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Europe PMC Annotations API provides text mining annotations contained in abstracts and open access full text articles, using the W3C Open Annotation Data Model
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.
List of annotations in JSON-LD format. It is only populated when the format parameter is equal to JSON-LD. To see details about JSON-LD go to http://europepmc.org/AnnotationsApi#jsonLD
,
articles (Array[ArticleResult], optional):
List of articles with the relative annotations. It is only populated when the format parameter is equal to either JSON or XML or ID_LIST
} AnnotationJsonLDDoc {
@context (string, optional):
JSON-LD context file
,
body (string, optional):
For named entity annotations (i.e. provided by Europe PMC) it represents the URI of the database resource the annotation is referring to. For sentence based annotations (i.e. provided by HES-SO / SIB Text Mining for Elixir, NaCTeM, IntAct) and annotations containing Gene Disease relationships (i.e. provided by Open Targets Platform and DisGeNET) it represents the portion of the article where the annotation is contained: "body": { "id": "http://europepmc.org/abstract/MED/15892892#geneRif_356408_P36159", # ann_link "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.", # exact "source": "http://europepmc.org/articles/MED/15892892", # ext_id "isPartOf": "Abstract" #section }
,
creator (string, optional):
Provider of the annotation
,
id (string, optional):
Link back to the specific sentence of the article that contains the annotation
,
memberOf (string, optional):
Field populated only for accession numbers or resource names annotations. It indicates the database name the annotations are belonging to.
,
target (string, optional):
For named entity annotations (i.e. provided by Europe PMC) it represents the portion of the article where the annotation is contained: "target": { "id": "http://europepmc.org/articles/MED/21494379#europepmc_1-1", # ann_link "source": "http://europepmc.org/articles/MED/21494379", # ext_id "isPartOf": "Title", # section "selector": { "type": "TextQuoteSelector", "exact": "Fluoride", "prefix": "", "suffix": " concentration of some brands of ferment" } }. For sentence based annotations (i.e. provided by HES-SO / SIB Text Mining for Elixir, NaCTeM, IntAct) it represents the URI of the database resource the annotation is referring to. For annotations containing Gene Disease relationships (i.e. provided by Open Targets Platform and DisGeNET) represents the URI of both gene and disease the annotation is referring to : "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" } ] # tags }.
,
type (string, optional):
Type of the resource
} ArticleResult {
annotations (Array[Annotation], optional):
Annotations contained in this article
,
extId (string, optional):
Identifier of the article connected with the domain specified by the source field (i.e. if SOURCE=MED it will be the PubMed ID or if SOURCE=PMC it will be a number representing the pmcid)
List of annotations in JSON-LD format. It is only populated when the format parameter is equal to JSON-LD. To see details about JSON-LD go to http://europepmc.org/AnnotationsApi#jsonLD
,
articles (Array[ArticleResult], optional):
List of articles with the relative annotations. It is only populated when the format parameter is equal to either JSON or XML or ID_LIST
,
cursorMark (number, optional):
CursorMark used in the current call to get the current page of the result set
,
nextCursorMark (number, optional):
CursorMark to be used in the next call to get the next page of the result set
} AnnotationJsonLDDoc {
@context (string, optional):
JSON-LD context file
,
body (string, optional):
For named entity annotations (i.e. provided by Europe PMC) it represents the URI of the database resource the annotation is referring to. For sentence based annotations (i.e. provided by HES-SO / SIB Text Mining for Elixir, NaCTeM, IntAct) and annotations containing Gene Disease relationships (i.e. provided by Open Targets Platform and DisGeNET) it represents the portion of the article where the annotation is contained: "body": { "id": "http://europepmc.org/abstract/MED/15892892#geneRif_356408_P36159", # ann_link "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.", # exact "source": "http://europepmc.org/articles/MED/15892892", # ext_id "isPartOf": "Abstract" #section }
,
creator (string, optional):
Provider of the annotation
,
id (string, optional):
Link back to the specific sentence of the article that contains the annotation
,
memberOf (string, optional):
Field populated only for accession numbers or resource names annotations. It indicates the database name the annotations are belonging to.
