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
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:
{ "@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 } } }
{ "@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 } }
{ "@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 } }