1 <?xml version="1.0" encoding="UTF-8"?>
2 <!-- *****************************************************************************
4 Version: $Revision: 1.3 $
5 Date: $Date: 2015/04/07 15:00:57 $
7 Copyright (c) 2011 UniProt consortium
9 *******************************************************************************-->
10 <xs:schema targetNamespace="http://uniprot.org/uniprot" xmlns:xs="http://www.w3.org/2001/XMLSchema"
11 xmlns="http://uniprot.org/uniprot" elementFormDefault="qualified">
12 <!-- XML Schema definition for the UniProtKB XML format
14 -XSV (XML Schema Validator), http://www.w3.org/2001/03/webdata/xsv
16 <!-- Root element definition begins -->
17 <xs:element name="uniprot">
19 <xs:documentation>Describes a collection of UniProtKB entries.</xs:documentation>
23 <xs:element ref="entry" maxOccurs="unbounded"/>
24 <xs:element ref="copyright" minOccurs="0"/>
28 <!-- Root element definition ends -->
30 <!-- Entry definition begins -->
31 <xs:element name="entry">
33 <xs:documentation>Describes a UniProtKB entry.</xs:documentation>
37 <xs:element name="accession" type="xs:string" maxOccurs="unbounded"/>
38 <xs:element name="name" type="xs:string" maxOccurs="unbounded"/>
39 <xs:element name="protein" type="proteinType"/>
40 <xs:element name="gene" type="geneType" minOccurs="0" maxOccurs="unbounded"/>
41 <xs:element name="organism" type="organismType" />
42 <xs:element name="organismHost" type="organismType" minOccurs="0" maxOccurs="unbounded"/>
43 <xs:element name="geneLocation" type="geneLocationType" minOccurs="0" maxOccurs="unbounded"/>
44 <xs:element name="reference" type="referenceType" maxOccurs="unbounded"/>
45 <xs:element name="comment" type="commentType" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
46 <xs:element name="dbReference" type="dbReferenceType" minOccurs="0" maxOccurs="unbounded"/>
47 <xs:element name="proteinExistence" type="proteinExistenceType"/>
48 <xs:element name="keyword" type="keywordType" minOccurs="0" maxOccurs="unbounded"/>
49 <xs:element name="feature" type="featureType" minOccurs="0" maxOccurs="unbounded"/>
50 <xs:element name="evidence" type="evidenceType" minOccurs="0" maxOccurs="unbounded"/>
51 <xs:element name="sequence" type="sequenceType"/>
53 <xs:attribute name="dataset" use="required">
55 <xs:restriction base="xs:string">
56 <xs:enumeration value="Swiss-Prot"/>
57 <xs:enumeration value="TrEMBL"/>
61 <xs:attribute name="created" type="xs:date" use="required"/>
62 <xs:attribute name="modified" type="xs:date" use="required"/>
63 <xs:attribute name="version" type="xs:int" use="required"/>
66 <!-- Entry definition ends -->
68 <xs:element name="copyright" type="xs:string"/>
70 <!-- Protein names definition begins -->
71 <xs:complexType name="proteinType">
73 <xs:documentation>Describes the names for the protein and parts thereof.
74 Equivalent to the flat file DE-line.</xs:documentation>
77 <xs:group ref="proteinNameGroup"/>
78 <xs:element name="domain" minOccurs="0" maxOccurs="unbounded">
80 <xs:documentation>Describes names of "domains".
81 Equivalent to the flat file DE-line Includes: section.</xs:documentation>
84 <xs:group ref="proteinNameGroup"/>
87 <xs:element name="component" minOccurs="0" maxOccurs="unbounded">
89 <xs:documentation>Describes names of processed products.
