BioSchemas - New pages [en]

RNAStructAlignmentML

Jkrueger — Wed, 21 Jun 2006 11:08:05 GMT

Summary:

RNAStructAlignmentML is a format for storing RNA secondary structure alignments as computed
by e.g. [http://bibiserv.techfak.uni-bielefeld.de/rnaforester RNAforester] or [http://www.tbi.univie.ac.at/~ivo/RNA/ RNAalifold] .
RNAStructAlignmentML uses an [[RNAStructML]]-like architecture, but bases on [[AlignmentML]] instead of [[SequenceML]].

== Example ==

==== FASTA DotBracket Format ====

'''>'''''gi|4972014|emb|AJ237949.1|SAC237949 Scenedesmus acuminatus [Scenedesmus acuminatus (modified and secondary structure added)]''
UCACCCCUCUC-UGC-CUU---U-UGGAGAGUUGGUCAGC-UC-UCAGCUGACCUUAGGGGUGGAUCUGGCUUUCCCAA-
U-U-GGUUUACUCCGA-UUGGGUUGGCUGAAGCUUAGAGGCUUAAGCAAGGACCCGAUAUGGGCUUCAACUGGAUAGGUA
GCACCGGCUCCUGCCGACUACACGAAGUUGUGGCUUGUGGACUUUGCUAGAGGCCAAGCAG-GA-A-A-CAUGCUUUGCA
UGUUUU-AAACUUU
(((((((((((-(.(-(..---.-.))))))..(((((((-..-...)))))))..)))))))).((.((((..(((((-
(-(-((......))))-)))))..)))))).((((...(((((.(((((((.((....(..((((.(((((......(((
(...((((....)))).))))....))))).))))..))).)))))))..)))))))))..-((-(-(-(((((...)))
))))))-.......
'''>'''''gi|37727738|gb|AY170854.1| Scenedesmus arcuatus var. arcuatus [Scenedesmus arcuatus var. arcuatus (modified and secondary structure added)]''
UCACCCCUC---C-CACCU-----UGU-GGGUCGGUUGGCUUG-CUAGCUAGCCUUAGGGGUGGAUCUGGCUUCCCCAA-
U-UUGCUUU--UGUGGAUUGGGUUGGCUGAAGUGUAGAGGCUUAAACAAGGACCCGAUAUGGGCUUCAACUGGAUAGGUA
GCACCGGCUC-UGCCGACUACACGAAGUUGUGGCCUGUGGACCUUGUUAGAGGCCAAGCAG-GA-A-A-CAUGCUUGGCA
UGU-UUUAAACUUU
(((((((((---(-(((..-----.))-)))..((((((((..-..))))))))..))))))))....((((..(((((-
(-(..(...--.)..)))))))..))))....(((...(((((.(((((((.((....(((((((.(((((......(((
(...((((..-.)))).))))....))))).))))))))).)))))))..)))))..))).-((-(-(-(((((...)))
)))-))).......

==== RNAStructAlignmentML Format ====

'''<?xml''' version="''1.0''" encoding="''UTF-8''"'''?>'''
'''<rnastructAlignmentML'''
xmlns="''http://hobit.sourceforge.net/xsds/20060515/rnastructAlignmentML''"
xmlns:xsi="''http://www.w3.org/2001/XMLSchema-instance''"
xsi:schemaLocation="''http://hobit.sourceforge.net/xsds/20060515/rnastructAlignmentML''
''http://bibiserv.techfak.uni-bielefeld.de/xsd/net/sourceforge/hobit/20060515/nastructAlignmentML.xsd''"'''>'''
'''<rnastructurealignment''' id="''IDDP8YM3vFxV''"'''>'''
'''<sequence''' seqID="''gi|4972014|emb|AJ237949.1|SAC237949''" size="''254''">'''
'''<name>'''''Scenedesmus acuminatus'''''</name>'''
'''<description>'''''Scenedesmus acuminatus'''''</description>'''
'''<alignedNucleicAcidSequence>'''''UCACCCCUCUC-UGC-CUU---U-UGGAGAGUUGGUCAGC-UC-UCA[http://bioschemas.sourceforge.net/download/xmlexamples/rnastructalignmentML.xml ....]'''''</alignedNucleicAcidSequence>'''
'''<structure>'''''(((((((((((-(.(-(..---.-.))))))..(((((((-..-...[http://bioschemas.sourceforge.net/download/xmlexamples/rnastructalignmentML.xml ....]'''''</structure>'''
'''<comment>'''''modified and secondary structure added'''''</comment>'''
'''</sequence>'''
'''<sequence''' seqID="''gi|37727738|gb|AY170854.1|''" size="''254''"'''>'''
'''<name>'''''Scenedesmus arcuatus var. arcuatus'''''</name>'''
'''<description>'''''Scenedesmus arcuatus var. arcuatus'''''</description>'''
'''<alignedNucleicAcidSequence>'''''UCACCCCUC---C-CACCU-----UGU-GGGUCGGUUGGCUUG-CUAG[http://bioschemas.sourceforge.net/download/xmlexamples/rnastructalignmentML.xml ....]'''''</alignedNucleicAcidSequence>'''
'''<structure>'''''(((((((((---(-(((..-----.))-)))..((((((((..-..)[http://bioschemas.sourceforge.net/download/xmlexamples/rnastructalignmentML.xml ....]'''''</structure>'''
'''<comment>'''''modified and secondary structure added'''''</comment>'''''
'''</sequence>'''
'''</rnastructurealignment>'''
'''</rnastructAlignmentML>'''

'''ATTENTION:''' To get a better overview of the XML structure, the sequence data is not complete in the shown XML example.
Download the complete example [http://bioschemas.sourceforge.net/download/xmlexamples/rnastructalignmentML.xml here].

== History ==
*Version 2.0 (2006/05/15) : [http://hobit.sourceforge.net/xsds/20060515/rnastructAlignmentML.xsd http://hobit.sourceforge.net/xsds/20060515/rnastructAlignmentML]
*Version 1.0 (2006/02/01) : [http://hobit.sourceforge.net/xsds/20060201/rnastructAlignmentML.xsd http://hobit.sourceforge.net/xsds/20060201/rnastructAlignmentML]
*Version 0.1 (2006/01/26) : [http://hobit.sourceforge.net/xsds/20060126/RNAStructAlignmentML.xsd http://hobit.sourceforge.net/xsds/20060126/RNAStructAlignmentML]

== Author ==
*[http://www.techfak.uni-bielefeld.de/ags/pi/pages/kloewent.htm Kai Löwenthal] : Contributor and Maintainer

--[[User:Jkrueger|Jkrueger]] 04:08, 21 June 2006 (PDT)

SequenceAnnotationML

Jkrueger — Wed, 21 Jun 2006 10:19:45 GMT

Summary:

SequenceAnnotationML is based on [[SequenceML]]. While [[SequenceML]] contains raw sequence information, SequenceAnnotationML allows additional annotations. Thus while [[SequenceML]] is often used as input for bioinformatic tools, SequenceAnnotationML can be used to store the result. SequenceAnnotationML allows modelling sites of interest of small sequences (DNA, RNA or protein). Furthermore it is possible to encapsulate whole genome annotations due to its recursive structure.

== History ==

*Version 1.1 (2006/05/05) - [http://hobit.sourceforge.net/xsds/20060505/sequenceAnnotationML.xsd http://hobit.sourceforge.net/xsds/20060505/sequenceAnnotationML]
*Version 1.0 (2005) - [http://hobit.sourceforge.net/xsds/2005/sequenceAnnotationML.xsd http://hobit.sourceforge.net/xsds/2005/sequenceAnnotationML.xsd]

== Authors ==

*[http://www.bioinf.med.uni-goettingen.de/people/ Knut Schwarzer] : Contributor and Maintainer

--[[User:Jkrueger|Jkrueger]] 03:20, 21 June 2006 (PDT)

AlignmentML

Jkrueger — Wed, 21 Jun 2006 10:06:37 GMT

Summary:

AlignmentML is a format describing (multiple) alignment information any alignment program like [http://bibiserv.techfak.uni-bielefeld.de/clustalw CLUSTALW], [http://bibiserv.techfak.uni-bielefeld.de/dca DCA] and [http://bibiserv.techfak.uni-bielefeld.de/dialign Dialign] can produce. Similar to [[SequenceML]], different sequence types are supported.

== Example ==

==== FASTA Format ====

'''>'''''gi|58374180|gb|AAW72226.1| HA [Influenza A virus (A/duck/Shandong/093/2004(H5N1))]''
m--eeivlllaivslvksdqicigyhannsteqvdtimeknvtvthaqdilekthngklcdldgvkplilrdcsvagwll
gnpmcdefinvpewsyivekanpandlcypgdfndyeelkhllsrinhfekiqiipksswsdheassgvssacpyngks-
sffrnvvwlik-knssyptikrsynntnqedllilwgihhpndaaeqtklyqnpttyisvgtstlnqrlvpkiatrskvn
gqsgrmeffwtilkpndainfesngnfiapeyayki---vk-kgdsaimkseleygnc-ntkcqtpm-gainssmpfhni
hpltigecpkyvksnrlvlatglrntpqrerrr-kkrglfgaiagfieggwqgmvdgwygyhhsneqgsgyaadkestqk
aidgvtnkvnsiidkmntqfeavgrefnnlerrienlnkkmedgfldvwtynaellvlmenertldfhdsnvknlydkvr
lqlrdnakelgngcfefyhkcdnecmesvkngtydypryseearlnreeisgvklesmgtyqilsiystvasslalaimv
aglslwmcsngslqcrici-----
'''>'''''gi|28849361|gb|AAO52863.1|AF509020_1 hemagglutinin [Influenza A virus (A/Pheasant/Hong Kong/FY155/01 (H5N1))]''
-------------slvksdqicigyhannsteqvdtimeknvtvthaqdilekthngklcdldgvkplilrdcsvagwll
gnpmcdefinvpewsyivekaspandlcypgdfndyeelkhllsrinhfekiqiipksswsnheassgvssacpylgks-
sffrnvvwlik-knnayptikrsynntnqedllvlwgihhpndaaeqtklyqnpttyisvgtstlnqrlvpkiatrskvn
gqsgrmeffwtilkpndainfesngnfiapeyayki---vk-kgdsaimkseleygnc-ntkcqtpm-gainssmpfhni
hpltigecpkyvksnrlvlatglrntpqrerrr-kkrglfgaiagfieggwqgmvdgwygyhhsneqgsgyaadkestqk
aidgvtnkvnsiidkmntqfeavgrefnnlerrienlnkkmedgfldvwtynaellvlmenertldfhdsnvknlydkvr
lqlrdnakelgngcfefyhkcdnecmesvkngtydypqylrkaglnreeisgvklesmgtyqilsiystvasslalaimv
aglslwmcsngslqcrici-----
'''>'''''gi|108671045|gb|ABF93441.1| hemagglutinin [Influenza A virus (St Jude H5N1 influenza seed virus 163222)]''
m--ekivlllaivslvksdqicigyhannsteqvdtimeknvtvthaqdilekthngklcdldgvkplilrdcsvagwll
gnpmcdeflnvpewsyivekinpandlcypgnfndyeelkhllsrinhfekiqiipksswsdheassgvssacpyqgrs-
sffrnvvwlik-knnayptikrsynntnqedllvlwgihhpndaaeqtrlyqnpttyisvgtstlnqrlvpkiatrskvn
gqsgrmeffwtilkpndainfesngnfiapenayki---vk-kgdstimkseleygnc-ntkcqtpi-gainssmpfhni
hpltigecpkyvksnrlvlatglrnspqie-----trglfgaiagfieggwqgmvdgwygyhhsneqgsgyaadkestqk
aidgvtnkvnsiidkmntqfeavgrefnnlerrienlnkkmedgfldvwtynaellvlmenertldfhdsnvknlydkvr
lqlrdnakelgngcfefyhrcdnecmesvrngtydypqyseearlkreeisgvklesigtyqilsiystvasslalaimv
aglslwmcsngslqcrici-----

==== AlignmentML Format ====

'''<?xml''' version="''1.0''" encoding="''utf-8''"'''?>'''
'''<alignmentML'''
xmlns="''http://hobit.sourceforge.net/xsds/20060602/alignmentML''"
xmlns:NS1="''http://www.w3.org/2001/XMLSchema-instance''"
NS1:schemaLocation="''http://hobit.sourceforge.net/xsds/20060602/alignmentML''
''http://bibiserv.techfak.uni-bielefeld.de/xsd/net/sourceforge/hobit/20060602/alignmentML.xsd''"'''>'''
'''<alignment>'''
'''<sequence''' seqID="''gi|58374180|gb|AAW72226.1|''"'''>'''
'''<name>'''''HA'''''</name>'''
'''<description>'''''Influenza A virus (A/duck/Shandong/093/2004(H5N1))'''''</description>'''
'''<alignedAminoAcidSequence>'''''M--EEIVLLLAIVSLVKSDQICIGYHANNSTEQVDTIMEK[http://bioschemas.sourceforge.net/download/xmlexamples/alignmentML.xml ....]'''''</alignedAminoAcidSequence>'''
'''</sequence>'''
'''<sequence''' seqID="''gi|28849361|gb|AAO52863.1|AF509020_1''"'''>'''
'''<name>'''''hemagglutinin'''''</name>'''
'''<description>'''''Influenza A virus (A/Pheasant/Hong Kong/FY155/01 (H5N1))'''''</description>'''
'''<alignedAminoAcidSequence>'''''-------------SLVKSDQICIGYHANNSTEQVDTIMEK[http://bioschemas.sourceforge.net/download/xmlexamples/alignmentML.xml ....]'''''</alignedAminoAcidSequence>'''
'''</sequence>'''
'''<sequence''' seqID="''gi|108671045|gb|ABF93441.1|''"'''>'''
'''<name>'''''hemagglutinin'''''</name>'''
'''<description>'''''Influenza A virus (St Jude H5N1 influenza seed virus 163222)'''''</description>'''
'''<alignedAminoAcidSequence>'''''M--EKIVLLLAIVSLVKSDQICIGYHANNSTEQVDTIMEK[http://bioschemas.sourceforge.net/download/xmlexamples/alignmentML.xml ....]'''''</alignedAminoAcidSequence>'''
'''</sequence>'''
'''</alignment>'''
'''</alignmentML>'''

'''ATTENTION:''' To get a better overview of the XML structure, the sequence data is not complete in the shown XML example.
Download the complete example [http://bioschemas.sourceforge.net/download/xmlexamples/alignmentML.xml here].

== History ==

* Version 1.2 (2006/06/02) : [http://hobit.sf.net/xsds/20060602/alignmentML.xsd http://hobit.sf.net/xsds/20060602/alignmentML]
* Version 1.1 (2006/02/01) : [http://hobit.sf.net/xsds/20060201/alignmentML.xsd http://hobit.sf.net/xsds/20060201/alignmentML]
* Version 1.0 (2006/01/26) : [http://hobit.sf.net/xsds/20060126/alignmentML.xsd http://hobit.sf.net/xsds/20060126/alignmentML]
* Version 0.1 (2005 - initial release) : [http://hobit.sf.net/xsds/2005/alignmentML.xsd http://hobit.sf.net/xsds/2005/alignmentML]

== Authors ==

*[http://www.techfak.uni-bielefeld.de/ags/pi/pages/shartmei.htm Sven Hartmeier] : Contributor
*[http://www.techfak.uni-bielefeld.de/ags/pi/pages/jkrueger.htm Jan Krüger] : Contributor and Maintainer
*[http://www.techfak.uni-bielefeld.de/ags/pi/pages/kloewent.htm Kai Löwenthal] : Contributor
*[http://www.henning-mersch.de Henning Mersch] : Inititator

--[[User:Jkrueger|Jkrueger]] 03:06, 21 June 2006 (PDT)

SequenceML

Jkrueger — Tue, 20 Jun 2006 12:19:39 GMT

Summary:

SequenceML deals with all kinds of simple sequence information often used as input
for several common bioinformatic tools. It is designed to be used as a XML
replacement of the [[FASTA]] format, containing all of FASTA's information
while avoiding that format's consistency problems. SequenceML
differentiates between nucleic- and aminoacid sequences following the IUPAC
standard and also allows the user to add free sequence information based on
basic types defined by [[BioTypes]]. SequenceML also supports
a mandatory sequence id and an optional detailed sequence description. SequenceML
does not contain any annotation information.

== Example ==

==== FASTA Format ====

'''>'''''gi|58374180|gb|AAW72226.1| HA [Influenza A virus (A/duck/Shandong/093/2004(H5N1))]''
meeivlllaivslvksdqicigyhannsteqvdtimeknvtvthaqdilekthngklcdldgvkplilrdcsvagwllgn
pmcdefinvpewsyivekanpandlcypgdfndyeelkhllsrinhfekiqiipksswsdheassgvssacpyngkssff
rnvvwlikknssyptikrsynntnqedllilwgihhpndaaeqtklyqnpttyisvgtstlnqrlvpkiatrskvngqsg
rmeffwtilkpndainfesngnfiapeyaykivkkgdsaimkseleygncntkcqtpmgainssmpfhnihpltigecpk
yvksnrlvlatglrntpqrerrrkkrglfgaiagfieggwqgmvdgwygyhhsneqgsgyaadkestqkaidgvtnkvns
iidkmntqfeavgrefnnlerrienlnkkmedgfldvwtynaellvlmenertldfhdsnvknlydkvrlqlrdnakelg
ngcfefyhkcdnecmesvkngtydypryseearlnreeisgvklesmgtyqilsiystvasslalaimvaglslwmcsng
slqcrici
'''>'''''gi|28849361|gb|AAO52863.1|AF509020_1 hemagglutinin [Influenza A virus (A/Pheasant/Hong Kong/FY155/01 (H5N1))]''
slvksdqicigyhannsteqvdtimeknvtvthaqdilekthngklcdldgvkplilrdcsvagwllgnpmcdefinvpe
wsyivekaspandlcypgdfndyeelkhllsrinhfekiqiipksswsnheassgvssacpylgkssffrnvvwlikknn
ayptikrsynntnqedllvlwgihhpndaaeqtklyqnpttyisvgtstlnqrlvpkiatrskvngqsgrmeffwtilkp
ndainfesngnfiapeyaykivkkgdsaimkseleygncntkcqtpmgainssmpfhnihpltigecpkyvksnrlvlat
glrntpqrerrrkkrglfgaiagfieggwqgmvdgwygyhhsneqgsgyaadkestqkaidgvtnkvnsiidkmntqfea
vgrefnnlerrienlnkkmedgfldvwtynaellvlmenertldfhdsnvknlydkvrlqlrdnakelgngcfefyhkcd
necmesvkngtydypqylrkaglnreeisgvklesmgtyqilsiystvasslalaimvaglslwmcsngslqcrici
'''>'''''gi|108671045|gb|ABF93441.1| hemagglutinin [Influenza A virus (St Jude H5N1 influenza seed virus 163222)]''
mekivlllaivslvksdqicigyhannsteqvdtimeknvtvthaqdilekthngklcdldgvkplilrdcsvagwllgnp
mcdeflnvpewsyivekinpandlcypgnfndyeelkhllsrinhfekiqiipksswsdheassgvssacpyqgrssffrn
vvwlikknnayptikrsynntnqedllvlwgihhpndaaeqtrlyqnpttyisvgtstlnqrlvpkiatrskvngqsgrme
ffwtilkpndainfesngnfiapenaykivkkgdstimkseleygncntkcqtpigainssmpfhnihpltigecpkyvks
nrlvlatglrnspqietrglfgaiagfieggwqgmvdgwygyhhsneqgsgyaadkestqkaidgvtnkvnsiidkmntqf
eavgrefnnlerrienlnkkmedgfldvwtynaellvlmenertldfhdsnvknlydkvrlqlrdnakelgngcfefyhrc
dnecmesvrngtydypqyseearlkreeisgvklesigtyqilsiystvasslalaimvaglslwmcsngslqcrici

==== SequenceML Format ====

'''<?xml''' version="''1.0''" encoding="''utf-8''"'''?>'''
'''<sequenceML'''
xmlns="''http://hobit.sourceforge.net/xsds/20060201/sequenceML''"
xmlns:NS1="''http://www.w3.org/2001/XMLSchema-instance''"
NS1:schemaLocation="''http://hobit.sourceforge.net/xsds/20060201/sequenceML''
''http://bibiserv.techfak.uni-bielefeld.de/xsd/net/sourceforge/hobit/20060201/sequenceML.xsd''"'''>'''
'''<sequence''' seqID="''gi|58374180|gb|AAW72226.1|''"'''>'''
'''<name>'''''HA'''''</name>'''
'''<description>'''''Influenza A virus (A/duck/Shandong/093/2004(H5N1))'''''</description>'''
'''<aminoAcidSequence>'''''MEEIVLLLAIVSLVKSDQICIGYHANNSTEQVDTIMEK[http://bioschemas.sourceforge.net/download/xmlexamples/sequenceML.xml ....]'''''</aminoAcidSequence>'''
'''</sequence>'''
'''<sequence''' seqID="''gi|28849361|gb|AAO52863.1|AF509020_1''"'''>'''
'''<name>''hemagglutinin'''''</name>'''
'''<description>'''''Influenza A virus (A/Pheasant/Hong Kong/FY155/01 (H5N1))'''''</description>'''
'''<aminoAcidSequence>'''''SLVKSDQICIGYHANNSTEQVDTIMEKNVTVTHAQDIL[http://bioschemas.sourceforge.net/download/xmlexamples/sequenceML.xml ....]'''''</aminoAcidSequence>'''
'''</sequence>'''
'''<sequence''' seqID="''gi|108671045|gb|ABF93441.1|''"'''>'''
'''<name>'''''hemagglutinin'''''</name>'''
'''<description>'''''Influenza A virus (St Jude H5N1 influenza seed virus 163222)'''''</description>'''
'''<aminoAcidSequence>'''''MEKIVLLLAIVSLVKSDQICIGYHANNSTEQVDTIMEK[http://bioschemas.sourceforge.net/download/xmlexamples/sequenceML.xml ....]'''''</aminoAcidSequence>'''
'''</sequence>'''
'''</sequenceML>'''

'''ATTENTION:''' To get a better overview of the XML structure, the sequence data is not complete in the shown XML example.
Download the complete example [http://bioschemas.sourceforge.net/download/xmlexamples/sequenceML.xml here].

== History ==
* Version 2.0 (2006/02/01) : [http://hobit.sf.net/xsds/20060201/sequenceML.xsd http://hobit.sf.net/xsds/20060201/sequenceML]
* Version 1.0 (2006/01/02) : [http://hobit.sf.net/xsds/20060102/sequenceML.xsd http://hobit.sf.net/xsds/20060102/sequenceML]
* Version 0.1 (2005 - initial release) : [http://hobit.sf.net/xsds/2005/sequenceML.xsd http://hobit.sf.net/xsds/2005/sequenceML]

== Authors ==
*[http://www.techfak.uni-bielefeld.de/ags/pi/pages/shartmei.htm Sven Hartmeier] : Contributor and Maintainer
*[http://www.techfak.uni-bielefeld.de/ags/pi/pages/jkrueger.htm Jan Krüger] : Contributor
*[http://www.techfak.uni-bielefeld.de/ags/pi/pages/kloewent.htm Kai Löwenthal] : Contributor
*[http://www.henning-mersch.de Henning Mersch] : Inititator

--[[User:Shartmei|Shartmei]] 03:19, 21 June 2006 (PDT)

RNAStructML

Jkrueger — Tue, 20 Jun 2006 12:15:29 GMT

Summary:

RNAStructML is a format for storing RNA secondary structure information.
The most widely used application for RNA tools, such as [http://bibiserv.techfak.uni-bielefeld.de/rnashapes RNAshapes],
[http://www.tbi.univie.ac.at/~ivo/RNA/ RNAfold] and [http://www.bioinfo.rpi.edu/applications/mfold/old/rna/form1.cgi Mfold]
is the proprosal of RNA secondary structures, based on thermodynamic principles.
RNAStructML is inspired by SequenceML and uses Vienna style DotBracket strings for storing the information about RNA secondary structure.

== Example ==

==== FASTA DotBracket Format ====

'''>'''''gi|4972014|emb|AJ237949.1|SAC237949 Scenedesmus acuminatus [Scenedesmus acuminatus (modified and secondary structure added)]''
UCACCCCUCUCUGCCUUUUGGAGAGUUGGUCAGCUCUCAGCUGACCUUAGGGGUGGAUCUGGCUUUCCCAAUUGGUUUAC
UCCGAUUGGGUUGGCUGAAGCUUAGAGGCUUAAGCAAGGACCCGAUAUGGGCUUCAACUGGAUAGGUAGCACCGGCUCCU
GCCGACUACACGAAGUUGUGGCUUGUGGACUUUGCUAGAGGCCAAGCAGGAAACAUGCUUUGCAUGUUUUAAACUUU
((((((((((((.((....))))))..(((((((.....)))))))..)))))))).((.((((..(((((((((.....
.)))))))))..)))))).((((...(((((.(((((((.((....(..((((.(((((......((((...((((....
)))).))))....))))).))))..))).)))))))..)))))))))..(((((((((...))))))))).......
'''>'''''gi|37727738|gb|AY170854.1| Scenedesmus arcuatus var. arcuatus [Scenedesmus arcuatus var. arcuatus (modified and secondary structure added)]''
UCACCCCUCCCACCUUGUGGGUCGGUUGGCUUGCUAGCUAGCCUUAGGGGUGGAUCUGGCUUCCCCAAUUUGCUUUUGUG
GAUUGGGUUGGCUGAAGUGUAGAGGCUUAAACAAGGACCCGAUAUGGGCUUCAACUGGAUAGGUAGCACCGGCUCUGCCG
ACUACACGAAGUUGUGGCCUGUGGACCUUGUUAGAGGCCAAGCAGGAAACAUGCUUGGCAUGUUUUAAACUUU
(((((((((((((...)))))..((((((((....))))))))..))))))))....((((..(((((((..(....)..
)))))))..))))....(((...(((((.(((((((.((....(((((((.(((((......((((...((((...))))
.))))....))))).))))))))).)))))))..)))))..))).(((((((((...))))))))).......

