syntax</a>).
</p>
- <table border="1" width="95%">
- <tr>
- <th>Field</th>
- <th>Example</th>
- <th>Description</th>
- </tr>
- <tr>
- <td>accession</td>
- <td><code>accession:P62988</code></td>
- <td>Lists all entries with the primary or secondary accession
- number P62988.</td>
- </tr>
- <tr>
- <td>active</td>
- <td><code>active:no </code></td>
- <td>Lists all obsolete entries.</td>
- </tr>
- <tr>
- <td>annotation</td>
- <td><code>
- annotation:(type:non-positional) <br />
- annotation:(type:positional) <br /> annotation:(type:mod_res
- "Pyrrolidone carboxylic acid" evidence:experimental)
- </code></td>
- <td>Lists all entries with:
- <ul>
- <li>any general annotation (comments [CC])</li>
- <li>any sequence annotation (features [FT])</li>
- <li>at least one amino acid modified with a Pyrrolidone
- carboxylic acid group</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>author</td>
- <td><code> author:ashburner </code></td>
- <td>Lists all entries with at least one reference co-authored
- by Michael Ashburner.</td>
- </tr>
- <tr>
- <td>cdantigen</td>
- <td><code> cdantigen:CD233 </code></td>
- <td>Lists all entries whose cluster of differentiation number
- is CD233.</td>
- </tr>
- <tr>
- <td>citation</td>
- <td><code>
- citation:("intracellular structural proteins") <br />
- citation:(author:ashburner journal:nature) citation:9169874
- </code></td>
- <td>Lists all entries with a literature citation:
- <ul>
- <li>containing the phrase "intracellular structural
- proteins" in either title or abstract</li>
- <li>co-authored by Michael Ashburner and published in
- Nature</li>
- <li>with the PubMed identifier 9169874</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>cluster</td>
- <td><code> cluster:UniRef90_A5YMT3 </code></td>
- <td>Lists all entries in the UniRef 90% identity cluster
- whose representative sequence is UniProtKB entry A5YMT3.</td>
- </tr>
- <tr>
- <td>count</td>
- <td><code>
- annotation:(type:transmem count:5)<br />
- annotation:(type:transmem count:[5 TO *])<br />
- annotation:(type:cofactor count:[3 TO *])
- </code></td>
- <td>Lists all entries with:
- <ul>
- <li>exactly 5 transmembrane regions</li>
- <li>5 or more transmembrane regions</li>
- <li>3 or more Cofactor comments</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>created</td>
- <td><code>
- created:[20121001 TO *]<br /> reviewed:yes AND
- created:[current TO *]
- </code></td>
- <td>Lists all entries created since October 1st 2012.<br />
- Lists all new UniProtKB/Swiss-Prot entries in the last release.
- </td>
- </tr>
- <tr>
- <td>database</td>
- <td><code>
- database:(type:pfam) <br /> database:(type:pdb 1aut)
- </code></td>
- <td>Lists all entries with:
- <ul>
- <li>a cross-reference to the Pfam database</li>
- <li>a cross-reference to the PDB database entry 1aut</li>
- </ul>
+<table border="1" width="95%">
+<thead>
+<tr>
+<th>rest.uniprot.org field</th>
+<th>rest.uniprot.org example</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>accession</td>
+<td>accession:P62988</td>
+<td>The old behaviour was to list all entries with primary or secondary accession number P62988. The new behaviour will list all primary / canonical isoform accessions P62988. To search over secondary accessions, we have introduced the <code>sec_acc</code> field.</td>
+</tr>
+<tr>
+<td>active</td>
+<td>active:false</td>
+<td>Lists all obsolete entries.</td>
+</tr>
+<tr>
+<td>Refer to the page: Sequence Annotations</td>
+<td></td>
+<td>Lists all entries with:<ol><li>any general annotation (comments [CC])</li> <li>any sequence annotation (features [FT])</li><li>at least one amino acid modified with a Pyrrolidone carboxylic acid group</li></ol></td>
+</tr>
+<tr>
+<td>lit_author</td>
+<td>lit_author:ashburner</td>
+<td>Lists all entries with at least one reference co-authored by Michael Ashburner.</td>
