1 <?xml version="1.0" encoding="UTF-8"?>
3 Retrieved for Jalview 04-Apr-2019 from https://www.uniprot.org/docs/uniprot.xsd
4 Uniprot Release 2018_11: https://www.uniprot.org/news/2018/12/05/release
5 Generate Java binding classes by running this command in the schemas parent directory:
6 xjc schemas/uniprot.xsd -d src -p jalview.xml.binding.uniprot
8 <!-- *****************************************************************************
13 Copyright (c) 2011 UniProt consortium
15 *******************************************************************************-->
16 <xs:schema targetNamespace="http://uniprot.org/uniprot" xmlns:xs="http://www.w3.org/2001/XMLSchema"
17 xmlns="http://uniprot.org/uniprot" elementFormDefault="qualified">
18 <!-- XML Schema definition for the UniProtKB XML format
20 -XSV (XML Schema Validator), http://www.w3.org/2001/03/webdata/xsv
24 <!-- Root element definition begins -->
25 <xs:element name="uniprot">
27 <xs:documentation>Describes a collection of UniProtKB entries.</xs:documentation>
31 <xs:element ref="entry" maxOccurs="unbounded"/>
32 <xs:element ref="copyright" minOccurs="0"/>
36 <!-- Root element definition ends -->
38 <!-- Entry definition begins -->
39 <xs:element name="entry">
41 <xs:documentation>Describes a UniProtKB entry.</xs:documentation>
45 <xs:element name="accession" type="xs:string" maxOccurs="unbounded"/>
46 <xs:element name="name" type="xs:string" maxOccurs="unbounded"/>
47 <xs:element name="protein" type="proteinType"/>
48 <xs:element name="gene" type="geneType" minOccurs="0" maxOccurs="unbounded"/>
49 <xs:element name="organism" type="organismType" />
50 <xs:element name="organismHost" type="organismType" minOccurs="0" maxOccurs="unbounded"/>
51 <xs:element name="geneLocation" type="geneLocationType" minOccurs="0" maxOccurs="unbounded"/>
52 <xs:element name="reference" type="referenceType" maxOccurs="unbounded"/>
53 <xs:element name="comment" type="commentType" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
54 <xs:element name="dbReference" type="dbReferenceType" minOccurs="0" maxOccurs="unbounded"/>
55 <xs:element name="proteinExistence" type="proteinExistenceType"/>
56 <xs:element name="keyword" type="keywordType" minOccurs="0" maxOccurs="unbounded"/>
57 <xs:element name="feature" type="featureType" minOccurs="0" maxOccurs="unbounded"/>
58 <xs:element name="evidence" type="evidenceType" minOccurs="0" maxOccurs="unbounded"/>
59 <xs:element name="sequence" type="sequenceType"/>
61 <xs:attribute name="dataset" use="required">
63 <xs:restriction base="xs:string">
64 <xs:enumeration value="Swiss-Prot"/>
65 <xs:enumeration value="TrEMBL"/>
69 <xs:attribute name="created" type="xs:date" use="required"/>
70 <xs:attribute name="modified" type="xs:date" use="required"/>
71 <xs:attribute name="version" type="xs:int" use="required"/>
74 <!-- Entry definition ends -->
76 <xs:element name="copyright" type="xs:string"/>
78 <!-- Protein names definition begins -->
79 <xs:complexType name="proteinType">
81 <xs:documentation>Describes the names for the protein and parts thereof.
82 Equivalent to the flat file DE-line.</xs:documentation>
85 <xs:group ref="proteinNameGroup"/>
86 <xs:element name="domain" minOccurs="0" maxOccurs="unbounded">
88 <xs:documentation>Describes names of "domains".
89 Equivalent to the flat file DE-line Includes: section.</xs:documentation>
92 <xs:group ref="proteinNameGroup"/>
95 <xs:element name="component" minOccurs="0" maxOccurs="unbounded">
97 <xs:documentation>Describes names of processed products.