==== RNAStructML Format ====

'''<?xml''' version="''1.0''" encoding="''utf-8''"'''?>'''
'''<rnastructML'''
xmlns="''http://hobit.sourceforge.net/xsds/20060201/rnastructML''"
xmlns:NS1="''http://www.w3.org/2001/XMLSchema-instance''"
NS1:schemaLocation="''http://hobit.sourceforge.net/xsds/20060201/rnastructML''
''http://bibiserv.techfak.uni-bielefeld.de/xsd/net/sourceforge/hobit/20060201/rnastructML.xsd''"'''>'''
'''<rnastructure''' id="''IDc4nOsqjgLG''"'''>'''
'''<sequence''' seqID="''gi|4972014|emb|AJ237949.1|SAC237949''"'''>'''
'''<name>'''''Scenedesmus acuminatus'''''</name>'''
'''<description>'''''Scenedesmus acuminatus'''''</description>'''
'''<nucleicAcidSequence>'''''UCACCCCUCUCUGCCUUUUGGAGAGUUGGUCAGCUCUCAGCUGACCUUAGGGGUGG[http://bioschemas.sourceforge.net/download/xmlexamples/rnastructML.xml ....]'''''</nucleicAcidSequence>'''
'''<comment>'''''modified and secondary structure added'''''</comment>'''
'''</sequence>'''
'''<structure>'''''((((((((((((.((....))))))..(((((((.....)))))))..)))))))).((.((((..(((([http://bioschemas.sourceforge.net/download/xmlexamples/rnastructML.xml ....]'''''</structure>'''
'''</rnastructure>'''
'''<rnastructure''' id="''IDMkBuPLmLAj''"'''>'''
'''<sequence''' seqID="''gi|37727738|gb|AY170854.1|''"'''>'''
'''<name>'''''Scenedesmus arcuatus var. arcuatus'''''</name>'''
'''<description>'''''Scenedesmus arcuatus var. arcuatus'''''</description>'''
'''<nucleicAcidSequence>'''''UCACCCCUCCCACCUUGUGGGUCGGUUGGCUUGCUAGCUAGCCUUAGGGGUGGAUC[http://bioschemas.sourceforge.net/download/xmlexamples/rnastructML.xml ....]'''''</nucleicAcidSequence>'''
'''<comment>'''''modified and secondary structure added'''''</comment>'''
'''</sequence>'''
'''<structure>'''''(((((((((((((...)))))..((((((((....))))))))..))))))))....((((..((((((([http://bioschemas.sourceforge.net/download/xmlexamples/rnastructML.xml ....]'''''</structure>'''
'''</rnastructure>'''
'''</rnastructML>'''

'''ATTENTION:''' To get a better overview of the XML structure, the sequence data is not complete in the shown XML example.
Download the complete example [http://bioschemas.sourceforge.net/download/xmlexamples/rnastructML.xml here].

== History ==

*Version 2.0 (2006/02/02) : [http://hobit.sourceforge.net/xsds/20060201/rnastructML.xsd http://hobit.sourceforge.net/xsds/20060201/rnastructML]
*Version 1.0 (2006/01/11) : [http://hobit.sourceforge.net/xsds/20060111/RNAStructML.xsd http://hobit.sourceforge.net/xsds/20060111/RNAStructML]

== Authors ==

*[http://www.techfak.uni-bielefeld.de/ags/pi/pages/shartmei.htm Sven Hartmeier] : Contributor
*[http://www.techfak.uni-bielefeld.de/ags/pi/pages/kloewent.htm Kai Löwenthal] : Contributor and Maintainer
*[http://www.techfak.uni-bielefeld.de/ags/pi/pages/jkrueger.htm Jan Krüger] : Contributor
*[http://www.biozentrum.uni-wuerzburg.de/faculty00.html Philipp Seibel] : Contributor

--[[User:Jkrueger|Jkrueger]] 05:15, 20 June 2006 (PDT)

GOA

Hampti — Wed, 14 Jun 2006 14:00:52 GMT

Summary:

The GOA schema describes [http://www.geneontology.org GO] annotations, i.e. annotates GO identifiers to an XML element and optionally one or more [http://www.geneontology.org/GO.evidence.shtml evidences] including evidence codes and the source of the evidence.

== Source code access ==

Get the latest release from the SVN repository:

<pre>https://svn.sourceforge.net/svnroot/bioschemas/goa/trunk</pre>

== History ==

These versions of BioTypes have been released or are under current development:

* [[GOA 0.1]]: ''open''

== Developers ==

* [http://szugat.gmxhome.de Martin Szugat]: Contributor and maintainer

== See also ==

* [[BioTypes]]: GOA makes use of BioTypes

[[Category:Building block]]

Guideline:New project

Hampti — Thu, 18 May 2006 02:29:18 GMT

Summary:

The new project must be added to

* SVN Repository
* Tracker (Bug and Feature requests)
* MediaWiki's Sidebar
* Mainpage
* Category

The simplest way to create a new project (called ''xyz'') is to use the existing template project ''bioschemas'' and make a copy of it in the repository:

<bash>$ svn -m "Created XYZ project" copy https://svn.sourceforge.net/svnroot/bioschemas/bioschemas https://svn.sourceforge.net/svnroot/bioschemas/xyz</bash>

Guideline:Schema releasing

Hampti — Thu, 18 May 2006 02:26:30 GMT

Summary:

== Compose ==

# Try to run the build process with the local files, especially execute the test run
# Commit all pending changes

== Build ==

# Make a seperate branch for the release
# Build the release
# Test it!

== Deploy ==

# Put it into Sourceforge's file release system
# Upload it to the namespace URL
# Tag the deployed version in the SVN repository

== Publish ==

# Add a news item
# Mention the new version in the wiki (i.e. in the history)

== See also ==

* [[Build Tools]]

ProML

Hampti — Wed, 17 May 2006 20:14:15 GMT

Summary:

ProML is an XML-schema for describing proteins and protein sets. ProML originally was developed as an XML-DTD by Daniel Hanisch et al. <nowiki>[</nowiki>[[#Literature|1]]<nowiki>]</nowiki>. Regarding flexibility and extensibility, DTD as an implementation standard had some less desirable characteristics. So we decided to reimplement the main properties of ProML as an XML-Schema. The schema has been used and extended in several projects (bachelors' thesis etc.) since.

== Goals and Applications ==

The main goal of ProML is not only to allow for the integration of protein data and features into a single data source (e.g. primary, secondary, tertiary structure) but also for the grouping of related proteins, including annotations of the essential characteristics underlying this group (e.g. specifical patterns, SCOP classification). New features can be applied to ProML by importing XML from other namespaces. In contrast to the former solution ProML is now based on the [[BioTypes]].

== History ==

* [http://www.bio.ifi.lmu.de/2005/proml/ ProML 1.0]: deprecated
* ProML 1.1: deprecated; not official released
* ProML 1.2: under development; complete redesign

== Developers ==

ProML was developed and is maintained at the [http://www.bio.ifi.lmu.de Bioinformatics unit] of the [http://www.lmu.de Ludwig Maximilians-University, Munich] in the [http://www.bio.ifi.lmu.de/forschung/struktur/index_en.html PROSEQO II] project.

* [http://www.bio.ifi.lmu.de/mitarbeiter/gewehr/ Gewehr, Jan Erik]: Project leader
* [mailto:Alessandro.Macri@ifi.lmu.de Macri, Alessandro Roberto]: Technical consultant
* [http://szugat.gmxhome.de/ Szugat, Martin]: Extended version of the ProML schema and its belonging stylesheets
* [mailto:zimek@cip.ifi.lmu.de Zimek, Arthur]: Initial version of the ProML schema

The current maintainer of the ProML project is [mailto:csaba@bio.ifi.lmu.de Gergely Csaba].

== Literature ==

# Hanisch,D., Zimmer,R., Lengauer,T.; "ProML - the Protein Markup Language for specification of protein sequences, structures and families"; In Silico Biology 2, 0029 (2002)

== See also ==

* [http://www.bioweka.org BioWeka]: Contains an XML-Stylesheet to convert ProML 1.0 files into Weka's ARFF format.

[[Category:Document format]]

XmlStatistic

Hampti — Wed, 17 May 2006 13:35:49 GMT

Summary:

XmlStatistic is a simple Visual Basic.NET program to calculate some statistics for one or more XML documents, e.g. the number of elements or attributes. It is also useful to estimate the ratio of metadata to real data, of (insignificant) whitespace to real data and of metadata plus (insignificant) whitespace to real data.

== Usage ==

<pre>XmlStatistic.exe Document1.xml Document2.xml ...</pre>

The output is written to <code>STDOUT</code> in a very simple XML format.

== Requirements ==

One of the following runtime libraries depending on the used operating system:

* [http://www.mono-project.de Mono-Runtime 1.1] for Windows, Linux, Mac or any other Unix-based OS
* [http://msdn.microsoft.com/netframework/downloads/updates/default.aspx Microsoft .NET Framework 1.1] for Windows

== Download ==

Download the latest release from the [http://sourceforge.net/project/showfiles.php?group_id=164851&package_id=186862 project site].

== Contact ==

Report bugs to the [http://sourceforge.net/tracker/?atid=833350&group_id=164851&func=browse Bug tracker] or ask your question in the [http://sourceforge.net/forum/forum.php?forum_id=560766 help forum].

== Developers ==

* [http://szugat.gmxhome.de Martin Szugat] (maintainer)

[[Category:Tool]]

External links

Hampti — Wed, 17 May 2006 12:19:08 GMT

Summary:

== Partner projects ==

* [http://biodom.sourceforge.net/ BioDOM]: The Bioinformatics XML Solution
* [http://hobit.sourceforge.net/ HOBIT]: Helmholtz Open BioInformatics Technology

== Other open projects ==

* [http://biojava.org/ BioJava]
* [http://www.bioweka.org BioWeka]: Knowledge Discovery and Data Analysis in Biology
* [http://protag.sourceforge.net ProTag]: Web Servicing the Biological Office

Browse

Hampti — Wed, 17 May 2006 12:10:30 GMT

Summary:

== This website ==

There are several options to browse the content of this website:

* [[Special:Categories|Categories]]: Browse the web pages by their (hierarchical) category
* [[Special:Allpages|All pages]]: Lists all pages on this website
* [[Special:Newpages|New pages]]: Displays only the new pages
* [[Special:Popularpages|Popular pages]]: Visit the most popular pages
* [[Special:Randompage|Random page]]: Navigate to a randomly selected page
* [[Special:Wantedpages|Wanted pages]]: See which pages need to be edited
* [[Special:Listusers|Users list]]: Lists all registered users of this website and their personal pages
* [[Special:Recentchanges|Recent changes]]: Be up-to-date of the recent changes to this website.

The recent changes are also available as [{{SERVER}}/index.php/Special:Recentchanges?feed=atom ATOM] and [{{SERVER}}/index.php/Special:Recentchanges?feed=rss RSS] feeds.

== Other BioSchemas sites ==

* [http://sourceforge.net/projects/bioschemas/ Project site]: Hosts the downloads and user forums and offers access to the source code (mainly for BioSchemas developers)
* [http://bioschemas.sourceforge.net/2005/ BioSchemas 2005]: Schemas released in 2005
* [http://bioschemas.sourceforge.net/2006/ BioSchemas 2006]: Schemas released in 2006

Other websites related to BioSchemas can be found under [[External links]].

ProThesaurus 0.1

Hampti — Wed, 17 May 2006 09:07:29 GMT

Summary:

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
== Specification ==

=== schema http://schemas.bioservices.net/2006/01/prothesaurus ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" title="code"><xml><xs:schema xmlns:pt="http://schemas.bioservices.net/2006/01/prothesaurus" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" targetNamespace="http://schemas.bioservices.net/2006/01/prothesaurus" elementFormDefault="qualified" attributeFormDefault="unqualified" id="prothesaurus" version="0.1" xml:lang="en"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== import http://schemas.bioservices.net/2006/01/biotypes ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:import schemaLocation="biotypes_1.1.xsd" namespace="http://schemas.bioservices.net/2006/01/biotypes"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType schemaVersion ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="schemaVersion">
<xs:restriction base="bt:version">
<xs:enumeration value="0.1"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType name ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="name">
<xs:restriction base="xs:string">
<xs:minLength value="1"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType synonym ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="synonym">
<xs:simpleContent>
<xs:extension base="pt:name">
<xs:anyAttribute namespace="##other" processContents="lax"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType entry ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="entry">
<xs:sequence>
<xs:element name="synonym" type="pt:synonym" minOccurs="0" maxOccurs="unbounded"/>
<xs:any namespace="##other" processContents="lax" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="name" type="pt:name" use="required"/>
<xs:attribute name="organism" type="pt:name" use="required"/>
<xs:anyAttribute namespace="##other" processContents="lax"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType prothesaurus ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="prothesaurus">
<xs:sequence>
<xs:any namespace="##other" processContents="lax" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="entry" type="pt:entry" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="schemaVersion" type="pt:schemaVersion" use="required"/>
<xs:anyAttribute namespace="##other" processContents="lax"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element prothesaurus ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="prothesaurus" type="pt:prothesaurus"/></xml></code>

ProThesaurus

Hampti — Wed, 17 May 2006 09:06:56 GMT

Summary:

== History ==

* [[ProThesaurus 0.1]]: ''open''

== See also ==

* [[BioTypes]] schema

[[Category:Document format]]

Guideline:Wiki editing

Hampti — Wed, 17 May 2006 09:06:18 GMT

Summary:

== Syntax highlight ==

On this Wiki the [http://www.wickle.com/wikis/index.php/Geshi_Syntax_Highlight_extension Geshi Syntax Highlight extension] is installed. Please use it to highlight your code.

== Minor edit ==

Minor edits, e.g. corrections that do not alter the syntax of a schema definition file or the semantic of a XML file, should be marked as ''This is a minor edit'' before the ''Save page'' button is pressed.

[[Category:Guideline]]

Guideline:Schema documentation

Hampti — Wed, 17 May 2006 09:05:09 GMT

Summary:

== Changelog order ==

New entries in a changelog should be put at first.

== Enumeration types ==

Enumeration types must be treated in a special way, because [http://xframe.sourceforge.net/xsddoc/ xsddoc] does not really supports documentating enumeration values. Here is an example how to do it:

<code><xml><xs:simpleType name="sourceName">
<xs:annotation><xs:documentation>
The name of a data source. The name could be any valid XML name (<code>xs:Name</code>
type, e.g. <code>my:db</code>). However the names of some well-known databases and
internet resources are provided as enumeration values. If the list contains an appropiate
entry you should use this instead of defining your own name.
<p><b>Attention</b>: XML names are case sensitive.</p>
<p>Predefined data source names:</p>
</xs:documentation></xs:annotation>
<xs:union memberTypes="xs:Name">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="default">
<xs:annotation><xs:documentation>
<li><code>default</code>: default source. Should be the default value for any element or attribute
of type <code>bs:sourceName</code>.</li>
</xs:documentation></xs:annotation>
</xs:enumeration>
<xs:enumeration value="aaindex">
<xs:annotation><xs:documentation>
<li><code>aaindex</code>: <a href="http://www.genome.jp/aaindex/">Amino acid index database.</a>]</li>
</xs:documentation></xs:annotation>
</xs:enumeration>
</xs:restriction>
</xs:simpleType>
</xs:union>
</xs:simpleType></xml></code>

== First sentence in a documentation ==

The first sentence in a <code><xs:documentation></code> element should not contain any markup because this sentence is used by [http://sut.sourceforge.net SUT] for the short description of the corresponding element, attribute, etc. in the overview page. Further it should concisely describe the element, attribute, etc.

== Examples ==

Every documentation should contain a short example how to use the corresponding element, attribute or type.

[[Category:Guideline]]

Guideline:Schema development

Hampti — Wed, 17 May 2006 09:04:12 GMT

Summary:

== Extension points and the empty namespace ==

Extension points should not only permit elements from a foreign namespace but also from the empty namespace. In addition extension elements should be located before the regular elements:

<code><xml><xs:sequence>
<xs:choice minOccurs="0" maxOccurs="unbounded">
<xs:any namespace="##other" processContents="lax"/>
<xs:any namespace="##local" processContents="lax"/>
</xs:choice>
<xs:element name="subelement" minOccurs="1" maxOccurs="unbounded"/>
</xs:sequence>
</xml></code>

== Optional attribute and key declarations ==

Optional attributes without a default value should not be used within a key declaration as a key field because a key requires every field to be set on the selected element. Thus it is best practice to declare an enumeration value <code>##missing</code> for the default value:

<code><xml><xs:simpleType name="missing">
<xs:restriction base="xs:token">
<xs:enumeration value="##missing"/>
</xs:restriction>
</xs:simpleType></xml></code>

The attribute type should be declared this way:

<code><xml><xs:simpleType name="key">
<xs:union memberTypes="xs:token missing"/>
</xs:simpleType></xml></code>

The attribute itself must use this type:

<code><xml><xs:attribute name="key" type="key" use="optional" default="##missing"/></xml></code>

The key may then be declared this way:

<code><xml><xs:key name="key">
<xs:selector xpath="element"/>
<xs:field xpath="@key"/>
</xs:key></xml></code>

== Namespace declaration for the schema itself ==

Every schema should declare its namespace using a prefix and <b>not</b> the default namespace (without prefix):

<code><xml>
<xs:schema
targetNamespace="http://schemas.bioservices.net/2005/biotypes/"
xmlns:xs="http://www.w3.org/2001/XMLSchema"
xmlns:bt="http://schemas.bioservices.net/2005/biotypes/"
elementFormDefault="qualified"
attributeFormDefault="unqualified"
id="biotypes" version="0.1"
>
</xml></code>

Otherwise you won't be able to declare keys and unique constraints using XPath, because XPath maps the default namespace to the empty namespace (<code>xmlns=""</code>):

<code><xml>
<xs:element name="source" type="bt:source">
<xs:key name="sourceItemKey">
<xs:annotation><xs:documentation>
</xs:documentation></xs:annotation>
<xs:selector xpath="./bt:item"/>
<xs:field xpath="@name"/>
</xs:key>
</xs:element>
</xml></code>

However attributes belong to the empty namespace as long as you do not qualify them! That's why you have to omit the prefix for attributes in XPath expressions.

== Nillable root elements ==

Root elements should be ''nillable'', so that e.g. web services can return an empty document for a query that does not match anything without violating the schema's specification:

<code><xml>
<xs:element name="root" nillable="true">
...
</xml></code>

It's not a good design to mark the subordinated elements as optional. Instead allow the root element to be nillable and set in the root element the <code>xsi:nil</code> attribute to <code>true</code>:

<code><xml>
<root
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:nil="true"
/>
</xml></code>

== xml:* Attributes ==

Every element you declare should explicitly allow the <code>xml:*</code> attributes, especially the <code>[http://www.w3.org/TR/xmlbase/ xml:base]</code> attribute. The latter is required for [http://www.w3.org/TR/2004/CR-xinclude-20040413/ XInclude] as described [http://norman.walsh.name/2005/04/01/xinclude here].

To allow the xml:* attributes or any other attributes from a foreign namespace include the following declaration in your type or element definition:

<code><xml><xs:anyAttribute namespace="##other" processContents="lax"/></xml></code>

== See also ==

* [http://www.xfront.com/BestPracticesHomepage.html XML Schemas: Best Practices]
* [http://www.aboutxml.de/ About XML]

[[Category:Guideline]]

CrossRefs 0.1

Hampti — Wed, 17 May 2006 09:02:53 GMT

Summary:

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
== Specification ==

=== schema http://schemas.bioservices.net/2006/01/crossrefs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" title="code"><xml><xs:schema xmlns:cr="http://schemas.bioservices.net/2006/01/crossrefs" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xmlns:xlink="http://www.w3.org/1999/xlink" targetNamespace="http://schemas.bioservices.net/2006/01/crossrefs" elementFormDefault="qualified" attributeFormDefault="unqualified" id="crossrefs" version="0.1" xml:lang="en"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The CrossRefs (Cross References) schema is a building block for including references to biological databases, websites, etc. into an XML document.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== import http://schemas.bioservices.net/2006/01/biotypes ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:import schemaLocation="biotypes_1.1.xsd" namespace="http://schemas.bioservices.net/2006/01/biotypes"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The CrossRefs schema supports cross references based on LSIDs as well as on BioTypes sources.
</div>

== Basics ==

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType abstractReference ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="abstractReference" abstract="true">
<xs:anyAttribute namespace="##other" processContents="lax"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractReference ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractReference" type="cr:abstractReference" abstract="true"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType schemaVersion ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="schemaVersion">
<xs:restriction base="xs:string">
<xs:enumeration value="0.1"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
List of valid versions.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType crossRefs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="crossRefs">
<xs:choice minOccurs="1" maxOccurs="unbounded">
<xs:element ref="cr:abstractReference"/>
</xs:choice>
<xs:attribute name="schemaVersion" type="cr:schemaVersion" use="optional"/>
<xs:anyAttribute namespace="##other" processContents="lax"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element crossRefs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="crossRefs" type="cr:crossRefs"/></xml></code>

== Database ==

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType databaseName ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="databaseName">
<xs:restriction base="xs:token">
<xs:minLength value="1"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType databaseEntry ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="databaseEntry">
<xs:restriction base="xs:token">
<xs:minLength value="1"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType databaseURL ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="databaseURL">
<xs:restriction base="xs:anyURI"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType databaseReference ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="databaseReference">
<xs:complexContent>
<xs:extension base="cr:abstractReference">
<xs:attribute name="name" type="cr:databaseName" use="required"/>
<xs:attribute name="entry" type="cr:databaseEntry" use="required"/>
<xs:attribute name="url" type="cr:databaseURL" use="optional"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element database ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="database" type="cr:databaseReference" substitutionGroup="cr:abstractReference"/></xml></code>

== URL ==

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType urlReference ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="urlReference">
<xs:complexContent>
<xs:extension base="cr:abstractReference">
<xs:attribute name="href" type="xs:anyURI" use="required"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element url ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="url" type="cr:urlReference" substitutionGroup="cr:abstractReference"/></xml></code>

== LSID ==

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType lsidReference ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="lsidReference">
<xs:complexContent>
<xs:extension base="cr:abstractReference">
<xs:attribute name="value" type="bt:lsid" use="required"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element lsid ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="lsid" type="cr:lsidReference" substitutionGroup="cr:abstractReference"/></xml></code>

== XLink ==

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType xlinkReference ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="xlinkReference">
<xs:complexContent>
<xs:extension base="cr:abstractReference">
<xs:anyAttribute namespace="http://www.w3.org/1999/xlink" processContents="strict"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element xlink ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="xlink" type="cr:xlinkReference" substitutionGroup="cr:abstractReference"/></xml></code>

== Source ==

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType sourceReference ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="sourceReference">
<xs:complexContent>
<xs:extension base="cr:abstractReference">
<xs:attribute name="uri" type="bt:sourceUri" use="required"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="required"/>
<xs:attribute name="date" type="bt:sourceDate" use="optional"/>
<xs:attribute name="version" type="bt:sourceVersion" use="optional"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element source ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="source" type="cr:sourceReference" substitutionGroup="cr:abstractReference"/></xml></code>

== User ==

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType userReference ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="userReference">
<xs:complexContent mixed="true">
<xs:extension base="cr:abstractReference">
<xs:sequence minOccurs="0" maxOccurs="unbounded">
<xs:any namespace="##any" processContents="skip"/>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element user ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="user" type="cr:userReference" substitutionGroup="cr:abstractReference"/></xml></code>

CrossRefs

Hampti — Wed, 17 May 2006 09:02:12 GMT

Summary:

== History ==

* [[CrossRefs 0.1]]: ''open''

== See also ==

* [[BioTypes]] schema

[[Category:Building block]]

Build Tools

Hampti — Wed, 17 May 2006 09:01:23 GMT

Summary:

The build tools automate XML Schema unit testing, documentation generation, version management and file releasing.

== Requirements ==

* [http://java.sun.com/ Java 1.4 or later]: Java runtime
* [http://ant.apache.org/ Apache Ant 1.6.4 or later]: Java-based build tool

== Components ==

Coming soon ...

== Usage ==

Coming soon ...

== Download ==

There is no official release, yet.

== Source code access ==

Get the latest release from the SVN repository:

<pre>https://svn.sourceforge.net/svnroot/bioschemas/bioschemas/trunk</pre>

== History ==

* ...

== Developers ==

* [http://szugat.gmx.home Martin Szugat]: Maintainer and contributor

[[Category:Tool]]

BioTypes 1.2

Hampti — Wed, 17 May 2006 08:57:01 GMT

Summary:

{{Header}}

== Introduction ==

For better reading and editing this schema is divided into different sections:

* [[#Basic|Basic]]: Basic type definitions.
* [[#Source|Source]]: Type definitions for specifying the source of biological data.
* [[#Sequence|Sequence]]: Type definitions for sequence data
* [[#Structure|Structure]]: Type definitions for structure data.
* [[#Classification|Classification]]: Type definitions for classification schemes.
* [[#Pattern|Pattern]]: Type definitions for sequence patterns.
* [[#Alignment|Alignment]]: Type definitions for sequence alignments.