,
target (string, optional):
For named entity annotations (i.e. provided by Europe PMC) it represents the portion of the article where the annotation is contained: "target": { "id": "http://europepmc.org/articles/MED/21494379#europepmc_1-1", # ann_link "source": "http://europepmc.org/articles/MED/21494379", # ext_id "isPartOf": "Title", # section "selector": { "type": "TextQuoteSelector", "exact": "Fluoride", "prefix": "", "suffix": " concentration of some brands of ferment" } }. For sentence based annotations (i.e. provided by HES-SO / SIB Text Mining for Elixir, NaCTeM, IntAct) it represents the URI of the database resource the annotation is referring to. For annotations containing Gene Disease relationships (i.e. provided by Open Targets Platform and DisGeNET) represents the URI of both gene and disease the annotation is referring to : "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" } ] # tags }.
,
type (string, optional):
Type of the resource
} ArticleResult {
annotations (Array[Annotation], optional):
Annotations contained in this article
,
extId (string, optional):
Identifier of the article connected with the domain specified by the source field (i.e. if SOURCE=MED it will be the PubMed ID or if SOURCE=PMC it will be a number representing the pmcid)
List of annotations in JSON-LD format. It is only populated when the format parameter is equal to JSON-LD. To see details about JSON-LD go to http://europepmc.org/AnnotationsApi#jsonLD
,
articles (Array[ArticleResult], optional):
List of articles with the relative annotations. It is only populated when the format parameter is equal to either JSON or XML or ID_LIST
,
cursorMark (number, optional):
CursorMark used in the current call to get the current page of the result set
,
nextCursorMark (number, optional):
CursorMark to be used in the next call to get the next page of the result set
} AnnotationJsonLDDoc {
@context (string, optional):
JSON-LD context file
,
body (string, optional):
For named entity annotations (i.e. provided by Europe PMC) it represents the URI of the database resource the annotation is referring to. For sentence based annotations (i.e. provided by HES-SO / SIB Text Mining for Elixir, NaCTeM, IntAct) and annotations containing Gene Disease relationships (i.e. provided by Open Targets Platform and DisGeNET) it represents the portion of the article where the annotation is contained: "body": { "id": "http://europepmc.org/abstract/MED/15892892#geneRif_356408_P36159", # ann_link "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.", # exact "source": "http://europepmc.org/articles/MED/15892892", # ext_id "isPartOf": "Abstract" #section }
,
creator (string, optional):
Provider of the annotation
,
id (string, optional):
Link back to the specific sentence of the article that contains the annotation
,
memberOf (string, optional):
Field populated only for accession numbers or resource names annotations. It indicates the database name the annotations are belonging to.
,
target (string, optional):
For named entity annotations (i.e. provided by Europe PMC) it represents the portion of the article where the annotation is contained: "target": { "id": "http://europepmc.org/articles/MED/21494379#europepmc_1-1", # ann_link "source": "http://europepmc.org/articles/MED/21494379", # ext_id "isPartOf": "Title", # section "selector": { "type": "TextQuoteSelector", "exact": "Fluoride", "prefix": "", "suffix": " concentration of some brands of ferment" } }. For sentence based annotations (i.e. provided by HES-SO / SIB Text Mining for Elixir, NaCTeM, IntAct) it represents the URI of the database resource the annotation is referring to. For annotations containing Gene Disease relationships (i.e. provided by Open Targets Platform and DisGeNET) represents the URI of both gene and disease the annotation is referring to : "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" } ] # tags }.