98 Equivalent to the flat file DE-line Contains: section.</xs:documentation>
101 <xs:group ref="proteinNameGroup"/>
106 <xs:group name="proteinNameGroup">
108 <xs:element name="recommendedName" minOccurs="0">
111 <xs:element name="fullName" type="evidencedStringType"/>
112 <xs:element name="shortName" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
113 <xs:element name="ecNumber" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
115 <!-- xs:attribute name="ref" type="xs:string" use="optional"/ -->
118 <xs:element name="alternativeName" minOccurs="0" maxOccurs="unbounded">
121 <xs:element name="fullName" type="evidencedStringType" minOccurs="0"/>
122 <xs:element name="shortName" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
123 <xs:element name="ecNumber" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
125 <!-- xs:attribute name="ref" type="xs:string" use="optional"/ -->
128 <xs:element name="submittedName" minOccurs="0" maxOccurs="unbounded">
131 <xs:element name="fullName" type="evidencedStringType"/>
132 <xs:element name="ecNumber" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
134 <!-- xs:attribute name="ref" type="xs:string" use="optional"/ -->
137 <xs:element name="allergenName" type="evidencedStringType" minOccurs="0"/>
138 <xs:element name="biotechName" type="evidencedStringType" minOccurs="0"/>
139 <xs:element name="cdAntigenName" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
140 <xs:element name="innName" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
143 <!-- Protein names definition ends -->
145 <!-- Gene names definition begins -->
146 <xs:complexType name="geneType">
148 <xs:documentation>Describes a gene.
149 Equivalent to the flat file GN-line.</xs:documentation>
152 <xs:element name="name" type="geneNameType" maxOccurs="unbounded"/>
155 <xs:complexType name="geneNameType">
157 <xs:documentation>Describes different types of gene designations.
158 Equivalent to the flat file GN-line.</xs:documentation>
161 <xs:extension base="xs:string">
162 <xs:attribute name="evidence" type="intListType" use="optional"/>
163 <xs:attribute name="type" use="required">
165 <xs:restriction base="xs:string">
166 <xs:enumeration value="primary"/>
167 <xs:enumeration value="synonym"/>
168 <xs:enumeration value="ordered locus"/>
169 <xs:enumeration value="ORF"/>
176 <!-- Gene names definition ends -->
178 <!-- Organism definition begins -->
179 <xs:complexType name="organismType">
181 <xs:documentation>Describes the source organism.</xs:documentation>
184 <xs:element name="name" type="organismNameType" maxOccurs="unbounded">
186 <xs:documentation>Describes the names of the source organism.
187 Equivalent to the flat file OS-line.</xs:documentation>
190 <xs:element name="dbReference" type="dbReferenceType" maxOccurs="unbounded">
192 <xs:documentation>Describes a cross-reference to the NCBI taxonomy database.
193 Equivalent to the flat file OX-line.</xs:documentation>
196 <xs:element name="lineage" minOccurs="0">
198 <xs:documentation>Describes the lineage of the source organism.
199 Equivalent to the flat file OC-line.</xs:documentation>
203 <xs:element name="taxon" type="xs:string" maxOccurs="unbounded"/>
208 <xs:attribute name="evidence" type="intListType" use="optional"/>
210 <xs:complexType name="organismNameType">
212 <xs:documentation>Describes different types of source organism names.</xs:documentation>
215 <xs:extension base="xs:string">
216 <xs:attribute name="type" use="required">
218 <xs:restriction base="xs:string">
219 <xs:enumeration value="common"/>
220 <xs:enumeration value="full"/>
221 <xs:enumeration value="scientific"/>
222 <xs:enumeration value="synonym"/>
223 <xs:enumeration value="abbreviation"/>
230 <!-- Organism definition ends -->
232 <!-- Gene location definition begins -->
233 <xs:complexType name="geneLocationType">
235 <xs:documentation>Describes non-nuclear gene locations (organelles and plasmids).
236 Equivalent to the flat file OG-line.</xs:documentation>
239 <xs:element name="name" type="statusType" minOccurs="0" maxOccurs="unbounded"/>
241 <xs:attribute name="type" use="required">
243 <xs:restriction base="xs:string">
244 <xs:enumeration value="apicoplast"/>
245 <xs:enumeration value="chloroplast"/>
246 <xs:enumeration value="organellar chromatophore"/>
247 <xs:enumeration value="cyanelle"/>
248 <xs:enumeration value="hydrogenosome"/>
249 <xs:enumeration value="mitochondrion"/>
250 <xs:enumeration value="non-photosynthetic plastid"/>
251 <xs:enumeration value="nucleomorph"/>
252 <xs:enumeration value="plasmid"/>
253 <xs:enumeration value="plastid"/>
257 <xs:attribute name="evidence" type="intListType" use="optional"/>
259 <xs:complexType name="statusType">
261 <xs:documentation>Indicates whether the name of a plasmid is known or unknown.</xs:documentation>
264 <xs:extension base="xs:string">
265 <xs:attribute name="status" use="optional" default="known">
267 <xs:restriction base="xs:string">
268 <xs:enumeration value="known"/>
269 <xs:enumeration value="unknown"/>
276 <!-- Gene location definition ends -->
278 <!-- Reference definition begins -->
279 <xs:complexType name="referenceType">
281 <xs:documentation>Describes a citation and a summary of its content.