The final release of this schema can be downloaded from http://schemas.bioservices.net/2005/.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
== Specification ==

=== schema http://schemas.bioservices.net/2005/biotypes ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" title="code"><xml><xs:schema xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" targetNamespace="http://schemas.bioservices.net/2005/biotypes" elementFormDefault="qualified" attributeFormDefault="unqualified" id="BioTypes" version="1.2" xml:lang="en"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The BioTypes schema provides a common XML type framework for biological data in analogy to the predefined XML Schema types. The recommended prefix for the BioTypes namespace is<i>bt</i>. For further information on usage visit<a href="http://schemas.bioservices.net">BioSchemas </a>.<p>To use BioTypes in an XML schema download a local copy of the BioTypes schema and include it via the <code>import</code> statement:</p><p><code>
<xs:import xmlns:xs="http://www.w3.org/2001/XMLSchema" schemaLocation="biotypes.xsd" namespace="http://schemas.bioservices.net/2005/biotypes"/></code></p><p>Content is available under <a href="http://creativecommons.org/licenses/by-sa/2.0/">Creative Commons Attribution-ShareAlike License</a>.</p>
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/tests.xsd'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/tests.xsd"><xml><xs:schema xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" targetNamespace="http://schemas.bioservices.net/2006/01/biotypes/tests" elementFormDefault="qualified" attributeFormDefault="unqualified">
<xs:import schemaLocation="../../biotypes.xsd" namespace="http://schemas.bioservices.net/2006/01/biotypes"/>
<xs:element name="root">
<xs:complexType>
<xs:sequence>
<xs:any namespace="##any" processContents="strict" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
<xs:anyAttribute namespace="##any" processContents="lax"/>
</xs:complexType>
</xs:element>
<xs:element name="index" type="bt:index"/>
<xs:element name="alphaIndex" type="bt:alphanumericIndex"/>
<xs:element name="version" type="bt:version"/>
<xs:element name="lsid" type="bt:lsid"/>
<xs:element name="sourceUri" type="bt:sourceUri"/>
<xs:element name="seq" type="bt:sequence"/>
<xs:element name="atomName" type="bt:atomName"/>
<xs:element name="container">
<xs:complexType>
<xs:complexContent>
<xs:extension base="bt:anyContent"/>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element name="item">
<xs:complexType>
<xs:attributeGroup ref="bt:dataAttrs"/>
</xs:complexType>
</xs:element>
<xs:element name="coord">
<xs:complexType>
<xs:attributeGroup ref="bt:coordinates3D"/>
</xs:complexType>
</xs:element>
<xs:element name="source" type="bt:source"/>
<xs:element name="atom" type="bt:atom" substitutionGroup="bt:abstractAtom"/>
<xs:element name="atomSeq" type="bt:atomSequence"/>
<xs:element name="patternProfile" type="bt:patternProfile"/>
<xs:element name="pattern" type="bt:pattern"/>
<xs:element name="aaMultipleAlignment" type="bt:multipleAlignment"/>
</xs:schema></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo"><xml><xs:appinfo>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="##missing">
<bt:mapping to="url"/>
<bt:mapping to="caption">Unknown</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:">
<bt:mapping to="url"/>
<bt:mapping to="caption">
<bt:attribute name="source"/>
</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:lsid:">
<bt:mapping to="url">lsidres:

<bt:attribute name="source"/>
</bt:mapping>
<bt:mapping to="caption">
<bt:attribute name="source"/>
</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:embl">
<bt:mapping to="caption">EMBL Nucleotide Sequence Database</bt:mapping>
<bt:mapping to="url">http://www.ebi.ac.uk/embl/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:entrez">
<bt:mapping to="caption">NCBI Entrez Gene</bt:mapping>
<bt:mapping to="url">http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:genbank">
<bt:mapping to="caption">NCBI GenBank</bt:mapping>
<bt:mapping to="url">http://www.ncbi.nlm.nih.gov/Genbank/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:hugo">
<bt:mapping to="caption">The Human Genome Organisation</bt:mapping>
<bt:mapping to="url">http://www.hugo-international.org/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:locuslink">
<bt:mapping to="caption">NCBI LocusLink</bt:mapping>
<bt:mapping to="url">http://www.ncbi.nlm.nih.gov/projects/LocusLink/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:mgd">
<bt:mapping to="caption">Mouse Genome Informatics</bt:mapping>
<bt:mapping to="url">http://www.informatics.jax.org/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:mgi">
<bt:mapping to="caption">Mouse Genome Informatics</bt:mapping>
<bt:mapping to="url">http://www.informatics.jax.org/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:rgd">
<bt:mapping to="caption">Rat Genome Database</bt:mapping>
<bt:mapping to="url">http://rgd.mcw.edu/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:sgd">
<bt:mapping to="caption">Saccharomyces Genome Database</bt:mapping>
<bt:mapping to="url">http://www.yeastgenome.org/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:pdb">
<bt:mapping to="caption">RCSB Protein Data Bank</bt:mapping>
<bt:mapping to="url">http://www.rcsb.org/pdb/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:swissprot">
<bt:mapping to="caption">Swiss-Prot</bt:mapping>
<bt:mapping to="url">http://au.expasy.org/sprot/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:dssp">
<bt:mapping to="caption">DSSP</bt:mapping>
<bt:mapping to="url">http://www.cmbi.kun.nl/gv/dssp/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:pdb">
<bt:mapping to="caption">RCSB Protein Data Bank</bt:mapping>
<bt:mapping to="url">http://www.rcsb.org/pdb/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:pdb">
<bt:mapping to="caption">RCSB Protein Data Bank</bt:mapping>
<bt:mapping to="url">http://www.rcsb.org/pdb/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:cath">
<bt:mapping to="caption">CATH</bt:mapping>
<bt:mapping to="url">http://www.ccbb.re.kr/irs/2_cath/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:scop">
<bt:mapping to="caption">SCOP</bt:mapping>
<bt:mapping to="url">http://scop.mrc-lmb.cam.ac.uk/scop/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:interpro">
<bt:mapping to="caption">EMBL Interpro</bt:mapping>
<bt:mapping to="url">http://www.ebi.ac.uk/interpro/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:pfam">
<bt:mapping to="caption">PFAM</bt:mapping>
<bt:mapping to="url">http://www.sanger.ac.uk/Software/Pfam/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:prodom">
<bt:mapping to="caption">ProDom</bt:mapping>
<bt:mapping to="url">http://protein.toulouse.inra.fr/prodom/current/html/home.php</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:prosite">
<bt:mapping to="caption">ExPASy PROSITE</bt:mapping>
<bt:mapping to="url">http://au.expasy.org/prosite/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:clustalw">
<bt:mapping to="caption">ClustalW</bt:mapping>
<bt:mapping to="url">http://www.ebi.ac.uk/clustalw/</bt:mapping>
</bt:source>
</xs:appinfo></xml></code>

'''references'''

* [http://schemas.bioservices.net/2005/biotypes BioTypes namespace URL]

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

== Basic ==

This section contains basic type definitions.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType index ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="index">
<xs:restriction base="xs:positiveInteger"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An one-based index. Indices should begin with 1 because zero-based indices might be confusing for humans and are a common source for errors, e.g. when a user assumes the numeration begins with 1.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestIndex.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestIndex.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<test:case test="with" result="pass" desc="index may be 1.">
<index>1</index>
</test:case>
<test:case test="with" result="fail" desc="index starts with 1.">
<index>0</index>
</test:case>
<test:case test="with" result="fail" desc="index must not be negative.">
<index>-1</index>
</test:case>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType alphanumericIndex ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="alphanumericIndex">
<xs:union memberTypes="bt:index">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:pattern value="[a-z]"/>
</xs:restriction>
</xs:simpleType>
</xs:union>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An alphanumeric index. Numeric indices should begin with 1. Alternatively the indices could be numbered using small letters: "a", "b", etc. A combination of letters is not allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAlphanumericIndex.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAlphanumericIndex.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<test:case test="with" result="pass" desc="alphaIndex may be 1.">
<alphaIndex>1</alphaIndex>
</test:case>
<test:case test="with" result="fail" desc="alphaIndex starts with 1.">
<alphaIndex>0</alphaIndex>
</test:case>
<test:case test="with" result="fail" desc="alphaIndex must not be negative.">
<alphaIndex>-1</alphaIndex>
</test:case>
<test:case test="with" result="pass" desc="alphaIndex may be a.">
<alphaIndex>a</alphaIndex>
</test:case>
<test:case test="with" result="fail" desc="alphaIndex must not be a uppercase letter.">
<alphaIndex>A</alphaIndex>
</test:case>
<test:case test="with" result="fail" desc="alphaIndex must not be empty.">
<alphaIndex/>
</test:case>
<test:case test="with" result="fail" desc="alphaIndex must not be a combination of letters.">
<alphaIndex>ab</alphaIndex>
</test:case>
</root></xml></code>

'''change log'''

* 06/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType version ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="version">
<xs:restriction base="xs:token">
<xs:pattern value="\d+(\.\d+)*"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A versioning number.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestVersion.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestVersion.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<test:case test="with" result="pass" desc="version may be a single digit.">
<version>1</version>
</test:case>
<test:case test="with" result="pass" desc="version may be a number.">
<version>11</version>
</test:case>
<test:case test="with" result="pass" desc="version may be a sequence of numbers.">
<version>11.0.1</version>
</test:case>
<test:case test="with" result="fail" desc="version must not be empty.">
<version/>
</test:case>
<test:case test="with" result="fail" desc="version must not end with a dot.">
<version>1.</version>
</test:case>
<test:case test="with" result="fail" desc="version must not contain characters other than digits.">
<version>1.x</version>
</test:case>
<test:case test="with" result="fail" desc="version must not contain two or more points in sequence.">
<version>1..1</version>
</test:case>
</root></xml></code>

'''change log'''

* 05/18/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType score ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="score">
<xs:restriction base="xs:double"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A scoring value. Scores can be positive or negative.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType anyContent ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="anyContent" mixed="true" abstract="true">
<xs:sequence minOccurs="0" maxOccurs="unbounded">
<xs:any namespace="##any" processContents="lax"/>
</xs:sequence>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Allows any mixed content, i.e. text and elements from any namespace.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestContainer.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestContainer.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<test:case test="with" result="pass" desc="A container may contain elements from foreign namespaces and text.">
<container>Prefix
<ext:item xmlns:ext="urn:other"/>
Infix
<ext2:item xmlns:ext2="urn:other2"/>
Postfix
</container>
</test:case>
<test:case test="with" result="pass" desc="A container may contain elements from the target namespace.">
<container>Prefix
<item/>
Infix
<item/>
Postfix
</container>
</test:case>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType dateOptionalTime ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="dateOptionalTime">
<xs:union memberTypes="xs:date xs:dateTime"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A date and eventually a time information.
</div>

'''change log'''

* 05/22/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType missing ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="missing">
<xs:restriction base="xs:token">
<xs:enumeration value="##missing"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Marks an optional attribute value as missing. This should be the default value for the attribute. This special enumeration value is necessary because optional attributes without a default value could not be used within a key declaration.
</div>

'''change log'''

* 05/22/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType sourceDate ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="sourceDate">
<xs:restriction base="bt:dateOptionalTime"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The date (and eventually time) the corresponding data item was retrieved from the data source.
</div>

'''change log'''

* 05/22/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType optionalSourceDate ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="optionalSourceDate">
<xs:union memberTypes="bt:sourceDate bt:missing"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The date (and eventually time) the corresponding data item was retrieved from the data source, or<code>##missing</code>as the default value.
</div>

'''change log'''

* 05/22/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType sourceVersion ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="sourceVersion">
<xs:restriction base="bt:version"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The version of the data source from whom the data item was retrieved.
</div>

'''change log'''

* 05/22/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType optionalSourceVersion ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="optionalSourceVersion">
<xs:union memberTypes="bt:sourceVersion bt:missing"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The version of the data source from whom the data item was retrieved, or<code>##missing</code>as the default value.
</div>

'''change log'''

* 05/22/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup dataAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="dataAttrs">
<xs:attribute name="version" type="bt:optionalSourceVersion" use="optional" default="##missing"/>
<xs:attribute name="date" type="bt:optionalSourceVersion" use="optional" default="##missing"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The attributes for a data item. A data item is an element which holds data that should be regarded as a single unit in contrast to a data collection which holds multiple units of data, i.e. data items. In addition to the optional<code>version</code>and<code>date</code>attributes, specifying the version of the data source and the date (and eventually the time) the data item was retrieved, a data item should declare a<code>source</code>attribute of type<code>sourceUri</code>and a<code>accNumber</code>attribute of type<code>accessionNumber</code>, specifying the data source of the data item and its accession number within the data source.
</div>

'''references'''

* [[#simpleType_sourceUri|simpleType sourceUri]]
* [[#simpleType_accessionNumber|simpleType accessionNumber]]

'''change log'''

* 05/22/05 by [http://szugat.gmxhome.de Martin Szugat]: Declared type dateOptionalTime.
* 05/10/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup scopeAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="scopeAttrs">
<xs:attribute name="from" type="bt:index" use="required"/>
<xs:attribute name="to" type="bt:index" use="required"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Attributes for setting a range.<code>from</code>should be less than<code>to</code>.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

== Source ==

This section contains type declarations for specifying the source of biological data.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType crossRefType ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="crossRefType">
<xs:sequence>
<xs:choice>
<xs:sequence>
<xs:element name="databaseName" type="xs:string">
<xs:annotation>
<xs:documentation>name of the database, should be from a controled vocabulary, to be done</xs:documentation>
</xs:annotation>
</xs:element>
<xs:element name="entryID" type="xs:string"/>
<xs:element name="databaseURL" type="xs:string" minOccurs="0"/>
</xs:sequence>
<xs:element name="lsid" type="bt:lsid"/>
</xs:choice>
</xs:sequence>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An element of type 'crossRefType' can be used to add a reference to a source of an object of biological data, by giving either its lsid or a database name and Entry Id (and optionally a DB URL)
</div>

'''change log'''
* 01/02/06 by [Sven Hartmeier]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType lsid ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="lsid">
<xs:restriction base="xs:anyURI">
<xs:pattern value="urn:lsid:(\c|/)+:(\c|/)+:\c+(:\c+)?"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A Life Sciences Identifier (LSID) is a URN that uniquely names an object. According to the<a href="http://lsid.sourceforge.net/">LSID Resolution Protocol Project</a>the syntax is<code>urn:lsid:<authority>:<namespace>:<value>:<version></code>where<code>authority</code>is the name of the organization that has defined an entity,<code>namespace</code>is a namespace within the authority for the Id,<code>value</code>is an alpha-numeric sequence that uniquely identifies an object to its authority, and<code>version</code>is an optional version number for an Id.<code>authority</code>and<code>namespace</code>can have hierarchical path elements separated by "/".
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestLSID.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestLSID.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<test:case test="with" result="pass" desc="lsid need not to have a revision.">
<lsid>urn:lsid:authority:namespace:identifier</lsid>
</test:case>
<test:case test="with" result="pass" desc="lsid may have a revision. ">
<lsid>urn:lsid:authority:namespace:identifier:1</lsid>
</test:case>
<test:case test="with" result="fail" desc="lsid must a have an urn prefix.">
<lsid>lsid:authority:namespace:identifier</lsid>
</test:case>
<test:case test="with" result="fail" desc="lsid must have a lsid prefix.">
<lsid>urn:authority:namespace:identifier</lsid>
</test:case>
<test:case test="with" result="fail" desc="lsid must have an identifier.">
<lsid>urn:lsid:authority:namespace</lsid>
</test:case>
<test:case test="with" result="fail" desc="lsid must have a namespace.">
<lsid>urn:lsid:authority::identifier</lsid>
</test:case>
<test:case test="with" result="fail" desc="lsid must have an authority.">
<lsid>urn:lsid::namespace:identifier</lsid>
</test:case>
<test:case test="with" result="pass" desc="authority and namespace may include slashes.">
<lsid>urn:lsid:authority/sub:namespace/sub:identifier</lsid>
</test:case>
</root></xml></code>

'''references'''
* [http://lsid.sourceforge.net LSID Resolution Protocol Project]

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType sourceUri ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="sourceUri" final="restriction">
<xs:union memberTypes="bt:lsid">
<xs:simpleType>
<xs:restriction base="xs:anyURI">
<xs:minLength value="1"/>
</xs:restriction>
</xs:simpleType>
</xs:union>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The URI of a data source. This may be an URL, an URN or a LSID.
</div>

'''references'''
* [[#simpleType_lsid|simpleType lsid]]
* [[#complexType_source|complexType source]]
* [http://lsid.sourceforge.net LSID Resolution Protocol Project]

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType optionalSourceUri ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="optionalSourceUri">
<xs:union memberTypes="bt:sourceUri bt:missing"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The URI of a data source. This may be an URL, an URN or a LSID or<code>##missing</code>as the default value.
</div>

'''change log'''

* 05/22/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType accessionNumber ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="accessionNumber">
<xs:restriction base="xs:token">
<xs:minLength value="1"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Specifies the accession number of a data item relative to its data source. The format of the accession number depends on the data source.
</div>

'''references'''
* [[#complexType_source|complexType source]]

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType source ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="source" mixed="true">
<xs:complexContent>
<xs:extension base="bt:anyContent">
<xs:attribute name="uri" type="bt:optionalSourceUri" use="required" form="unqualified"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The description of a data source. The data source is identified by the<code>uri</code>attribute. The content may be source specific. It may consist e.g. of one or more<code>mapping</code>elements which map the source URI to an URL or a caption. Such a mapping is demonstrated by the<a href="http://schemas.bioservices.net/index.php?title=BioTypes_stylesheet">BioTypes stylesheet</a>.
</div>

'''references'''
* [[#element_source|element source]]
* [[#element_mapping|element mapping]]
* [[BioTypes stylesheet]]

'''change log'''

* 05/10/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element source ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="source">
<xs:complexType>
<xs:complexContent>
<xs:extension base="bt:source">
<xs:anyAttribute namespace="##other" processContents="lax"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The description of a data source.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestSource.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestSource.xml"><xml><bst:root xmlns:bst="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<bst:source uri="test">
<test:attribute name="uri" result="fail" desc="source must have a uri."/>
<test:attribute name="uri" value="urn:bts:cath" result="pass" desc="source uri may be a predefined name."/>
<test:attribute name="uri" value="urn:org.db:id" result="pass" desc="source uri may be a custom URN."/>
<test:attribute name="uri" value="http://www.db.org/id" result="pass" desc="source uri may be a custom URL."/>
<test:attribute name="uri" value="urn:lsid:authority:namespace:identifier" result="pass" desc="source uri may be a LSID."/>
<test:attribute name="uri" value="##missing" result="pass" desc="source uri may be ##missing."/>
<test:case test="with" result="pass" desc="source may contain any content.">
Prefix<ext:item xmlns:ext="urn:other">Infix</ext:item>Postfix
</test:case>
</bst:source>
</bst:root></xml></code>

'''references'''

* [[#complexType_source|complexType source]]

'''change log'''

* 01/02/06 by [http://szugat.gmxhome.de Martin Szugat]: Added tests
* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element mapping ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="mapping">
<xs:complexType>
<xs:complexContent>
<xs:extension base="bt:anyContent">
<xs:attribute name="to" use="required">
<xs:simpleType>
<xs:union memberTypes="xs:token">
<xs:simpleType>
<xs:restriction base="xs:token">
<xs:enumeration value="url"/>
<xs:enumeration value="caption"/>
</xs:restriction>
</xs:simpleType>
</xs:union>
</xs:simpleType>
</xs:attribute>
<xs:anyAttribute namespace="##other" processContents="lax"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The mapping of a value to another representation. The<code>to</code>attribute specifies the representation. A mapping is used e.g. within a<code>source</code>element to map the data source URI to an URL. It is used by the<a href="http://schemas.bioservices.net/index.php?title=BioTypes_stylesheet">BioTypes stylesheet</a>. Its content may be mapping specific, e.g. text and one or more<code>attribute</code>elements. For each subordinated element the processing application or stylesheet should be ready to process it, i.e. there must be appropiate template.
</div>

'''references'''

* [[BioTypes stylesheet]]

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element attribute ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="attribute">
<xs:complexType>
<xs:attribute name="name" type="xs:Name" use="required"/>
<xs:attribute name="namespace" type="xs:anyURI" use="optional"/>
<xs:anyAttribute namespace="##other" processContents="lax"/>
</xs:complexType>
</xs:element></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Evaluates an attribute. This element can be used e.g. inside a<code>mapping</code>element. During the mapping process it should be replaced by the concrete value of the attribute.
</div>

