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Controlled vocabulary

Last modified September 11, 2015

Journals (citations/publications)

The Controlled vocabulary of journals lists the journal abbreviations used in UniProtKB/Swiss-Prot. The abbreviations are those proposed by the ISO (International Organization for Standardization) and they generally correspond to those used by the National Library of Medicine (NLM) in PubMed.

UniProtKB/Swiss-Prot document: Controlled vocabulary of journals
UniProt web page: Literature citations
User manual: References

What journal abbreviations are used in UniProtKB?
On what basis are literature references inserted in UniProtKB/Swiss-Prot entries?

Keywords

The Controlled vocabulary of keywords lists the keywords and keyword categories used in the UniProt knowledgebase (Swiss-Prot and TrEMBL).

UniProtKB/Swiss-Prot document: Controlled vocabulary of keywords
UniProt web page: Keywords
User manual: Keywords

What are the differences between UniProtKB keywords and the GO terms?

Subcellular locations

The Controlled vocabulary of subcellular locations and membrane topologies and orientations lists the UniProtKB controlled vocabulary used for the subcellular locations (including the membrane topologies and orientations terms) in the ‘Subcellular location’ section.

UniProtKB/Swiss-Prot document: Controlled vocabulary of subcellular locations and membrane topologies and orientations
User manual: Subcellular location
UniProt web page: Subcellular locations

Pathways

The Controlled vocabulary of metabolic pathways lists the UniProtKB controlled vocabulary used for the subsection ‘Pathway’ of the ‘Function’ section. It provides definitions of the terms as well as other relevant information for UniPathway concepts (pathway, sub-pathway, enzymatic reaction (step))

UniProtKB/Swiss-Prot document: Controlled vocabulary of metabolic pathways
UniProtKB/Swiss-Prot document: Index of metabolic and biosynthesis pathways

User manual: Pathway

Plasmids

The Controlled vocabulary of plasmids lists the currently valid values for the plasmids cited in the Encoded on subsection of the ‘Names and origin’ section and in the Reference section of UniProtKB/Swiss-Prot entries.

UniProtKB/Swiss-Prot document: Controlled vocabulary of plasmids
User manual: Encoded on

Post-translational modifications

The Controlled vocabulary of posttranslational modifications lists the posttranslational modifications (PTM) used in the sequence annotation section of the UniProt knowledgebase (Swiss-Prot and TrEMBL). Additional information such as amino acid target, subcellular location, monoisotopic mass difference, average mass difference, taxonomic range, corresponding keyword etc. are listed when available.

UniProtKB/Swiss-Prot document: Controlled vocabulary of posttranslational modifications

How are protein sequence variety and protein diversity represented in UniProtKB?

Taxonomy

Species

The Controlled vocabulary of species contains two sublists: the Real organism codes, which are used in both UniProtKB/Swiss-Prot and UniProtKB/TrEMBL and which correspond to a specific and specified organism; the Virtual organism codes that regroup organisms at a certain taxonomic level. They generally correspond to a ‘pool’ of organisms and are used only in UniProtKB/TrEMBL.

UniProtKB/Swiss-Prot document: Controlled vocabulary of species
UniProt web page: Taxonomy

Strains

The Controlled vocabulary of strains lists the most frequently occurring values for the ‘Strain’ topic in the Reference section of UniProtKB/Swiss-Prot entries.

UniProtKB/Swiss-Prot document: Controlled vocabulary of strains
UniProt web page: Taxonomy/strains

Tissues

The Controlled vocabulary of tissues lists the currently valid values and their synomym(s) for the tissues cited in the Reference section of UniProtKB/Swiss-Prot entries.

UniProtKB/Swiss-Prot document: Controlled vocabulary of tissues

Human diseases

The Controlled vocabulary of human diseases lists the controlled vocabulary that is used for the annotation of human diseases in UniProtKB/Swiss-Prot. Each record in this file consists of a disease identifier, acronym, and description, as well as known disease synonyms, links to OMIM, Medical Subject Headings (MeSH) and associated UniProtKB keywords.

UniProt web page: Human diseases
UniProtKB/Swiss-Prot document: Controlled vocabulary of human diseases
Related keyword: Disease mutation
Relevant UniProtKB/Swiss-Prot entries cross-referenced to the OMIM database

How can I get all the proteins involved in a given disease?
How can I get medical advice from UniProtKB?

Extracellular domains

The document: Nomenclature of extracellular domains lists the nomenclature proposal for domains (or modules) found mainly in extracellular proteins of higher eukaryotes. These domains are described in the ‘Sequence annotation’ section of entries.

UniProtKB/Swiss-Prot document: Nomenclature of extracellular domains