282 Equivalent to the flat file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines.</xs:documentation>
285 <xs:element name="citation" type="citationType"/>
286 <xs:group ref="sptrCitationGroup"/>
288 <xs:attribute name="evidence" type="intListType" use="optional"/>
289 <xs:attribute name="key" type="xs:string" use="required"/>
291 <!-- Reference definition ends -->
293 <!-- Citation definition begins -->
294 <xs:complexType name="citationType">
296 <xs:documentation>Describes different types of citations.
297 Equivalent to the flat file RX-, RG-, RA-, RT- and RL-lines.</xs:documentation>
300 <xs:element name="title" type="xs:string" minOccurs="0">
302 <xs:documentation>Describes the title of a citation.
303 Equivalent to the flat file RT-line.</xs:documentation>
306 <xs:element name="editorList" type="nameListType" minOccurs="0">
308 <xs:documentation>Describes the editors of a book (only used for books).
309 Equivalent to part of the flat file RL-line of books.</xs:documentation>
312 <xs:element name="authorList" type="nameListType" minOccurs="0">
314 <xs:documentation>Describes the authors of a citation.
315 Equivalent to the flat file RA-line.</xs:documentation>
318 <xs:element name="locator" type="xs:string" minOccurs="0">
320 <xs:documentation>Describes the location (URL) of an online journal article.
321 No flat file equivalent.</xs:documentation>
324 <xs:element name="dbReference" type="dbReferenceType" minOccurs="0" maxOccurs="unbounded">
326 <xs:documentation>Describes cross-references to bibliography databases (MEDLINE, PubMed, AGRICOLA) or other online resources (DOI).
327 Equivalent to the flat file RX-line.</xs:documentation>
331 <xs:attribute name="type" use="required">
333 <xs:documentation>Describes the type of a citation.</xs:documentation>
336 <xs:restriction base="xs:string">
337 <xs:enumeration value="book"/>
338 <xs:enumeration value="journal article"/>
339 <xs:enumeration value="online journal article"/>
340 <xs:enumeration value="patent"/>
341 <xs:enumeration value="submission"/>
342 <xs:enumeration value="thesis"/>
343 <xs:enumeration value="unpublished observations"/>
347 <xs:attribute name="date" use="optional">
349 <xs:union memberTypes="xs:date xs:gYearMonth xs:gYear"/>
352 <xs:attribute name="name" type="xs:string" use="optional">
354 <xs:documentation>Describes the name of an (online) journal or book.</xs:documentation>
357 <xs:attribute name="volume" type="xs:string" use="optional">
359 <xs:documentation>Describes the volume of a journal or book.</xs:documentation>
362 <xs:attribute name="first" type="xs:string" use="optional">
364 <xs:documentation>Describes the first page of an article.</xs:documentation>
367 <xs:attribute name="last" type="xs:string" use="optional">
369 <xs:documentation>Describes the last page of an article.</xs:documentation>
372 <xs:attribute name="publisher" type="xs:string" use="optional">
374 <xs:documentation>Describes the publisher of a book.</xs:documentation>
377 <xs:attribute name="city" type="xs:string" use="optional">
379 <xs:documentation>Describes the city where a book was published.</xs:documentation>
382 <xs:attribute name="db" type="xs:string" use="optional">
384 <xs:documentation>Describes the database name of submissions.</xs:documentation>
387 <xs:attribute name="number" type="xs:string" use="optional">
389 <xs:documentation>Describes a patent number.</xs:documentation>
392 <xs:attribute name="institute" type="xs:string" use="optional">
394 <xs:documentation>Describes the institute where a thesis was made.</xs:documentation>
397 <xs:attribute name="country" type="xs:string" use="optional">
399 <xs:documentation>Describes the country where a thesis was made.</xs:documentation>
403 <xs:complexType name="consortiumType">
405 <xs:documentation>Describes the authors of a citation when these are represented by a consortium.
