neXtProt - The knowledge resource on human proteins

This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project

See: https://www.nextprot.org/

neXtprot advanced search example queries

Example queries for neXtProt advanced searches (SPARQL).

Naming convention

For queries to be published, use:

NXQ_nnnnn.rq where nnnnn is a five digit number

For queries used internally or which need further validation, use:

NXQ_nnnnn.rq.unpub

File content structure

The file contains meta-information fields followed by the SPARQL query itself. The meta-inoformation fields are:

• #id: identifies the query (should correspond to file name without extension)
• #title: english free text translation of the SPARQL query
• #comment: useful info about query (multiple lines prefixed with #comment are allowed)
• #tags: a list of comma separated categories for classifying & searching queries
  • add tag snorql-only for queries not returning protein entries
• #acs: a sample of uniprot style protein accession codes returned by the query
• #count: the count of entries returned by the query (approximative)

Example:

#id:NXQ_00001
#title:Proteins phosphorylated and located in the cytoplasm
#comment:In this query we use the keyword "Phosphorylation" (KW-0597) and the UniProt subcellur location ontology term "Cytoplasm" (SL-0886).
#comment:Using the "childOf" allows to select for subcellular locations that are, in that ontology, children of cytoplasm like for example "Cell cortex".
#tags:subcellular location,cellular component,PTM,phosphorylation
#acs:A1A4S6,A1KZ92,A1L020
#count:3680
select distinct ?entry where {
  ?entry :isoform ?iso.
  ?iso :keyword / :term cv:KW-0597.
  ?iso :cellularComponent /:term /:childOf cv:SL-0086.
}