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

== Sequence ==

This section contains type declarations for biological sequence data.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType sequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="sequence">
<xs:restriction base="xs:string">
<xs:minLength value="1"/>
<xs:whiteSpace value="preserve"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of character data of length greater than zero.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<seq>
<test:case test="with" result="fail" desc="sequence must not be empty."/>
<test:case test="with" result="pass" desc="sequence may contain any number of characters.">ABCDEFGHIJKLMNOPQRSTVWXYZabcdefghijklmnopqrstvwxyz</test:case>
<test:case test="with" result="pass" desc="sequence may contain whitespace and line breaks.">
AA
AA
</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAmbiguousNucleotideSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAmbiguousNucleotideSequence">
<xs:restriction base="bt:sequence">
<xs:pattern value="(A|G|C|T|U|R|Y|M|K|S|W|H|B|V|D|N|X|\-)+"/>
<xs:whiteSpace value="collapse"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of nucleotides (RNA and DNA) or its placeholders in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedAmbiguousNucleotideSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedAmbiguousNucleotideSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedAmbiguousNucleotideSequence">
<test:case test="with" result="fail" desc="gapped ambiguous nucleotide sequence must not be empty."/>
<test:case test="with" result="fail" desc="gapped ambiguous nucleotide sequence must not contain lower case characters.">a</test:case>
<test:case test="with" result="pass" desc="gapped ambiguous nucleotide sequence may contain any number of nucleotides, ambiguous characters and gaps.">ACGTURYMKSWHBVDNX-</test:case>
<test:case test="with" result="pass" desc="gapped ambiguous nucleotide sequence may contain line breaks at the beginning and at the end.">
AAAA
</test:case>
<test:case test="with" result="fail" desc="gapped ambiguous nucleotide must not contain line breaks in between.">
AA
AA
</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedNucleotideSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedNucleotideSequence">
<xs:restriction base="bt:gappedAmbiguousNucleotideSequence">
<xs:pattern value="(A|G|C|T|U|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of nucleotides (RNA and DNA) in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedNucleotideSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedNucleotideSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedNucleotideSequence">
<test:case test="with" result="fail" desc="gapped nucleotide sequence must not contain ambiguous characters.">RYMKSWHBVDNX</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType ambiguousNucleotideSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="ambiguousNucleotideSequence">
<xs:restriction base="bt:gappedAmbiguousNucleotideSequence">
<xs:pattern value="(A|G|C|T|U|R|Y|M|K|S|W|H|B|V|D|N|X)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of nucleotides (RNA and DNA) or its placeholders in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAmbiguousNucleotideSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAmbiguousNucleotideSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<seq xsi:type="bt:ambiguousNucleotideSequence">
<test:case test="with" result="fail" desc="ambiguous nucleotide sequence must not contain gap characters.">-</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType nucleotideSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="nucleotideSequence">
<xs:restriction base="bt:ambiguousNucleotideSequence">
<xs:pattern value="(A|G|C|T|U)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of nucleotides (RNA and DNA) in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestNucleotideSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestNucleotideSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<seq xsi:type="bt:nucleotideSequence">
<test:case test="with" result="fail" desc="nucleotide sequence must not contain gap characters or ambiguous characters.">-X</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType nucleotideSequenceSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="nucleotideSequenceSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:embl"/>
<xs:enumeration value="urn:bts:entrez"/>
<xs:enumeration value="urn:bts:genbank"/>
<xs:enumeration value="urn:bts:hugo"/>
<xs:enumeration value="urn:bts:locuslink"/>
<xs:enumeration value="urn:bts:mgd"/>
<xs:enumeration value="urn:bts:mgi"/>
<xs:enumeration value="urn:bts:rgd"/>
<xs:enumeration value="urn:bts:sgd"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined nucleotide sequence source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType nucleotideSequenceSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="nucleotideSequenceSource">
<xs:union memberTypes="bt:sourceUri bt:nucleotideSequenceSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of a nucleotide sequence. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_nucleotideSequenceSources|simpleType nucleotideSequenceSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup nucleotideSequenceAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="nucleotideSequenceAttrs">
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
<xs:attribute name="source" type="bt:nucleotideSequenceSource" use="optional"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Attributes for nucleotide sequences.<code>source</code>specifies the source of the sequence. In addition<code>accNumber</code>can be set to an accession number dependant on the data source if<code>source</code>identifies only the data source (e.g. database) but not the data item itself.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAmbiguousDnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAmbiguousDnaSequence">
<xs:restriction base="bt:gappedAmbiguousNucleotideSequence">
<xs:pattern value="(A|G|C|T|R|Y|M|K|S|W|H|B|V|D|N|X|\-)+"/>
<xs:whiteSpace value="collapse"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of DNAs or its placeholders in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedAmbiguousDnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedAmbiguousDnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedAmbiguousDnaSequence">
<test:case test="with" result="fail" desc="gapped ambiguous dna sequence must not contain Uracil.">U</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedDnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedDnaSequence">
<xs:restriction base="bt:gappedAmbiguousDnaSequence">
<xs:pattern value="(A|G|C|T|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of DNAs in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedDnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedDnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedDnaSequence">
<test:case test="with" result="fail" desc="gapped dna sequence must not contain ambiguous characters.">RYMKSWHBVDNX</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType ambiguousDnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="ambiguousDnaSequence">
<xs:restriction base="bt:gappedAmbiguousDnaSequence">
<xs:pattern value="(A|G|C|T|R|Y|M|K|S|W|H|B|V|D|N|X)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of DNAs or its placeholders in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAmbiguousDnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAmbiguousDnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<seq xsi:type="bt:ambiguousDnaSequence">
<test:case test="with" result="fail" desc="ambiguous dna sequence must not contain gap characters.">-</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType dnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="dnaSequence">
<xs:restriction base="bt:ambiguousDnaSequence">
<xs:pattern value="(A|G|C|T)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of DNAs in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestDnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestDnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<seq xsi:type="bt:dnaSequence">
<test:case test="with" result="fail" desc="dna sequence must not contain gap characters or ambiguous characters.">-X</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAmbiguousRnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAmbiguousRnaSequence">
<xs:restriction base="bt:gappedAmbiguousNucleotideSequence">
<xs:pattern value="(A|G|C|U|R|Y|M|K|S|W|H|B|V|D|N|X|\-)+"/>
<xs:whiteSpace value="collapse"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of RNAs or its placeholders in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedAmbiguousRnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedAmbiguousRnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedAmbiguousRnaSequence">
<test:case test="with" result="fail" desc="gapped ambiguous rna sequence must not contain Thymin.">T</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedRnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedRnaSequence">
<xs:restriction base="bt:gappedAmbiguousRnaSequence">
<xs:pattern value="(A|G|C|U|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of DNAs in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedRnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedRnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedRnaSequence">
<test:case test="with" result="fail" desc="gapped rna sequence must not contain ambiguous characters.">RYMKSWHBVDNX</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType ambiguousRnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="ambiguousRnaSequence">
<xs:restriction base="bt:gappedAmbiguousRnaSequence">
<xs:pattern value="(A|G|C|U|R|Y|M|K|S|W|H|B|V|D|N|X)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of RNAs or its placeholders in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAmbiguousRnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAmbiguousRnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<seq xsi:type="bt:ambiguousRnaSequence">
<test:case test="with" result="fail" desc="ambiguous rna sequence must not contain gap characters.">-</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType rnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="rnaSequence">
<xs:restriction base="bt:ambiguousRnaSequence">
<xs:pattern value="(A|G|C|U)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of RNAs in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestRnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestRnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<seq xsi:type="bt:rnaSequence">
<test:case test="with" result="fail" desc="rna sequence must not contain gap characters or ambiguous characters.">-X</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAmbiguousTerminalAminoAcidOneLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAmbiguousTerminalAminoAcidOneLetterSequence">
<xs:restriction base="bt:sequence">
<xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|X|B|Z|\-|\*)+"/>
<xs:whiteSpace value="collapse"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case one letter code including the terminal symbol *, ambigiuous and gap characters. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAmbiguousAminoAcidOneLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAmbiguousAminoAcidOneLetterSequence">
<xs:restriction base="bt:gappedAmbiguousTerminalAminoAcidOneLetterSequence">
<xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|X|B|Z|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case one letter code, ambigiuous and gap characters. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 05/10/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType ambiguousAminoAcidOneLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="ambiguousAminoAcidOneLetterSequence">
<xs:restriction base="bt:gappedAmbiguousTerminalAminoAcidOneLetterSequence">
<xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|X|B|Z)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case one letter code and ambigiuous characters. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAminoAcidOneLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAminoAcidOneLetterSequence">
<xs:restriction base="bt:gappedAmbiguousTerminalAminoAcidOneLetterSequence">
<xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case one letter code and gap characters. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType terminalAminoAcidOneLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="terminalAminoAcidOneLetterSequence">
<xs:restriction base="bt:gappedAmbiguousTerminalAminoAcidOneLetterSequence">
<xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|\*)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case one letter code including the terminal symbol *. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType aminoAcidOneLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="aminoAcidOneLetterSequence">
<xs:restriction base="bt:ambiguousAminoAcidOneLetterSequence">
<xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case one letter code. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType terminalAminoAcidThreeLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="terminalAminoAcidThreeLetterSequence">
<xs:restriction base="bt:sequence">
<xs:pattern value="(ALA|ARG|ASN|ASP|CYS|GLN|GLU|GLY|HIS|ILE|LEU|LYS|MET|PHE|PRO|SER|THR|SEC|TRP|TYR|VAL|TER)+"/>
<xs:whiteSpace value="collapse"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case three letter code including the terminal symbol TER. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestTerminalAminoAcidThreeLetterSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestTerminalAminoAcidThreeLetterSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<seq xsi:type="bt:terminalAminoAcidThreeLetterSequence">
<test:case test="with" result="fail" desc="terminal amino acid three letter sequence must not be empty."/>
<test:case test="with" result="fail" desc="terminal amino acid three letter sequence must not contain lower case characters.">ala</test:case>
<test:case test="with" result="fail" desc="terminal amino acid three letter sequence must not contain illegal character combinations.">XZY</test:case>
<test:case test="with" result="pass" desc="terminal amino acid thre letter sequence may contain any number of amino acids in three letter code and the terminal signal.">ALAARGASNASPCYSGLNGLUGLYHISILELEULYSMETPHEPROSERTHRSECTRPTYRVALTER</test:case>
</seq>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType aminoAcidThreeLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="aminoAcidThreeLetterSequence">
<xs:restriction base="bt:terminalAminoAcidThreeLetterSequence">
<xs:pattern value="(ALA|ARG|ASN|ASP|CYS|GLN|GLU|GLY|HIS|ILE|LEU|LYS|MET|PHE|PRO|SER|THR|SEC|TRP|TYR|VAL)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case three letter code. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAminoAcidThreeLetterSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAminoAcidThreeLetterSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<seq xsi:type="bt:aminoAcidThreeLetterSequence">
<test:case test="with" result="fail" desc="amino acid three letter sequence must not contain the terminal signal.">TER</test:case>
</seq>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType aminoAcidSequenceSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="aminoAcidSequenceSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:pdb"/>
<xs:enumeration value="urn:bts:swissprot"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined amino acid sequence source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType aminoAcidSequenceSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="aminoAcidSequenceSource">
<xs:union memberTypes="bt:sourceUri bt:aminoAcidSequenceSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of a amino acid sequence. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_aminoAcidSequenceSources|simpleType aminoAcidSequenceSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup aminoAcidSequenceAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="aminoAcidSequenceAttrs">
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
<xs:attribute name="source" type="bt:aminoAcidSequenceSource" use="optional"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Attributes for amino acid sequences.<code>source</code>specifies the source of the sequence. In addition<code>accNumber</code>can be set to an accession number dependant on the data source if<code>source</code>identifies only the data source (e.g. database) but not the data item itself.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAmbiguousSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAmbiguousSecondaryStructureSequence">
<xs:restriction base="bt:sequence">
<xs:pattern value="(C|H|G|I|E|B|T|S|_|X|\-)+"/>
<xs:whiteSpace value="replace"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of secondary structure assignments or its placeholder in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedAmbiguousSecondaryStructureSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedAmbiguousSecondaryStructureSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedAmbiguousSecondaryStructureSequence">
<test:case test="with" result="fail" desc="gapped ambiguous secondary structure sequence must not be empty."/>
<test:case test="with" result="fail" desc="gapped ambiguous secondary structure sequence must not contain lower case characters.">a</test:case>
<test:case test="with" result="pass" desc="gapped ambiguous secondary structure sequence may contain any number of secondary structures, ambiguous characters and gaps.">CHGIEBTS_X-</test:case>
<test:case test="with" result="fail" desc="gapped ambiguous secondary structure must not contain line breaks in between.">
SS
SS
</test:case>
</seq>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType ambiguousSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="ambiguousSecondaryStructureSequence">
<xs:restriction base="bt:gappedAmbiguousSecondaryStructureSequence">
<xs:pattern value="(C|H|G|I|E|B|T|S|_|X)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of secondary structure assignments or its placeholder in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAmbiguousSecondaryStructureSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAmbiguousSecondaryStructureSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<seq xsi:type="bt:ambiguousSecondaryStructureSequence">
<test:case test="with" result="fail" desc="ambiguous secondary structure sequence must not contain gap characters.">-</test:case>
</seq>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedSecondaryStructureSequence">
<xs:restriction base="bt:gappedAmbiguousSecondaryStructureSequence">
<xs:pattern value="(C|H|G|I|E|B|T|S|_|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of secondary structure assignments in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedSecondaryStructureSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedSecondaryStructureSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedSecondaryStructureSequence">
<test:case test="with" result="fail" desc="gapped secondary structure sequence must not contain ambiguous character.">X</test:case>
</seq>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType secondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="secondaryStructureSequence">
<xs:restriction base="bt:gappedAmbiguousSecondaryStructureSequence">
<xs:pattern value="(C|H|G|I|E|B|T|S|_)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of secondary structure assignments in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestSecondaryStructureSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestSecondaryStructureSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<seq xsi:type="bt:secondaryStructureSequence">
<test:case test="with" result="fail" desc="secondary structure sequence must not contain ambiguous character or gap character.">X-</test:case>
</seq>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType secondaryStructureSequenceSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="secondaryStructureSequenceSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:dssp"/>
<xs:enumeration value="urn:bts:pdb"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined secondary structure sequence source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType secondaryStructureSequenceSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="secondaryStructureSequenceSource">
<xs:union memberTypes="bt:sourceUri bt:secondaryStructureSequenceSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of a secondary structure sequence. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_secondaryStructureSequenceSources|simpleType secondaryStructureSequenceSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup secondaryStructureSequenceAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="secondaryStructureSequenceAttrs">
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
<xs:attribute name="source" type="bt:secondaryStructureSequenceSource" use="optional"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Attributes for secondary structure sequences.<code>source</code>specifies the source of the sequence. In addition<code>accNumber</code>can be set to an accession number dependant on the data source if<code>source</code>identifies only the data source (e.g. database) but not the data item itself.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedRnaSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedRnaSecondaryStructureSequence">
<xs:restriction base="bt:sequence">
<xs:pattern value="($|$|\[|\]|\{|\}|<|>|\.|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of secondary structure assignments in dot-bracket format and gap characters. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 01/02/06 by [http://bibiserv.techfak.uni-bielefeld.de Kai Loewenthal]: added bracket-pair < > for pseudoknot structures
* 11/04/05 by [http://bibiserv.techfak.uni-bielefeld.de Jan Krueger]: add additional bracket-pairs for pseudoknot structures
* 10/19/05 by [http://biozentrum.uni-wuerzburg.de Philipp Seibel]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType rnaSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="rnaSecondaryStructureSequence">
<xs:restriction base="bt:gappedRnaSecondaryStructureSequence">
<xs:pattern value="($|$|\[|\]|\{|\}|<|>|\.)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of rna secondary structure assignments in dot-bracket notation. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 01/02/06 by [http://bibiserv.techfak.uni-bielefeld.de Kai Loewenthal]: added bracket-pair < > for pseudoknot structures
* 11/04/05 by [http://bibiserv.techfak.uni-bielefeld.de Jan Krueger]: add additional bracket-pairs for pseudoknot structures
* 10/19/05 by [http://biozentrum.uni-wuerzburg.de Philipp Seibel]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType rnaSecondaryStructureSequenceClass ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="rnaSecondaryStructureSequenceClass">
<xs:restriction base="bt:sequence">
<xs:pattern value="($|$|\[|\]|\{|\}|<|>|_)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A class of rna secondary structure sequences in shape notation.
</div>

'''change log'''

* 01/02/06 by [http://bibiserv.techfak.uni-bielefeld.de Kai Loewenthal]: Initial declaration.

== Structure ==

This section contains type, attribute and element declarations for atom structures.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType atomNames ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="atomNames">
<xs:restriction base="xs:token">
<xs:enumeration value="H"/>
<xs:enumeration value="C"/>
<xs:enumeration value="CA"/>
<xs:enumeration value="CB"/>
<xs:enumeration value="O"/>
<xs:enumeration value="N"/>
<xs:enumeration value="S"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined atom names.<p>This list contains the following atom names:</p><ul><li><code>H</code>: hydrogen atom</li><li><code>C</code>: carbon atom</li><li><code>CA</code>: alpha carbon atom</li><li><code>CB</code>: beta carbon atom</li><li><code>O</code>: oxygen atom</li><li><code>N</code>: nitrogen atom</li><li><code>S</code>: sulphur atom</li></ul>
</div>

'''references'''
* [[#simpleType_atomName|simpleType atomName]]

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType atomName ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="atomName">
<xs:union memberTypes="bt:atomNames">
<xs:simpleType>
<xs:restriction base="xs:token">
<xs:minLength value="1"/>
</xs:restriction>
</xs:simpleType>
</xs:union>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The (abbreviated) name of an atom within a biological molecule. The name must be at least one character long and may contain numbers but not at the beginning.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAtomName.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAtomName.xml"><xml><root xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<test:case test="with" result="fail" desc="atom name must not be empty.">
<atomName/>
</test:case>
<test:case test="with" result="pass" desc="atom name may contain any number of token characters.">
<atomName>B1</atomName>
</test:case>
<test:case test="with" result="pass" desc="atom name must not start with a digit.">
<atomName>1B</atomName>
</test:case>
</root></xml></code>

'''references'''
* [[#simpleType_atomNames|simpleType atomNames]]

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType coordinate ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="coordinate">
<xs:restriction base="xs:double"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A coordinate in a n-dimensional space.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType distance ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="distance">
<xs:restriction base="xs:double">
<xs:minInclusive value="0.0"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A distance in a n-dimensional space. A distance may not be negative.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType distanceUnits ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="distanceUnits">
<xs:restriction base="xs:token">
<xs:enumeration value="angstroem"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of possible distance units.<p>This list contains the following entries:</p><ul><li><code>angstroem</code>: Angstroem</li></ul>
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType atomStructureSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="atomStructureSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:pdb"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined atom structure source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType atomStructureSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="atomStructureSource">
<xs:union memberTypes="bt:sourceUri bt:atomStructureSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of an atom structure. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_atomSequenceSources|simpleType atomSequenceSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup coordinates3D ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="coordinates3D">
<xs:attribute name="x" type="bt:coordinate" use="required" form="unqualified"/>
<xs:attribute name="y" type="bt:coordinate" use="required" form="unqualified"/>
<xs:attribute name="z" type="bt:coordinate" use="required" form="unqualified"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Coordinates in a 3-dimensional space.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestCoordinates3D.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestCoordinates3D.xml"><xml><coord xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" y="1.0" z="1.0" x="1.0" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<test:attribute id="x" name="x" result="fail" desc="3-D-coordinates must have a x value."/>
<test:attribute name="y" result="fail" desc="3-D-coordinates must have a y value."/>
<test:attribute name="z" result="fail" desc="3-D-coordinates must have a z value."/>
</coord></xml></code>

'''change log'''

* 04/26/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType atom ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="atom" block="restriction" final="restriction">
<xs:attributeGroup ref="bt:coordinates3D"/>
<xs:attribute name="type" type="bt:atomName" use="required" form="unqualified"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A single atom including its coordinates in 3-dimensional space and its type.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAtom.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAtom.xml"><xml><atom xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd" x="1.0" y="1.0" z="1.0" type="C">
<test:attribute name="type" result="fail" desc="atom must have a type."/>
</atom></xml></code>

'''references'''
* [[#attributeGroup_coordinates3D|attributeGroup coordinates3D]]

'''change log'''

* 04/26/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractAtom ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractAtom" type="bt:atom" abstract="true" block="restriction" final="restriction"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An abstract atom element for the atomSeq element.
</div>

'''references'''
* [[#complexType_atom|complexType atom]]
* [[#complexType_atomSeq|complexType atomSeq]]

'''change log'''

* 04/26/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup structureAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="structureAttrs">
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
<xs:attribute name="source" type="bt:atomStructureSource" use="optional"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Attributes for structure data.<code>source</code>specifies the source of the structure data. In addition<code>accNumber</code>can be set to an accession number dependant on the data source if<code>source</code>identifies only the data source (e.g. database) but not the data item itself.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType atomSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="atomSequence" block="restriction" final="restriction">
<xs:sequence>
<xs:element ref="bt:abstractAtom" minOccurs="1" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attributeGroup ref="bt:structureAttrs"/>
<xs:attribute name="unit" type="bt:distanceUnits" use="optional" default="angstroem"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of atoms. An atom sequence must contain at least one atom. The<code>abstractAtom</code>element must be replaced by a concrete element of type<code>atom</code>. This is done via a substitution group:<p><code>
<xs:element xmlns:xs="http://www.w3.org/2001/XMLSchema" name="atom" type="bt:atom" substitutionGroup="bt:abstractAtom"/></code>.</p><p>The coordinates of each atom are relative to the specified distance unit (default is Angstroem).</p>
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAtomSeq.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAtomSeq.xml"><xml><atomSeq xmlns="http://schemas.bioservices.net/2006/01/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2006/01/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2006/01/biotypes/tests tests.xsd">
<test:case test="with" result="fail" desc="atomSeq must not be empty."/>
<test:case test="with" result="pass" desc="atomSeq may contain one or more atoms.">
<atom y="1.0" z="1.0" type="C" x="1.0"/>
<atom y="1.0" z="1.0" type="C" x="1.0"/>
</test:case>
</atomSeq></xml></code>

'''references'''
* [[#complexType_atom|complexType atom]]
* [[#element_atom|element atom]]

'''change log'''

* 04/26/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType atomConnection ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="atomConnection" abstract="true" block="restriction" final="restriction">
<xs:attribute name="atomType1" type="bt:atomName" use="required"/>
<xs:attribute name="atomType2" type="bt:atomName" use="required"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Specifies a connection between two atoms identified by<code>atomType1</code>and<code>atomType2</code>. A connection can be e.g. a bond or a contact.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType atomContact ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="atomContact">
<xs:complexContent>
<xs:extension base="bt:atomConnection">
<xs:attribute name="distance" type="bt:distance" use="required"/>
<xs:attribute name="unit" type="bt:distanceUnits" use="optional" default="angstroem"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Specifies a (close) contact between two atoms. The distance of the two atoms is specified by<code>distance</code>. The unit of the distance depends on<code>unit</code>. The default setting for<code>unit</code>is<code>angstroem</code>.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

== Classification ==

This section contains type declaration for the classification of biological objects.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType classificationSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="classificationSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:cath"/>
<xs:enumeration value="urn:bts:scop"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined classification source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType classificationSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="classificationSource">
<xs:union memberTypes="bt:sourceUri bt:classificationSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of a classification. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_classificationSources|simpleType classificationSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType classificationValue ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="classificationValue">
<xs:restriction base="xs:token">
<xs:minLength value="1"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Obsolete.
</div>

'''change log'''

* 05/22/05 by [http://szugat.gmxhome.de Martin Szugat]: Declared as obsolete.
* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType classification ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="classification">
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="source" type="bt:classificationSource" use="required"/>
<xs:attribute name="accNumber" type="bt:classificationValue" use="required"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Specifies a classification. The classification scheme is identified by<code>source</code>. The classification itself is specified by<code>accNumber</code>.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

== Pattern ==

This section contains type declaration for sequence patterns.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType patternSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="patternSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:interpro"/>
<xs:enumeration value="urn:bts:pfam"/>
<xs:enumeration value="urn:bts:prodom"/>
<xs:enumeration value="urn:bts:prosite"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined sequence pattern source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType patternSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="patternSource">
<xs:union memberTypes="bt:sourceUri bt:patternSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of a sequence pattern. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_patternSources|simpleType patternSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup patternAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="patternAttrs">
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="source" type="bt:patternSource" use="required"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="required"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Attributes for pattern data.<code>source</code>specifies the source of the pattern data. In addition<code>accNumber</code>can be set to an accession number dependant on the data source if<code>source</code>identifies only the data source (e.g. database) but not the data item itself.
</div>

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType patternBase ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="patternBase" mixed="true">
<xs:complexContent>
<xs:extension base="bt:anyContent">
<xs:attributeGroup ref="bt:patternAttrs"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence pattern. The content of a pattern element is the pattern itself, e.g. a consensus sequence or a HMM, and may contain elements from any namespace and text.
</div>

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType patternProfile ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="patternProfile">
<xs:sequence>
<xs:element ref="bt:abstractPatternProfileMember" minOccurs="1" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="source" type="bt:patternSource" use="optional"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence pattern profile. A profile must contain at least one pattern reference.
</div>

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Made pattern abstract.
* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType patternProfileMember ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="patternProfileMember" block="restriction" final="restriction">
<xs:complexContent>
<xs:extension base="bt:patternBase">
<xs:attribute name="occurence" type="xs:positiveInteger" use="required"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A member of a pattern profile. The number of occurences of the pattern in the sequence(s) must be specified.
</div>

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Made pattern abstract.
* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractPatternProfileMember ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractPatternProfileMember" type="bt:patternProfileMember" abstract="true" block="restriction" final="restriction"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Abstract pattern element for a pattern profile.
</div>

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Made pattern abstract.
* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType pattern ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="pattern" mixed="true">
<xs:complexContent>
<xs:extension base="bt:patternBase">
<xs:attributeGroup ref="bt:scopeAttrs"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A single sequence pattern. The location of the pattern inside the sequence is identified by the attributes<code>from</code>and<code>to</code>.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

== Alignment ==

This section contains type declaration for sequence alignments.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType alignmentSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="alignmentSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:clustalw"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined sequence alignment source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType alignmentSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="alignmentSource">
<xs:union memberTypes="bt:sourceUri bt:alignmentSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of a sequence alignment. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_alignmentSources|simpleType alignmentSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType multipleAlignment ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="multipleAlignment" final="restriction" block="restriction">
<xs:choice>
<xs:sequence minOccurs="2" maxOccurs="unbounded">
<xs:element ref="bt:abstractAlignedRnaSequence"/>
</xs:sequence>
<xs:sequence minOccurs="2" maxOccurs="unbounded">
<xs:element ref="bt:abstractAlignedDnaSequence"/>
</xs:sequence>
<xs:sequence minOccurs="2" maxOccurs="unbounded">
<xs:element ref="bt:abstractAlignedSecondaryStructureSequence"/>
</xs:sequence>
<xs:sequence minOccurs="2" maxOccurs="unbounded">
<xs:element ref="bt:abstractAlignedAminoAcidSequence"/>
</xs:sequence>
<xs:sequence minOccurs="2" maxOccurs="unbounded">
<xs:element ref="bt:abstractAlignedRnaSecondaryStructureSequence"/>
</xs:sequence>
</xs:choice>
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="score" type="bt:score" use="optional"/>
<xs:attribute name="source" type="bt:alignmentSource" use="optional"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A multiple sequence alignment. A overall score may be assigned to the multiple alignment using the<code>score</code>attribute. The source of the multiple alignment can be specified using the attributes<code>source</code>and<code>accNumber</code>. A multiple alignment must contain at least two aligned sequences. Thus one or more of the abstract elements<code>abstractAlignedRnaSequence</code>,<code>abstractAlignedDnaSequence</code>,<code>abstractAlignedSecondaryStructureSequence</code>,<code>abstractAlignedAminoAcidSequence</code>or<code>abstractAlignedRnaSecondaryStructureSequence</code>must be replaced by a concrete element. This can be done via a substitution group.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.
* 10/18/05 by [http://biozentrum.uni-wuerzburg.de/bioinformatik Philipp Seibel]: Rna secondary structure added.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup alignedSequenceAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="alignedSequenceAttrs">
<xs:attribute name="score" type="bt:score" use="optional"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The attributes for an aligned sequence. The individual score for an aligned sequence may be set using the<code>score</code>attribute.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType alignedRnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="alignedRnaSequence">
<xs:simpleContent>
<xs:extension base="bt:gappedAmbiguousRnaSequence">
<xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An aligned RNA sequence.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractAlignedRnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractAlignedRnaSequence" type="bt:alignedRnaSequence" abstract="true" final="restriction" block="restriction"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An abstract aligned RNA sequence element for the multiple alignment.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType alignedDnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="alignedDnaSequence">
<xs:simpleContent>
<xs:extension base="bt:gappedAmbiguousDnaSequence">
<xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An aligned DNA sequence.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractAlignedDnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractAlignedDnaSequence" type="bt:alignedDnaSequence" abstract="true" final="restriction" block="restriction"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An abstract aligned DNA sequence element for the multiple alignment.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType alignedSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="alignedSecondaryStructureSequence">
<xs:simpleContent>
<xs:extension base="bt:gappedAmbiguousSecondaryStructureSequence">
<xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An aligned secondary structure sequence.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractAlignedSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractAlignedSecondaryStructureSequence" type="bt:alignedSecondaryStructureSequence" abstract="true" final="restriction" block="restriction"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An abstract aligned secondary structure sequence element for the multiple alignment.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType alignedRnaSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="alignedRnaSecondaryStructureSequence">
<xs:simpleContent>
<xs:extension base="bt:gappedRnaSecondaryStructureSequence">
<xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An aligned rna secondary structure sequence.
</div>

'''change log'''

* 10/19/05 by [http://biozentrum.uni-wuerzburg.de/bioinformatik Philipp Seibel]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractAlignedRnaSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractAlignedRnaSecondaryStructureSequence" type="bt:alignedRnaSecondaryStructureSequence" abstract="true" final="restriction" block="restriction"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An abstract aligned rna secondary structure sequence element for the multiple alignment.
</div>

'''change log'''

* 10/19/05 by [http://biozentrum.uni-wuerzburg.de/bioinformatik Philipp Seibel]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType alignedAminoAcidSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="alignedAminoAcidSequence">
<xs:simpleContent>
<xs:extension base="bt:gappedAmbiguousAminoAcidOneLetterSequence">
<xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An aligned amino acid sequence.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractAlignedAminoAcidSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractAlignedAminoAcidSequence" type="bt:alignedAminoAcidSequence" abstract="true" final="restriction" block="restriction"/></xml></code>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

BioTypes 1.1

Hampti — Wed, 17 May 2006 08:54:07 GMT

Summary:

{{Schema:Header}}

== Introduction ==

For better reading and editing this schema is divided into different sections:

* [[#Basic|Basic]]: Basic type definitions.
* [[#Source|Source]]: Type definitions for specifying the source of biological data.
* [[#Sequence|Sequence]]: Type definitions for sequence data
* [[#Structure|Structure]]: Type definitions for structure data.
* [[#Classification|Classification]]: Type definitions for classification schemes.
* [[#Pattern|Pattern]]: Type definitions for sequence patterns.
* [[#Alignment|Alignment]]: Type definitions for sequence alignments.