406 Equivalent to the flat file RG-line.</xs:documentation>
408 <xs:attribute name="name" type="xs:string" use="required"/>
410 <xs:complexType name="personType">
411 <xs:attribute name="name" type="xs:string" use="required"/>
413 <xs:complexType name="nameListType">
414 <xs:choice maxOccurs="unbounded">
415 <xs:element name="consortium" type="consortiumType"/>
416 <xs:element name="person" type="personType"/>
419 <!-- Citation definition ends -->
421 <!-- Citation summary definition begins -->
422 <xs:group name="sptrCitationGroup">
424 <xs:documentation>Groups a citation's scope and source descriptions.</xs:documentation>
427 <xs:element name="scope" type="xs:string" maxOccurs="unbounded">
429 <xs:documentation>Describes the scope of a citation.
430 Equivalent to the flat file RP-line.</xs:documentation>
433 <xs:element name="source" type="sourceDataType" minOccurs="0"/>
436 <xs:complexType name="sourceDataType">
438 <xs:documentation>Describes the source of the sequence according to the citation.
439 Equivalent to the flat file RC-line.</xs:documentation>
441 <xs:choice maxOccurs="unbounded">
442 <xs:element name="strain">
445 <xs:extension base="xs:string">
446 <xs:attribute name="evidence" type="intListType" use="optional"/>
451 <xs:element name="plasmid">
454 <xs:extension base="xs:string">
455 <xs:attribute name="evidence" type="intListType" use="optional"/>
460 <xs:element name="transposon">
463 <xs:extension base="xs:string">
464 <xs:attribute name="evidence" type="intListType" use="optional"/>
469 <xs:element name="tissue">
472 <xs:extension base="xs:string">
473 <xs:attribute name="evidence" type="intListType" use="optional"/>
480 <!-- Citation summary definition ends -->
482 <!-- Comment definition begins -->
483 <xs:complexType name="commentType">
485 <xs:documentation>Describes different types of general annotations.
486 Equivalent to the flat file CC-line.</xs:documentation>
489 <xs:element name="molecule" type="moleculeType" minOccurs="0"/>
490 <xs:choice minOccurs="0">
491 <xs:group ref="bpcCommentGroup"/>
495 <xs:documentation>Used in 'catalytic activity' annotations.</xs:documentation>
497 <xs:element name="reaction" type="reactionType"/>
498 <xs:element name="physiologicalReaction" type="physiologicalReactionType" minOccurs="0" maxOccurs="2"/>
503 <xs:documentation>Used in 'cofactor' annotations.</xs:documentation>
505 <xs:element name="cofactor" type="cofactorType" maxOccurs="unbounded"/>
510 <xs:documentation>Used in 'subcellular location' annotations.</xs:documentation>
512 <xs:element name="subcellularLocation" type="subcellularLocationType" maxOccurs="unbounded"/>
515 <xs:element name="conflict">
517 <xs:documentation>Used in 'sequence caution' annotations.</xs:documentation>
521 <xs:element name="sequence" minOccurs="0">
523 <xs:attribute name="resource" use="required">
525 <xs:restriction base="xs:string">
526 <xs:enumeration value="EMBL-CDS"/>
527 <xs:enumeration value="EMBL"/>
531 <xs:attribute name="id" type="xs:string" use="required"/>
532 <xs:attribute name="version" type="xs:int" use="optional"/>
536 <xs:attribute name="type" use="required">
538 <xs:restriction base="xs:string">
539 <xs:enumeration value="frameshift"/>
540 <xs:enumeration value="erroneous initiation"/>
541 <xs:enumeration value="erroneous termination"/>
542 <xs:enumeration value="erroneous gene model prediction"/>
543 <xs:enumeration value="erroneous translation"/>
544 <xs:enumeration value="miscellaneous discrepancy"/>
548 <xs:attribute name="ref" type="xs:string" use="optional">
550 <xs:documentation>Refers to the 'key' attribute of a 'reference' element.</xs:documentation>
557 <xs:element name="link" minOccurs="0" maxOccurs="unbounded">
559 <xs:documentation>Used in 'online information' annotations.</xs:documentation>
562 <xs:attribute name="uri" type="xs:anyURI" use="required"/>
569 <xs:documentation>Used in 'alternative products' annotations.</xs:documentation>
