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 bt. For further information on usage visit BioSchemas .

To use BioTypes in an XML schema download a local copy of the BioTypes schema and include it via the import statement:

Content is available under Creative Commons Attribution-ShareAlike License.

lsidres: EMBL Nucleotide Sequence Database http://www.ebi.ac.uk/embl/ NCBI Entrez Gene http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene NCBI GenBank http://www.ncbi.nlm.nih.gov/Genbank/ The Human Genome Organisation http://www.hugo-international.org/ NCBI LocusLink http://www.ncbi.nlm.nih.gov/projects/LocusLink/ Mouse Genome Informatics http://www.informatics.jax.org/ Mouse Genome Informatics http://www.informatics.jax.org/ Rat Genome Database http://rgd.mcw.edu/ Saccharomyces Genome Database http://www.yeastgenome.org/ RCSB Protein Data Bank http://www.rcsb.org/pdb/ Swiss-Prot http://au.expasy.org/sprot/ DSSP http://www.cmbi.kun.nl/gv/dssp/ RCSB Protein Data Bank http://www.rcsb.org/pdb/ RCSB Protein Data Bank http://www.rcsb.org/pdb/ CATH http://www.ccbb.re.kr/irs/2_cath/ SCOP http://scop.mrc-lmb.cam.ac.uk/scop/ EMBL Interpro http://www.ebi.ac.uk/interpro/ PFAM http://www.sanger.ac.uk/Software/Pfam/ ProDom http://protein.toulouse.inra.fr/prodom/current/html/home.php ExPASy PROSITE http://au.expasy.org/prosite/ ClustalW http://www.ebi.ac.uk/clustalw/ 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. A versioning number. A scoring value. Scores can be positive or negative. Allows any mixed content, i.e. text and elements from any namespace. 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 version and date 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 source attribute of type sourceUri and a accNumber attribute of type accessionNumber, specifying the data source of the data item and its accession number within the data source. Attributes for setting a range. from should be less than to. A Life Sciences Identifier (LSID) is a URN that uniquely names an object. According to the LSID Resolution Protocol Project the syntax is urn:lsid:<authority>:<namespace>:<value>:<version> where authority is the name of the organization that has defined an entity, namespace is a namespace within the authority for the Id, value is an alpha-numeric sequence that uniquely identifies an object to its authority, and version is an optional version number for an Id. authority and namespace can have hierarchical path elements separated by "/". The URI of a data source - may be a LSID. Specifies the accession number of a data item relative to its data source. The format of the accession number depends on the data source. The description of a data source. The data source is identified by the uri attribute. The content may be source specific. It may consist e.g. of one or more mapping elements which map the source URI to an URL or a caption. Such a mapping is demonstrated by the BioTypes stylesheet. The description of a data source. The mapping of a value to another representation. The to attribute specifies the representation. A mapping is used e.g. within a source element to map the data source URI to an URL. It is used by the BioTypes stylesheet. Its content may be mapping specific, e.g. text and one or more attribute elements. For each subordinated element the processing application or stylesheet should be ready to process it, i.e. there must be appropiate template. Evaluates an attribute. This element can be used e.g. inside a mapping element. During the mapping process it should be replaced by the concrete value of the attribute. A sequence of character data of length greater than zero. A sequence of nucleotides (RNA and DNA) or its placeholders in upper case letters and gap characters. Only leading and trailing whitespace is allowed. A sequence of nucleotides (RNA and DNA) in upper case letters and gap characters. Only leading and trailing whitespace is allowed. A sequence of nucleotides (RNA and DNA) or its placeholders in upper case letters. Only leading and trailing whitespace is allowed. A sequence of nucleotides (RNA and DNA) in upper case letters. Only leading and trailing whitespace is allowed. A list of predefined nucleotide sequence source names. The source of a nucleotide sequence. May be an URI, a LSID or one of the predefined source names. Attributes for nucleotide sequences. source specifies the source of the sequence. In addition accNumber can be set to an accession number dependant on the data source if source identifies only the data source (e.g. database) but not the data item itself. A sequence of DNAs or its placeholders in upper case letters and gap characters. Only leading and trailing whitespace is allowed. A sequence of DNAs in upper case letters and gap characters. Only leading and trailing whitespace is allowed. A sequence of DNAs or its placeholders in upper case letters. Only leading and trailing whitespace is allowed. A sequence of DNAs in upper case letters. Only leading and trailing whitespace is allowed. A sequence of RNAs or its placeholders in upper case letters and gap characters. Only leading and trailing whitespace is allowed. A sequence of DNAs in upper case letters and gap characters. Only leading and trailing whitespace is allowed. A sequence of RNAs or its placeholders in upper case letters. Only leading and trailing whitespace is allowed. A sequence of RNAs in upper case letters. Only leading and trailing whitespace is allowed. 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. A sequence of amino acids in upper case one letter code, ambigiuous and gap characters. Only leading and trailing whitespace is allowed. A sequence of amino acids in upper case one letter code and ambigiuous characters. Only leading and trailing whitespace is allowed. A sequence of amino acids in upper case one letter code and gap characters. Only leading and trailing whitespace is allowed. A sequence of amino acids in upper case one letter code including the terminal symbol *. Only leading and trailing whitespace is allowed. A sequence of amino acids in upper case one letter code. Only leading and trailing whitespace is allowed. A sequence of amino acids in upper case three letter code including the terminal symbol TER. Only leading and trailing whitespace is allowed. A sequence of amino acids in upper case three letter code. Only leading and trailing whitespace is allowed. A list of predefined amino acid sequence source names. The source of a amino acid sequence. May be an URI, a LSID or one of the predefined source names. Attributes for amino acid sequences. source specifies the source of the sequence. In addition accNumber can be set to an accession number dependant on the data source if source identifies only the data source (e.g. database) but not the data item itself. A sequence of secondary structure assignments or its placeholder in upper case letters and gap characters. Only leading and trailing whitespace is allowed. A sequence of secondary structure assignments or its placeholder in upper case letters. Only leading and trailing whitespace is allowed. A sequence of secondary structure assignments in upper case letters and gap characters. Only leading and trailing whitespace is allowed. A sequence of secondary structure assignments in upper case letters. Only leading and trailing whitespace is allowed. A list of predefined secondary structure sequence source names. The source of a secondary structure sequence. May be an URI, a LSID or one of the predefined source names. Attributes for secondary structure sequences. source specifies the source of the sequence. In addition accNumber can be set to an accession number dependant on the data source if source identifies only the data source (e.g. database) but not the data item itself. A list of predefined atom names.

