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Europe PMC Annotations API

Europe PMC Annotations API provides text mining annotations contained in abstracts and open access full text articles, using the W3C Open Annotation Data Model

Created by
Europe PMC

We advise that you read our Privacy Notice before using this API. By using our public API you agree to accept the terms of the Europe PMC website Privacy Notice.

Annotation types and sources

The Annotations platform hosts annotations from various providers, covering different annotation types (e.g. Named entities and relationships). The table below lists the types of annotations and the corresponding providers.

Named Entities (Accessions, Genes/Proteins, Chemicals, Organisms, Diseases, Gene Ontology, Resources, Experimental Methods) Gene Mutations Gene-Disease relationships Gene Functional annotations, COVoc accession numbers Protein-protein interaction Transcription factor - Target gene relationships Biological event (Phosphosrylation events) Cells, Cell Lines, Clinical Drugs, Sequences, Molecular Processes, Organ Tissues Cells, Phenotypes, Molecules, Anatomy, Pathways Sample-Material, Body-Site, Host, State, Site, Place, Date, Engineered, Ecoregion, Treatment, Kit, Primer, Gene, LS, LCM, Sequencing
Europe PMC
HES-SO/SIB
DisGeNET
Open Targets Platform
IntAct
NaCTEM
PubTator (NCBI)
ExTRI(NTNU/CNIO/BSC)
OntoGene
PheneBank
Metagenomics (EMERALD)

If you are a text-mining group and can supply annotations in the format we require read here

JSON-LD Annotations format

This paragraph describes details on providing annotations data as JSON-LD. JSON-LD (JSON for Linking Data) is a variant of JSON that enables linking data from different resources. For more details on JSON-LD refer to the following links: JSON-LD definition and JSON-LD syntax.

The annotations are modelled in the Web Annotations Data Model (OA). For more details on the OA model, refer to the following links: OA definition and OA vocabulary.

To represent annotations as JSON-LD a context must be provided (represented by the keyword @context in JSON-LD). The context allows applications to interpret the data being exchanged (using a set of URIs linking to various terms in specified vocabularies and ontologies). For the the purpose of Annotation API, the context file can be found here.

According to the type of annotations there are different types of JSON-LD representations:

  • Named entities annotations (i.e. provided by Europe PMC)
    {
       "@context": "http://europepmc.org/docs/europepmc-annotation-api-vocab.json", # context file
       "id": "http://europepmc.org/article/MED/21494379#europepmc_1-1", # annotation link back
       "type": "Annotation",
       "creator": "europepmc", # provider
       "body": "http://purl.obolibrary.org/obo/CHEBI_29228", # uri of the tagged database entity
       "target": {
          "id": "http://europepmc.org/article/MED/21494379#europepmc_1-1", # annotation link back
          "source": "http://europepmc.org/article/MED/21494379", # article page url
          "isPartOf": "Title", # section of the article where the annotation appears
          "selector": {
             "type": "TextQuoteSelector",
             "exact": "Fluoride", # text of the annotation inside the article
             "prefix": "", # prefix of the annotation inside the article
             "suffix": " concentration of some brands of ferment" # suffix of the annotation inside the article
          }
       }
    }
    
  • Sentence based annotations (i.e. provided by HES-SO / SIB Text Mining for Elixir, NaCTeM, IntAct)
    {
       "@context": "http://europepmc.org/docs/europepmc-annotation-api-vocab.json", # context file
       "id": "http://europepmc.org/abstract/MED/15892892#geneRif_356408_P36159", # annotation link back
       "type": "Annotation",
       "creator": "HES-SO / SIB Text Mining for Elixir", # provider
       "target": "http://purl.uniprot.org/uniprot/P36159", # uri of the tagged database entity
       "body": {
          "id": "http://europepmc.org/abstract/MED/15892892#geneRif_356408_P36159", # annotation link back
          "type": "TextualBody",
          "value": "In this work, we show that the yeast homolog of ELAC2, encoded by TRZ1 (tRNase Z 1), is involved genetically in RNA processing.", # text of the annotation inside the article
          "source": "http://europepmc.org/article/MED/15892892", # article page url
          "isPartOf": "Abstract" # section of the article where the annotation appears
       }
    }
    
  • Annotations containing Gene Disease relationships (i.e. provided by Open Targets Platform and DisGeNET)
    {
       "@context": "http://europepmc.org/docs/europepmc-annotation-api-vocab.json", # context file
       "id": "http://europepmc.org/articles/PMC3691765#openTargets_1563_Q14790_EFO_0001668", # annotation link back
       "type": "Annotation",
       "creator": "OpenTargets", # provider
       "target": {
          "type": "List",
          "items": [ { "id": "http://purl.uniprot.org/uniprot/Q14790", "label": "caspase 8" }, { "id": "http://www.ebi.ac.uk/efo/EFO_0001668", "label": "HPV" } ] # uri of the tagged database entities
       },
       "body": {
          "id": "http://europepmc.org/articles/PMC3691765#openTargets_1563_Q14790_EFO_0001668", # annotation link back
          "type": "TextualBody",
          "value": "caspase 8 (HPV" ,# text of the annotation inside the article
          "source": "http://europepmc.org/articles/PMC3691765", # article page url
          "isPartOf": "Table" # section of the article where the annotation appears
       }
    }