90 Equivalent to the flat file DE-line Contains: section.</xs:documentation>
93 <xs:group ref="proteinNameGroup"/>
98 <xs:group name="proteinNameGroup">
100 <xs:element name="recommendedName" minOccurs="0">
103 <xs:element name="fullName" type="evidencedStringType"/>
104 <xs:element name="shortName" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
105 <xs:element name="ecNumber" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
107 <!-- xs:attribute name="ref" type="xs:string" use="optional"/ -->
110 <xs:element name="alternativeName" minOccurs="0" maxOccurs="unbounded">
113 <xs:element name="fullName" type="evidencedStringType" minOccurs="0"/>
114 <xs:element name="shortName" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
115 <xs:element name="ecNumber" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
117 <!-- xs:attribute name="ref" type="xs:string" use="optional"/ -->
120 <xs:element name="submittedName" minOccurs="0" maxOccurs="unbounded">
123 <xs:element name="fullName" type="evidencedStringType"/>
124 <xs:element name="ecNumber" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
126 <!-- xs:attribute name="ref" type="xs:string" use="optional"/ -->
129 <xs:element name="allergenName" type="evidencedStringType" minOccurs="0"/>
130 <xs:element name="biotechName" type="evidencedStringType" minOccurs="0"/>
131 <xs:element name="cdAntigenName" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
132 <xs:element name="innName" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
135 <!-- Protein names definition ends -->
137 <!-- Gene names definition begins -->
138 <xs:complexType name="geneType">
140 <xs:documentation>Describes a gene.
141 Equivalent to the flat file GN-line.</xs:documentation>
144 <xs:element name="name" type="geneNameType" maxOccurs="unbounded"/>
147 <xs:complexType name="geneNameType">
149 <xs:documentation>Describes different types of gene designations.
150 Equivalent to the flat file GN-line.</xs:documentation>
153 <xs:extension base="xs:string">
154 <xs:attribute name="evidence" type="intListType" use="optional"/>
155 <xs:attribute name="type" use="required">
157 <xs:restriction base="xs:string">
158 <xs:enumeration value="primary"/>
159 <xs:enumeration value="synonym"/>
160 <xs:enumeration value="ordered locus"/>
161 <xs:enumeration value="ORF"/>
168 <!-- Gene names definition ends -->
170 <!-- Organism definition begins -->
171 <xs:complexType name="organismType">
173 <xs:documentation>Describes the source organism.</xs:documentation>
176 <xs:element name="name" type="organismNameType" maxOccurs="unbounded">
178 <xs:documentation>Describes the names of the source organism.
179 Equivalent to the flat file OS-line.</xs:documentation>
182 <xs:element name="dbReference" type="dbReferenceType" maxOccurs="unbounded">
184 <xs:documentation>Describes a cross-reference to the NCBI taxonomy database.
185 Equivalent to the flat file OX-line.</xs:documentation>
188 <xs:element name="lineage" minOccurs="0">
190 <xs:documentation>Describes the lineage of the source organism.
191 Equivalent to the flat file OC-line.</xs:documentation>
195 <xs:element name="taxon" type="xs:string" maxOccurs="unbounded"/>
200 <xs:attribute name="evidence" type="intListType" use="optional"/>
202 <xs:complexType name="organismNameType">
204 <xs:documentation>Describes different types of source organism names.</xs:documentation>
207 <xs:extension base="xs:string">
208 <xs:attribute name="type" use="required">
210 <xs:restriction base="xs:string">
211 <xs:enumeration value="common"/>
212 <xs:enumeration value="full"/>
213 <xs:enumeration value="scientific"/>
214 <xs:enumeration value="synonym"/>
215 <xs:enumeration value="abbreviation"/>
222 <!-- Organism definition ends -->
224 <!-- Gene location definition begins -->
225 <xs:complexType name="geneLocationType">
227 <xs:documentation>Describes non-nuclear gene locations (organelles and plasmids).
228 Equivalent to the flat file OG-line.</xs:documentation>
231 <xs:element name="name" type="statusType" minOccurs="0" maxOccurs="unbounded"/>
233 <xs:attribute name="type" use="required">
235 <xs:restriction base="xs:string">
236 <xs:enumeration value="apicoplast"/>
237 <xs:enumeration value="chloroplast"/>
238 <xs:enumeration value="organellar chromatophore"/>
239 <xs:enumeration value="cyanelle"/>
240 <xs:enumeration value="hydrogenosome"/>
241 <xs:enumeration value="mitochondrion"/>
242 <xs:enumeration value="non-photosynthetic plastid"/>
243 <xs:enumeration value="nucleomorph"/>
244 <xs:enumeration value="plasmid"/>
245 <xs:enumeration value="plastid"/>
249 <xs:attribute name="evidence" type="intListType" use="optional"/>
251 <xs:complexType name="statusType">
253 <xs:documentation>Indicates whether the name of a plasmid is known or unknown.</xs:documentation>
256 <xs:extension base="xs:string">
257 <xs:attribute name="status" use="optional" default="known">
259 <xs:restriction base="xs:string">
260 <xs:enumeration value="known"/>
261 <xs:enumeration value="unknown"/>
268 <!-- Gene location definition ends -->
270 <!-- Reference definition begins -->
271 <xs:complexType name="referenceType">
273 <xs:documentation>Describes a citation and a summary of its content.
