Evidence & citations

Every UniProt annotation can be backed by evidence: a statement that says why the annotation is trusted - usually a literature citation, sometimes a curator’s own judgement, sometimes an automated pipeline. This page shows how that evidence is modeled in RDF, and how to query it.

UniProt records this with the standard RDF reification pattern: instead of attaching evidence directly to a triple (which isn’t possible - RDF triples aren’t things you can point to), UniProt creates an rdf:Statement resource that describes the triple (rdf:subject/rdf:predicate/rdf:object), and attaches an up:Attribution to that. The attribution links to the up:source (typically a up:Journal_Citation) and, often, an up:evidence code from the Evidence & Conclusion Ontology (ECO).

Evidence tags on an annotation

base <http://purl.uniprot.org/uniprot/>
prefix up: <http://purl.uniprot.org/core/>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix citations: <http://purl.uniprot.org/citations/>
prefix attribution: <http://purl.uniprot.org/attribution/>
prefix ECO: <http://purl.obolibrary.org/obo/ECO_>

<P99999> a up:Protein ;
  up:annotation <P99999#VAR_001>, <P99999#FUNC_001> .

<P99999#VAR_001> a up:Natural_Variant_Annotation .

<P99999#FUNC_001> a up:Function_Annotation .

# The reified statement: "<P99999> up:annotation <P99999#VAR_001>" is itself
# a resource here, so we can attach an up:attribution to it.
_:linkVar a rdf:Statement ;
  rdf:subject <P99999> ;
  rdf:predicate up:annotation ;
  rdf:object <P99999#VAR_001> ;
  up:attribution attribution:VAR_ATT_1 .

_:linkFunc a rdf:Statement ;
  rdf:subject <P99999> ;
  rdf:predicate up:annotation ;
  rdf:object <P99999#FUNC_001> ;
  up:attribution attribution:FUNC_ATT_1 .

attribution:VAR_ATT_1 a up:Attribution ;
  up:source citations:12345678 ;
  up:evidence ECO:0000269 .

attribution:FUNC_ATT_1 a up:Attribution ;
  up:source citations:12345678 ;
  up:evidence ECO:0000305 .

citations:12345678 a up:Journal_Citation .

Find natural variant annotations linked to a PubMed article

Adapted from sparql-examples #19: find all natural variant annotations that are, via an evidence tag, associated with an article that has a PubMed identifier.

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX up: <http://purl.uniprot.org/core/>

SELECT
    ?accession
    ?annotation_acc
    ?pubmed
WHERE
{
        ?protein a up:Protein ;
            up:annotation ?annotation .
        ?annotation a up:Natural_Variant_Annotation .
        ?linkToEvidence rdf:object ?annotation ;
                        up:attribution ?attribution .
        ?attribution up:source ?source .
        ?source a up:Journal_Citation .
  BIND(SUBSTR(STR(?protein),33) AS ?accession)
  BIND(IF(CONTAINS(STR(?annotation), "#SIP"), SUBSTR(STR(?annotation),33), SUBSTR(STR(?annotation),36))AS?annotation_acc)
  BIND(SUBSTR(STR(?source),35) AS ?pubmed)
}

How often is a citation used across evidence tags?

Adapted from sparql-examples #20 (the original restricts to human proteins; that restriction is dropped here since this toy dataset only has one protein).

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX up: <http://purl.uniprot.org/core/>

SELECT
    ?source
    (COUNT(?attribution) AS ?attributions)
WHERE
{
        ?protein a up:Protein ;
            up:annotation ?annotation .
        ?linkToEvidence rdf:object ?annotation ;
                        up:attribution ?attribution .
        ?attribution up:source ?source .
        ?source a up:Journal_Citation .
} GROUP BY ?source ORDER BY DESC(COUNT(?attribution))

Illustrative: which ECO evidence code backs each annotation?

(Hand-written for this page - sparql-examples doesn’t currently have a dedicated example selecting up:evidence directly, only up:source.)

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX up: <http://purl.uniprot.org/core/>

SELECT ?annotation ?evidenceCode ?source
WHERE {
  ?linkToEvidence rdf:object ?annotation ;
                  up:attribution ?attribution .
  ?attribution up:evidence ?evidenceCode ;
               up:source ?source .
}
ORDER BY ?annotation

Protein existence: how well-characterized is an entry?

Separately from evidence on individual annotations, every UniProt entry has one overall up:existence value - a coarse confidence level for the existence of the protein itself, from direct protein-level evidence down to purely computational prediction.

base <http://purl.uniprot.org/uniprot/>
prefix up: <http://purl.uniprot.org/core/>

<P10001> a up:Protein ; up:reviewed true ; up:existence up:Evidence_at_Protein_Level_Existence .
<P10002> a up:Protein ; up:reviewed true ; up:existence up:Evidence_at_Protein_Level_Existence .
<P10003> a up:Protein ; up:reviewed true ; up:existence up:Evidence_at_Transcript_Level_Existence .
<P10004> a up:Protein ; up:reviewed true ; up:existence up:Inferred_from_Homology_Existence .
<P10005> a up:Protein ; up:reviewed true ; up:existence up:Predicted_Existence .

Break down reviewed proteins by existence evidence level

Adapted from sparql-examples #216 (the original restricts to human, taxon:9606; dropped here since our toy proteins have no organism).

PREFIX up: <http://purl.uniprot.org/core/>

SELECT
  ?existence
  (COUNT(*) AS ?proteinCount)
WHERE {
  ?protein a up:Protein ;
    up:reviewed true ;
    up:existence ?existence .
}
GROUP BY ?existence
ORDER BY DESC(?proteinCount)

Citation statements: what scope was a citation used for?

A protein can cite the same article for several different reasons - one citation might document the original sequence determination, another mention might document a specific disease variant. UniProt records the plain triple <protein> up:citation <citation> for direct traversal, and separately reifies that same triple as an up:Citation_Statement so it can attach a up:scope to the specific citation relationship, not to the citation as a whole.

base <http://purl.uniprot.org/uniprot/>
prefix up: <http://purl.uniprot.org/core/>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix citations: <http://purl.uniprot.org/citations/>

<P99999> up:citation citations:12345678, citations:87654321 .

_:stmt1 a up:Citation_Statement ;
  rdf:subject <P99999> ;
  rdf:predicate up:citation ;
  rdf:object citations:12345678 ;
  up:scope "Disease variant p.Arg273His" .

_:stmt2 a up:Citation_Statement ;
  rdf:subject <P99999> ;
  rdf:predicate up:citation ;
  rdf:object citations:87654321 ;
  up:scope "Sequence determination" .

Find what a citation was used for

Adapted from sparql-examples #158 (originally run against human insulin, P01308; here against the toy protein P99999).

PREFIX up: <http://purl.uniprot.org/core/>
PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

SELECT
  DISTINCT
    ?citation
    ?scope
WHERE {
  ?statement a up:Citation_Statement ;
    rdf:subject uniprotkb:P99999 ;
    rdf:predicate up:citation ;
    rdf:object ?citation ;
    up:scope ?scope .
}