+</tr>
+<tr>
+<td>protein_name</td>
+<td>protein_name:CD233</td>
+<td>Lists all entries whose cluster of differentiation number is CD233 (see cdlist.txt).</td>
+</tr>
+<tr>
+<td>chebi</td>
+<td>chebi:18420</td>
+<td>Lists all entries which are associated with the small molecule corresponding to ChEBI identifier 18420, Mg(2+) (see How can I search UniProt for chemical or reaction data?).</td>
+</tr>
+<tr>
+<td>uniprot_id (/uniref), then uniref_cluster_90 (/uniprotkb)</td>
+<td><ol><li>uniprot_id:A5YMT3 to find cluster UniRef90_P00395</li><li>uniref_cluster_90:UniRef90_P00395</li></ol></td>
+<td>Find all entries in the UniRef 90% identity cluster whose representative sequence is UniProtKB entry A5YMT3 (about UniRef).</td>
+</tr>
+<tr>
+<td>xref<em>count_pdb (or xref_count</em>)</td>
+<td>xref_count_pdb:[20 TO *]</td>
+<td>Lists all entries with 20 or more cross-references to PDB</td>
+</tr>
+<tr>
+<td>date_created</td>
+<td>date_created:[2012-10-01 TO *]</td>
+<td>Lists all entries created since October 1st 2012.</td>
+</tr>
+<tr>
+<td>database, xref</td>
+<td><ol><li>database:pfam</li><li>xref:pdb-1aut</li></ol></td>
+<td>Lists all entries with:<ol><li>a cross-reference to the Pfam database</li><li>a cross-reference to the PDB database entry 1aut</li></ol> (see Databases cross-referenced in UniProtKB and Database mapping)</td>
+</tr>
+<tr>
+<td>ec</td>
+<td>ec:3.2.1.23</td>
+<td>Lists all beta-galactosidases (Enzyme nomenclature database).</td>
+</tr>
+<tr>
+<td>Refer to the pages: Comments or Sequence Annotations</td>
+<td></td>
+<td>Lists all entries with: <ol><li>a signal sequence whose positions have been experimentally proven</li> <li>experimentally proven phosphoserine sites</li> <li>a function manually asserted according to rules</li></ol>(see Evidence attribution)</td>
+</tr>
+<tr>
+<td>existence</td>
+<td>existence:3</td>
+<td>See Protein existence criteria.</td>
+</tr>
+<tr>
+<td>family</td>
+<td>family:serpin</td>
+<td>Lists all entries belonging to the Serpin family of proteins (Index of protein domains and families).</td>
+</tr>
+<tr>
+<td>fragment</td>
+<td>fragment:true</td>
+<td>Lists all entries with an incomplete sequence.</td>
+</tr>
+<tr>
+<td>gene</td>
+<td>gene:HPSE</td>
+<td>Lists all entries for proteins encoded by gene HPSE, but also by HPSE2.</td>
+</tr>
+<tr>
+<td>gene_exact</td>
+<td>gene_exact:HPSE</td>
+<td>Lists all entries for proteins encoded by gene HPSE, but excluding variations like HPSE2 or HPSE_0.</td>
+</tr>
+<tr>
+<td>go</td>
+<td>go:0015629)</td>
+<td>Lists all entries associated with the GO term Actin cytoskeleton and any subclasses</td>
+</tr>
+<tr>
+<td>virus_host_name, virus_host_id</td>
+<td>virus_host_id:10090</td>
+<td>Lists all entries for viruses infecting Mus musculus (Mouse)</td>
+</tr>
+<tr>
+<td>accession_id</td>
+<td>accession_id:P00750</td>
+<td>Returns the entry with the primary accession number P00750.</td>
+</tr>
+<tr>
+<td>inchikey</td>
+<td>inchikey:WQZGKKKJIJFFOK-GASJEMHNSA-N</td>
+<td>Returns entries associated with the small molecule identified by the InChIKey WQZGKKKJIJFFOK-GASJEMHNSA-N, i.e. D-glucopyranose (see How can I search UniProt for chemical or reaction data?). To get the CHEBI identifier for an Inchikey value, one can now use the advanced search builder.</td>
+</tr>
+<tr>
+<td>protein_name</td>
+<td>protein_name:Anakinra</td>
+<td>Lists all entries whose protein name includes the "International Nonproprietary Name" is Anakinra.</td>
+</tr>
+<tr>
+<td>interactor</td>
+<td>interactor:P00520</td>
+<td>Lists all entries describing interactions with the protein described by entry P00520.</td>
+</tr>
+<tr>
+<td>keyword</td>
+<td><ol><li>keyword:toxin</li><li>keyword:KW-0800</li></ol></td>