274 Equivalent to the flat file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines.</xs:documentation>
277 <xs:element name="citation" type="citationType"/>
278 <xs:group ref="sptrCitationGroup"/>
280 <xs:attribute name="evidence" type="intListType" use="optional"/>
281 <xs:attribute name="key" type="xs:string" use="required"/>
283 <!-- Reference definition ends -->
285 <!-- Citation definition begins -->
286 <xs:complexType name="citationType">
288 <xs:documentation>Describes different types of citations.
289 Equivalent to the flat file RX-, RG-, RA-, RT- and RL-lines.</xs:documentation>
292 <xs:element name="title" type="xs:string" minOccurs="0">
294 <xs:documentation>Describes the title of a citation.
295 Equivalent to the flat file RT-line.</xs:documentation>
298 <xs:element name="editorList" type="nameListType" minOccurs="0">
300 <xs:documentation>Describes the editors of a book (only used for books).
301 Equivalent to part of the flat file RL-line of books.</xs:documentation>
304 <xs:element name="authorList" type="nameListType" minOccurs="0">
306 <xs:documentation>Describes the authors of a citation.
307 Equivalent to the flat file RA-line.</xs:documentation>
310 <xs:element name="locator" type="xs:string" minOccurs="0">
312 <xs:documentation>Describes the location (URL) of an online journal article.
313 No flat file equivalent.</xs:documentation>
316 <xs:element name="dbReference" type="dbReferenceType" minOccurs="0" maxOccurs="unbounded">
318 <xs:documentation>Describes cross-references to bibliography databases (MEDLINE, PubMed, AGRICOLA) or other online resources (DOI).
319 Equivalent to the flat file RX-line.</xs:documentation>
323 <xs:attribute name="type" use="required">
325 <xs:documentation>Describes the type of a citation.</xs:documentation>
328 <xs:restriction base="xs:string">
329 <xs:enumeration value="book"/>
330 <xs:enumeration value="journal article"/>
331 <xs:enumeration value="online journal article"/>
332 <xs:enumeration value="patent"/>
333 <xs:enumeration value="submission"/>
334 <xs:enumeration value="thesis"/>
335 <xs:enumeration value="unpublished observations"/>
339 <xs:attribute name="date" use="optional">
341 <xs:union memberTypes="xs:date xs:gYearMonth xs:gYear"/>
344 <xs:attribute name="name" type="xs:string" use="optional">
346 <xs:documentation>Describes the name of an (online) journal or book.</xs:documentation>
349 <xs:attribute name="volume" type="xs:string" use="optional">
351 <xs:documentation>Describes the volume of a journal or book.</xs:documentation>
354 <xs:attribute name="first" type="xs:string" use="optional">
356 <xs:documentation>Describes the first page of an article.</xs:documentation>
359 <xs:attribute name="last" type="xs:string" use="optional">
361 <xs:documentation>Describes the last page of an article.</xs:documentation>
364 <xs:attribute name="publisher" type="xs:string" use="optional">
366 <xs:documentation>Describes the publisher of a book.</xs:documentation>
369 <xs:attribute name="city" type="xs:string" use="optional">
371 <xs:documentation>Describes the city where a book was published.</xs:documentation>
374 <xs:attribute name="db" type="xs:string" use="optional">
376 <xs:documentation>Describes the database name of submissions.</xs:documentation>
379 <xs:attribute name="number" type="xs:string" use="optional">
381 <xs:documentation>Describes a patent number.</xs:documentation>
384 <xs:attribute name="institute" type="xs:string" use="optional">
386 <xs:documentation>Describes the institute where a thesis was made.</xs:documentation>
389 <xs:attribute name="country" type="xs:string" use="optional">
391 <xs:documentation>Describes the country where a thesis was made.</xs:documentation>
395 <xs:complexType name="consortiumType">
397 <xs:documentation>Describes the authors of a citation when these are represented by a consortium.