The final release of this schema can be downloaded from http://schemas.bioservices.net/2005/.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">

== Specification ==

=== schema http://schemas.bioservices.net/2005/biotypes ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" title="code"><xml><xs:schema xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="http://schemas.bioservices.net/2005/biotypes" elementFormDefault="qualified" attributeFormDefault="unqualified" id="BioTypes" version="1.1" xml:lang="en"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The BioTypes schema provides a common XML type framework for biological data in analogy to the predefined XML Schema types. The recommended prefix for the BioTypes namespace is <i>bt</i>. For further information on usage visit <a href="http://schemas.bioservices.net">BioSchemas </a>.
<p>To use BioTypes in an XML schema download a local copy of the BioTypes schema and include it via the <code>import</code> statement:</p><p><code>
<xs:import xmlns:xs="http://www.w3.org/2001/XMLSchema" schemaLocation="biotypes.xsd" namespace="http://schemas.bioservices.net/2005/biotypes"/></code></p><p>Content is available under <a href="http://creativecommons.org/licenses/by-sa/2.0/">Creative Commons Attribution-ShareAlike License</a>.</p>
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/tests.xsd'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/tests.xsd"><xml><xs:schema xmlns:bt="http://schemas.bioservices.net/2005/biotypes" targetNamespace="http://schemas.bioservices.net/2005/biotypes/tests" elementFormDefault="qualified" attributeFormDefault="unqualified">
<xs:import schemaLocation="../../biotypes.xsd" namespace="http://schemas.bioservices.net/2005/biotypes"/>
<xs:element name="root">
<xs:complexType>
<xs:sequence>
<xs:any namespace="##any" processContents="strict" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
<xs:anyAttribute namespace="##any" processContents="lax"/>
</xs:complexType>
</xs:element>
<xs:element name="index" type="bt:index"/>
<xs:element name="alphaIndex" type="bt:alphanumericIndex"/>
<xs:element name="version" type="bt:version"/>
<xs:element name="lsid" type="bt:lsid"/>
<xs:element name="sourceUri" type="bt:sourceUri"/>
<xs:element name="seq" type="bt:sequence"/>
<xs:element name="atomName" type="bt:atomName"/>
<xs:element name="container">
<xs:complexType>
<xs:complexContent>
<xs:extension base="bt:anyContent"/>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element name="item">
<xs:complexType>
<xs:attributeGroup ref="bt:dataAttrs"/>
</xs:complexType>
</xs:element>
<xs:element name="coord">
<xs:complexType>
<xs:attributeGroup ref="bt:coordinates3D"/>
</xs:complexType>
</xs:element>
<xs:element name="source" type="bt:source"/>
<xs:element name="atom" type="bt:atom" substitutionGroup="bt:abstractAtom"/>
<xs:element name="atomSeq" type="bt:atomSequence"/>
<xs:element name="patternProfile" type="bt:patternProfile"/>
<xs:element name="pattern" type="bt:pattern"/>
<xs:element name="aaMultipleAlignment" type="bt:multipleAlignment"/>
</xs:schema></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo"><xml><xs:appinfo>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="##missing">
<bt:mapping to="url"/>
<bt:mapping to="caption">Unknown</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:">
<bt:mapping to="url"/>
<bt:mapping to="caption">
<bt:attribute name="source"/>
</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:lsid:">
<bt:mapping to="url">lsidres:
<bt:attribute name="source"/>
</bt:mapping>
<bt:mapping to="caption">
<bt:attribute name="source"/>
</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:embl">
<bt:mapping to="caption">EMBL Nucleotide Sequence Database</bt:mapping>
<bt:mapping to="url">http://www.ebi.ac.uk/embl/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:entrez">
<bt:mapping to="caption">NCBI Entrez Gene</bt:mapping>
<bt:mapping to="url">http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:genbank">
<bt:mapping to="caption">NCBI GenBank</bt:mapping>
<bt:mapping to="url">http://www.ncbi.nlm.nih.gov/Genbank/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:hugo">
<bt:mapping to="caption">The Human Genome Organisation</bt:mapping>
<bt:mapping to="url">http://www.hugo-international.org/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:locuslink">
<bt:mapping to="caption">NCBI LocusLink</bt:mapping>
<bt:mapping to="url">http://www.ncbi.nlm.nih.gov/projects/LocusLink/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:mgd">
<bt:mapping to="caption">Mouse Genome Informatics</bt:mapping>
<bt:mapping to="url">http://www.informatics.jax.org/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:mgi">
<bt:mapping to="caption">Mouse Genome Informatics</bt:mapping>
<bt:mapping to="url">http://www.informatics.jax.org/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:rgd">
<bt:mapping to="caption">Rat Genome Database</bt:mapping>
<bt:mapping to="url">http://rgd.mcw.edu/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:sgd">
<bt:mapping to="caption">Saccharomyces Genome Database</bt:mapping>
<bt:mapping to="url">http://www.yeastgenome.org/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:pdb">
<bt:mapping to="caption">RCSB Protein Data Bank</bt:mapping>
<bt:mapping to="url">http://www.rcsb.org/pdb/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:swissprot">
<bt:mapping to="caption">Swiss-Prot</bt:mapping>
<bt:mapping to="url">http://au.expasy.org/sprot/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:dssp">
<bt:mapping to="caption">DSSP</bt:mapping>
<bt:mapping to="url">http://www.cmbi.kun.nl/gv/dssp/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:pdb">
<bt:mapping to="caption">RCSB Protein Data Bank</bt:mapping>
<bt:mapping to="url">http://www.rcsb.org/pdb/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:pdb">
<bt:mapping to="caption">RCSB Protein Data Bank</bt:mapping>
<bt:mapping to="url">http://www.rcsb.org/pdb/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:cath">
<bt:mapping to="caption">CATH</bt:mapping>
<bt:mapping to="url">http://www.ccbb.re.kr/irs/2_cath/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:scop">
<bt:mapping to="caption">SCOP</bt:mapping>
<bt:mapping to="url">http://scop.mrc-lmb.cam.ac.uk/scop/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:interpro">
<bt:mapping to="caption">EMBL Interpro</bt:mapping>
<bt:mapping to="url">http://www.ebi.ac.uk/interpro/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:pfam">
<bt:mapping to="caption">PFAM</bt:mapping>
<bt:mapping to="url">http://www.sanger.ac.uk/Software/Pfam/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:prodom">
<bt:mapping to="caption">ProDom</bt:mapping>
<bt:mapping to="url">http://protein.toulouse.inra.fr/prodom/current/html/home.php</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:prosite">
<bt:mapping to="caption">ExPASy PROSITE</bt:mapping>
<bt:mapping to="url">http://au.expasy.org/prosite/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:clustalw">
<bt:mapping to="caption">ClustalW</bt:mapping>
<bt:mapping to="url">http://www.ebi.ac.uk/clustalw/</bt:mapping>
</bt:source>
</xs:appinfo></xml></code>

'''references'''

* [http://schemas.bioservices.net/2005/biotypes BioTypes namespace URL]

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

== Basic ==

This section contains basic type definitions.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType index ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="index">
<xs:restriction base="xs:positiveInteger"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An one-based index. Indices should begin with 1 because zero-based indices might be confusing for humans and are a common source for errors, e.g. when a user assumes the numeration begins with 1.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestIndex.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestIndex.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<test:case test="with" result="pass" desc="index may be 1.">
<index>1</index>
</test:case>
<test:case test="with" result="fail" desc="index starts with 1.">
<index>0</index>
</test:case>
<test:case test="with" result="fail" desc="index must not be negative.">
<index>-1</index>
</test:case>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType alphanumericIndex ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="alphanumericIndex">
<xs:union memberTypes="bt:index">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:pattern value="[a-z]"/>
</xs:restriction>
</xs:simpleType>
</xs:union>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An alphanumeric index. Numeric indices should begin with 1. Alternatively the indices could be numbered using small letters: "a", "b", etc. A combination of letters is not allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAlphanumericIndex.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAlphanumericIndex.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<test:case test="with" result="pass" desc="alphaIndex may be 1.">
<alphaIndex>1</alphaIndex>
</test:case>
<test:case test="with" result="fail" desc="alphaIndex starts with 1.">
<alphaIndex>0</alphaIndex>
</test:case>
<test:case test="with" result="fail" desc="alphaIndex must not be negative.">
<alphaIndex>-1</alphaIndex>
</test:case>
<test:case test="with" result="pass" desc="alphaIndex may be a.">
<alphaIndex>a</alphaIndex>
</test:case>
<test:case test="with" result="fail" desc="alphaIndex must not be a uppercase letter.">
<alphaIndex>A</alphaIndex>
</test:case>
<test:case test="with" result="fail" desc="alphaIndex must not be empty.">
<alphaIndex/>
</test:case>
<test:case test="with" result="fail" desc="alphaIndex must not be a combination of letters.">
<alphaIndex>ab</alphaIndex>
</test:case>
</root></xml></code>

'''change log'''

* 06/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">

=== simpleType version ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="version">
<xs:restriction base="xs:token">
<xs:pattern value="\d+(\.\d+)*"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A versioning number.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestVersion.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestVersion.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<test:case test="with" result="pass" desc="version may be a single digit.">
<version>1</version>
</test:case>
<test:case test="with" result="pass" desc="version may be a number.">
<version>11</version>
</test:case>
<test:case test="with" result="pass" desc="version may be a sequence of numbers.">
<version>11.0.1</version>
</test:case>
<test:case test="with" result="fail" desc="version must not be empty.">
<version/>
</test:case>
<test:case test="with" result="fail" desc="version must not end with a dot.">
<version>1.</version>
</test:case>
<test:case test="with" result="fail" desc="version must not contain characters other than digits.">
<version>1.x</version>
</test:case>
<test:case test="with" result="fail" desc="version must not contain two or more points in sequence.">
<version>1..1</version>
</test:case>
</root></xml></code>

'''change log'''

* 05/18/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType score ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="score">
<xs:restriction base="xs:double"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A scoring value. Scores can be positive or negative.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType anyContent ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="anyContent" mixed="true" abstract="true">
<xs:sequence minOccurs="0" maxOccurs="unbounded">
<xs:any namespace="##any" processContents="lax"/>
</xs:sequence>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Allows any mixed content, i.e. text and elements from any namespace.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestContainer.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestContainer.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<test:case test="with" result="pass" desc="A container may contain elements from foreign namespaces and text.">
<container>Prefix
<ext:item xmlns:ext="urn:other"/>
Infix
<ext2:item xmlns:ext2="urn:other2"/>
Postfix
</container>
</test:case>
<test:case test="with" result="pass" desc="A container may contain elements from the target namespace.">
<container>Prefix
<item/>
Infix
<item/>
Postfix
</container>
</test:case>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType dateOptionalTime ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="dateOptionalTime">
<xs:union memberTypes="xs:date xs:dateTime"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A date and eventually a time information.
</div>

'''change log'''

* 05/22/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType missing ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="missing">
<xs:restriction base="xs:token">
<xs:enumeration value="##missing"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Marks an optional attribute value as missing. This should be the default value for the attribute. This special enumeration value is necessary because optional attributes without a default value could not be used within a key declaration.
</div>

'''change log'''

* 05/22/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType sourceDate ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="sourceDate">
<xs:restriction base="bt:dateOptionalTime"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The date (and eventually time) the corresponding data item was retrieved from the data source.
</div>

'''change log'''

* 05/22/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType optionalSourceDate ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="optionalSourceDate">
<xs:union memberTypes="bt:sourceDate bt:missing"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The date (and eventually time) the corresponding data item was retrieved from the data source, or <code>##missing</code> as the default value.
</div>

'''change log'''

* 05/22/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType sourceVersion ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="sourceVersion">
<xs:restriction base="bt:version"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The version of the data source from whom the data item was retrieved.
</div>

'''change log'''

* 05/22/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType optionalSourceVersion ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="optionalSourceVersion">
<xs:union memberTypes="bt:sourceVersion bt:missing"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The version of the data source from whom the data item was retrieved, or <code>##missing</code> as the default value.
</div>

'''change log'''

* 05/22/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup dataAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="dataAttrs">
<xs:attribute name="version" type="bt:optionalSourceVersion" use="optional" default="##missing"/>
<xs:attribute name="date" type="bt:optionalSourceVersion" use="optional" default="##missing"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The attributes for a data item. A data item is an element which holds data that should be regarded as a single unit in contrast to a data collection which holds multiple units of data, i.e. data items. In addition to the optional <code>version</code> and <code>date</code> attributes, specifying the version of the data source and the date (and eventually the time) the data item was retrieved, a data item should declare a <code>source</code> attribute of type <code>sourceUri</code> and a <code>accNumber</code> attribute of type <code>accessionNumber</code>, specifying the data source of the data item and its accession number within the data source.
</div>

'''references'''

* [[#simpleType_sourceUri|simpleType sourceUri]]
* [[#simpleType_accessionNumber|simpleType accessionNumber]]

'''change log'''

* 05/22/05 by [http://szugat.gmxhome.de Martin Szugat]: Declared type dateOptionalTime.
* 05/10/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup scopeAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="scopeAttrs">
<xs:attribute name="from" type="bt:index" use="required"/>
<xs:attribute name="to" type="bt:index" use="required"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Attributes for setting a range. <code>from</code> should be less than <code>to</code>.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

== Source ==

This section contains type declarations for specifying the source of biological data.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">

=== simpleType lsid ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="lsid">
<xs:restriction base="xs:anyURI">
<xs:pattern value="urn:lsid:(\c|/)+:(\c|/)+:\c+(:\c+)?"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A Life Sciences Identifier (LSID) is a URN that uniquely names an object. According to the <a href="http://lsid.sourceforge.net/">LSID Resolution Protocol Project</a> the syntax is <code>urn:lsid:<authority>:<namespace>:<value>:<version></code> where <code>authority</code> is the name of the organization that has defined an entity, <code>namespace</code> is a namespace within the authority for the Id, <code>value</code> is an alpha-numeric sequence that uniquely identifies an object to its authority, and <code>version</code> is an optional version number for an Id. <code>authority</code> and <code>namespace</code> can have hierarchical path elements separated by "/".
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestLSID.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestLSID.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<test:case test="with" result="pass" desc="lsid need not to have a revision.">
<lsid>urn:lsid:authority:namespace:identifier</lsid>
</test:case>
<test:case test="with" result="pass" desc="lsid may have a revision. ">
<lsid>urn:lsid:authority:namespace:identifier:1</lsid>
</test:case>
<test:case test="with" result="fail" desc="lsid must a have an urn prefix.">
<lsid>lsid:authority:namespace:identifier</lsid>
</test:case>
<test:case test="with" result="fail" desc="lsid must have a lsid prefix.">
<lsid>urn:authority:namespace:identifier</lsid>
</test:case>
<test:case test="with" result="fail" desc="lsid must have an identifier.">
<lsid>urn:lsid:authority:namespace</lsid>
</test:case>
<test:case test="with" result="fail" desc="lsid must have a namespace.">
<lsid>urn:lsid:authority::identifier</lsid>
</test:case>
<test:case test="with" result="fail" desc="lsid must have an authority.">
<lsid>urn:lsid::namespace:identifier</lsid>
</test:case>
<test:case test="with" result="pass" desc="authority and namespace may include slashes.">
<lsid>urn:lsid:authority/sub:namespace/sub:identifier</lsid>
</test:case>
</root></xml></code>

'''references'''
* [http://lsid.sourceforge.net LSID Resolution Protocol Project]

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType sourceUri ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="sourceUri" final="restriction">
<xs:union memberTypes="bt:lsid">
<xs:simpleType>
<xs:restriction base="xs:anyURI">
<xs:minLength value="1"/>
</xs:restriction>
</xs:simpleType>
</xs:union>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The URI of a data source. This may be an URL, an URN or a LSID.
</div>

'''references'''
* [[#simpleType_lsid|simpleType lsid]]
* [[#complexType_source|complexType source]]
* [http://lsid.sourceforge.net LSID Resolution Protocol Project]

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType optionalSourceUri ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="optionalSourceUri">
<xs:union memberTypes="bt:sourceUri bt:missing"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The URI of a data source. This may be an URL, an URN or a LSID or <code>##missing</code> as the default value.
</div>

'''change log'''

* 05/22/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType accessionNumber ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="accessionNumber">
<xs:restriction base="xs:token">
<xs:minLength value="1"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Specifies the accession number of a data item relative to its data source. The format of the accession number depends on the data source.
</div>

'''references'''
* [[#complexType_source|complexType source]]

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType source ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="source" mixed="true">
<xs:complexContent>
<xs:extension base="bt:anyContent">
<xs:attribute name="uri" type="bt:optionalSourceUri" use="required" form="unqualified"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The description of a data source. The data source is identified by the <code>uri</code> attribute. The content may be source specific. It may consist e.g. of one or more <code>mapping</code> elements which map the source URI to an URL or a caption. Such a mapping is demonstrated by the <a href="http://schemas.bioservices.net/index.php?title=BioTypes_stylesheet">BioTypes stylesheet</a>.
</div>

'''references'''
* [[#element_source|element source]]
* [[#element_mapping|element mapping]]
* [[BioTypes stylesheet]]

'''change log'''

* 05/10/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element source ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="source">
<xs:complexType>
<xs:complexContent>
<xs:extension base="bt:source">
<xs:anyAttribute namespace="##other" processContents="lax"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The description of a data source.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestSource.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestSource.xml"><xml><bst:root xmlns:bst="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<bst:source uri="test">
<test:attribute name="uri" result="fail" desc="source must have a uri."/>
<test:attribute name="uri" value="urn:bts:cath" result="pass" desc="source uri may be a predefined name."/>
<test:attribute name="uri" value="urn:org.db:id" result="pass" desc="source uri may be a custom URN."/>
<test:attribute name="uri" value="http://www.db.org/id" result="pass" desc="source uri may be a custom URL."/>
<test:attribute name="uri" value="urn:lsid:authority:namespace:identifier" result="pass" desc="source uri may be a LSID."/>
<test:attribute name="uri" value="##missing" result="pass" desc="source uri may be ##missing."/>
<test:case test="with" result="pass" desc="source may contain any content.">
Prefix<ext:item xmlns:ext="urn:other">Infix</ext:item>Postfix
</test:case>
</bst:source>
</bst:root></xml></code>

'''references'''

* [[#complexType_source|complexType source]]

'''change log'''

* 01/02/06 by [http://szugat.gmxhome.de Martin Szugat]: Added tests
* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">

=== element mapping ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="mapping">
<xs:complexType>
<xs:complexContent>
<xs:extension base="bt:anyContent">
<xs:attribute name="to" use="required">
<xs:simpleType>
<xs:union memberTypes="xs:token">
<xs:simpleType>
<xs:restriction base="xs:token">
<xs:enumeration value="url"/>
<xs:enumeration value="caption"/>
</xs:restriction>
</xs:simpleType>
</xs:union>
</xs:simpleType>
</xs:attribute>
<xs:anyAttribute namespace="##other" processContents="lax"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The mapping of a value to another representation. The <code>to</code> attribute specifies the representation. A mapping is used e.g. within a <code>source</code> element to map the data source URI to an URL. It is used by the <a href="http://schemas.bioservices.net/index.php?title=BioTypes_stylesheet">BioTypes stylesheet</a>. Its content may be mapping specific, e.g. text and one or more <code>attribute</code> elements. For each subordinated element the processing application or stylesheet should be ready to process it, i.e. there must be appropiate template.
</div>

'''references'''

* [[BioTypes stylesheet]]

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element attribute ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="attribute">
<xs:complexType>
<xs:attribute name="name" type="xs:Name" use="required"/>
<xs:attribute name="namespace" type="xs:anyURI" use="optional"/>
<xs:anyAttribute namespace="##other" processContents="lax"/>
</xs:complexType>
</xs:element></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Evaluates an attribute. This element can be used e.g. inside a <code>mapping</code> element. During the mapping process it should be replaced by the concrete value of the attribute.
</div>

