X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Funiprotqueryfields.html;fp=help%2Fhelp%2Fhtml%2Ffeatures%2Funiprotqueryfields.html;h=66082f2bf81c9be4736e37e38ea1e50ff23a3874;hp=182b2061303ed113ac204cb3dab78a925d351b77;hb=b9b1f47cc74bbec8c28b75776e1d00c258215dfb;hpb=f07e07b4ab966a2f617a0f9b25ee9f94b92b5825 diff --git a/help/help/html/features/uniprotqueryfields.html b/help/help/html/features/uniprotqueryfields.html index 182b206..66082f2 100644 --- a/help/help/html/features/uniprotqueryfields.html +++ b/help/help/html/features/uniprotqueryfields.html @@ -33,359 +33,238 @@ syntax).

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
FieldExampleDescription
accessionaccession:P62988Lists all entries with the primary or secondary accession - number P62988.
activeactive:no Lists all obsolete entries.
annotation - annotation:(type:non-positional)
- annotation:(type:positional)
annotation:(type:mod_res - "Pyrrolidone carboxylic acid" evidence:experimental) - 		Lists all entries with: -
    -
  • any general annotation (comments [CC])
    • -
  • any sequence annotation (features [FT])
    • -
  • at least one amino acid modified with a Pyrrolidone - carboxylic acid group
    • -
-
author author:ashburner Lists all entries with at least one reference co-authored - by Michael Ashburner.
cdantigen cdantigen:CD233 Lists all entries whose cluster of differentiation number - is CD233.
citation - citation:("intracellular structural proteins")
- citation:(author:ashburner journal:nature) citation:9169874 - 		Lists all entries with a literature citation: -
    -
  • containing the phrase "intracellular structural - proteins" in either title or abstract
    • -
  • co-authored by Michael Ashburner and published in - Nature
    • -
  • with the PubMed identifier 9169874
    • -
-
cluster cluster:UniRef90_A5YMT3 Lists all entries in the UniRef 90% identity cluster - whose representative sequence is UniProtKB entry A5YMT3.
count - annotation:(type:transmem count:5)
- annotation:(type:transmem count:[5 TO *])
- annotation:(type:cofactor count:[3 TO *]) - 		Lists all entries with: -
    -
  • exactly 5 transmembrane regions
    • -
  • 5 or more transmembrane regions
    • -
  • 3 or more Cofactor comments
    • -
-
created - created:[20121001 TO *]
reviewed:yes AND - created:[current TO *] - 		Lists all entries created since October 1st 2012.
- Lists all new UniProtKB/Swiss-Prot entries in the last release. -
database - database:(type:pfam)
database:(type:pdb 1aut) - 		Lists all entries with: -
    -
  • a cross-reference to the Pfam database
    • -
  • a cross-reference to the PDB database entry 1aut
    • -
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
rest.uniprot.org fieldrest.uniprot.org exampleDescription
accessionaccession:P62988The 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 sec_acc field.
activeactive:falseLists all obsolete entries.
Refer to the page: Sequence AnnotationsLists all entries with:
  1. any general annotation (comments [CC])
  2. any sequence annotation (features [FT])
  3. at least one amino acid modified with a Pyrrolidone carboxylic acid group
lit_authorlit_author:ashburnerLists all entries with at least one reference co-authored by Michael Ashburner.
protein_nameprotein_name:CD233Lists all entries whose cluster of differentiation number is CD233 (see cdlist.txt).
chebichebi:18420Lists 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?).
uniprot_id (/uniref), then uniref_cluster_90 (/uniprotkb)
  1. uniprot_id:A5YMT3 to find cluster UniRef90_P00395
  2. uniref_cluster_90:UniRef90_P00395
Find all entries in the UniRef 90% identity cluster whose representative sequence is UniProtKB entry A5YMT3 (about UniRef).
xrefcount_pdb (or xref_count)xref_count_pdb:[20 TO *]Lists all entries with 20 or more cross-references to PDB
date_createddate_created:[2012-10-01 TO *]Lists all entries created since October 1st 2012.
database, xref
  1. database:pfam
  2. xref:pdb-1aut
Lists all entries with:
  1. a cross-reference to the Pfam database
  2. a cross-reference to the PDB database entry 1aut
(see Databases cross-referenced in UniProtKB and Database mapping)
ecec:3.2.1.23Lists all beta-galactosidases (Enzyme nomenclature database).