398 Equivalent to the flat file RG-line.</xs:documentation>
400 <xs:attribute name="name" type="xs:string" use="required"/>
402 <xs:complexType name="personType">
403 <xs:attribute name="name" type="xs:string" use="required"/>
405 <xs:complexType name="nameListType">
406 <xs:choice maxOccurs="unbounded">
407 <xs:element name="consortium" type="consortiumType"/>
408 <xs:element name="person" type="personType"/>
411 <!-- Citation definition ends -->
413 <!-- Citation summary definition begins -->
414 <xs:group name="sptrCitationGroup">
416 <xs:documentation>Groups a citation's scope and source descriptions.</xs:documentation>
419 <xs:element name="scope" type="xs:string" maxOccurs="unbounded">
421 <xs:documentation>Describes the scope of a citation.
422 Equivalent to the flat file RP-line.</xs:documentation>
425 <xs:element name="source" type="sourceDataType" minOccurs="0"/>
428 <xs:complexType name="sourceDataType">
430 <xs:documentation>Describes the source of the sequence according to the citation.
431 Equivalent to the flat file RC-line.</xs:documentation>
433 <xs:choice maxOccurs="unbounded">
434 <xs:element name="strain">
437 <xs:extension base="xs:string">
438 <xs:attribute name="evidence" type="intListType" use="optional"/>
443 <xs:element name="plasmid">
446 <xs:extension base="xs:string">
447 <xs:attribute name="evidence" type="intListType" use="optional"/>
452 <xs:element name="transposon">
455 <xs:extension base="xs:string">
456 <xs:attribute name="evidence" type="intListType" use="optional"/>
461 <xs:element name="tissue">
464 <xs:extension base="xs:string">
465 <xs:attribute name="evidence" type="intListType" use="optional"/>
472 <!-- Citation summary definition ends -->
474 <!-- Comment definition begins -->
475 <xs:complexType name="commentType">
477 <xs:documentation>Describes different types of general annotations.
478 Equivalent to the flat file CC-line.</xs:documentation>
481 <xs:element name="molecule" type="moleculeType" minOccurs="0"/>
482 <xs:choice minOccurs="0">
483 <xs:group ref="bpcCommentGroup"/>
487 <xs:documentation>Used in 'cofactor' annotations.</xs:documentation>
489 <xs:element name="cofactor" type="cofactorType" maxOccurs="unbounded"/>
494 <xs:documentation>Used in 'subcellular location' annotations.</xs:documentation>
496 <xs:element name="subcellularLocation" type="subcellularLocationType" maxOccurs="unbounded"/>
499 <xs:element name="conflict">
501 <xs:documentation>Used in 'sequence caution' annotations.</xs:documentation>
505 <xs:element name="sequence" minOccurs="0">
507 <xs:attribute name="resource" use="required">
509 <xs:restriction base="xs:string">
510 <xs:enumeration value="EMBL-CDS"/>
511 <xs:enumeration value="EMBL"/>
515 <xs:attribute name="id" type="xs:string" use="required"/>
516 <xs:attribute name="version" type="xs:int" use="optional"/>
520 <xs:attribute name="type" use="required">
522 <xs:restriction base="xs:string">
523 <xs:enumeration value="frameshift"/>
524 <xs:enumeration value="erroneous initiation"/>
525 <xs:enumeration value="erroneous termination"/>
526 <xs:enumeration value="erroneous gene model prediction"/>
527 <xs:enumeration value="erroneous translation"/>
528 <xs:enumeration value="miscellaneous discrepancy"/>
532 <xs:attribute name="ref" type="xs:string" use="optional">
534 <xs:documentation>Refers to the 'key' attribute of a 'reference' element.</xs:documentation>
541 <xs:element name="link" minOccurs="0" maxOccurs="unbounded">
543 <xs:documentation>Used in 'online information' annotations.</xs:documentation>
546 <xs:attribute name="uri" type="xs:anyURI" use="required"/>
553 <xs:documentation>Used in 'alternative products' annotations.</xs:documentation>
555 <xs:element name="event" type="eventType" maxOccurs="4"/>
556 <xs:element name="isoform" type="isoformType" minOccurs="0" maxOccurs="unbounded"/>
561 <xs:documentation>Used in 'interaction' annotations.</xs:documentation>