This list contains the following atom names:

H: hydrogen atom
C: carbon atom
CA: alpha carbon atom
CB: beta carbon atom
O: oxygen atom
N: nitrogen atom
S: sulphur atom

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. A coordinate in a n-dimensional space. A distance in a n-dimensional space. A distance may not be negative. A list of possible distance units.

This list contains the following entries:

angstroem: Angstroem

A list of predefined atom structure source names. The source of an atom structure. May be an URI, a LSID or one of the predefined source names. Coordinates in a 3-dimensional space. A single atom including its coordinates in 3-dimensional space and its type. An abstract atom element for the atomSeq element. Attributes for structure data. source specifies the source of the structure data. In addition accNumber can be set to an accession number dependant on the data source if source identifies only the data source (e.g. database) but not the data item itself. A sequence of atoms. An atom sequence must contain at least one atom. The abstractAtom element must be replaced by a concrete element of type atom. This is done via a substitution group:

The coordinates of each atom are relative to the specified distance unit (default is Angstroem).

Specifies a connection between two atoms identified by atomType1 and atomType2. A connection can be e.g. a bond or a contact. Specifies a (close) contact between two atoms. The distance of the two atoms is specified by distance. The unit of the distance depends on unit. The default setting for unit is angstroem. A list of predefined classification source names. The source of a classification. May be an URI, a LSID or one of the predefined source names. Specifies a classification. The classification scheme is identified by source. The classification itself is specified by accNumber. A list of predefined sequence pattern source names. The source of a sequence pattern. May be an URI, a LSID or one of the predefined source names. Attributes for pattern data. source specifies the source of the pattern data. In addition accNumber can be set to an accession number dependant on the data source if source identifies only the data source (e.g. database) but not the data item itself. 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. A sequence pattern profile. A profile must contain at least one pattern reference. A member of a pattern profile. The number of occurences of the pattern in the sequence(s) must be specified. Abstract pattern element for a pattern profile. A single sequence pattern. The location of the pattern inside the sequence is identified by the attributes from and to. A list of predefined sequence alignment source names. The source of a sequence alignment. May be an URI, a LSID or one of the predefined source names. A multiple sequence alignment. A overall score may be assigned to the multiple alignment using the score attribute. The source of the multiple alignment can be specified using the attributes source and accNumber. A multiple alignment must contain at least two aligned sequences. Thus one or more of the abstract elements abstractAlignedRnaSequence, abstractAlignedDnaSequence, abstractAlignedSecondaryStructureSequence or abstractAlignedAminoAcidSequence must be replaced by a concrete element. This can be done via a substitution group. The attributes for an aligned sequence. The individual score for an aligned sequence may be set using the score attribute. An aligned RNA sequence. An abstract aligned RNA sequence element for the multiple alignment. An aligned DNA sequence. An abstract aligned DNA sequence element for the multiple alignment. An aligned secondary structure sequence. An abstract aligned secondary structure sequence element for the multiple alignment. An aligned amino acid sequence. An abstract aligned amino acid sequence element for the multiple alignment.