571 <xs:element name="event" type="eventType" maxOccurs="4"/>
572 <xs:element name="isoform" type="isoformType" minOccurs="0" maxOccurs="unbounded"/>
577 <xs:documentation>Used in 'interaction' annotations.</xs:documentation>
579 <xs:element name="interactant" type="interactantType" minOccurs="2" maxOccurs="2"/>
580 <xs:element name="organismsDiffer" type="xs:boolean" default="false"/>
581 <xs:element name="experiments" type="xs:int"/>
584 <xs:element name="disease">
586 <xs:documentation>Used in 'disease' annotations.</xs:documentation>
590 <xs:element name="name" type="xs:string"/>
591 <xs:element name="acronym" type="xs:string"/>
592 <xs:element name="description" type="xs:string"/>
593 <xs:element name="dbReference" type="dbReferenceType"/>
595 <xs:attribute name="id" type="xs:string" use="required"/>
601 <xs:element name="location" type="locationType" minOccurs="0" maxOccurs="unbounded">
603 <xs:documentation>Used in 'mass spectrometry' and 'sequence caution' annotations.</xs:documentation>
607 <xs:element name="text" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
611 <xs:attribute name="type" use="required">
613 <xs:documentation>Describes the type of a general annotation.
614 Equivalent to the flat file CC comment topics (except for "DATABASE" which is translated to "online information").</xs:documentation>
617 <xs:restriction base="xs:string">
618 <xs:enumeration value="allergen"/>
619 <xs:enumeration value="alternative products"/>
620 <xs:enumeration value="biotechnology"/>
621 <xs:enumeration value="biophysicochemical properties"/>
622 <xs:enumeration value="catalytic activity"/>
623 <xs:enumeration value="caution"/>
624 <xs:enumeration value="cofactor"/>
625 <xs:enumeration value="developmental stage"/>
626 <xs:enumeration value="disease"/>
627 <xs:enumeration value="domain"/>
628 <xs:enumeration value="disruption phenotype"/>
629 <xs:enumeration value="activity regulation"/>
630 <xs:enumeration value="function"/>
631 <xs:enumeration value="induction"/>
632 <xs:enumeration value="miscellaneous"/>
633 <xs:enumeration value="pathway"/>
634 <xs:enumeration value="pharmaceutical"/>
635 <xs:enumeration value="polymorphism"/>
636 <xs:enumeration value="PTM"/>
637 <xs:enumeration value="RNA editing"/>
638 <xs:enumeration value="similarity"/>
639 <xs:enumeration value="subcellular location"/>
640 <xs:enumeration value="sequence caution"/>
641 <xs:enumeration value="subunit"/>
642 <xs:enumeration value="tissue specificity"/>
643 <xs:enumeration value="toxic dose"/>
644 <xs:enumeration value="online information"/>
645 <xs:enumeration value="mass spectrometry"/>
646 <xs:enumeration value="interaction"/>
651 <xs:attribute name="locationType" type="xs:string" use="optional">
653 <xs:documentation>Describes the type of sequence location in 'RNA editing' annotations. Common values are "Not_applicable" and "Undetermined".</xs:documentation>
657 <xs:attribute name="name" type="xs:string" use="optional">
659 <xs:documentation>Describes an optional name for an 'online information'.</xs:documentation>
663 <xs:attribute name="mass" type="xs:float" use="optional">
665 <xs:documentation>Describes the molecular mass in 'mass spectrometry' annotations.</xs:documentation>
668 <xs:attribute name="error" type="xs:string" use="optional">
670 <xs:documentation>Describes the error of the mass measurement in 'mass spectrometry' annotations.</xs:documentation>
673 <xs:attribute name="method" type="xs:string" use="optional">
675 <xs:documentation>Describes the experimental method in 'mass spectrometry' annotations.</xs:documentation>
679 <xs:attribute name="evidence" type="intListType" use="optional"/>
682 <xs:group name="bpcCommentGroup">
684 <xs:documentation>Describes different types of biophysicochemical properties.</xs:documentation>
687 <xs:element name="absorption" minOccurs="0">
690 <xs:element name="max" type="evidencedStringType" minOccurs="0"/>
691 <xs:element name="text" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