563 <xs:element name="interactant" type="interactantType" minOccurs="2" maxOccurs="2"/>
564 <xs:element name="organismsDiffer" type="xs:boolean" default="false"/>
565 <xs:element name="experiments" type="xs:int"/>
568 <xs:element name="disease">
570 <xs:documentation>Used in 'disease' annotations.</xs:documentation>
574 <xs:element name="name" type="xs:string"/>
575 <xs:element name="acronym" type="xs:string"/>
576 <xs:element name="description" type="xs:string"/>
577 <xs:element name="dbReference" type="dbReferenceType"/>
579 <xs:attribute name="id" type="xs:string" use="required"/>
585 <xs:element name="location" type="locationType" minOccurs="0" maxOccurs="unbounded">
587 <xs:documentation>Used in 'mass spectrometry' and 'sequence caution' annotations.</xs:documentation>
591 <xs:element name="text" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
595 <xs:attribute name="type" use="required">
597 <xs:documentation>Describes the type of a general annotation.
598 Equivalent to the flat file CC comment topics (except for "DATABASE" which is translated to "online information").</xs:documentation>
601 <xs:restriction base="xs:string">
602 <xs:enumeration value="allergen"/>
603 <xs:enumeration value="alternative products"/>
604 <xs:enumeration value="biotechnology"/>
605 <xs:enumeration value="biophysicochemical properties"/>
606 <xs:enumeration value="catalytic activity"/>
607 <xs:enumeration value="caution"/>
608 <xs:enumeration value="cofactor"/>
609 <xs:enumeration value="developmental stage"/>
610 <xs:enumeration value="disease"/>
611 <xs:enumeration value="domain"/>
612 <xs:enumeration value="disruption phenotype"/>
613 <xs:enumeration value="activity regulation"/>
614 <xs:enumeration value="function"/>
615 <xs:enumeration value="induction"/>
616 <xs:enumeration value="miscellaneous"/>
617 <xs:enumeration value="pathway"/>
618 <xs:enumeration value="pharmaceutical"/>
619 <xs:enumeration value="polymorphism"/>
620 <xs:enumeration value="PTM"/>
621 <xs:enumeration value="RNA editing"/>
622 <xs:enumeration value="similarity"/>
623 <xs:enumeration value="subcellular location"/>
624 <xs:enumeration value="sequence caution"/>
625 <xs:enumeration value="subunit"/>
626 <xs:enumeration value="tissue specificity"/>
627 <xs:enumeration value="toxic dose"/>
628 <xs:enumeration value="online information"/>
629 <xs:enumeration value="mass spectrometry"/>
630 <xs:enumeration value="interaction"/>
635 <xs:attribute name="locationType" type="xs:string" use="optional">
637 <xs:documentation>Describes the type of sequence location in 'RNA editing' annotations. Common values are "Not_applicable" and "Undetermined".</xs:documentation>
641 <xs:attribute name="name" type="xs:string" use="optional">
643 <xs:documentation>Describes an optional name for an 'online information'.</xs:documentation>
647 <xs:attribute name="mass" type="xs:float" use="optional">
649 <xs:documentation>Describes the molecular mass in 'mass spectrometry' annotations.</xs:documentation>
652 <xs:attribute name="error" type="xs:string" use="optional">
654 <xs:documentation>Describes the error of the mass measurement in 'mass spectrometry' annotations.</xs:documentation>
657 <xs:attribute name="method" type="xs:string" use="optional">
659 <xs:documentation>Describes the experimental method in 'mass spectrometry' annotations.</xs:documentation>
663 <xs:attribute name="evidence" type="intListType" use="optional"/>
666 <xs:group name="bpcCommentGroup">
668 <xs:documentation>Describes different types of biophysicochemical properties.</xs:documentation>
671 <xs:element name="absorption" minOccurs="0">
674 <xs:element name="max" type="evidencedStringType" minOccurs="0"/>
675 <xs:element name="text" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
679 <xs:element name="kinetics" minOccurs="0">
682 <xs:element name="KM" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
683 <xs:element name="Vmax" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