+<td><ol><li>Lists all entries associated with a keyword matching "Toxin" in its name or description (UniProtKB Keywords).</li> <li>Lists all entries associated with the UniProtKB keyword Toxin.</li></ol></td>
+</tr>
+<tr>
+<td>length</td>
+<td>length:[500 TO 700]</td>
+<td>Lists all entries describing sequences of length between 500 and 700 residues.</td>
+</tr>
+<tr>
+<td>mass</td>
+<td>mass:[500000 TO *]</td>
+<td>Lists all entries describing sequences with a mass of at least 500,000 Da.</td>
+</tr>
+<tr>
+<td>cc_mass_spectrometry</td>
+<td>cc_mass_spectrometry:maldi</td>
+<td>Lists all entries for proteins identified by: matrix-assisted laser desorption/ionization (MALDI), crystallography (X-Ray). The <code>method</code> field searches names of physico-chemical identification methods in the 'Biophysicochemical properties' subsection of the 'Function' section, the 'Publications' and 'Cross-references' sections.</td>
+</tr>
+<tr>
+<td>date_modified</td>
+<td>modified:[2012-01-01 TO 2019-03-01] AND active:true</td>
+<td>Lists all active entries that were last modified between January and March 2019.</td>
+</tr>
+<tr>
+<td>protein_name</td>
+<td>protein_name:"prion protein"</td>
+<td>Lists all entries for prion proteins.</td>
+</tr>
+<tr>
+<td>organelle</td>
+<td>organelle:Mitochondrion</td>
+<td>Lists all entries for proteins encoded by a gene of the mitochondrial chromosome.</td>
+</tr>
+<tr>
+<td>organism_name, organism_id</td>
+<td><ol><li>organism_name:"Ovis aries"</li><li>organism_id:9940</li><li>organism_name:sheep</li></ol></td>
+<td>Lists all entries for proteins expressed in sheep (first 2 examples) and organisms whose name contains the term "sheep" (UniProt taxonomy).</td>
+</tr>
+<tr>
+<td>plasmid</td>
+<td>plasmid:ColE1</td>
+<td>Lists all entries for proteins encoded by a gene of plasmid ColE1 (Controlled vocabulary of plasmids).</td>
+</tr>
+<tr>
+<td>proteome</td>
+<td>proteome:UP000005640</td>
+<td>Lists all entries from the human proteome.</td>
+</tr>
+<tr>
+<td>proteomecomponent</td>
+<td>proteomecomponent:"chromosome 1" AND organism_id:9606</td>
+<td>Lists all entries from the human chromosome 1.</td>
+</tr>
+<tr>
+<td>sec_acc</td>
+<td>sec_acc:P02023</td>
+<td>Lists all entries that were created from a merge with entry P02023 (see FAQ).</td>
+</tr>
+<tr>
+<td>reviewed</td>
+<td>reviewed:true</td>
+<td>Lists all UniProtKB/Swiss-Prot entries (about UniProtKB).</td>
+</tr>
+<tr>
+<td>scope</td>
+<td>scope:mutagenesis</td>
+<td>Lists all entries containing a reference that was used to gather information about mutagenesis (Entry view: "Cited for", See 'Publications' section of the user manual).</td>
+</tr>
+<tr>
+<td>sec_acc</td>
+<td>sec_acc:P62988</td>
+<td>Lists all entries containing a secondary accession P62988.</td>
+</tr>
+<tr>
+<td>sequence</td>
+<td>accession:P05067-9 AND is_isoform:true</td>
+<td>Lists all entries containing a link to isoform 9 of the sequence described in entry P05067. Allows searching by specific sequence identifier.</td>
+</tr>
+<tr>
+<td>date_sequence_modified</td>
+<td><ol><li>date_sequence_modified:[2012-01-01 TO 2012-03-01]</li><li>date_sequence_modified:[2012-01-01 TO 2012-03-01]</li></ol></td>
+<td><ol><li>Lists all entries whose sequences were last modified between January and March 2012.</li><li>Lists all UniProtKB/Swiss-Prot entries whose sequences were modified after the start of 2012.</li></ol></td>
+</tr>
+<tr>
+<td>strain</td>
+<td>strain:wistar</td>
+<td>Lists all entries containing a reference relevant to strain wistar (Lists of strains in reference comments and Taxonomy help: organism strains).</td>
+</tr>
+<tr>
+<td>taxonomy_name, taxonomy_id</td>
+<td><ol><li>taxonomy_name:mammal</li><li>taxonomy_id:40674</li></ol></td>
+<td>Lists all entries for proteins expressed in Mammals. This field is used to retrieve entries for all organisms classified below a given taxonomic node (taxonomy classification).</td>