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

== Sequence ==

This section contains type declarations for biological sequence data.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType sequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="sequence">
<xs:restriction base="xs:string">
<xs:minLength value="1"/>
<xs:whiteSpace value="preserve"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of character data of length greater than zero.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq>
<test:case test="with" result="fail" desc="sequence must not be empty."/>
<test:case test="with" result="pass" desc="sequence may contain any number of characters.">ABCDEFGHIJKLMNOPQRSTVWXYZabcdefghijklmnopqrstvwxyz</test:case>
<test:case test="with" result="pass" desc="sequence may contain whitespace and line breaks.">
AA
AA
</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAmbiguousNucleotideSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAmbiguousNucleotideSequence">
<xs:restriction base="bt:sequence">
<xs:pattern value="(A|G|C|T|U|R|Y|M|K|S|W|H|B|V|D|N|X|\-)+"/>
<xs:whiteSpace value="collapse"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of nucleotides (RNA and DNA) or its placeholders in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedAmbiguousNucleotideSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedAmbiguousNucleotideSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedAmbiguousNucleotideSequence">
<test:case test="with" result="fail" desc="gapped ambiguous nucleotide sequence must not be empty."/>
<test:case test="with" result="fail" desc="gapped ambiguous nucleotide sequence must not contain lower case characters.">a</test:case>
<test:case test="with" result="pass" desc="gapped ambiguous nucleotide sequence may contain any number of nucleotides, ambiguous characters and gaps.">ACGTURYMKSWHBVDNX-</test:case>
<test:case test="with" result="pass" desc="gapped ambiguous nucleotide sequence may contain line breaks at the beginning and at the end.">
AAAA
</test:case>
<test:case test="with" result="fail" desc="gapped ambiguous nucleotide must not contain line breaks in between.">
AA
AA
</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedNucleotideSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedNucleotideSequence">
<xs:restriction base="bt:gappedAmbiguousNucleotideSequence">
<xs:pattern value="(A|G|C|T|U|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of nucleotides (RNA and DNA) in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedNucleotideSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedNucleotideSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedNucleotideSequence">
<test:case test="with" result="fail" desc="gapped nucleotide sequence must not contain ambiguous characters.">RYMKSWHBVDNX</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType ambiguousNucleotideSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="ambiguousNucleotideSequence">
<xs:restriction base="bt:gappedAmbiguousNucleotideSequence">
<xs:pattern value="(A|G|C|T|U|R|Y|M|K|S|W|H|B|V|D|N|X)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of nucleotides (RNA and DNA) or its placeholders in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAmbiguousNucleotideSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAmbiguousNucleotideSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:ambiguousNucleotideSequence">
<test:case test="with" result="fail" desc="ambiguous nucleotide sequence must not contain gap characters.">-</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType nucleotideSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="nucleotideSequence">
<xs:restriction base="bt:ambiguousNucleotideSequence">
<xs:pattern value="(A|G|C|T|U)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of nucleotides (RNA and DNA) in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestNucleotideSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestNucleotideSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:nucleotideSequence">
<test:case test="with" result="fail" desc="nucleotide sequence must not contain gap characters or ambiguous characters.">-X</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType nucleotideSequenceSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="nucleotideSequenceSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:embl"/>
<xs:enumeration value="urn:bts:entrez"/>
<xs:enumeration value="urn:bts:genbank"/>
<xs:enumeration value="urn:bts:hugo"/>
<xs:enumeration value="urn:bts:locuslink"/>
<xs:enumeration value="urn:bts:mgd"/>
<xs:enumeration value="urn:bts:mgi"/>
<xs:enumeration value="urn:bts:rgd"/>
<xs:enumeration value="urn:bts:sgd"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined nucleotide sequence source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType nucleotideSequenceSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="nucleotideSequenceSource">
<xs:union memberTypes="bt:sourceUri bt:nucleotideSequenceSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of a nucleotide sequence. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_nucleotideSequenceSources|simpleType nucleotideSequenceSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup nucleotideSequenceAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="nucleotideSequenceAttrs">
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
<xs:attribute name="source" type="bt:nucleotideSequenceSource" use="optional"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Attributes for nucleotide sequences. <code>source</code> specifies the source of the sequence. In addition <code>accNumber</code> can be set to an accession number dependant on the data source if <code>source</code> identifies only the data source (e.g. database) but not the data item itself.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAmbiguousDnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAmbiguousDnaSequence">
<xs:restriction base="bt:gappedAmbiguousNucleotideSequence">
<xs:pattern value="(A|G|C|T|R|Y|M|K|S|W|H|B|V|D|N|X|\-)+"/>
<xs:whiteSpace value="collapse"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of DNAs or its placeholders in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedAmbiguousDnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedAmbiguousDnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedAmbiguousDnaSequence">
<test:case test="with" result="fail" desc="gapped ambiguous dna sequence must not contain Uracil.">U</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedDnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedDnaSequence">
<xs:restriction base="bt:gappedAmbiguousDnaSequence">
<xs:pattern value="(A|G|C|T|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of DNAs in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedDnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedDnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedDnaSequence">
<test:case test="with" result="fail" desc="gapped dna sequence must not contain ambiguous characters.">RYMKSWHBVDNX</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType ambiguousDnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="ambiguousDnaSequence">
<xs:restriction base="bt:gappedAmbiguousDnaSequence">
<xs:pattern value="(A|G|C|T|R|Y|M|K|S|W|H|B|V|D|N|X)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of DNAs or its placeholders in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAmbiguousDnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAmbiguousDnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:ambiguousDnaSequence">
<test:case test="with" result="fail" desc="ambiguous dna sequence must not contain gap characters.">-</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType dnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="dnaSequence">
<xs:restriction base="bt:ambiguousDnaSequence">
<xs:pattern value="(A|G|C|T)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of DNAs in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestDnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestDnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:dnaSequence">
<test:case test="with" result="fail" desc="dna sequence must not contain gap characters or ambiguous characters.">-X</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAmbiguousRnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAmbiguousRnaSequence">
<xs:restriction base="bt:gappedAmbiguousNucleotideSequence">
<xs:pattern value="(A|G|C|U|R|Y|M|K|S|W|H|B|V|D|N|X|\-)+"/>
<xs:whiteSpace value="collapse"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of RNAs or its placeholders in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedAmbiguousRnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedAmbiguousRnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedAmbiguousRnaSequence">
<test:case test="with" result="fail" desc="gapped ambiguous rna sequence must not contain Thymin.">T</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedRnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedRnaSequence">
<xs:restriction base="bt:gappedAmbiguousRnaSequence">
<xs:pattern value="(A|G|C|U|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of DNAs in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedRnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedRnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedRnaSequence">
<test:case test="with" result="fail" desc="gapped rna sequence must not contain ambiguous characters.">RYMKSWHBVDNX</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType ambiguousRnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="ambiguousRnaSequence">
<xs:restriction base="bt:gappedAmbiguousRnaSequence">
<xs:pattern value="(A|G|C|U|R|Y|M|K|S|W|H|B|V|D|N|X)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of RNAs or its placeholders in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAmbiguousRnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAmbiguousRnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:ambiguousRnaSequence">
<test:case test="with" result="fail" desc="ambiguous rna sequence must not contain gap characters.">-</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType rnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="rnaSequence">
<xs:restriction base="bt:ambiguousRnaSequence">
<xs:pattern value="(A|G|C|U)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of RNAs in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestRnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestRnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:rnaSequence">
<test:case test="with" result="fail" desc="rna sequence must not contain gap characters or ambiguous characters.">-X</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAmbiguousTerminalAminoAcidOneLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAmbiguousTerminalAminoAcidOneLetterSequence">
<xs:restriction base="bt:sequence">
<xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|X|B|Z|\-|\*)+"/>
<xs:whiteSpace value="collapse"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case one letter code including the terminal symbol *, ambigiuous and gap characters. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAmbiguousAminoAcidOneLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAmbiguousAminoAcidOneLetterSequence">
<xs:restriction base="bt:gappedAmbiguousTerminalAminoAcidOneLetterSequence">
<xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|X|B|Z|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case one letter code, ambigiuous and gap characters. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 05/10/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType ambiguousAminoAcidOneLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="ambiguousAminoAcidOneLetterSequence">
<xs:restriction base="bt:gappedAmbiguousTerminalAminoAcidOneLetterSequence">
<xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|X|B|Z)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case one letter code and ambigiuous characters. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAminoAcidOneLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAminoAcidOneLetterSequence">
<xs:restriction base="bt:gappedAmbiguousTerminalAminoAcidOneLetterSequence">
<xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case one letter code and gap characters. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType terminalAminoAcidOneLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="terminalAminoAcidOneLetterSequence">
<xs:restriction base="bt:gappedAmbiguousTerminalAminoAcidOneLetterSequence">
<xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|\*)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case one letter code including the terminal symbol *. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType aminoAcidOneLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="aminoAcidOneLetterSequence">
<xs:restriction base="bt:ambiguousAminoAcidOneLetterSequence">
<xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case one letter code. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType terminalAminoAcidThreeLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="terminalAminoAcidThreeLetterSequence">
<xs:restriction base="bt:sequence">
<xs:pattern value="(ALA|ARG|ASN|ASP|CYS|GLN|GLU|GLY|HIS|ILE|LEU|LYS|MET|PHE|PRO|SER|THR|SEC|TRP|TYR|VAL|TER)+"/>
<xs:whiteSpace value="collapse"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case three letter code including the terminal symbol TER. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestTerminalAminoAcidThreeLetterSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestTerminalAminoAcidThreeLetterSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:terminalAminoAcidThreeLetterSequence">
<test:case test="with" result="fail" desc="terminal amino acid three letter sequence must not be empty."/>
<test:case test="with" result="fail" desc="terminal amino acid three letter sequence must not contain lower case characters.">ala</test:case>
<test:case test="with" result="fail" desc="terminal amino acid three letter sequence must not contain illegal character combinations.">XZY</test:case>
<test:case test="with" result="pass" desc="terminal amino acid thre letter sequence may contain any number of amino acids in three letter code and the terminal signal.">ALAARGASNASPCYSGLNGLUGLYHISILELEULYSMETPHEPROSERTHRSECTRPTYRVALTER</test:case>
</seq>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType aminoAcidThreeLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="aminoAcidThreeLetterSequence">
<xs:restriction base="bt:terminalAminoAcidThreeLetterSequence">
<xs:pattern value="(ALA|ARG|ASN|ASP|CYS|GLN|GLU|GLY|HIS|ILE|LEU|LYS|MET|PHE|PRO|SER|THR|SEC|TRP|TYR|VAL)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case three letter code. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAminoAcidThreeLetterSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAminoAcidThreeLetterSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:aminoAcidThreeLetterSequence">
<test:case test="with" result="fail" desc="amino acid three letter sequence must not contain the terminal signal.">TER</test:case>
</seq>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType aminoAcidSequenceSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="aminoAcidSequenceSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:pdb"/>
<xs:enumeration value="urn:bts:swissprot"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined amino acid sequence source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType aminoAcidSequenceSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="aminoAcidSequenceSource">
<xs:union memberTypes="bt:sourceUri bt:aminoAcidSequenceSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of a amino acid sequence. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_aminoAcidSequenceSources|simpleType aminoAcidSequenceSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup aminoAcidSequenceAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="aminoAcidSequenceAttrs">
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
<xs:attribute name="source" type="bt:aminoAcidSequenceSource" use="optional"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Attributes for amino acid sequences. <code>source</code> specifies the source of the sequence. In addition <code>accNumber</code> can be set to an accession number dependant on the data source if <code>source</code> identifies only the data source (e.g. database) but not the data item itself.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAmbiguousSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAmbiguousSecondaryStructureSequence">
<xs:restriction base="bt:sequence">
<xs:pattern value="(C|H|G|I|E|B|T|S|_|X|\-)+"/>
<xs:whiteSpace value="replace"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of secondary structure assignments or its placeholder in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedAmbiguousSecondaryStructureSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedAmbiguousSecondaryStructureSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedAmbiguousSecondaryStructureSequence">
<test:case test="with" result="fail" desc="gapped ambiguous secondary structure sequence must not be empty."/>
<test:case test="with" result="fail" desc="gapped ambiguous secondary structure sequence must not contain lower case characters.">a</test:case>
<test:case test="with" result="pass" desc="gapped ambiguous secondary structure sequence may contain any number of secondary structures, ambiguous characters and gaps.">CHGIEBTS_X-</test:case>
<test:case test="with" result="fail" desc="gapped ambiguous secondary structure must not contain line breaks in between.">
SS
SS
</test:case>
</seq>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType ambiguousSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="ambiguousSecondaryStructureSequence">
<xs:restriction base="bt:gappedAmbiguousSecondaryStructureSequence">
<xs:pattern value="(C|H|G|I|E|B|T|S|_|X)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of secondary structure assignments or its placeholder in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAmbiguousSecondaryStructureSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAmbiguousSecondaryStructureSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:ambiguousSecondaryStructureSequence">
<test:case test="with" result="fail" desc="ambiguous secondary structure sequence must not contain gap characters.">-</test:case>
</seq>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedSecondaryStructureSequence">
<xs:restriction base="bt:gappedAmbiguousSecondaryStructureSequence">
<xs:pattern value="(C|H|G|I|E|B|T|S|_|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of secondary structure assignments in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedSecondaryStructureSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedSecondaryStructureSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedSecondaryStructureSequence">
<test:case test="with" result="fail" desc="gapped secondary structure sequence must not contain ambiguous character.">X</test:case>
</seq>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType secondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="secondaryStructureSequence">
<xs:restriction base="bt:gappedAmbiguousSecondaryStructureSequence">
<xs:pattern value="(C|H|G|I|E|B|T|S|_)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of secondary structure assignments in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestSecondaryStructureSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestSecondaryStructureSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:secondaryStructureSequence">
<test:case test="with" result="fail" desc="secondary structure sequence must not contain ambiguous character or gap character.">X-</test:case>
</seq>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType secondaryStructureSequenceSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="secondaryStructureSequenceSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:dssp"/>
<xs:enumeration value="urn:bts:pdb"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined secondary structure sequence source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType secondaryStructureSequenceSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="secondaryStructureSequenceSource">
<xs:union memberTypes="bt:sourceUri bt:secondaryStructureSequenceSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of a secondary structure sequence. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_secondaryStructureSequenceSources|simpleType secondaryStructureSequenceSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup secondaryStructureSequenceAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="secondaryStructureSequenceAttrs">
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
<xs:attribute name="source" type="bt:secondaryStructureSequenceSource" use="optional"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Attributes for secondary structure sequences. <code>source</code> specifies the source of the sequence. In addition <code>accNumber</code> can be set to an accession number dependant on the data source if <code>source</code> identifies only the data source (e.g. database) but not the data item itself.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedRnaSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedRnaSecondaryStructureSequence">
<xs:restriction base="bt:sequence">
<xs:pattern value="($|$|\[|\]|\{|\}|<|>|\.|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of secondary structure assignments in dot-bracket format and gap characters. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 01/02/06 by [http://bibiserv.techfak.uni-bielefeld.de Kai Loewenthal]: added bracket-pair < > for pseudoknot structures
* 11/04/05 by [http://bibiserv.techfak.uni-bielefeld.de Jan Krueger]: add additional bracket-pairs for pseudoknot structures
* 10/19/05 by [http://biozentrum.uni-wuerzburg.de Philipp Seibel]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">

=== simpleType rnaSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="rnaSecondaryStructureSequence">
<xs:restriction base="bt:gappedRnaSecondaryStructureSequence">
<xs:pattern value="($|$|\[|\]|\{|\}|<|>|\.)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of rna secondary structure assignments in dot-bracket notation. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 01/02/06 by [http://bibiserv.techfak.uni-bielefeld.de Kai Loewenthal]: added bracket-pair < > for pseudoknot structures
* 11/04/05 by [http://bibiserv.techfak.uni-bielefeld.de Jan Krueger]: add additional bracket-pairs for pseudoknot structures
* 10/19/05 by [http://biozentrum.uni-wuerzburg.de Philipp Seibel]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">

=== simpleType rnaSecondaryStructureSequenceClass ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="rnaSecondaryStructureSequenceClass">
<xs:restriction base="bt:sequence">
<xs:pattern value="($|$|\[|\]|\{|\}|<|>|_)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A class of rna secondary structure sequences in shape notation.
</div>

'''change log'''

* 01/02/06 by [http://bibiserv.techfak.uni-bielefeld.de Kai Loewenthal]: Initial declaration.

== Structure ==

This section contains type, attribute and element declarations for atom structures.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType atomNames ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="atomNames">
<xs:restriction base="xs:token">
<xs:enumeration value="H"/>
<xs:enumeration value="C"/>
<xs:enumeration value="CA"/>
<xs:enumeration value="CB"/>
<xs:enumeration value="O"/>
<xs:enumeration value="N"/>
<xs:enumeration value="S"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined atom names. <p>This list contains the following atom names:</p><ul><li><code>H</code>: hydrogen atom</li><li><code>C</code>: carbon atom</li><li><code>CA</code>: alpha carbon atom</li><li><code>CB</code>: beta carbon atom</li><li><code>O</code>: oxygen atom</li><li><code>N</code>: nitrogen atom</li><li><code>S</code>: sulphur atom</li></ul>
</div>

'''references'''
* [[#simpleType_atomName|simpleType atomName]]

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType atomName ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="atomName">
<xs:union memberTypes="bt:atomNames">
<xs:simpleType>
<xs:restriction base="xs:token">
<xs:minLength value="1"/>
</xs:restriction>
</xs:simpleType>
</xs:union>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The (abbreviated) name of an atom within a biological molecule. The name must be at least one character long and may contain numbers but not at the beginning.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAtomName.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAtomName.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<test:case test="with" result="fail" desc="atom name must not be empty.">
<atomName/>
</test:case>
<test:case test="with" result="pass" desc="atom name may contain any number of token characters.">
<atomName>B1</atomName>
</test:case>
<test:case test="with" result="pass" desc="atom name must not start with a digit.">
<atomName>1B</atomName>
</test:case>
</root></xml></code>

'''references'''
* [[#simpleType_atomNames|simpleType atomNames]]

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType coordinate ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="coordinate">
<xs:restriction base="xs:double"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A coordinate in a n-dimensional space.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType distance ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="distance">
<xs:restriction base="xs:double">
<xs:minInclusive value="0.0"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A distance in a n-dimensional space. A distance may not be negative.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType distanceUnits ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="distanceUnits">
<xs:restriction base="xs:token">
<xs:enumeration value="angstroem"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of possible distance units. <p>This list contains the following entries:</p><ul><li><code>angstroem</code>: Angstroem</li></ul>
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType atomStructureSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="atomStructureSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:pdb"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined atom structure source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType atomStructureSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="atomStructureSource">
<xs:union memberTypes="bt:sourceUri bt:atomStructureSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of an atom structure. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_atomSequenceSources|simpleType atomSequenceSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup coordinates3D ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="coordinates3D">
<xs:attribute name="x" type="bt:coordinate" use="required" form="unqualified"/>
<xs:attribute name="y" type="bt:coordinate" use="required" form="unqualified"/>
<xs:attribute name="z" type="bt:coordinate" use="required" form="unqualified"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Coordinates in a 3-dimensional space.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestCoordinates3D.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestCoordinates3D.xml"><xml><coord xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" y="1.0" z="1.0" x="1.0" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<test:attribute id="x" name="x" result="fail" desc="3-D-coordinates must have a x value."/>
<test:attribute name="y" result="fail" desc="3-D-coordinates must have a y value."/>
<test:attribute name="z" result="fail" desc="3-D-coordinates must have a z value."/>
</coord></xml></code>

'''change log'''

* 04/26/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType atom ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="atom" block="restriction" final="restriction">
<xs:attributeGroup ref="bt:coordinates3D"/>
<xs:attribute name="type" type="bt:atomName" use="required" form="unqualified"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A single atom including its coordinates in 3-dimensional space and its type.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAtom.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAtom.xml"><xml><atom xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd" x="1.0" y="1.0" z="1.0" type="C">
<test:attribute name="type" result="fail" desc="atom must have a type."/>
</atom></xml></code>

'''references'''
* [[#attributeGroup_coordinates3D|attributeGroup coordinates3D]]

'''change log'''

* 04/26/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractAtom ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractAtom" type="bt:atom" abstract="true" block="restriction" final="restriction"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An abstract atom element for the atomSeq element.
</div>

'''references'''
* [[#complexType_atom|complexType atom]]
* [[#complexType_atomSeq|complexType atomSeq]]

'''change log'''

* 04/26/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup structureAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="structureAttrs">
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
<xs:attribute name="source" type="bt:atomStructureSource" use="optional"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Attributes for structure data. <code>source</code> specifies the source of the structure data. In addition <code>accNumber</code> can be set to an accession number dependant on the data source if <code>source</code> identifies only the data source (e.g. database) but not the data item itself.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType atomSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="atomSequence" block="restriction" final="restriction">
<xs:sequence>
<xs:element ref="bt:abstractAtom" minOccurs="1" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attributeGroup ref="bt:structureAttrs"/>
<xs:attribute name="unit" type="bt:distanceUnits" use="optional" default="angstroem"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of atoms. An atom sequence must contain at least one atom. The <code>abstractAtom</code> element must be replaced by a concrete element of type <code>atom</code>. This is done via a substitution group:
<p><code>
<xs:element xmlns:xs="http://www.w3.org/2001/XMLSchema" name="atom" type="bt:atom" substitutionGroup="bt:abstractAtom"/></code>.</p><p>The coordinates of each atom are relative to the specified distance unit (default is Angstroem).</p>
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAtomSeq.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAtomSeq.xml"><xml><atomSeq xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<test:case test="with" result="fail" desc="atomSeq must not be empty."/>
<test:case test="with" result="pass" desc="atomSeq may contain one or more atoms.">
<atom y="1.0" z="1.0" type="C" x="1.0"/>
<atom y="1.0" z="1.0" type="C" x="1.0"/>
</test:case>
</atomSeq></xml></code>

'''references'''
* [[#complexType_atom|complexType atom]]
* [[#element_atom|element atom]]

'''change log'''

* 04/26/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType atomConnection ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="atomConnection" abstract="true" block="restriction" final="restriction">
<xs:attribute name="atomType1" type="bt:atomName" use="required"/>
<xs:attribute name="atomType2" type="bt:atomName" use="required"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Specifies a connection between two atoms identified by <code>atomType1</code> and <code>atomType2</code>. A connection can be e.g. a bond or a contact.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType atomContact ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="atomContact">
<xs:complexContent>
<xs:extension base="bt:atomConnection">
<xs:attribute name="distance" type="bt:distance" use="required"/>
<xs:attribute name="unit" type="bt:distanceUnits" use="optional" default="angstroem"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Specifies a (close) contact between two atoms. The distance of the two atoms is specified by <code>distance</code>. The unit of the distance depends on <code>unit</code>. The default setting for <code>unit</code> is <code>angstroem</code>.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

== Classification ==

This section contains type declaration for the classification of biological objects.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType classificationSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="classificationSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:cath"/>
<xs:enumeration value="urn:bts:scop"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined classification source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType classificationSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="classificationSource">
<xs:union memberTypes="bt:sourceUri bt:classificationSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of a classification. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_classificationSources|simpleType classificationSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType classificationValue ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="classificationValue">
<xs:restriction base="xs:token">
<xs:minLength value="1"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Obsolete.
</div>

'''change log'''

* 05/22/05 by [http://szugat.gmxhome.de Martin Szugat]: Declared as obsolete.
* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType classification ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="classification">
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="source" type="bt:classificationSource" use="required"/>
<xs:attribute name="accNumber" type="bt:classificationValue" use="required"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Specifies a classification. The classification scheme is identified by <code>source</code>. The classification itself is specified by <code>accNumber</code>.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

== Pattern ==

This section contains type declaration for sequence patterns.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType patternSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="patternSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:interpro"/>
<xs:enumeration value="urn:bts:pfam"/>
<xs:enumeration value="urn:bts:prodom"/>
<xs:enumeration value="urn:bts:prosite"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined sequence pattern source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType patternSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="patternSource">
<xs:union memberTypes="bt:sourceUri bt:patternSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of a sequence pattern. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_patternSources|simpleType patternSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup patternAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="patternAttrs">
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="source" type="bt:patternSource" use="required"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="required"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Attributes for pattern data. <code>source</code> specifies the source of the pattern data. In addition <code>accNumber</code> can be set to an accession number dependant on the data source if <code>source</code> identifies only the data source (e.g. database) but not the data item itself.
</div>

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType patternBase ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="patternBase" mixed="true">
<xs:complexContent>
<xs:extension base="bt:anyContent">
<xs:attributeGroup ref="bt:patternAttrs"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence pattern. The content of a pattern element is the pattern itself, e.g. a consensus sequence or a HMM, and may contain elements from any namespace and text.
</div>

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType patternProfile ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="patternProfile">
<xs:sequence>
<xs:element ref="bt:abstractPatternProfileMember" minOccurs="1" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="source" type="bt:patternSource" use="optional"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence pattern profile. A profile must contain at least one pattern reference.
</div>

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Made pattern abstract.
* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType patternProfileMember ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="patternProfileMember" block="restriction" final="restriction">
<xs:complexContent>
<xs:extension base="bt:patternBase">
<xs:attribute name="occurence" type="xs:positiveInteger" use="required"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A member of a pattern profile. The number of occurences of the pattern in the sequence(s) must be specified.
</div>

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Made pattern abstract.
* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractPatternProfileMember ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractPatternProfileMember" type="bt:patternProfileMember" abstract="true" block="restriction" final="restriction"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Abstract pattern element for a pattern profile.
</div>

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Made pattern abstract.
* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType pattern ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="pattern" mixed="true">
<xs:complexContent>
<xs:extension base="bt:patternBase">
<xs:attributeGroup ref="bt:scopeAttrs"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A single sequence pattern. The location of the pattern inside the sequence is identified by the attributes <code>from</code> and <code>to</code>.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

== Alignment ==

This section contains type declaration for sequence alignments.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType alignmentSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="alignmentSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:clustalw"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined sequence alignment source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType alignmentSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="alignmentSource">
<xs:union memberTypes="bt:sourceUri bt:alignmentSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of a sequence alignment. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_alignmentSources|simpleType alignmentSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType multipleAlignment ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="multipleAlignment" final="restriction" block="restriction">
<xs:choice>
<xs:sequence minOccurs="2" maxOccurs="unbounded">
<xs:element ref="bt:abstractAlignedRnaSequence"/>
</xs:sequence>
<xs:sequence minOccurs="2" maxOccurs="unbounded">
<xs:element ref="bt:abstractAlignedDnaSequence"/>
</xs:sequence>
<xs:sequence minOccurs="2" maxOccurs="unbounded">
<xs:element ref="bt:abstractAlignedSecondaryStructureSequence"/>
</xs:sequence>
<xs:sequence minOccurs="2" maxOccurs="unbounded">
<xs:element ref="bt:abstractAlignedAminoAcidSequence"/>
</xs:sequence>
<xs:sequence minOccurs="2" maxOccurs="unbounded">
<xs:element ref="bt:abstractAlignedRnaSecondaryStructureSequence"/>
</xs:sequence>
</xs:choice>
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="score" type="bt:score" use="optional"/>
<xs:attribute name="source" type="bt:alignmentSource" use="optional"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A multiple sequence alignment. A overall score may be assigned to the multiple alignment using the <code>score</code> attribute. The source of the multiple alignment can be specified using the attributes <code>source</code> and <code>accNumber</code>. A multiple alignment must contain at least two aligned sequences. Thus one or more of the abstract elements <code>abstractAlignedRnaSequence</code>, <code>abstractAlignedDnaSequence</code>, <code>abstractAlignedSecondaryStructureSequence</code>,<code>abstractAlignedAminoAcidSequence</code> or <code>abstractAlignedRnaSecondaryStructureSequence</code> must be replaced by a concrete element. This can be done via a substitution group.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.
* 10/18/05 by [http://biozentrum.uni-wuerzburg.de/bioinformatik Philipp Seibel]: Rna secondary structure added.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">

=== attributeGroup alignedSequenceAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="alignedSequenceAttrs">
<xs:attribute name="score" type="bt:score" use="optional"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The attributes for an aligned sequence. The individual score for an aligned sequence may be set using the <code>score</code> attribute.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType alignedRnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="alignedRnaSequence">
<xs:simpleContent>
<xs:extension base="bt:gappedAmbiguousRnaSequence">
<xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An aligned RNA sequence.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractAlignedRnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractAlignedRnaSequence" type="bt:alignedRnaSequence" abstract="true" final="restriction" block="restriction"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An abstract aligned RNA sequence element for the multiple alignment.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType alignedDnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="alignedDnaSequence">
<xs:simpleContent>
<xs:extension base="bt:gappedAmbiguousDnaSequence">
<xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An aligned DNA sequence.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractAlignedDnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractAlignedDnaSequence" type="bt:alignedDnaSequence" abstract="true" final="restriction" block="restriction"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An abstract aligned DNA sequence element for the multiple alignment.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType alignedSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="alignedSecondaryStructureSequence">
<xs:simpleContent>
<xs:extension base="bt:gappedAmbiguousSecondaryStructureSequence">
<xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An aligned secondary structure sequence.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractAlignedSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractAlignedSecondaryStructureSequence" type="bt:alignedSecondaryStructureSequence" abstract="true" final="restriction" block="restriction"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An abstract aligned secondary structure sequence element for the multiple alignment.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">

=== complexType alignedRnaSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="alignedRnaSecondaryStructureSequence">
<xs:simpleContent>
<xs:extension base="bt:gappedRnaSecondaryStructureSequence">
<xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An aligned rna secondary structure sequence.
</div>

'''change log'''

* 10/19/05 by [http://biozentrum.uni-wuerzburg.de/bioinformatik Philipp Seibel]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractAlignedRnaSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractAlignedRnaSecondaryStructureSequence" type="bt:alignedRnaSecondaryStructureSequence" abstract="true" final="restriction" block="restriction"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An abstract aligned rna secondary structure sequence element for the multiple alignment.
</div>

'''change log'''

* 10/19/05 by [http://biozentrum.uni-wuerzburg.de/bioinformatik Philipp Seibel]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType alignedAminoAcidSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="alignedAminoAcidSequence">
<xs:simpleContent>
<xs:extension base="bt:gappedAmbiguousAminoAcidOneLetterSequence">
<xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An aligned amino acid sequence.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractAlignedAminoAcidSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractAlignedAminoAcidSequence" type="bt:alignedAminoAcidSequence" abstract="true" final="restriction" block="restriction"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An abstract aligned amino acid sequence element for the multiple alignment.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

BioTypes 1.0

Hampti — Wed, 17 May 2006 08:53:13 GMT

Summary:

{{Schema:Header}}

== Introduction ==

For better reading and editing this schema is divided into different sections:

* [[#Basic|Basic]]: Basic type definitions.
* [[#Source|Source]]: Type definitions for specifying the source of biological data.
* [[#Sequence|Sequence]]: Type definitions for sequence data
* [[#Structure|Structure]]: Type definitions for structure data.
* [[#Classification|Classification]]: Type definitions for classification schemes.
* [[#Pattern|Pattern]]: Type definitions for sequence patterns.
* [[#Alignment|Alignment]]: Type definitions for sequence alignments.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
== Specification ==

