BioXSD: The common XML Schema (canonical data model) for bioinformatics Web services and everyday bioinformatics. Defines XML exchange formats for: sequences, sequence annotations, sequence similarity/alignments, references and supporting types of data Nucleotide sequence, possibly with ambiguous ("degenerate") bases Amino-acid sequence, possibly with ambiguous residues (Asx, Xle, Glx, Xaa/Unk) and additional residues (Pyl and Sec) Nucleotide or amino-acid sequence, possibly with ambiguous bases and residues Nucleotide sequence without ambiguous ("degenerate") bases Amino-acid sequence without ambiguous and additional residues (Pyl, Sec) Nucleotide or amino-acid sequence record including the generic sequence and optional metadata Biological source of the sequence/biopolymer Identification of the sequence record. May refer to data the sequence originates from: a database entry or an explicit super-sequence. NB. ID/accession is part of the 'reference' Nucleotide sequence record including the generic nucleotide sequence and optional metadata Biological source of the sequence/biopolymer Identification of the sequence record. May refer to data the sequence originates from: a database entry or an explicit super-sequence. NB. ID/accession is part of the 'reference' Amino-acid sequence record including the generic amino-acid sequence and optional metadata Biological source of the sequence/biopolymer Identification of the sequence record. May refer to data the sequence originates from: a database entry or an explicit super-sequence. NB. ID/accession is part of the 'reference' Nucleotide sequence record including the unambiguous nucleotide sequence and optional metadata Biological source of the sequence/biopolymer Identification of the sequence record. May refer to data the sequence originates from: a database entry or an explicit super-sequence. NB. ID/accession is part of the 'reference' Amino-acid sequence record including the unambiguous amino-acid sequence and optional metadata Biological source of the sequence/biopolymer Identification of the sequence record. May refer to data the sequence originates from: a database entry or an explicit super-sequence. NB. ID/accession is part of the 'reference' Alignment of 2..n generic nucleotide or amino-acid sequences. A *multiple sequence alignment* in the sense that all sequences are treated equally Alignment of 2..n generic nucleotide sequences. A *multiple sequence alignment* in the sense that all sequences are treated equally Alignment of 2..n generic amino-acid sequences. A *multiple sequence alignment* in the sense that all sequences are treated equally Alignment of 2..n nucleotide sequences. A *multiple sequence alignment* in the sense that all sequences are treated equally Alignment of 2..n amino-acid sequences. A *multiple sequence alignment* in the sense that all sequences are treated equally Single gap in an aligned sequence Single insert in an aligned sequence Frame-shift in an aligned amino-acid sequence Coordinates of the locally aligned sub-sequence. (Not present means global alignment) Coordinates of a sub-sequence within the chromosome Coordinates of the locally aligned sub-sequence. (Not present means global alignment) Coordinates of the locally aligned sub-sequence. (Not present means global alignment) Coordinates of the locally aligned sub-sequence. (Not present means global alignment) Coordinates of the locally aligned sub-sequence. (Not present means global alignment) Annotation by a particular feature. That is, a single-feature sequence annotation track for one particular reference sequence Human-readable display name of the feature Alternative human-readable display name of the feature More generic class of features containing this feature (human-readable display name of the class) Specific properties of a feature Pointer to a database entry specifying the feature-type details Occurrence of a feature in a reference sequence. Positioned or non-positioned (non-positioned means applied to the whole sequence) NB. Should be 0 for non-translated but transcribed features. Should be 'strand'*(('min'-1) mod 3 + 1) for translated features within a whole-chromosome annotation NB. Corresponds to a position within the feature occurrence Features of a sequence/biopolymer (or a genome/metagenome). The reference sequence may me included explicitly, referred to remotely, or implicit The *reference* sequence that is annotated Coordinates of a sub-sequence within the chromosome Annotation by a particular feature or property. Corresponds to one sequence annotation track Annotation by a particular feature or property. Corresponds to one sequence annotation track Type of score of an experiment or computation Score of an experiment or computation NB. Corresponds to a position in the (sub)sequence the score belongs to Position in the sequence, referring to a single point (base, residue, or C-alpha atom), possibly with a certain level of uncertainty NB. Omit 'pos' attribute only if 'certainty'="Unknown" Certain position in the sequence, referring to a single point (base, residue, or C-alpha atom) Position of an insertion into the sequence, possibly with a certain level of uncertainty. NB. Insertion *behind* (to the right of) the given point in the direction of the sequence; *-1* for preceeding the sequence NB. Omit 'pos' attribute only if 'certainty'="Unknown" Certain position of an insertion into the sequence. NB. Insertion *behind* (to the right of) the given point in the direction of the sequence; *-1* for preceeding the sequence Position outside of the reference sequence, referring to a single point (a nucleotide, residue, or C-alpha atom), possibly uncertain NB. Omit 'pos' attribute only if 'certainty'="Unknown" Certain position outside of the reference sequence, referring to a single point (a nucleotide, residue, or C-alpha atom) Position in the sequence referring to a continuous segment of the sequence, possibly uncertain NB. Keep 'min' < 'max', use 'strand' if necessary. Omit 'min' attribute only if 'minCertainty'="Unknown" NB. Keep 'max' > 'min', use 'strand' if necessary. Omit 'max' attribute only if 'maxCertainty'="Unknown" Certain position in the sequence referring to a scontinuous segment of the sequence NB. Keep 'min' < 'max', use 'strand' if necessary NB. Keep 'max' > 'min', use 'strand' if necessary Position outside of the reference sequence, referring to a continuous segment, possibly