Refer to the pages: Comments or Sequence AnnotationsLists all entries with:
  1. a signal sequence whose positions have been experimentally proven
  2. experimentally proven phosphoserine sites
  3. a function manually asserted according to rules
(see Evidence attribution)
existenceexistence:3See Protein existence criteria.
familyfamily:serpinLists all entries belonging to the Serpin family of proteins (Index of protein domains and families).
fragmentfragment:trueLists all entries with an incomplete sequence.
genegene:HPSELists all entries for proteins encoded by gene HPSE, but also by HPSE2.
gene_exactgene_exact:HPSELists all entries for proteins encoded by gene HPSE, but excluding variations like HPSE2 or HPSE_0.
gogo:0015629)Lists all entries associated with the GO term Actin cytoskeleton and any subclasses
virus_host_name, virus_host_idvirus_host_id:10090Lists all entries for viruses infecting Mus musculus (Mouse)
accession_idaccession_id:P00750Returns the entry with the primary accession number P00750.
inchikeyinchikey:WQZGKKKJIJFFOK-GASJEMHNSA-NReturns 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.
protein_nameprotein_name:AnakinraLists all entries whose protein name includes the "International Nonproprietary Name" is Anakinra.
interactorinteractor:P00520Lists all entries describing interactions with the protein described by entry P00520.
keyword
  1. keyword:toxin
  2. keyword:KW-0800
  1. Lists all entries associated with a keyword matching "Toxin" in its name or description (UniProtKB Keywords).
  2. Lists all entries associated with the UniProtKB keyword Toxin.
lengthlength:[500 TO 700]Lists all entries describing sequences of length between 500 and 700 residues.
massmass:[500000 TO *]Lists all entries describing sequences with a mass of at least 500,000 Da.
cc_mass_spectrometrycc_mass_spectrometry:maldiLists all entries for proteins identified by: matrix-assisted laser desorption/ionization (MALDI), crystallography (X-Ray). The method field searches names of physico-chemical identification methods in the 'Biophysicochemical properties' subsection of the 'Function' section, the 'Publications' and 'Cross-references' sections.
date_modifiedmodified:[2012-01-01 TO 2019-03-01] AND active:trueLists all active entries that were last modified between January and March 2019.
protein_nameprotein_name:"prion protein"Lists all entries for prion proteins.
organelleorganelle:MitochondrionLists all entries for proteins encoded by a gene of the mitochondrial chromosome.
organism_name, organism_id
  1. organism_name:"Ovis aries"
  2. organism_id:9940
  3. organism_name:sheep
Lists all entries for proteins expressed in sheep (first 2 examples) and organisms whose name contains the term "sheep" (UniProt taxonomy).
plasmidplasmid:ColE1Lists all entries for proteins encoded by a gene of plasmid ColE1 (Controlled vocabulary of plasmids).
proteomeproteome:UP000005640Lists all entries from the human proteome.
proteomecomponentproteomecomponent:"chromosome 1" AND organism_id:9606Lists all entries from the human chromosome 1.
sec_accsec_acc:P02023Lists all entries that were created from a merge with entry P02023 (see FAQ).
reviewedreviewed:trueLists all UniProtKB/Swiss-Prot entries (about UniProtKB).
scopescope:mutagenesisLists all entries containing a reference that was used to gather information about mutagenesis (Entry view: "Cited for", See 'Publications' section of the user manual).
sec_accsec_acc:P62988Lists all entries containing a secondary accession P62988.
sequenceaccession:P05067-9 AND is_isoform:trueLists all entries containing a link to isoform 9 of the sequence described in entry P05067. Allows searching by specific sequence identifier.
date_sequence_modified
  1. date_sequence_modified:[2012-01-01 TO 2012-03-01]
  2. date_sequence_modified:[2012-01-01 TO 2012-03-01]
  1. Lists all entries whose sequences were last modified between January and March 2012.
  2. Lists all UniProtKB/Swiss-Prot entries whose sequences were modified after the start of 2012.
strainstrain:wistarLists all entries containing a reference relevant to strain wistar (Lists of strains in reference comments and Taxonomy help: organism strains).
taxonomy_name, taxonomy_id
  1. taxonomy_name:mammal
  2. taxonomy_id:40674
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).
tissuetissue:liverLists all entries containing a reference describing the protein sequence obtained from a clone isolated from liver (Controlled vocabulary of tissues).
cc_webresourcecc_webresource:wikipediaLists all entries for proteins that are described in Wikipedia.