+</tr>
+<tr>
+<td>tissue</td>
+<td>tissue:liver</td>
+<td>Lists all entries containing a reference describing the protein sequence obtained from a clone isolated from liver (Controlled vocabulary of tissues).</td>
+</tr>
+<tr>
+<td>cc_webresource</td>
+<td>cc_webresource:wikipedia</td>
+<td>Lists all entries for proteins that are described in Wikipedia.</td>
+</tr>
+</tbody>
+</table>
- </td>
- </tr>
- <tr>
- <td>domain</td>
- <td><code> domain:VWFA </code></td>
- <td>Lists all entries with a Von Willebrand factor type A
- domain described in the 'Family and Domains' section.</td>
- </tr>
- <tr>
- <td>ec</td>
- <td><code> ec:3.2.1.23 </code></td>
- <td>Lists all beta-galactosidases.</td>
- </tr>
- <tr>
- <td>evidence</td>
- <td><code>
- annotation:(type:signal evidence:ECO_0000269)<br />
- (type:mod_res phosphoserine evidence:ECO_0000269)<br />
- annotation:(type:function AND evidence:ECO_0000255)
- </code></td>
- <td>Lists all entries with:
- <ul>
- <li>a signal sequence whose positions have been
- experimentally proven</li>
- <li>experimentally proven phosphoserine sites</li>
- <li>a function manually asserted according to rules</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>family</td>
- <td><code> family:serpin </code></td>
- <td>Lists all entries belonging to the Serpin family of
- proteins.</td>
- </tr>
- <tr>
- <td>fragment</td>
- <td><code> fragment:yes </code></td>
- <td>Lists all entries with an incomplete sequence.</td>
- </tr>
-
- <tr>
- <td>gene</td>
- <td><code> gene:HSPC233 </code></td>
- <td>Lists all entries for proteins encoded by gene HSPC233.</td>
- </tr>
- <tr>
- <td>go</td>
- <td><code>
- go:cytoskeleton <br /> go:0015629
- </code></td>
- <td>Lists all entries associated with:
- <ul>
- <li>a GO term containing the word "cytoskeleton"</li>
- <li>the GO term Actin cytoskeleton and any subclasses</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>host</td>
- <td><code>
- host:mouse <br /> host:10090 <br /> host:40674
- </code></td>
- <td>Lists all entries for viruses infecting:
- <ul>
- <li>organisms with a name containing the word "mouse"</li>
- <li>Mus musculus (Mouse)</li>
- <li>all mammals (all taxa classified under the taxonomy
- node for Mammalia)</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>id</td>
- <td><code>id:P00750</code></td>
- <td>Returns the entry with the primary accession number
- P00750.</td>
- </tr>
- <tr>
- <td>inn</td>
- <td><code> inn:Anakinra </code></td>
- <td>Lists all entries whose "International Nonproprietary
- Name" is Anakinra.</td>
- </tr>
- <tr>
- <td>interactor</td>
- <td><code> interactor:P00520 </code></td>
- <td>Lists all entries describing interactions with the
- protein described by entry P00520.</td>
- </tr>
- <tr>
- <td>keyword</td>
- <td><code> keyword:toxin </code></td>
- <td>Lists all entries associated with the keyword Toxin.</td>
- </tr>
- <tr>
- <td>length</td>
- <td><code> length:[500 TO 700] </code></td>
- <td>Lists all entries describing sequences of length between
- 500 and 700 residues.</td>
- </tr>
- <tr>
- <td>lineage</td>
- <td />
- <td>This field is a synonym for the field <code>taxonomy</code>.
- </td>
- </tr>
- <tr>
- <td>mass</td>
- <td><code> mass:[500000 TO *] </code></td>
- <td>Lists all entries describing sequences with a mass of at
- least 500,000 Da.</td>
- </tr>
- <tr>
- <td>method</td>
- <td><code>
- method:maldi <br /> method:xray
- </code></td>
- <td>Lists all entries for proteins identified by:
- matrix-assisted laser desorption/ionization (MALDI),
- crystallography (X-Ray). The <code>method</code> field searches
- names of physico-chemical identification methods in the
- 'Biophysicochemical properties' subsection of the 'Function'
- section, the 'Publications' and 'Cross-references' sections.