684 <xs:element name="text" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
688 <xs:element name="phDependence" minOccurs="0">
691 <xs:element name="text" type="evidencedStringType" maxOccurs="unbounded"/>
695 <xs:element name="redoxPotential" minOccurs="0">
698 <xs:element name="text" type="evidencedStringType" maxOccurs="unbounded"/>
702 <xs:element name="temperatureDependence" minOccurs="0">
705 <xs:element name="text" type="evidencedStringType" maxOccurs="unbounded"/>
712 <xs:complexType name="cofactorType">
714 <xs:documentation>Describes a cofactor.</xs:documentation>
717 <xs:element name="name" type="xs:string"/>
718 <xs:element name="dbReference" type="dbReferenceType"/>
720 <xs:attribute name="evidence" type="intListType" use="optional"/>
723 <xs:complexType name="subcellularLocationType">
725 <xs:documentation>Describes the subcellular location and optionally the topology and orientation of a molecule.</xs:documentation>
728 <xs:element name="location" type="evidencedStringType" maxOccurs="unbounded"/>
729 <xs:element name="topology" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
730 <xs:element name="orientation" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
734 <xs:complexType name="eventType">
736 <xs:documentation>Describes the type of events that cause alternative products.</xs:documentation>
738 <xs:attribute name="type" use="required">
740 <xs:restriction base="xs:string">
741 <xs:enumeration value="alternative splicing"/>
742 <xs:enumeration value="alternative initiation"/>
743 <xs:enumeration value="alternative promoter"/>
744 <xs:enumeration value="ribosomal frameshifting"/>
750 <xs:complexType name="isoformType">
752 <xs:documentation>Describes isoforms in 'alternative products' annotations.</xs:documentation>
755 <xs:element name="id" type="xs:string" maxOccurs="unbounded"/>
756 <xs:element name="name" maxOccurs="unbounded">
759 <xs:extension base="xs:string">
760 <xs:attribute name="evidence" type="intListType" use="optional"/>
765 <xs:element name="sequence">
767 <xs:attribute name="type" use="required">
769 <xs:restriction base="xs:string">
770 <xs:enumeration value="not described"/>
771 <xs:enumeration value="described"/>
772 <xs:enumeration value="displayed"/>
773 <xs:enumeration value="external"/>
777 <xs:attribute name="ref" type="xs:string" use="optional"/>
780 <xs:element name="text" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
784 <xs:group name="interactantGroup">
786 <xs:element name="id" type="xs:string"/>
787 <xs:element name="label" type="xs:string" minOccurs="0"/>
790 <xs:complexType name="interactantType">
791 <xs:group ref="interactantGroup" minOccurs="0"/>
792 <xs:attribute name="intactId" type="xs:string" use="required"/>
794 <!-- Comment definition ends -->
796 <!-- Database cross-reference definition begins -->
797 <xs:complexType name="dbReferenceType">
799 <xs:documentation>Describes a database cross-reference.
800 Equivalent to the flat file DR-line.
804 <xs:element name="molecule" type="moleculeType" minOccurs="0"/>
805 <xs:element name="property" type="propertyType" minOccurs="0" maxOccurs="unbounded"/>
807 <xs:attribute name="type" type="xs:string" use="required">
809 <xs:documentation>Describes the name of the database.</xs:documentation>
812 <xs:attribute name="id" type="xs:string" use="required">
814 <xs:documentation>Describes a unique database identifier.</xs:documentation>
817 <xs:attribute name="evidence" type="intListType" use="optional"/>
818 <!-- xs:attribute name="key" type="xs:string" use="optional"/ -->
821 <xs:complexType name="propertyType">
822 <xs:attribute name="type" type="xs:string" use="required"/>
823 <xs:attribute name="value" type="xs:string" use="required"/>
825 <!-- Database cross-reference definition ends -->
827 <!-- Protein existence definition begins -->
828 <xs:complexType name="proteinExistenceType">
830 <xs:documentation>Describes the evidence for the protein's existence.