695 <xs:element name="kinetics" minOccurs="0">
698 <xs:element name="KM" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
699 <xs:element name="Vmax" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
700 <xs:element name="text" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
704 <xs:element name="phDependence" minOccurs="0">
707 <xs:element name="text" type="evidencedStringType" maxOccurs="unbounded"/>
711 <xs:element name="redoxPotential" minOccurs="0">
714 <xs:element name="text" type="evidencedStringType" maxOccurs="unbounded"/>
718 <xs:element name="temperatureDependence" minOccurs="0">
721 <xs:element name="text" type="evidencedStringType" maxOccurs="unbounded"/>
728 <xs:complexType name="reactionType">
730 <xs:documentation>Describes a chemical reaction.</xs:documentation>
733 <xs:element name="text" type="xs:string"/>
734 <xs:element name="dbReference" type="dbReferenceType" minOccurs="1" maxOccurs="unbounded"/>
736 <xs:attribute name="evidence" type="intListType" use="optional"/>
739 <xs:complexType name="physiologicalReactionType">
741 <xs:documentation>Describes a physiological reaction.</xs:documentation>
744 <xs:element name="dbReference" type="dbReferenceType"/>
746 <xs:attribute name="direction" use="required">
748 <xs:restriction base="xs:string">
749 <xs:enumeration value="left-to-right"/>
750 <xs:enumeration value="right-to-left"/>
754 <xs:attribute name="evidence" type="intListType" use="optional"/>
757 <xs:complexType name="cofactorType">
759 <xs:documentation>Describes a cofactor.</xs:documentation>
762 <xs:element name="name" type="xs:string"/>
763 <xs:element name="dbReference" type="dbReferenceType"/>
765 <xs:attribute name="evidence" type="intListType" use="optional"/>
768 <xs:complexType name="subcellularLocationType">
770 <xs:documentation>Describes the subcellular location and optionally the topology and orientation of a molecule.</xs:documentation>
773 <xs:element name="location" type="evidencedStringType" maxOccurs="unbounded"/>
774 <xs:element name="topology" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
775 <xs:element name="orientation" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
779 <xs:complexType name="eventType">
781 <xs:documentation>Describes the type of events that cause alternative products.</xs:documentation>
783 <xs:attribute name="type" use="required">
785 <xs:restriction base="xs:string">
786 <xs:enumeration value="alternative splicing"/>
787 <xs:enumeration value="alternative initiation"/>
788 <xs:enumeration value="alternative promoter"/>
789 <xs:enumeration value="ribosomal frameshifting"/>
795 <xs:complexType name="isoformType">
797 <xs:documentation>Describes isoforms in 'alternative products' annotations.</xs:documentation>
800 <xs:element name="id" type="xs:string" maxOccurs="unbounded"/>
801 <xs:element name="name" maxOccurs="unbounded">
804 <xs:extension base="xs:string">
805 <xs:attribute name="evidence" type="intListType" use="optional"/>
810 <xs:element name="sequence">
812 <xs:attribute name="type" use="required">
814 <xs:restriction base="xs:string">
815 <xs:enumeration value="not described"/>
816 <xs:enumeration value="described"/>
817 <xs:enumeration value="displayed"/>
818 <xs:enumeration value="external"/>
822 <xs:attribute name="ref" type="xs:string" use="optional"/>
825 <xs:element name="text" type="evidencedStringType" minOccurs="0" maxOccurs="unbounded"/>
829 <xs:group name="interactantGroup">
831 <xs:element name="id" type="xs:string"/>
832 <xs:element name="label" type="xs:string" minOccurs="0"/>
835 <xs:complexType name="interactantType">
836 <xs:group ref="interactantGroup" minOccurs="0"/>
837 <xs:attribute name="intactId" type="xs:string" use="required"/>
839 <!-- Comment definition ends -->
841 <!-- Database cross-reference definition begins -->
842 <xs:complexType name="dbReferenceType">
844 <xs:documentation>Describes a database cross-reference.