- </td>
- </tr>
- <tr>
- <td>mnemonic</td>
- <td><code> mnemonic:ATP6_HUMAN </code></td>
- <td>Lists all entries with entry name (ID) ATP6_HUMAN.
- Searches also obsolete entry names.</td>
- </tr>
- <tr>
- <td>modified</td>
- <td><code>
- modified:[20120101 TO 20120301]<br /> reviewed:yes AND
- modified:[current TO *]
- </code></td>
- <td>Lists all entries that were last modified between January
- and March 2012.<br /> Lists all UniProtKB/Swiss-Prot entries
- modified in the last release.
- </td>
- </tr>
- <tr>
- <td>name</td>
- <td><code> name:"prion protein" </code></td>
- <td>Lists all entries for prion proteins.</td>
- </tr>
- <tr>
- <td>organelle</td>
- <td><code> organelle:Mitochondrion </code></td>
- <td>Lists all entries for proteins encoded by a gene of the
- mitochondrial chromosome.</td>
- </tr>
- <tr>
- <td>organism</td>
- <td><code>
- organism:"Ovis aries" <br /> organism:9940 <br />
- organism:sheep <br />
- </code></td>
- <td>Lists all entries for proteins expressed in sheep (first
- 2 examples) and organisms whose name contains the term "sheep".
- </td>
- </tr>
-
- <tr>
- <td>plasmid</td>
- <td><code> plasmid:ColE1 </code></td>
- <td>Lists all entries for proteins encoded by a gene of
- plasmid ColE1.</td>
- </tr>
- <tr>
- <td>proteome</td>
- <td><code> proteome:UP000005640 </code></td>
- <td>Lists all entries from the human proteome.</td>
- </tr>
- <tr>
- <td>proteomecomponent</td>
- <td><code> proteomecomponent:"chromosome 1" and
- organism:9606 </code></td>
- <td>Lists all entries from the human chromosome 1.</td>
- </tr>
- <tr>
- <td>replaces</td>
- <td><code> replaces:P02023 </code></td>
- <td>Lists all entries that were created from a merge with
- entry P02023.</td>
- </tr>
- <tr>
- <td>reviewed</td>
- <td><code> reviewed:yes </code></td>
- <td>Lists all UniProtKB/Swiss-Prot entries.</td>
- </tr>
- <tr>
- <td>scope</td>
- <td><code> scope:mutagenesis </code></td>
- <td>Lists all entries containing a reference that was used to
- gather information about mutagenesis.</td>
- </tr>
- <tr>
- <td>sequence</td>
- <td><code> sequence:P05067-9 </code></td>
- <td>Lists all entries containing a link to isoform 9 of the
- sequence described in entry P05067. Allows searching by specific
- sequence identifier.</td>
- </tr>
- <tr>
- <td>sequence_modified</td>
- <td><code>
- sequence_modified:[20120101 TO 20120301]<br /> reviewed:yes
- AND sequence_modified:[current TO *]
- </code></td>
- <td>Lists all entries whose sequences were last modified
- between January and March 2012.<br /> Lists all
- UniProtKB/Swiss-Prot entries whose sequences were modified in
- the last release.
- </td>
- </tr>
- <tr>
- <td>source</td>
- <td><code> source:intact </code></td>
- <td>Lists all entries containing a GO term whose annotation
- source is the IntAct database.</td>
- </tr>
- <tr>
- <td>strain</td>
- <td><code> strain:wistar </code></td>
- <td>Lists all entries containing a reference relevant to
- strain wistar.</td>
- </tr>
- <tr>
- <td>taxonomy</td>
- <td><code> taxonomy:40674 </code></td>
- <td>Lists all entries for proteins expressed in Mammals. This
- field is used to retrieve entries for all organisms classified
- below a given taxonomic node taxonomy classification).</td>
- </tr>
- <tr>
- <td>tissue</td>
- <td><code> tissue:liver </code></td>
- <td>Lists all entries containing a reference describing the
- protein sequence obtained from a clone isolated from liver.</td>
- </tr>
- <tr>
- <td>web</td>
- <td><code> web:wikipedia </code></td>
- <td>Lists all entries for proteins that are described in
- Wikipedia.</td>
- </tr>
- </table>
</body>
-</html>
\ No newline at end of file
+</html>
git://source.jalview.org / jalview.git / blobdiff