-
domain domain:VWFA Lists all entries with a Von Willebrand factor type A - domain described in the 'Family and Domains' section.
ec ec:3.2.1.23 Lists all beta-galactosidases.
evidence - annotation:(type:signal evidence:ECO_0000269)
- (type:mod_res phosphoserine evidence:ECO_0000269)
- annotation:(type:function AND evidence:ECO_0000255) - 		Lists all entries with: -
    -
  • a signal sequence whose positions have been - experimentally proven
    • -
  • experimentally proven phosphoserine sites
    • -
  • a function manually asserted according to rules
    • -
-
family family:serpin Lists all entries belonging to the Serpin family of - proteins.
fragment fragment:yes Lists all entries with an incomplete sequence.
gene gene:HSPC233 Lists all entries for proteins encoded by gene HSPC233.
go - go:cytoskeleton
go:0015629 - 		Lists all entries associated with: -
    -
  • a GO term containing the word "cytoskeleton"
    • -
  • the GO term Actin cytoskeleton and any subclasses
    • -
-
host - host:mouse
host:10090
host:40674 - 		Lists all entries for viruses infecting: -
    -
  • organisms with a name containing the word "mouse"
    • -
  • Mus musculus (Mouse)
    • -
  • all mammals (all taxa classified under the taxonomy - node for Mammalia)
    • -
-
idid:P00750Returns the entry with the primary accession number - P00750.
inn inn:Anakinra Lists all entries whose "International Nonproprietary - Name" is Anakinra.
interactor interactor:P00520 Lists all entries describing interactions with the - protein described by entry P00520.
keyword keyword:toxin Lists all entries associated with the keyword Toxin.
length length:[500 TO 700] Lists all entries describing sequences of length between - 500 and 700 residues.
lineage - This field is a synonym for the field taxonomy. -
mass mass:[500000 TO *] Lists all entries describing sequences with a mass of at - least 500,000 Da.
method - method:maldi
method:xray - 		Lists all entries for proteins identified by: - matrix-assisted laser desorption/ionization (MALDI), - crystallography (X-Ray). The method field searches - names of physico-chemical identification methods in the - 'Biophysicochemical properties' subsection of the 'Function' - section, the 'Publications' and 'Cross-references' sections. -
mnemonic mnemonic:ATP6_HUMAN Lists all entries with entry name (ID) ATP6_HUMAN. - Searches also obsolete entry names.
modified - modified:[20120101 TO 20120301]
reviewed:yes AND - modified:[current TO *] - 		Lists all entries that were last modified between January - and March 2012.
Lists all UniProtKB/Swiss-Prot entries - modified in the last release. -
name name:"prion protein" Lists all entries for prion proteins.
organelle organelle:Mitochondrion Lists all entries for proteins encoded by a gene of the - mitochondrial chromosome.
organism - organism:"Ovis aries"
organism:9940
- organism:sheep
- 		Lists all entries for proteins expressed in sheep (first - 2 examples) and organisms whose name contains the term "sheep". -
plasmid plasmid:ColE1 Lists all entries for proteins encoded by a gene of - plasmid ColE1.
proteome proteome:UP000005640 Lists all entries from the human proteome.
proteomecomponent proteomecomponent:"chromosome 1" and - organism:9606 Lists all entries from the human chromosome 1.
replaces replaces:P02023 Lists all entries that were created from a merge with - entry P02023.
reviewed reviewed:yes Lists all UniProtKB/Swiss-Prot entries.
scope scope:mutagenesis Lists all entries containing a reference that was used to - gather information about mutagenesis.
sequence sequence:P05067-9 Lists all entries containing a link to isoform 9 of the - sequence described in entry P05067. Allows searching by specific - sequence identifier.
sequence_modified - sequence_modified:[20120101 TO 20120301]
reviewed:yes - AND sequence_modified:[current TO *] - 		Lists all entries whose sequences were last modified - between January and March 2012.
Lists all - UniProtKB/Swiss-Prot entries whose sequences were modified in - the last release. -
source source:intact Lists all entries containing a GO term whose annotation - source is the IntAct database.
strain strain:wistar Lists all entries containing a reference relevant to - strain wistar.
taxonomy taxonomy:40674 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).
tissue tissue:liver Lists all entries containing a reference describing the - protein sequence obtained from a clone isolated from liver.
web web:wikipedia Lists all entries for proteins that are described in - Wikipedia.
- \ No newline at end of file +