X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Funiprotqueryfields.html;h=182b2061303ed113ac204cb3dab78a925d351b77;hb=dde303bc73617ab4eb3e681e67cf899e6a971318;hp=eaee3087cb0e305dde41beaf8a73918e286ccd93;hpb=528c0f1815bc67b54618ad5b16c2162946974caf;p=jalview.git diff --git a/help/html/features/uniprotqueryfields.html b/help/html/features/uniprotqueryfields.html index eaee308..182b206 100644 --- a/help/html/features/uniprotqueryfields.html +++ b/help/html/features/uniprotqueryfields.html @@ -33,571 +33,359 @@ syntax).

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
FieldExampleDescription
accession - accession:P62988 - - Lists all entries with the primary or secondary - accession number P62988. -
active - active: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.
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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
    • -
- -
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. -
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
    • +
-
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)
    • -
-
id - id:P00750 - - Returns 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. -
+
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.
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