845 Equivalent to the flat file DR-line.
849 <xs:element name="molecule" type="moleculeType" minOccurs="0"/>
850 <xs:element name="property" type="propertyType" minOccurs="0" maxOccurs="unbounded"/>
852 <xs:attribute name="type" type="xs:string" use="required">
854 <xs:documentation>Describes the name of the database.</xs:documentation>
857 <xs:attribute name="id" type="xs:string" use="required">
859 <xs:documentation>Describes a unique database identifier.</xs:documentation>
862 <xs:attribute name="evidence" type="intListType" use="optional"/>
863 <!-- xs:attribute name="key" type="xs:string" use="optional"/ -->
866 <xs:complexType name="propertyType">
867 <xs:attribute name="type" type="xs:string" use="required"/>
868 <xs:attribute name="value" type="xs:string" use="required"/>
870 <!-- Database cross-reference definition ends -->
872 <!-- Protein existence definition begins -->
873 <xs:complexType name="proteinExistenceType">
875 <xs:documentation>Describes the evidence for the protein's existence.
876 Equivalent to the flat file PE-line.</xs:documentation>
878 <xs:attribute name="type" use="required">
880 <xs:restriction base="xs:string">
881 <xs:enumeration value="evidence at protein level"/>
882 <xs:enumeration value="evidence at transcript level"/>
883 <xs:enumeration value="inferred from homology"/>
884 <xs:enumeration value="predicted"/>
885 <xs:enumeration value="uncertain"/>
890 <!-- Protein existence definition ends -->
892 <!-- Keyword definition begins -->
893 <xs:complexType name="keywordType">
895 <xs:extension base="xs:string">
896 <xs:attribute name="evidence" type="intListType" use="optional"/>
897 <xs:attribute name="id" type="xs:string" use="required"/>
901 <!-- Keyword definition ends -->
903 <!-- Feature definition begins -->
904 <xs:complexType name="featureType">
906 <xs:documentation>Describes different types of sequence annotations.
907 Equivalent to the flat file FT-line.</xs:documentation>
910 <xs:element name="original" type="xs:string" minOccurs="0">
912 <xs:documentation>Describes the original sequence in annotations that describe natural or artifical sequence variations.</xs:documentation>
915 <xs:element name="variation" type="xs:string" minOccurs="0" maxOccurs="unbounded">
917 <xs:documentation>Describes the variant sequence in annotations that describe natural or artifical sequence variations.</xs:documentation>
920 <xs:element name="location" type="locationType">
922 <xs:documentation>Describes the sequence coordinates of the annotation.</xs:documentation>
926 <xs:attribute name="type" use="required">
928 <xs:documentation>Describes the type of a sequence annotation.
929 Equivalent to the flat file FT feature keys, but using full terms instead of acronyms.</xs:documentation>
932 <xs:restriction base="xs:string">
933 <xs:enumeration value="active site"/>
934 <xs:enumeration value="binding site"/>
935 <xs:enumeration value="calcium-binding region"/>
936 <xs:enumeration value="chain"/>
937 <xs:enumeration value="coiled-coil region"/>
938 <xs:enumeration value="compositionally biased region"/>
939 <xs:enumeration value="cross-link"/>
940 <xs:enumeration value="disulfide bond"/>
941 <xs:enumeration value="DNA-binding region"/>
942 <xs:enumeration value="domain"/>
943 <xs:enumeration value="glycosylation site"/>
944 <xs:enumeration value="helix"/>
945 <xs:enumeration value="initiator methionine"/>
946 <xs:enumeration value="lipid moiety-binding region"/>
947 <xs:enumeration value="metal ion-binding site"/>
948 <xs:enumeration value="modified residue"/>
949 <xs:enumeration value="mutagenesis site"/>
950 <xs:enumeration value="non-consecutive residues"/>
951 <xs:enumeration value="non-terminal residue"/>
952 <xs:enumeration value="nucleotide phosphate-binding region"/>
953 <xs:enumeration value="peptide"/>
954 <xs:enumeration value="propeptide"/>
955 <xs:enumeration value="region of interest"/>
956 <xs:enumeration value="repeat"/>
957 <xs:enumeration value="non-standard amino acid"/>
958 <xs:enumeration value="sequence conflict"/>
959 <xs:enumeration value="sequence variant"/>
960 <xs:enumeration value="short sequence motif"/>
961 <xs:enumeration value="signal peptide"/>
962 <xs:enumeration value="site"/>
963 <xs:enumeration value="splice variant"/>
964 <xs:enumeration value="strand"/>