831 Equivalent to the flat file PE-line.</xs:documentation>
833 <xs:attribute name="type" use="required">
835 <xs:restriction base="xs:string">
836 <xs:enumeration value="evidence at protein level"/>
837 <xs:enumeration value="evidence at transcript level"/>
838 <xs:enumeration value="inferred from homology"/>
839 <xs:enumeration value="predicted"/>
840 <xs:enumeration value="uncertain"/>
845 <!-- Protein existence definition ends -->
847 <!-- Keyword definition begins -->
848 <xs:complexType name="keywordType">
850 <xs:extension base="xs:string">
851 <xs:attribute name="evidence" type="intListType" use="optional"/>
852 <xs:attribute name="id" type="xs:string" use="required"/>
856 <!-- Keyword definition ends -->
858 <!-- Feature definition begins -->
859 <xs:complexType name="featureType">
861 <xs:documentation>Describes different types of sequence annotations.
862 Equivalent to the flat file FT-line.</xs:documentation>
865 <xs:element name="original" type="xs:string" minOccurs="0">
867 <xs:documentation>Describes the original sequence in annotations that describe natural or artifical sequence variations.</xs:documentation>
870 <xs:element name="variation" type="xs:string" minOccurs="0" maxOccurs="unbounded">
872 <xs:documentation>Describes the variant sequence in annotations that describe natural or artifical sequence variations.</xs:documentation>
875 <xs:element name="location" type="locationType">
877 <xs:documentation>Describes the sequence coordinates of the annotation.</xs:documentation>
881 <xs:attribute name="type" use="required">
883 <xs:documentation>Describes the type of a sequence annotation.
884 Equivalent to the flat file FT feature keys, but using full terms instead of acronyms.</xs:documentation>
887 <xs:restriction base="xs:string">
888 <xs:enumeration value="active site"/>
889 <xs:enumeration value="binding site"/>
890 <xs:enumeration value="calcium-binding region"/>
891 <xs:enumeration value="chain"/>
892 <xs:enumeration value="coiled-coil region"/>
893 <xs:enumeration value="compositionally biased region"/>
894 <xs:enumeration value="cross-link"/>
895 <xs:enumeration value="disulfide bond"/>
896 <xs:enumeration value="DNA-binding region"/>
897 <xs:enumeration value="domain"/>
898 <xs:enumeration value="glycosylation site"/>
899 <xs:enumeration value="helix"/>
900 <xs:enumeration value="initiator methionine"/>
901 <xs:enumeration value="lipid moiety-binding region"/>
902 <xs:enumeration value="metal ion-binding site"/>
903 <xs:enumeration value="modified residue"/>
904 <xs:enumeration value="mutagenesis site"/>
905 <xs:enumeration value="non-consecutive residues"/>
906 <xs:enumeration value="non-terminal residue"/>
907 <xs:enumeration value="nucleotide phosphate-binding region"/>
908 <xs:enumeration value="peptide"/>
909 <xs:enumeration value="propeptide"/>
910 <xs:enumeration value="region of interest"/>
911 <xs:enumeration value="repeat"/>
912 <xs:enumeration value="non-standard amino acid"/>
913 <xs:enumeration value="sequence conflict"/>
914 <xs:enumeration value="sequence variant"/>
915 <xs:enumeration value="short sequence motif"/>
916 <xs:enumeration value="signal peptide"/>
917 <xs:enumeration value="site"/>
918 <xs:enumeration value="splice variant"/>
919 <xs:enumeration value="strand"/>
920 <xs:enumeration value="topological domain"/>
921 <xs:enumeration value="transit peptide"/>
922 <xs:enumeration value="transmembrane region"/>
923 <xs:enumeration value="turn"/>
924 <xs:enumeration value="unsure residue"/>
925 <xs:enumeration value="zinc finger region"/>
926 <xs:enumeration value="intramembrane region"/>
930 <xs:attribute name="status" use="optional">
932 <xs:restriction base="xs:string">
933 <xs:enumeration value="by similarity"/>
934 <xs:enumeration value="probable"/>
935 <xs:enumeration value="potential"/>
939 <xs:attribute name="id" type="xs:string" use="optional"/>
