X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Funiprot.xsd;fp=schemas%2Funiprot.xsd;h=13df214ff56028b87f091e904ea53e4df671037f;hb=88515cdb74e4603a40c8c1dca14107b5ca503e04;hp=0000000000000000000000000000000000000000;hpb=28c232b27469433dd85d3a09ecf8b6e2ff09eead;p=jalview.git diff --git a/schemas/uniprot.xsd b/schemas/uniprot.xsd new file mode 100644 index 0000000..13df214 --- /dev/null +++ b/schemas/uniprot.xsd @@ -0,0 +1,1072 @@ + + + + + + + + Describes a collection of UniProtKB entries. + + + + + + + + + + + + + + Describes a UniProtKB entry. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Describes the names for the protein and parts thereof. + Equivalent to the flat file DE-line. + + + + + + Describes names of "domains". + Equivalent to the flat file DE-line Includes: section. + + + + + + + + Describes names of processed products. + Equivalent to the flat file DE-line Contains: section. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Describes a gene. + Equivalent to the flat file GN-line. + + + + + + + + Describes different types of gene designations. + Equivalent to the flat file GN-line. + + + + + + + + + + + + + + + + + + + + + + + Describes the source organism. + + + + + Describes the names of the source organism. + Equivalent to the flat file OS-line. + + + + + Describes a cross-reference to the NCBI taxonomy database. + Equivalent to the flat file OX-line. + + + + + Describes the lineage of the source organism. + Equivalent to the flat file OC-line. + + + + + + + + + + + + + Describes different types of source organism names. + + + + + + + + + + + + + + + + + + + + + + + Describes non-nuclear gene locations (organelles and plasmids). + Equivalent to the flat file OG-line. + + + + + + + + + + + + + + + + + + + + + + + + + Indicates whether the name of a plasmid is known or unknown. + + + + + + + + + + + + + + + + + + + + Describes a citation and a summary of its content. + Equivalent to the flat file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines. + + + + + + + + + + + + + + Describes different types of citations. + Equivalent to the flat file RX-, RG-, RA-, RT- and RL-lines. + + + + + Describes the title of a citation. + Equivalent to the flat file RT-line. + + + + + Describes the editors of a book (only used for books). + Equivalent to part of the flat file RL-line of books. + + + + + Describes the authors of a citation. + Equivalent to the flat file RA-line. + + + + + Describes the location (URL) of an online journal article. + No flat file equivalent. + + + + + Describes cross-references to bibliography databases (MEDLINE, PubMed, AGRICOLA) or other online resources (DOI). + Equivalent to the flat file RX-line. + + + + + + Describes the type of a citation. + + + + + + + + + + + + + + + + + + + + + Describes the name of an (online) journal or book. + + + + + Describes the volume of a journal or book. + + + + + Describes the first page of an article. + + + + + Describes the last page of an article. + + + + + Describes the publisher of a book. + + + + + Describes the city where a book was published. + + + + + Describes the database name of submissions. + + + + + Describes a patent number. + + + + + Describes the institute where a thesis was made. + + + + + Describes the country where a thesis was made. + + + + + + Describes the authors of a citation when these are represented by a consortium. + Equivalent to the flat file RG-line. + + + + + + + + + + + + + + + + + + Groups a citation's scope and source descriptions. + + + + + Describes the scope of a citation. + Equivalent to the flat file RP-line. + + + + + + + + Describes the source of the sequence according to the citation. + Equivalent to the flat file RC-line. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Describes different types of general annotations. + Equivalent to the flat file CC-line. + + + + + + + + + Used in 'cofactor' annotations. + + + + + + + Used in 'subcellular location' annotations. + + + + + + + Used in 'sequence caution' annotations. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Refers to the 'key' attribute of a 'reference' element. + + + + + + + + + Used in 'online information' annotations. + + + + + + + + + + Used in 'alternative products' annotations. + + + + + + + + Used in 'interaction' annotations. + + + + + + + + + Used in 'disease' annotations. + + + + + + + + + + + + + + + + + Used in 'mass spectrometry' and 'sequence caution' annotations. + + + + + + + + + + Describes the type of a general annotation. + Equivalent to the flat file CC comment topics (except for "DATABASE" which is translated to "online information"). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Describes the type of sequence location in 'RNA editing' annotations. Common values are "Not_applicable" and "Undetermined". + + + + + + Describes an optional name for an 'online information'. + + + + + + Describes the molecular mass in 'mass spectrometry' annotations. + + + + + Describes the error of the mass measurement in 'mass spectrometry' annotations. + + + + + Describes the experimental method in 'mass spectrometry' annotations. + + + + + + + + + Describes different types of biophysicochemical properties. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Describes a cofactor. + + + + + + + + + + + Describes the subcellular location and optionally the topology and orientation of a molecule. + + + + + + + + + + + Describes the type of events that cause alternative products. + + + + + + + + + + + + + + + + Describes isoforms in 'alternative products' annotations. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Describes a database cross-reference. + Equivalent to the flat file DR-line. + + + + + + + + + Describes the name of the database. + + + + + Describes a unique database identifier. + + + + + + + + + + + + + + + + Describes the evidence for the protein's existence. + Equivalent to the flat file PE-line. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Describes different types of sequence annotations. + Equivalent to the flat file FT-line. + + + + + Describes the original sequence in annotations that describe natural or artifical sequence variations. + + + + + Describes the variant sequence in annotations that describe natural or artifical sequence variations. + + + + + Describes the sequence coordinates of the annotation. + + + + + + Describes the type of a sequence annotation. + Equivalent to the flat file FT feature keys, but using full terms instead of acronyms. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Describes a sequence location as either a range with a begin and end or as a position. The 'sequence' attribute is only used when the location is not on the canonical sequence displayed in the current entry. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Describes a molecule by name or unique identifier. + + + + + + + + + + + + + Describes the evidence for an annotation. + No flat file equivalent. + + + + + + + + Describes the type of an evidence using the Evidence Code Ontology (http://www.obofoundry.org/cgi-bin/detail.cgi?id=evidence_code). + + + + + A unique key to link annotations (via 'evidence' attributes) to evidences. + + + + + + Describes the source of the data using a database cross-reference (or a 'ref' attribute when the source cannot be found in a public data source, such as PubMed, and is cited only within the UniProtKB entry). + + + + + + + + + Describes the source of the evidence, when it is not assigned by UniProt, but imported from an external database. + + + + + + + + + + + + + + + + + + + + + + + + + + + +