=== schema http://schemas.bioservices.net/2005/biotypes ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" title="code"><xml><xs:schema xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="http://schemas.bioservices.net/2005/biotypes" elementFormDefault="qualified" attributeFormDefault="unqualified" id="BioTypes" version="1.0" xml:lang="en"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The BioTypes schema provides a common XML type framework for biological data in analogy to the predefined XML Schema types. The recommended prefix for the BioTypes namespace is <i>bt</i>. For further information on usage visit <a href="http://schemas.bioservices.net">BioSchemas </a>.
<p>To use BioTypes in an XML schema download a local copy of the BioTypes schema and include it via the <code>import</code> statement:</p><p><code>
<xs:import xmlns:xs="http://www.w3.org/2001/XMLSchema" schemaLocation="biotypes.xsd" namespace="http://schemas.bioservices.net/2005/biotypes"/></code></p><p>Content is available under <a href="http://creativecommons.org/licenses/by-sa/2.0/">Creative Commons Attribution-ShareAlike License</a>.</p>
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/tests.xsd'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/tests.xsd"><xml><xs:schema xmlns:bt="http://schemas.bioservices.net/2005/biotypes" targetNamespace="http://schemas.bioservices.net/2005/biotypes/tests" elementFormDefault="qualified" attributeFormDefault="unqualified">
<xs:import schemaLocation="../../biotypes.xsd" namespace="http://schemas.bioservices.net/2005/biotypes"/>
<xs:element name="root">
<xs:complexType>
<xs:sequence>
<xs:any namespace="##any" processContents="strict" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
<xs:anyAttribute namespace="##any" processContents="lax"/>
</xs:complexType>
</xs:element>
<xs:element name="index" type="bt:index"/>
<xs:element name="version" type="bt:version"/>
<xs:element name="lsid" type="bt:lsid"/>
<xs:element name="sourceUri" type="bt:sourceUri"/>
<xs:element name="seq" type="bt:sequence"/>
<xs:element name="atomName" type="bt:atomName"/>
<xs:element name="container">
<xs:complexType>
<xs:complexContent>
<xs:extension base="bt:anyContent"/>
</xs:complexContent>
</xs:complexType>
</xs:element>
<xs:element name="item">
<xs:complexType>
<xs:attributeGroup ref="bt:dataAttrs"/>
</xs:complexType>
</xs:element>
<xs:element name="coord">
<xs:complexType>
<xs:attributeGroup ref="bt:coordinates3D"/>
</xs:complexType>
</xs:element>
<xs:element name="source" type="bt:source"/>
<xs:element name="atom" type="bt:atom" substitutionGroup="bt:abstractAtom"/>
<xs:element name="atomSeq" type="bt:atomSequence"/>
<xs:element name="patternProfile" type="bt:patternProfile"/>
<xs:element name="pattern" type="bt:pattern"/>
<xs:element name="aaMultipleAlignment" type="bt:multipleAlignment"/>
</xs:schema></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo"><xml><xs:appinfo>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:">
<bt:mapping to="url"/>
<bt:mapping to="caption">
<bt:attribute name="source"/>
</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:lsid:">
<bt:mapping to="url">lsidres:
<bt:attribute name="source"/>
</bt:mapping>
<bt:mapping to="caption">
<bt:attribute name="source"/>
</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:embl">
<bt:mapping to="caption">EMBL Nucleotide Sequence Database</bt:mapping>
<bt:mapping to="url">http://www.ebi.ac.uk/embl/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:entrez">
<bt:mapping to="caption">NCBI Entrez Gene</bt:mapping>
<bt:mapping to="url">http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:genbank">
<bt:mapping to="caption">NCBI GenBank</bt:mapping>
<bt:mapping to="url">http://www.ncbi.nlm.nih.gov/Genbank/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:hugo">
<bt:mapping to="caption">The Human Genome Organisation</bt:mapping>
<bt:mapping to="url">http://www.hugo-international.org/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:locuslink">
<bt:mapping to="caption">NCBI LocusLink</bt:mapping>
<bt:mapping to="url">http://www.ncbi.nlm.nih.gov/projects/LocusLink/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:mgd">
<bt:mapping to="caption">Mouse Genome Informatics</bt:mapping>
<bt:mapping to="url">http://www.informatics.jax.org/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:mgi">
<bt:mapping to="caption">Mouse Genome Informatics</bt:mapping>
<bt:mapping to="url">http://www.informatics.jax.org/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:rgd">
<bt:mapping to="caption">Rat Genome Database</bt:mapping>
<bt:mapping to="url">http://rgd.mcw.edu/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:sgd">
<bt:mapping to="caption">Saccharomyces Genome Database</bt:mapping>
<bt:mapping to="url">http://www.yeastgenome.org/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:pdb">
<bt:mapping to="caption">RCSB Protein Data Bank</bt:mapping>
<bt:mapping to="url">http://www.rcsb.org/pdb/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:swissprot">
<bt:mapping to="caption">Swiss-Prot</bt:mapping>
<bt:mapping to="url">http://au.expasy.org/sprot/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:dssp">
<bt:mapping to="caption">DSSP</bt:mapping>
<bt:mapping to="url">http://www.cmbi.kun.nl/gv/dssp/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:pdb">
<bt:mapping to="caption">RCSB Protein Data Bank</bt:mapping>
<bt:mapping to="url">http://www.rcsb.org/pdb/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:pdb">
<bt:mapping to="caption">RCSB Protein Data Bank</bt:mapping>
<bt:mapping to="url">http://www.rcsb.org/pdb/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:cath">
<bt:mapping to="caption">CATH</bt:mapping>
<bt:mapping to="url">http://www.ccbb.re.kr/irs/2_cath/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:scop">
<bt:mapping to="caption">SCOP</bt:mapping>
<bt:mapping to="url">http://scop.mrc-lmb.cam.ac.uk/scop/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:interpro">
<bt:mapping to="caption">EMBL Interpro</bt:mapping>
<bt:mapping to="url">http://www.ebi.ac.uk/interpro/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:pfam">
<bt:mapping to="caption">PFAM</bt:mapping>
<bt:mapping to="url">http://www.sanger.ac.uk/Software/Pfam/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:prodom">
<bt:mapping to="caption">ProDom</bt:mapping>
<bt:mapping to="url">http://protein.toulouse.inra.fr/prodom/current/html/home.php</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:prosite">
<bt:mapping to="caption">ExPASy PROSITE</bt:mapping>
<bt:mapping to="url">http://au.expasy.org/prosite/</bt:mapping>
</bt:source>
<bt:source xmlns:bt="http://schemas.bioservices.net/2005/biotypes" uri="urn:bts:clustalw">
<bt:mapping to="caption">ClustalW</bt:mapping>
<bt:mapping to="url">http://www.ebi.ac.uk/clustalw/</bt:mapping>
</bt:source>
</xs:appinfo></xml></code>

'''references'''

* [http://schemas.bioservices.net/2005/biotypes BioTypes namespace URL]

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

== Basic ==

This section contains basic type definitions.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType index ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="index">
<xs:restriction base="xs:positiveInteger"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An one-based index. Indices should begin with 1 because zero-based indices might be confusing for humans and are a common source for errors, e.g. when a user assumes the numeration begins with 1.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestIndex.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestIndex.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<test:case test="with" result="pass" desc="index may be 1.">
<index>1</index>
</test:case>
<test:case test="with" result="fail" desc="index starts with 1.">
<index>0</index>
</test:case>
<test:case test="with" result="fail" desc="index must not be negative.">
<index>-1</index>
</test:case>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType version ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="version">
<xs:restriction base="xs:token">
<xs:pattern value="\d+(\.\d+)*"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A versioning number.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestVersion.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestVersion.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<test:case test="with" result="pass" desc="version may be a single digit.">
<version>1</version>
</test:case>
<test:case test="with" result="pass" desc="version may be a number.">
<version>11</version>
</test:case>
<test:case test="with" result="pass" desc="version may be a sequence of numbers.">
<version>11.0.1</version>
</test:case>
<test:case test="with" result="fail" desc="version must not be empty.">
<version/>
</test:case>
<test:case test="with" result="fail" desc="version must not end with a dot.">
<version>1.</version>
</test:case>
<test:case test="with" result="fail" desc="version must not contain characters other than digits.">
<version>1.x</version>
</test:case>
<test:case test="with" result="fail" desc="version must not contain two or more points in sequence.">
<version>1..1</version>
</test:case>
</root></xml></code>

'''change log'''

* 05/18/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType score ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="score">
<xs:restriction base="xs:double"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A scoring value. Scores can be positive or negative.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType anyContent ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="anyContent" mixed="true" abstract="true">
<xs:sequence minOccurs="0" maxOccurs="unbounded">
<xs:any namespace="##any" processContents="lax"/>
</xs:sequence>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Allows any mixed content, i.e. text and elements from any namespace.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestContainer.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestContainer.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<test:case test="with" result="pass" desc="A container may contain elements from foreign namespaces and text.">
<container>Prefix
<ext:item xmlns:ext="urn:other"/>
Infix
<ext2:item xmlns:ext2="urn:other2"/>
Postfix
</container>
</test:case>
<test:case test="with" result="pass" desc="A container may contain elements from the target namespace.">
<container>Prefix
<item/>
Infix
<item/>
Postfix
</container>
</test:case>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup dataAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="dataAttrs">
<xs:attribute name="version" type="bt:version" use="optional"/>
<xs:attribute name="date" use="optional">
<xs:simpleType>
<xs:union memberTypes="xs:date xs:dateTime"/>
</xs:simpleType>
</xs:attribute>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The attributes for a data item. A data item is an element which holds data that should be regarded as a single unit in contrast to a data collection which holds multiple units of data, i.e. data items. In addition to the optional <code>version</code> and <code>date</code> attributes, specifying the version of the data source and the date (and eventually the time) the data item was retrieved, a data item should declare a <code>source</code> attribute of type <code>sourceUri</code> and a <code>accNumber</code> attribute of type <code>accessionNumber</code>, specifying the data source of the data item and its accession number within the data source.
</div>

'''references'''

* [[#simpleType_sourceUri|simpleType sourceUri]]
* [[#simpleType_accessionNumber|simpleType accessionNumber]]

'''change log'''

* 05/10/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup scopeAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="scopeAttrs">
<xs:attribute name="from" type="bt:index" use="required"/>
<xs:attribute name="to" type="bt:index" use="required"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Attributes for setting a range. <code>from</code> should be less than <code>to</code>.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

== Source ==

This section contains type declarations for specifying the source of biological data.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType lsid ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="lsid">
<xs:restriction base="xs:anyURI">
<xs:pattern value="urn:lsid:(\c|/)+:(\c|/)+:\c+(:\c+)?"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A Life Sciences Identifier (LSID) is a URN that uniquely names an object. According to the <a href="http://lsid.sourceforge.net/">LSID Resolution Protocol Project</a> the syntax is <code>urn:lsid:<authority>:<namespace>:<value>:<version></code> where <code>authority</code> is the name of the organization that has defined an entity, <code>namespace</code> is a namespace within the authority for the Id, <code>value</code> is an alpha-numeric sequence that uniquely identifies an object to its authority, and <code>version</code> is an optional version number for an Id. <code>authority</code> and <code>namespace</code> can have hierarchical path elements separated by "/".
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestLSID.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestLSID.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<test:case test="with" result="pass" desc="lsid need not to have a revision.">
<lsid>urn:lsid:authority:namespace:identifier</lsid>
</test:case>
<test:case test="with" result="pass" desc="lsid may have a revision. ">
<lsid>urn:lsid:authority:namespace:identifier:1</lsid>
</test:case>
<test:case test="with" result="fail" desc="lsid must a have an urn prefix.">
<lsid>lsid:authority:namespace:identifier</lsid>
</test:case>
<test:case test="with" result="fail" desc="lsid must have a lsid prefix.">
<lsid>urn:authority:namespace:identifier</lsid>
</test:case>
<test:case test="with" result="fail" desc="lsid must have an identifier.">
<lsid>urn:lsid:authority:namespace</lsid>
</test:case>
<test:case test="with" result="fail" desc="lsid must have a namespace.">
<lsid>urn:lsid:authority::identifier</lsid>
</test:case>
<test:case test="with" result="fail" desc="lsid must have an authority.">
<lsid>urn:lsid::namespace:identifier</lsid>
</test:case>
<test:case test="with" result="pass" desc="authority and namespace may include slashes.">
<lsid>urn:lsid:authority/sub:namespace/sub:identifier</lsid>
</test:case>
</root></xml></code>

'''references'''
* [http://lsid.sourceforge.net LSID Resolution Protocol Project]

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType sourceUri ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="sourceUri" final="restriction">
<xs:union memberTypes="bt:lsid">
<xs:simpleType>
<xs:restriction base="xs:anyURI">
<xs:minLength value="1"/>
</xs:restriction>
</xs:simpleType>
</xs:union>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The URI of a data source - may be a LSID.
</div>

'''references'''
* [[#simpleType_lsid|simpleType lsid]]
* [[#complexType_source|complexType source]]
* [http://lsid.sourceforge.net LSID Resolution Protocol Project]

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType accessionNumber ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="accessionNumber">
<xs:restriction base="xs:token">
<xs:minLength value="1"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Specifies the accession number of a data item relative to its data source. The format of the accession number depends on the data source.
</div>

'''references'''
* [[#complexType_source|complexType source]]

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType source ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="source" mixed="true">
<xs:complexContent>
<xs:extension base="bt:anyContent">
<xs:attribute name="uri" type="bt:sourceUri" use="required" form="unqualified"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The description of a data source. The data source is identified by the <code>uri</code> attribute. The content may be source specific. It may consist e.g. of one or more <code>mapping</code> elements which map the source URI to an URL or a caption. Such a mapping is demonstrated by the <a href="http://schemas.bioservices.net/index.php?title=BioTypes_stylesheet">BioTypes stylesheet</a>.
</div>

'''references'''
* [[#element_source|element source]]
* [[#element_mapping|element mapping]]
* [[BioTypes stylesheet]]

'''change log'''

* 05/10/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element source ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="source">
<xs:complexType>
<xs:complexContent>
<xs:extension base="bt:source">
<xs:anyAttribute namespace="##other" processContents="lax"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The description of a data source.
</div>

'''references'''

* [[#complexType_source|complexType source]]

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element mapping ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="mapping">
<xs:complexType>
<xs:complexContent>
<xs:extension base="bt:anyContent">
<xs:attribute name="to" use="required">
<xs:simpleType>
<xs:union memberTypes="xs:token">
<xs:simpleType>
<xs:restriction base="xs:token">
<xs:enumeration value="url"/>
<xs:enumeration value="caption"/>
</xs:restriction>
</xs:simpleType>
</xs:union>
</xs:simpleType>
</xs:attribute>
<xs:anyAttribute namespace="##other" processContents="lax"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
</xs:element></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The mapping of a value to another representation. The <code>to</code> attribute specifies the representation. A mapping is used e.g. within a <code>source</code> element to map the data source URI to an URL. It is used by the <a href="http://schemas.bioservices.net/index.php?title=BioTypes_stylesheet">BioTypes stylesheet</a>. Its content may be mapping specific, e.g. text and one or more <code>attribute</code> elements. For each subordinated element the processing application or stylesheet should be ready to process it, i.e. there must be appropiate template.
</div>

'''references'''

* [[BioTypes stylesheet]]

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element attribute ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="attribute">
<xs:complexType>
<xs:attribute name="name" type="xs:Name" use="required"/>
<xs:attribute name="namespace" type="xs:anyURI" use="optional"/>
<xs:anyAttribute namespace="##other" processContents="lax"/>
</xs:complexType>
</xs:element></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Evaluates an attribute. This element can be used e.g. inside a <code>mapping</code> element. During the mapping process it should be replaced by the concrete value of the attribute.
</div>

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

== Sequence ==

This section contains type declarations for biological sequence data.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType sequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="sequence">
<xs:restriction base="xs:string">
<xs:minLength value="1"/>
<xs:whiteSpace value="preserve"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of character data of length greater than zero.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq>
<test:case test="with" result="fail" desc="sequence must not be empty."/>
<test:case test="with" result="pass" desc="sequence may contain any number of characters.">ABCDEFGHIJKLMNOPQRSTVWXYZabcdefghijklmnopqrstvwxyz</test:case>
<test:case test="with" result="pass" desc="sequence may contain whitespace and line breaks.">
AA
AA
</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAmbiguousNucleotideSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAmbiguousNucleotideSequence">
<xs:restriction base="bt:sequence">
<xs:pattern value="(A|G|C|T|U|R|Y|M|K|S|W|H|B|V|D|N|X|\-)+"/>
<xs:whiteSpace value="collapse"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of nucleotides (RNA and DNA) or its placeholders in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedAmbiguousNucleotideSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedAmbiguousNucleotideSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedAmbiguousNucleotideSequence">
<test:case test="with" result="fail" desc="gapped ambiguous nucleotide sequence must not be empty."/>
<test:case test="with" result="fail" desc="gapped ambiguous nucleotide sequence must not contain lower case characters.">a</test:case>
<test:case test="with" result="pass" desc="gapped ambiguous nucleotide sequence may contain any number of nucleotides, ambiguous characters and gaps.">ACGTURYMKSWHBVDNX-</test:case>
<test:case test="with" result="pass" desc="gapped ambiguous nucleotide sequence may contain line breaks at the beginning and at the end.">
AAAA
</test:case>
<test:case test="with" result="fail" desc="gapped ambiguous nucleotide must not contain line breaks in between.">
AA
AA
</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedNucleotideSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedNucleotideSequence">
<xs:restriction base="bt:gappedAmbiguousNucleotideSequence">
<xs:pattern value="(A|G|C|T|U|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of nucleotides (RNA and DNA) in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedNucleotideSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedNucleotideSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedNucleotideSequence">
<test:case test="with" result="fail" desc="gapped nucleotide sequence must not contain ambiguous characters.">RYMKSWHBVDNX</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType ambiguousNucleotideSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="ambiguousNucleotideSequence">
<xs:restriction base="bt:gappedAmbiguousNucleotideSequence">
<xs:pattern value="(A|G|C|T|U|R|Y|M|K|S|W|H|B|V|D|N|X)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of nucleotides (RNA and DNA) or its placeholders in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAmbiguousNucleotideSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAmbiguousNucleotideSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:ambiguousNucleotideSequence">
<test:case test="with" result="fail" desc="ambiguous nucleotide sequence must not contain gap characters.">-</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType nucleotideSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="nucleotideSequence">
<xs:restriction base="bt:ambiguousNucleotideSequence">
<xs:pattern value="(A|G|C|T|U)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of nucleotides (RNA and DNA) in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestNucleotideSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestNucleotideSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:nucleotideSequence">
<test:case test="with" result="fail" desc="nucleotide sequence must not contain gap characters or ambiguous characters.">-X</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType nucleotideSequenceSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="nucleotideSequenceSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:embl"/>
<xs:enumeration value="urn:bts:entrez"/>
<xs:enumeration value="urn:bts:genbank"/>
<xs:enumeration value="urn:bts:hugo"/>
<xs:enumeration value="urn:bts:locuslink"/>
<xs:enumeration value="urn:bts:mgd"/>
<xs:enumeration value="urn:bts:mgi"/>
<xs:enumeration value="urn:bts:rgd"/>
<xs:enumeration value="urn:bts:sgd"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined nucleotide sequence source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType nucleotideSequenceSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="nucleotideSequenceSource">
<xs:union memberTypes="bt:sourceUri bt:nucleotideSequenceSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of a nucleotide sequence. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_nucleotideSequenceSources|simpleType nucleotideSequenceSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup nucleotideSequenceAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="nucleotideSequenceAttrs">
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
<xs:attribute name="source" type="bt:nucleotideSequenceSource" use="optional"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Attributes for nucleotide sequences. <code>source</code> specifies the source of the sequence. In addition <code>accNumber</code> can be set to an accession number dependant on the data source if <code>source</code> identifies only the data source (e.g. database) but not the data item itself.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAmbiguousDnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAmbiguousDnaSequence">
<xs:restriction base="bt:gappedAmbiguousNucleotideSequence">
<xs:pattern value="(A|G|C|T|R|Y|M|K|S|W|H|B|V|D|N|X|\-)+"/>
<xs:whiteSpace value="collapse"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of DNAs or its placeholders in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedAmbiguousDnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedAmbiguousDnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedAmbiguousDnaSequence">
<test:case test="with" result="fail" desc="gapped ambiguous dna sequence must not contain Uracil.">U</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedDnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedDnaSequence">
<xs:restriction base="bt:gappedAmbiguousDnaSequence">
<xs:pattern value="(A|G|C|T|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of DNAs in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedDnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedDnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedDnaSequence">
<test:case test="with" result="fail" desc="gapped dna sequence must not contain ambiguous characters.">RYMKSWHBVDNX</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType ambiguousDnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="ambiguousDnaSequence">
<xs:restriction base="bt:gappedAmbiguousDnaSequence">
<xs:pattern value="(A|G|C|T|R|Y|M|K|S|W|H|B|V|D|N|X)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of DNAs or its placeholders in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAmbiguousDnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAmbiguousDnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:ambiguousDnaSequence">
<test:case test="with" result="fail" desc="ambiguous dna sequence must not contain gap characters.">-</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType dnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="dnaSequence">
<xs:restriction base="bt:ambiguousDnaSequence">
<xs:pattern value="(A|G|C|T)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of DNAs in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestDnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestDnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:dnaSequence">
<test:case test="with" result="fail" desc="dna sequence must not contain gap characters or ambiguous characters.">-X</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAmbiguousRnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAmbiguousRnaSequence">
<xs:restriction base="bt:gappedAmbiguousNucleotideSequence">
<xs:pattern value="(A|G|C|U|R|Y|M|K|S|W|H|B|V|D|N|X|\-)+"/>
<xs:whiteSpace value="collapse"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of RNAs or its placeholders in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedAmbiguousRnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedAmbiguousRnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedAmbiguousRnaSequence">
<test:case test="with" result="fail" desc="gapped ambiguous rna sequence must not contain Thymin.">T</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedRnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedRnaSequence">
<xs:restriction base="bt:gappedAmbiguousRnaSequence">
<xs:pattern value="(A|G|C|U|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of DNAs in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedRnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedRnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedRnaSequence">
<test:case test="with" result="fail" desc="gapped rna sequence must not contain ambiguous characters.">RYMKSWHBVDNX</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType ambiguousRnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="ambiguousRnaSequence">
<xs:restriction base="bt:gappedAmbiguousRnaSequence">
<xs:pattern value="(A|G|C|U|R|Y|M|K|S|W|H|B|V|D|N|X)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of RNAs or its placeholders in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAmbiguousRnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAmbiguousRnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:ambiguousRnaSequence">
<test:case test="with" result="fail" desc="ambiguous rna sequence must not contain gap characters.">-</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType rnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="rnaSequence">
<xs:restriction base="bt:ambiguousRnaSequence">
<xs:pattern value="(A|G|C|U)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of RNAs in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestRnaSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestRnaSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:rnaSequence">
<test:case test="with" result="fail" desc="rna sequence must not contain gap characters or ambiguous characters.">-X</test:case>
</seq>
</root></xml></code>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAmbiguousTerminalAminoAcidOneLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAmbiguousTerminalAminoAcidOneLetterSequence">
<xs:restriction base="bt:sequence">
<xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|X|B|Z|\-|\*)+"/>
<xs:whiteSpace value="collapse"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case one letter code including the terminal symbol *, ambigiuous and gap characters. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAmbiguousAminoAcidOneLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAmbiguousAminoAcidOneLetterSequence">
<xs:restriction base="bt:gappedAmbiguousTerminalAminoAcidOneLetterSequence">
<xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|X|B|Z|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case one letter code, ambigiuous and gap characters. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 05/10/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType ambiguousAminoAcidOneLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="ambiguousAminoAcidOneLetterSequence">
<xs:restriction base="bt:gappedAmbiguousTerminalAminoAcidOneLetterSequence">
<xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|X|B|Z)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case one letter code and ambigiuous characters. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAminoAcidOneLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAminoAcidOneLetterSequence">
<xs:restriction base="bt:gappedAmbiguousTerminalAminoAcidOneLetterSequence">
<xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case one letter code and gap characters. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType terminalAminoAcidOneLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="terminalAminoAcidOneLetterSequence">
<xs:restriction base="bt:gappedAmbiguousTerminalAminoAcidOneLetterSequence">
<xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V|\*)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case one letter code including the terminal symbol *. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType aminoAcidOneLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="aminoAcidOneLetterSequence">
<xs:restriction base="bt:ambiguousAminoAcidOneLetterSequence">
<xs:pattern value="(A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|U|W|Y|V)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case one letter code. Only leading and trailing whitespace is allowed.
</div>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType terminalAminoAcidThreeLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="terminalAminoAcidThreeLetterSequence">
<xs:restriction base="bt:sequence">
<xs:pattern value="(ALA|ARG|ASN|ASP|CYS|GLN|GLU|GLY|HIS|ILE|LEU|LYS|MET|PHE|PRO|SER|THR|SEC|TRP|TYR|VAL|TER)+"/>
<xs:whiteSpace value="collapse"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case three letter code including the terminal symbol TER. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestTerminalAminoAcidThreeLetterSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestTerminalAminoAcidThreeLetterSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:terminalAminoAcidThreeLetterSequence">
<test:case test="with" result="fail" desc="terminal amino acid three letter sequence must not be empty."/>
<test:case test="with" result="fail" desc="terminal amino acid three letter sequence must not contain lower case characters.">ala</test:case>
<test:case test="with" result="fail" desc="terminal amino acid three letter sequence must not contain illegal character combinations.">XZY</test:case>
<test:case test="with" result="pass" desc="terminal amino acid thre letter sequence may contain any number of amino acids in three letter code and the terminal signal.">ALAARGASNASPCYSGLNGLUGLYHISILELEULYSMETPHEPROSERTHRSECTRPTYRVALTER</test:case>
</seq>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType aminoAcidThreeLetterSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="aminoAcidThreeLetterSequence">
<xs:restriction base="bt:terminalAminoAcidThreeLetterSequence">
<xs:pattern value="(ALA|ARG|ASN|ASP|CYS|GLN|GLU|GLY|HIS|ILE|LEU|LYS|MET|PHE|PRO|SER|THR|SEC|TRP|TYR|VAL)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of amino acids in upper case three letter code. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAminoAcidThreeLetterSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAminoAcidThreeLetterSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:aminoAcidThreeLetterSequence">
<test:case test="with" result="fail" desc="amino acid three letter sequence must not contain the terminal signal.">TER</test:case>
</seq>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType aminoAcidSequenceSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="aminoAcidSequenceSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:pdb"/>
<xs:enumeration value="urn:bts:swissprot"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined amino acid sequence source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType aminoAcidSequenceSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="aminoAcidSequenceSource">
<xs:union memberTypes="bt:sourceUri bt:aminoAcidSequenceSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of a amino acid sequence. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_aminoAcidSequenceSources|simpleType aminoAcidSequenceSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup aminoAcidSequenceAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="aminoAcidSequenceAttrs">
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
<xs:attribute name="source" type="bt:aminoAcidSequenceSource" use="optional"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Attributes for amino acid sequences. <code>source</code> specifies the source of the sequence. In addition <code>accNumber</code> can be set to an accession number dependant on the data source if <code>source</code> identifies only the data source (e.g. database) but not the data item itself.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedAmbiguousSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedAmbiguousSecondaryStructureSequence">
<xs:restriction base="bt:sequence">
<xs:pattern value="(C|H|G|I|E|B|T|S|_|X|\-)+"/>
<xs:whiteSpace value="replace"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of secondary structure assignments or its placeholder in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedAmbiguousSecondaryStructureSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedAmbiguousSecondaryStructureSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedAmbiguousSecondaryStructureSequence">
<test:case test="with" result="fail" desc="gapped ambiguous secondary structure sequence must not be empty."/>
<test:case test="with" result="fail" desc="gapped ambiguous secondary structure sequence must not contain lower case characters.">a</test:case>
<test:case test="with" result="pass" desc="gapped ambiguous secondary structure sequence may contain any number of secondary structures, ambiguous characters and gaps.">CHGIEBTS_X-</test:case>
<test:case test="with" result="fail" desc="gapped ambiguous secondary structure must not contain line breaks in between.">
SS
SS
</test:case>
</seq>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType ambiguousSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="ambiguousSecondaryStructureSequence">
<xs:restriction base="bt:gappedAmbiguousSecondaryStructureSequence">
<xs:pattern value="(C|H|G|I|E|B|T|S|_|X)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of secondary structure assignments or its placeholder in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAmbiguousSecondaryStructureSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAmbiguousSecondaryStructureSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:ambiguousSecondaryStructureSequence">
<test:case test="with" result="fail" desc="ambiguous secondary structure sequence must not contain gap characters.">-</test:case>
</seq>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType gappedSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="gappedSecondaryStructureSequence">
<xs:restriction base="bt:gappedAmbiguousSecondaryStructureSequence">
<xs:pattern value="(C|H|G|I|E|B|T|S|_|\-)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of secondary structure assignments in upper case letters and gap characters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestGappedSecondaryStructureSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestGappedSecondaryStructureSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:gappedSecondaryStructureSequence">
<test:case test="with" result="fail" desc="gapped secondary structure sequence must not contain ambiguous character.">X</test:case>
</seq>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType secondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="secondaryStructureSequence">
<xs:restriction base="bt:gappedAmbiguousSecondaryStructureSequence">
<xs:pattern value="(C|H|G|I|E|B|T|S|_)+"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of secondary structure assignments in upper case letters. Only leading and trailing whitespace is allowed.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestSecondaryStructureSequence.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestSecondaryStructureSequence.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<seq xsi:type="bt:secondaryStructureSequence">
<test:case test="with" result="fail" desc="secondary structure sequence must not contain ambiguous character or gap character.">X-</test:case>
</seq>
</root></xml></code>

