Annotation types & information

The Annotations platform hosts annotations of different types, e.g. Genes, Chemicals, Diseases, etc. For the full list, see the "Annotation types & information" section of Europe PMC About SciLite annotations page.

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
    }
  }