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 />
+ <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>
-
- </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>
+ </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>
- <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>
+ </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>
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git://source.jalview.org / jalview.git / blobdiff