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType secondaryStructureSequenceSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="secondaryStructureSequenceSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:dssp"/>
<xs:enumeration value="urn:bts:pdb"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined secondary structure sequence source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType secondaryStructureSequenceSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="secondaryStructureSequenceSource">
<xs:union memberTypes="bt:sourceUri bt:secondaryStructureSequenceSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of a secondary structure sequence. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_secondaryStructureSequenceSources|simpleType secondaryStructureSequenceSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup secondaryStructureSequenceAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="secondaryStructureSequenceAttrs">
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
<xs:attribute name="source" type="bt:secondaryStructureSequenceSource" use="optional"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Attributes for secondary structure sequences. <code>source</code> specifies the source of the sequence. In addition <code>accNumber</code> can be set to an accession number dependant on the data source if <code>source</code> identifies only the data source (e.g. database) but not the data item itself.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

== Structure ==

This section contains type, attribute and element declarations for atom structures.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType atomNames ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="atomNames">
<xs:restriction base="xs:token">
<xs:enumeration value="H"/>
<xs:enumeration value="C"/>
<xs:enumeration value="CA"/>
<xs:enumeration value="CB"/>
<xs:enumeration value="O"/>
<xs:enumeration value="N"/>
<xs:enumeration value="S"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined atom names. <p>This list contains the following atom names:</p><ul><li><code>H</code>: hydrogen atom</li><li><code>C</code>: carbon atom</li><li><code>CA</code>: alpha carbon atom</li><li><code>CB</code>: beta carbon atom</li><li><code>O</code>: oxygen atom</li><li><code>N</code>: nitrogen atom</li><li><code>S</code>: sulphur atom</li></ul>
</div>

'''references'''
* [[#simpleType_atomName|simpleType atomName]]

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType atomName ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="atomName">
<xs:union memberTypes="bt:atomNames">
<xs:simpleType>
<xs:restriction base="xs:token">
<xs:minLength value="1"/>
</xs:restriction>
</xs:simpleType>
</xs:union>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The (abbreviated) name of an atom within a biological molecule. The name must be at least one character long and may contain numbers but not at the beginning.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAtomName.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAtomName.xml"><xml><root xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<test:case test="with" result="fail" desc="atom name must not be empty.">
<atomName/>
</test:case>
<test:case test="with" result="pass" desc="atom name may contain any number of token characters.">
<atomName>B1</atomName>
</test:case>
<test:case test="with" result="pass" desc="atom name must not start with a digit.">
<atomName>1B</atomName>
</test:case>
</root></xml></code>

'''references'''
* [[#simpleType_atomNames|simpleType atomNames]]

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType coordinate ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="coordinate">
<xs:restriction base="xs:double"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A coordinate in a n-dimensional space.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType distance ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="distance">
<xs:restriction base="xs:double">
<xs:minInclusive value="0.0"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A distance in a n-dimensional space. A distance may not be negative.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType distanceUnits ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="distanceUnits">
<xs:restriction base="xs:token">
<xs:enumeration value="angstroem"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of possible distance units. <p>This list contains the following entries:</p><ul><li><code>angstroem</code>: Angstroem</li></ul>
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType atomStructureSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="atomStructureSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:pdb"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined atom structure source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType atomStructureSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="atomStructureSource">
<xs:union memberTypes="bt:sourceUri bt:atomStructureSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of an atom structure. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_atomSequenceSources|simpleType atomSequenceSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup coordinates3D ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="coordinates3D">
<xs:attribute name="x" type="bt:coordinate" use="required" form="unqualified"/>
<xs:attribute name="y" type="bt:coordinate" use="required" form="unqualified"/>
<xs:attribute name="z" type="bt:coordinate" use="required" form="unqualified"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Coordinates in a 3-dimensional space.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestCoordinates3D.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestCoordinates3D.xml"><xml><coord xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" y="1.0" z="1.0" x="1.0" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<test:attribute id="x" name="x" result="fail" desc="3-D-coordinates must have a x value."/>
<test:attribute name="y" result="fail" desc="3-D-coordinates must have a y value."/>
<test:attribute name="z" result="fail" desc="3-D-coordinates must have a z value."/>
</coord></xml></code>

'''change log'''

* 04/26/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType atom ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="atom" block="restriction" final="restriction">
<xs:attributeGroup ref="bt:coordinates3D"/>
<xs:attribute name="type" type="bt:atomName" use="required" form="unqualified"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A single atom including its coordinates in 3-dimensional space and its type.
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAtom.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAtom.xml"><xml><atom xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd" x="1.0" y="1.0" z="1.0" type="C">
<test:attribute name="type" result="fail" desc="atom must have a type."/>
</atom></xml></code>

'''references'''
* [[#attributeGroup_coordinates3D|attributeGroup coordinates3D]]

'''change log'''

* 04/26/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractAtom ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractAtom" type="bt:atom" abstract="true" block="restriction" final="restriction"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An abstract atom element for the atomSeq element.
</div>

'''references'''
* [[#complexType_atom|complexType atom]]
* [[#complexType_atomSeq|complexType atomSeq]]

'''change log'''

* 04/26/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup structureAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="structureAttrs">
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
<xs:attribute name="source" type="bt:atomStructureSource" use="optional"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Attributes for structure data. <code>source</code> specifies the source of the structure data. In addition <code>accNumber</code> can be set to an accession number dependant on the data source if <code>source</code> identifies only the data source (e.g. database) but not the data item itself.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType atomSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="atomSequence" block="restriction" final="restriction">
<xs:sequence>
<xs:element ref="bt:abstractAtom" minOccurs="1" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attributeGroup ref="bt:structureAttrs"/>
<xs:attribute name="unit" type="bt:distanceUnits" use="optional" default="angstroem"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence of atoms. An atom sequence must contain at least one atom. The <code>abstractAtom</code> element must be replaced by a concrete element of type <code>atom</code>. This is done via a substitution group:
<p><code>
<xs:element xmlns:xs="http://www.w3.org/2001/XMLSchema" name="atom" type="bt:atom" substitutionGroup="bt:abstractAtom"/></code>.</p><p>The coordinates of each atom are relative to the specified distance unit (default is Angstroem).</p>
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''appinfo biotypes/tests/TestAtomSeq.xml'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="appinfo biotypes/tests/TestAtomSeq.xml"><xml><atomSeq xmlns="http://schemas.bioservices.net/2005/biotypes/tests" xmlns:test="http://www.powerware.com/nz/XMLSchemaUnitTest" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:bt="http://schemas.bioservices.net/2005/biotypes" xsi:schemaLocation="http://www.powerware.com/nz/XMLSchemaUnitTest ../../sut.xsd http://schemas.bioservices.net/2005/biotypes/tests tests.xsd">
<test:case test="with" result="fail" desc="atomSeq must not be empty."/>
<test:case test="with" result="pass" desc="atomSeq may contain one or more atoms.">
<atom y="1.0" z="1.0" type="C" x="1.0"/>
<atom y="1.0" z="1.0" type="C" x="1.0"/>
</test:case>
</atomSeq></xml></code>

'''references'''
* [[#complexType_atom|complexType atom]]
* [[#element_atom|element atom]]

'''change log'''

* 04/26/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType atomConnection ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="atomConnection" abstract="true" block="restriction" final="restriction">
<xs:attribute name="atomType1" type="bt:atomName" use="required"/>
<xs:attribute name="atomType2" type="bt:atomName" use="required"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Specifies a connection between two atoms identified by <code>atomType1</code> and <code>atomType2</code>. A connection can be e.g. a bond or a contact.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType atomContact ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="atomContact">
<xs:complexContent>
<xs:extension base="bt:atomConnection">
<xs:attribute name="distance" type="bt:distance" use="required"/>
<xs:attribute name="unit" type="bt:distanceUnits" use="optional" default="angstroem"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Specifies a (close) contact between two atoms. The distance of the two atoms is specified by <code>distance</code>. The unit of the distance depends on <code>unit</code>. The default setting for <code>unit</code> is <code>angstroem</code>.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

== Classification ==

This section contains type declaration for the classification of biological objects.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType classificationSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="classificationSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:cath"/>
<xs:enumeration value="urn:bts:scop"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined classification source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType classificationSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="classificationSource">
<xs:union memberTypes="bt:sourceUri bt:classificationSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of a classification. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_classificationSources|simpleType classificationSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType classificationValue ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="classificationValue">
<xs:restriction base="xs:token">
<xs:minLength value="1"/>
</xs:restriction>
</xs:simpleType></xml></code>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType classification ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="classification">
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="source" type="bt:classificationSource" use="required"/>
<xs:attribute name="accNumber" type="bt:classificationValue" use="required"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Specifies a classification. The classification scheme is identified by <code>source</code>. The classification itself is specified by <code>accNumber</code>.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

== Pattern ==

This section contains type declaration for sequence patterns.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType patternSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="patternSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:interpro"/>
<xs:enumeration value="urn:bts:pfam"/>
<xs:enumeration value="urn:bts:prodom"/>
<xs:enumeration value="urn:bts:prosite"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined sequence pattern source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType patternSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="patternSource">
<xs:union memberTypes="bt:sourceUri bt:patternSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of a sequence pattern. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_patternSources|simpleType patternSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup patternAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="patternAttrs">
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="source" type="bt:patternSource" use="required"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="required"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Attributes for pattern data. <code>source</code> specifies the source of the pattern data. In addition <code>accNumber</code> can be set to an accession number dependant on the data source if <code>source</code> identifies only the data source (e.g. database) but not the data item itself.
</div>

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType patternBase ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="patternBase" mixed="true">
<xs:complexContent>
<xs:extension base="bt:anyContent">
<xs:attributeGroup ref="bt:patternAttrs"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence pattern. The content of a pattern element is the pattern itself, e.g. a consensus sequence or a HMM, and may contain elements from any namespace and text.
</div>

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType patternProfile ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="patternProfile">
<xs:sequence>
<xs:element ref="bt:abstractPatternProfileMember" minOccurs="1" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="source" type="bt:patternSource" use="optional"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A sequence pattern profile. A profile must contain at least one pattern reference.
</div>

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Made pattern abstract.
* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType patternProfileMember ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="patternProfileMember" block="restriction" final="restriction">
<xs:complexContent>
<xs:extension base="bt:patternBase">
<xs:attribute name="occurence" type="xs:positiveInteger" use="required"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A member of a pattern profile. The number of occurences of the pattern in the sequence(s) must be specified.
</div>

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Made pattern abstract.
* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractPatternProfileMember ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractPatternProfileMember" type="bt:patternProfileMember" abstract="true" block="restriction" final="restriction"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
Abstract pattern element for a pattern profile.
</div>

'''change log'''

* 05/19/05 by [http://szugat.gmxhome.de Martin Szugat]: Made pattern abstract.
* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType pattern ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="pattern" mixed="true">
<xs:complexContent>
<xs:extension base="bt:patternBase">
<xs:attributeGroup ref="bt:scopeAttrs"/>
</xs:extension>
</xs:complexContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A single sequence pattern. The location of the pattern inside the sequence is identified by the attributes <code>from</code> and <code>to</code>.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

== Alignment ==

This section contains type declaration for sequence alignments.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType alignmentSources ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="alignmentSources">
<xs:restriction base="xs:token">
<xs:enumeration value="urn:bts:clustalw"/>
</xs:restriction>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A list of predefined sequence alignment source names.
</div>

'''change log'''

* 04/23/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== simpleType alignmentSource ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:simpleType name="alignmentSource">
<xs:union memberTypes="bt:sourceUri bt:alignmentSources"/>
</xs:simpleType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The source of a sequence alignment. May be an URI, a LSID or one of the predefined source names.
</div>

'''references'''
* [[#simpleType_alignmentSources|simpleType alignmentSources]]

'''change log'''

* 05/09/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType multipleAlignment ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="multipleAlignment" final="restriction" block="restriction">
<xs:choice>
<xs:sequence minOccurs="2" maxOccurs="unbounded">
<xs:element ref="bt:abstractAlignedRnaSequence"/>
</xs:sequence>
<xs:sequence minOccurs="2" maxOccurs="unbounded">
<xs:element ref="bt:abstractAlignedDnaSequence"/>
</xs:sequence>
<xs:sequence minOccurs="2" maxOccurs="unbounded">
<xs:element ref="bt:abstractAlignedSecondaryStructureSequence"/>
</xs:sequence>
<xs:sequence minOccurs="2" maxOccurs="unbounded">
<xs:element ref="bt:abstractAlignedAminoAcidSequence"/>
</xs:sequence>
</xs:choice>
<xs:attributeGroup ref="bt:dataAttrs"/>
<xs:attribute name="score" type="bt:score" use="optional"/>
<xs:attribute name="source" type="bt:alignmentSource" use="optional"/>
<xs:attribute name="accNumber" type="bt:accessionNumber" use="optional"/>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
A multiple sequence alignment. A overall score may be assigned to the multiple alignment using the <code>score</code> attribute. The source of the multiple alignment can be specified using the attributes <code>source</code> and <code>accNumber</code>. A multiple alignment must contain at least two aligned sequences. Thus one or more of the abstract elements <code>abstractAlignedRnaSequence</code>, <code>abstractAlignedDnaSequence</code>, <code>abstractAlignedSecondaryStructureSequence</code> or <code>abstractAlignedAminoAcidSequence</code> must be replaced by a concrete element. This can be done via a substitution group.
</div>

'''change log'''

* 05/11/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== attributeGroup alignedSequenceAttrs ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:attributeGroup name="alignedSequenceAttrs">
<xs:attribute name="score" type="bt:score" use="optional"/>
</xs:attributeGroup></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
The attributes for an aligned sequence. The individual score for an aligned sequence may be set using the <code>score</code> attribute.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType alignedRnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="alignedRnaSequence">
<xs:simpleContent>
<xs:extension base="bt:gappedAmbiguousRnaSequence">
<xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An aligned RNA sequence.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractAlignedRnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractAlignedRnaSequence" type="bt:alignedRnaSequence" abstract="true" final="restriction" block="restriction"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An abstract aligned RNA sequence element for the multiple alignment.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType alignedDnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="alignedDnaSequence">
<xs:simpleContent>
<xs:extension base="bt:gappedAmbiguousDnaSequence">
<xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An aligned DNA sequence.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractAlignedDnaSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractAlignedDnaSequence" type="bt:alignedDnaSequence" abstract="true" final="restriction" block="restriction"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An abstract aligned DNA sequence element for the multiple alignment.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType alignedSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="alignedSecondaryStructureSequence">
<xs:simpleContent>
<xs:extension base="bt:gappedAmbiguousSecondaryStructureSequence">
<xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An aligned secondary structure sequence.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractAlignedSecondaryStructureSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractAlignedSecondaryStructureSequence" type="bt:alignedSecondaryStructureSequence" abstract="true" final="restriction" block="restriction"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An abstract aligned secondary structure sequence element for the multiple alignment.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== complexType alignedAminoAcidSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:complexType name="alignedAminoAcidSequence">
<xs:simpleContent>
<xs:extension base="bt:gappedAmbiguousAminoAcidOneLetterSequence">
<xs:attributeGroup ref="bt:alignedSequenceAttrs"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An aligned amino acid sequence.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
=== element abstractAlignedAminoAcidSequence ===

'''code'''
</div>

<code xmlns="http://www.w3.org/1999/xhtml" xmlns:xs="http://www.w3.org/2001/XMLSchema" title="code"><xml><xs:element name="abstractAlignedAminoAcidSequence" type="bt:alignedAminoAcidSequence" abstract="true" final="restriction" block="restriction"/></xml></code>

<div xmlns="http://www.w3.org/1999/xhtml" title="ignore">
'''documentation'''
</div>

<div xmlns="http://www.w3.org/1999/xhtml" title="documentation">
An abstract aligned amino acid sequence element for the multiple alignment.
</div>

'''change log'''

* 05/13/05 by [http://szugat.gmxhome.de Martin Szugat]: Initial declaration.

Contribute

Hampti — Wed, 17 May 2006 08:30:04 GMT

Summary:

This page describes how to contribute to the BioSchemas project by releasing your own XML-schema(s) to BioSchemas or by extending an existing XML-schema.

== How to become a BioSchemas developer ==

[http://sourceforge.net/tracker/?func=add&group_id=164851&atid=833351 Request] a membership. Please tell us your full name, the user name for your sourceforge account (if you have one), your email address and the name of the organisation you work for. As category set <code>Membership</code>. We will create an account for the Wiki and the Sourceforge project.

For any further requests, e.g. if you like to create your own project, please also use the [http://sourceforge.net/tracker/?atid=833351&group_id=164851&func=browse Support page].

== How to become an informed BioSchemas developer ==

* Fill your [[Special:Watchlist|watchlist]] with the pages you are interested in or monitor all changes to this wiki using the [[Special:Recentchanges|recent changes]] page which is also available as [{{SERVER}}{{localurl:Special:Recentchanges|feed=rss}} RSS ]and [{{SERVER}}{{localurl:Special:Recentchanges|feed=rss}} Atom] feed
* Subscribe to the following mailing lists:
** [http://lists.sourceforge.net/mailman/listinfo/bioschemas-developers bioschemas-developers]: developer discussions
** [http://lists.sourceforge.net/mailman/listinfo/bioschemas-svnnotify bioschemas-svnnotify]: notifications of commits to the repository
** [http://lists.sourceforge.net/mailman/listinfo/bioschemas-tracker bioschemas-tracker]: notifications of new bug reports or feature requests or changes to the tracked items
* Monitor the [http://sourceforge.net/forum/?group_id=164851 user forums].
* Subscribe to the [http://sourceforge.net/export/rss2_projnews.php?group_id=164851&rss_fulltext=1 news feed].

== How to become a good BioSchemas developer ==

Read and follow some guidelines:

* [[Guideline:Wiki editing|Wiki editing]]
* [[Guideline:New project|New project]]
* [[Guideline:Schema development|Schema development]]
* [[Guideline:Schema documentation|Schema documentation]]
* [[Guideline:Schema releasing|Schema releasing]]

== How to become a productive BioSchemas developer ==

* Use the [[Build Tools]]

Use

Hampti — Wed, 17 May 2006 08:29:27 GMT

Summary:

== Preface ==

Feel free to use any of the XML-schemas provided on this website, but please

* read the license info, some schemas maybe released in the public domain, others may be open source licensed.
* mention the authors and this website in your scientific work.
* give us valuable feedback by using the discussion page for the respective XML-schema (see above) or edit the XML-schema directly (if possible).

== Schemas ==

The schemas are categorized as follows:

* [[:Category:Type library|Type libraries]]: basic types
* [[:Category:Building block|Building blocks]]: common structures
* [[:Category:Document format|Document formats]]: whole formats

== Download ==

The latest releases of the BioSchemas can be downloaded from the [http://sourceforge.net/project/showfiles.php?group_id=164851 project site].

== Help ==

Bug reports or feature requests are highly [http://sourceforge.net/tracker/?group_id=164851 welcome]. If you have any questions [http://sourceforge.net/forum/?group_id=164851 tell us]. If you like to contribute bug fixes, additional features, etc. read [[Contribute|this]]. If you don't know how to use a Wiki please read this http://meta.wikimedia.org/wiki/Help:Contents.

__NOTOC__

Sandbox

Hampti — Fri, 05 May 2006 16:48:37 GMT

Summary:

Test it

BioTypes

Hampti — Tue, 18 Apr 2006 22:42:43 GMT

Summary:

The BioTypes schema provides a common XML type framework for biological data in analogy to the predefined XML Schema types. It is not intended to be used as a standalone schema but as a satellite schema that can be imported into other schemas. Thus the development of new schemas for biological data becomes easier and the schemas also share a common basis, which increases the interoperability.

== Source code access ==

Get the latest release from the SVN repository:

<pre>https://svn.sourceforge.net/svnroot/bioschemas/biotypes/trunk</pre>

== History ==

These versions of BioTypes have been released or are under current development:

* [[BioTypes 1.0]]: ''released''
* [[BioTypes 1.1]]: ''released''
* [[BioTypes 1.2]]: ''open''

'''Note''': Only those versions that have a state of ''open'' may be edited. For practice the latest ''released'' version of BioTypes should be used.

== Developers ==

* [http://szugat.gmxhome.de Martin Szugat]: Contributor and maintainer
* [http://biozentrum.uni-wuerzburg.de/ Philipp Seibel]: Contributor
* [http://bibiserv.techfak.uni-bielefeld.de/ Jan Krüger]: Contributor
* Sven Hartmeier: Contributor
* [http://bibiserv.techfak.uni-bielefeld.de Kai Loewenthal]: Contributor

== See also ==

* [http://schemas.bioservices.net/2005/biotypes BioTypes namespace URL]
* [http://www.bio.ifi.lmu.de/2005/proml ProML]

[[Category:Type library]]

Start

Hampti — Tue, 18 Apr 2006 22:41:13 GMT

Summary:

''Schemas are interfaces / contracts between applications / developers''. Therefore, schemas should not be owned nor defined by a single person or institution. They have to be defined in a collaborative way - thus BioSchemas.

== Introduction ==

The need for data exchange especially in life sciences is a key factor for success. Because of that many organizations and companies gone over to replace their flat file formats by [http://www.w3.org/XML XML]-based formats. This offers a whole lot of advantages over flat file formats:

* A common, easy and well-known syntax and in case of [http://www.w3.org/XML/Schema XML Schema] also a common, extensive and flexible type system.
* Both, XML and XML Schema, are supported by many programming languages, operating systems, application platforms, software libraries, authoring tools and additional specifications and also by major organizations and companies.
* The possibility to validate XML documents against their appropriate schemas without the need for extra programming tasks.

However many XML-based formats for biological data are not compatible to each other. What is missing is a common type framework in analogy to the [http://www.w3.org/TR/xmlschema-2/ XML Schema Types] and the standardization of element and attribute names. Only the concrete arrangement of the different elements and attributes should be open to the Application-specific formats.

== What is BioSchemas? ==

[[image:ESA.jpg|500px|right]]
Although, XML stands for "Extensible Markup Language", most XML formats are not extensible, i.e. they do not allow to incorporate data from foreign formats. The BioSchemas project tries to overcome this limitation by using an ''Extensible Schema Architecture'' which is mainly based on a common type framework, multiple replaceable building blocks and flexible lightweight document formats - see picture on the right side.

The aim of the BioSchemas project is to provide an XML Schema framework by offering libraries of basic types and frequently used building blocks, so that XML formats share a common foundation. This will improve the interoperability in biological data exchange by eliminating awkward type conversations and structure transformations.

Besides, the development of new specifications becomes easier, because existing definitions and declarations can be imported into new schemas and so decrease the expense of development.

To guarantee that the schemas provided here fulfill the requirements for a broad range of applications the development of the schemas is driven by an open community process and thus all members affected are involved in the evolution of this project.

== What next? ==

If you think these are the right answers to your problems, feel welcome to [[Use|use our solutions]]. If you think there is a better solution, feel free to [[Contribute|contribute it]]. You want to know more? Then [[Browse|browse]] or [[Special:Search|search]] our website. You want to know who we are? Then visit the [http://hobit.sourceforge.net HOBITs]