940 <xs:attribute name="description" type="xs:string" use="optional"/>
941 <xs:attribute name="evidence" type="intListType" use="optional"/>
942 <xs:attribute name="ref" type="xs:string" use="optional"/>
945 <xs:complexType name="locationType">
947 <xs:documentation>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.</xs:documentation>
951 <xs:element name="begin" type="positionType"/>
952 <xs:element name="end" type="positionType"/>
954 <xs:element name="position" type="positionType"/>
956 <xs:attribute name="sequence" type="xs:string" use="optional"/>
959 <xs:complexType name="positionType">
960 <xs:attribute name="position" type="xs:unsignedLong" use="optional"/>
961 <xs:attribute name="status" use="optional" default="certain">
963 <xs:restriction base="xs:string">
964 <xs:enumeration value="certain"/>
965 <xs:enumeration value="uncertain"/>
966 <xs:enumeration value="less than"/>
967 <xs:enumeration value="greater than"/>
968 <xs:enumeration value="unknown"/>
972 <xs:attribute name="evidence" type="intListType" use="optional"/>
974 <!-- Feature definition ends -->
976 <!-- Sequence definition begins -->
977 <xs:complexType name="sequenceType">
979 <xs:extension base="xs:string">
980 <xs:attribute name="length" type="xs:int" use="required"/>
981 <xs:attribute name="mass" type="xs:int" use="required"/>
982 <xs:attribute name="checksum" type="xs:string" use="required"/>
983 <xs:attribute name="modified" type="xs:date" use="required"/>
984 <xs:attribute name="version" type="xs:int" use="required"/>
985 <xs:attribute name="precursor" type="xs:boolean" use="optional"/>
986 <xs:attribute name="fragment" use="optional">
988 <xs:restriction base="xs:string">
989 <xs:enumeration value="single"/>
990 <xs:enumeration value="multiple"/>
997 <!-- Sequence definition ends -->
999 <!-- Molecule definition begins -->
1000 <xs:complexType name="moleculeType">
1002 <xs:documentation>Describes a molecule by name or unique identifier.</xs:documentation>
1005 <xs:extension base="xs:string">
1006 <xs:attribute name="id" type="xs:string" use="optional"/>
1010 <!-- Molecule definition ends -->
1012 <!-- Evidence definition begins -->
1013 <xs:complexType name="evidenceType">
1015 <xs:documentation>Describes the evidence for an annotation.
1016 No flat file equivalent.</xs:documentation>
1019 <xs:element name="source" type="sourceType" minOccurs="0"/>
1020 <xs:element name="importedFrom" type="importedFromType" minOccurs="0"/>
1022 <xs:attribute name="type" type="xs:string" use="required">
1024 <xs:documentation>Describes the type of an evidence using the Evidence Code Ontology (http://www.obofoundry.org/cgi-bin/detail.cgi?id=evidence_code).</xs:documentation>
1027 <xs:attribute name="key" type="xs:integer" use="required">
1029 <xs:documentation>A unique key to link annotations (via 'evidence' attributes) to evidences.</xs:documentation>
1033 <xs:complexType name="sourceType">
1035 <xs:documentation>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).</xs:documentation>
1038 <xs:element name="dbReference" type="dbReferenceType" minOccurs="0"/>
1040 <xs:attribute name="ref" type="xs:integer" use="optional"/>
1042 <xs:complexType name="importedFromType">
1044 <xs:documentation>Describes the source of the evidence, when it is not assigned by UniProt, but imported from an external database.</xs:documentation>
1047 <xs:element name="dbReference" type="dbReferenceType"/>
1050 <!-- Evidence definition ends -->
1052 <xs:complexType name="evidencedStringType">
1054 <xs:extension base="xs:string">
1055 <xs:attribute name="evidence" type="intListType" use="optional"/>
1056 <xs:attribute name="status" use="optional">
1058 <xs:restriction base="xs:string">
1059 <xs:enumeration value="by similarity"/>
1060 <xs:enumeration value="probable"/>
1061 <xs:enumeration value="potential"/>
1069 <xs:simpleType name="intListType">
1070 <xs:list itemType="xs:int"/>