uncertain NB. Keep 'min' < 'max', use 'strand' if necessary. Omit 'min' attribute only if 'minCertainty'="Unknown" NB. Keep 'max' > 'min', use 'strand' if necessary. Omit 'max' attribute only if 'maxCertainty'="Unknown" Certain position outside of the reference sequence, referring to a continuous segment NB. Keep 'min' < 'max', use 'strand' if necessary NB. Keep 'max' > 'min', use 'strand' if necessary NB. Omit 'max' attribute only if 'certainty'="Unknown" Position in the sequence, referring either to a subsequence, a single point, an insertion, or outside of the sequence, possibly uncertain Certain position in the sequence, referring either to a subsequence, a single point, an insertion, or outside of the sequence Position outside of the sequence, possibly uncertain Certain position outside of the sequence Particular genetic code (codon encoding) Codon code consisting of 3 bases (possibly ambiguous, "degenerate") One amino-acid (possibly ambiguous). NB. If the same codon codes for multiple amino-acids, use multiple 'codon' elements and fill in the 'note' attribute A reference to a SOAP Web service Date when this Web-service reference was fully valid: created or last time updated Reference to a database General URI of the database Reference to an entry in a database Date when this reference was fully valid: created or last time updated Reference to an ontology, controlled vocabulary, or a collection of semantic concepts General URI of the controlled vocabulary (ontology) Reference to a concept from an ontology or the Semantic Web, or a term from a controlled vocabulary The local ID of the semantic concept within an ontology, vocabulary, or a collection of concepts. Note: The local ID is supposed to be persistent (an accession) Human-readable term, or a name of an ontology concept. NB. Does not have to be always up to date and canonical. (Use also 'conceptUri' or 'accession': up-to-date name and other properties of the concept should be downloadable given the 'conceptUri' or 'accession') Reference to a species (can be used also for a phenotype, cell line, tissue, sample, geo location, ...) Custom human-readable name of the species. NB. Does not have to be always up to date and canonical. Use also entryUri or accession if possible Formal reference to a sequence in a database or an explicit super-sequence Coordinates of the sub-sequence within the referenced sequence Explicit super-sequence, in case it is not desired or not possible to point to a database entry Custom name of the super-sequence, in case it is not desired or not possible to point to a database entry Identifier for local references within a data record. NB. Objects define their local identifier always in their 'localId' attribute Generalisation of bioinformatics accession numbers (stable primary keys/stable unique identifiers), or bioinformatics primary keys/unique identifiers (where no stable accessions) UniProt accession number, optionally with version after a dot (.) or the variant (isoform) suffix after a hyphen (-) UniProt accession number, without the sequence version and splice-variant suffix GenBank/EMBL/DDBJ nucleotide accession number GenBank/EMBL/DDBJ protein accession number GenBank/EMBL/DDBJ WGS accession number GenBank/EMBL/DDBJ MGA accession number NCBI Taxonomy ID (0 ... 999999999; i.e. a subset of 32-bit (4B) signed int) NCBI ID of a genetic code (1 ... 99) Predefined, recommended verdict of a predicted or experimental evidence Predefined, recommended reliability of an experimental evidence Qualitative certainty tag The reffered value completely unknown, not the certainty unknown Correspondance of the outside positions to the reference sequence The outside position is in the nucleotide sequence of the either explicitly given chromosome or scaffold/contig, or the chromosome/scaffold/contig of the reference sequence. Outside-positions 1..m are positions in the chromosome The outside position is in an explicitly referenced nucleotide or amino-acid sequence. Can but does not have to be a supersequence of the reference sequence. Outside-positions 1..m are in the explicitly referenced supersequence. Fill in the 'explicitSequenceReference' element The outside position is in a nucleotide or amino-acid supersequence (respectively) of the reference subsequence. Positions 1..n correspond, position -1 is the preceding (next point to the left) from 1 The outside position is in a nucleotide sequence. Position 1 corresponds to the 1st base of the 1st translated codon within the reference isoform, position -1 is the next to the left from 1 (NB. CDSs include the start and stop codons: do not use this correspondance option for outside features of CDSs) The outside position is in a nucleotide sequence. Position 1 corresponds to the 1st base transcribed within the reference isoform, position -1 is the next to the left from 1 Predefined, recommended database name of a public database Predefined, recommended name of a public ontology or controlled vocabulary Any integer number (~-9.2x10^18 ... ~9.2x10^18). Represented by a 64-bit (8B) signed long integer (long, long long, int64, same as xs:long, different from xs:integer) Non-negative integer number (0 ... ~9.2x10^18). Represented by a 64-bit (8B) signed long integer Non-zero integer number (~-9.2x10^18 ... -1, 1 ... ~9.2x10^18). Represented by a 64-bit (8B) signed long integer Insertion-point specific integer number (-1, 1 ... ~9.2x10^18). Represented by a 64-bit (8B) signed long integer Positive integer number (1 ... ~9.2x10^18). Represented by a 64-bit (8B) signed long integer Any decimal number with double precision (-INF, ~-1.7E308 ... 0, ~5E-324 subnormal ... ~2.3E-308 ... ~1.7E308, INF; +NaN). Represented by a 64-bit (8B) signed floating point number (double, long double, same as xs:double, different from xs:decimal) Probability with double precision (0 ... 1). Represented by a 64-bit (8B) signed floating point number Quantitave or qualitative certainty An absolute Unified Resource Identifier (URI), possibly a Web link. NB. Supports a subset of RFC 3986 generic syntax (selected schemes, DNS only, no user info, constrained port and characters) Any plain text (possibly formatted) Name of a public or private database (predefined or arbitrary name) Name of a public or private ontology or controlled vocabulary (predefined or arbitrary name) Phase of an incomplete peptide-coding nucleotide sequence, in the direction of translation