965 <xs:enumeration value="topological domain"/>
966 <xs:enumeration value="transit peptide"/>
967 <xs:enumeration value="transmembrane region"/>
968 <xs:enumeration value="turn"/>
969 <xs:enumeration value="unsure residue"/>
970 <xs:enumeration value="zinc finger region"/>
971 <xs:enumeration value="intramembrane region"/>
975 <xs:attribute name="status" use="optional">
977 <xs:restriction base="xs:string">
978 <xs:enumeration value="by similarity"/>
979 <xs:enumeration value="probable"/>
980 <xs:enumeration value="potential"/>
984 <xs:attribute name="id" type="xs:string" use="optional"/>
985 <xs:attribute name="description" type="xs:string" use="optional"/>
986 <xs:attribute name="evidence" type="intListType" use="optional"/>
987 <xs:attribute name="ref" type="xs:string" use="optional"/>
990 <xs:complexType name="locationType">
992 <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>
996 <xs:element name="begin" type="positionType"/>
997 <xs:element name="end" type="positionType"/>
999 <xs:element name="position" type="positionType"/>
1001 <xs:attribute name="sequence" type="xs:string" use="optional"/>
1004 <xs:complexType name="positionType">
1005 <xs:attribute name="position" type="xs:unsignedLong" use="optional"/>
1006 <xs:attribute name="status" use="optional" default="certain">
1008 <xs:restriction base="xs:string">
1009 <xs:enumeration value="certain"/>
1010 <xs:enumeration value="uncertain"/>
1011 <xs:enumeration value="less than"/>
1012 <xs:enumeration value="greater than"/>
1013 <xs:enumeration value="unknown"/>
1017 <xs:attribute name="evidence" type="intListType" use="optional"/>
1019 <!-- Feature definition ends -->
1021 <!-- Sequence definition begins -->
1022 <xs:complexType name="sequenceType">
1024 <xs:extension base="xs:string">
1025 <xs:attribute name="length" type="xs:int" use="required"/>
1026 <xs:attribute name="mass" type="xs:int" use="required"/>
1027 <xs:attribute name="checksum" type="xs:string" use="required"/>
1028 <xs:attribute name="modified" type="xs:date" use="required"/>
1029 <xs:attribute name="version" type="xs:int" use="required"/>
1030 <xs:attribute name="precursor" type="xs:boolean" use="optional"/>
1031 <xs:attribute name="fragment" use="optional">
1033 <xs:restriction base="xs:string">
1034 <xs:enumeration value="single"/>
1035 <xs:enumeration value="multiple"/>
1042 <!-- Sequence definition ends -->
1044 <!-- Molecule definition begins -->
1045 <xs:complexType name="moleculeType">
1047 <xs:documentation>Describes a molecule by name or unique identifier.</xs:documentation>
1050 <xs:extension base="xs:string">
1051 <xs:attribute name="id" type="xs:string" use="optional"/>
1055 <!-- Molecule definition ends -->
1057 <!-- Evidence definition begins -->
1058 <xs:complexType name="evidenceType">
1060 <xs:documentation>Describes the evidence for an annotation.
1061 No flat file equivalent.</xs:documentation>
1064 <xs:element name="source" type="sourceType" minOccurs="0"/>
1065 <xs:element name="importedFrom" type="importedFromType" minOccurs="0"/>
1067 <xs:attribute name="type" type="xs:string" use="required">
1069 <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>
1072 <xs:attribute name="key" type="xs:integer" use="required">
1074 <xs:documentation>A unique key to link annotations (via 'evidence' attributes) to evidences.</xs:documentation>
1078 <xs:complexType name="sourceType">
1080 <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>
1083 <xs:element name="dbReference" type="dbReferenceType" minOccurs="0"/>
1085 <xs:attribute name="ref" type="xs:integer" use="optional"/>
1087 <xs:complexType name="importedFromType">
1089 <xs:documentation>Describes the source of the evidence, when it is not assigned by UniProt, but imported from an external database.</xs:documentation>
1092 <xs:element name="dbReference" type="dbReferenceType"/>
1095 <!-- Evidence definition ends -->
1097 <xs:complexType name="evidencedStringType">
1099 <xs:extension base="xs:string">
1100 <xs:attribute name="evidence" type="intListType" use="optional"/>
1101 <xs:attribute name="status" use="optional">
1103 <xs:restriction base="xs:string">
1104 <xs:enumeration value="by similarity"/>
1105 <xs:enumeration value="probable"/>
1106 <xs:enumeration value="potential"/>
1114 <xs:simpleType name="intListType">
1115 <xs:list itemType="xs:int"/>