,
type (string, optional):
Type of the resource
} ArticleResult {
annotations (Array[Annotation], optional):
Annotations contained in this article
,
extId (string, optional):
Identifier of the article connected with the domain specified by the source field (i.e. if SOURCE=MED it will be the PubMed ID or if SOURCE=PMC it will be a number representing the pmcid)
List of annotations in JSON-LD format. It is only populated when the format parameter is equal to JSON-LD. To see details about JSON-LD go to http://europepmc.org/AnnotationsApi#jsonLD
,
articles (Array[ArticleResult], optional):
List of articles with the relative annotations. It is only populated when the format parameter is equal to either JSON or XML or ID_LIST
,
cursorMark (number, optional):
CursorMark used in the current call to get the current page of the result set
,
nextCursorMark (number, optional):
CursorMark to be used in the next call to get the next page of the result set
} AnnotationJsonLDDoc {
@context (string, optional):
JSON-LD context file
,
body (string, optional):
For named entity annotations (i.e. provided by Europe PMC) it represents the URI of the database resource the annotation is referring to. For sentence based annotations (i.e. provided by HES-SO / SIB Text Mining for Elixir, NaCTeM, IntAct) and annotations containing Gene Disease relationships (i.e. provided by Open Targets Platform and DisGeNET) it represents the portion of the article where the annotation is contained: "body": { "id": "http://europepmc.org/abstract/MED/15892892#geneRif_356408_P36159", # ann_link "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.", # exact "source": "http://europepmc.org/articles/MED/15892892", # ext_id "isPartOf": "Abstract" #section }
,
creator (string, optional):
Provider of the annotation
,
id (string, optional):
Link back to the specific sentence of the article that contains the annotation
,
memberOf (string, optional):
Field populated only for accession numbers or resource names annotations. It indicates the database name the annotations are belonging to.
,
target (string, optional):
For named entity annotations (i.e. provided by Europe PMC) it represents the portion of the article where the annotation is contained: "target": { "id": "http://europepmc.org/articles/MED/21494379#europepmc_1-1", # ann_link "source": "http://europepmc.org/articles/MED/21494379", # ext_id "isPartOf": "Title", # section "selector": { "type": "TextQuoteSelector", "exact": "Fluoride", "prefix": "", "suffix": " concentration of some brands of ferment" } }. For sentence based annotations (i.e. provided by HES-SO / SIB Text Mining for Elixir, NaCTeM, IntAct) it represents the URI of the database resource the annotation is referring to. For annotations containing Gene Disease relationships (i.e. provided by Open Targets Platform and DisGeNET) represents the URI of both gene and disease the annotation is referring to : "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" } ] # tags }.
,
type (string, optional):
Type of the resource
} ArticleResult {
annotations (Array[Annotation], optional):
Annotations contained in this article
,
extId (string, optional):
Identifier of the article connected with the domain specified by the source field (i.e. if SOURCE=MED it will be the PubMed ID or if SOURCE=PMC it will be a number representing the pmcid)
List of annotations in JSON-LD format. It is only populated when the format parameter is equal to JSON-LD. To see details about JSON-LD go to http://europepmc.org/AnnotationsApi#jsonLD
,
articles (Array[ArticleResult], optional):
List of articles with the relative annotations. It is only populated when the format parameter is equal to either JSON or XML or ID_LIST
,
cursorMark (number, optional):
CursorMark used in the current call to get the current page of the result set
,
nextCursorMark (number, optional):
CursorMark to be used in the next call to get the next page of the result set
} AnnotationJsonLDDoc {
@context (string, optional):
JSON-LD context file
,
body (string, optional):
For named entity annotations (i.e. provided by Europe PMC) it represents the URI of the database resource the annotation is referring to. For sentence based annotations (i.e. provided by HES-SO / SIB Text Mining for Elixir, NaCTeM, IntAct) and annotations containing Gene Disease relationships (i.e. provided by Open Targets Platform and DisGeNET) it represents the portion of the article where the annotation is contained: "body": { "id": "http://europepmc.org/abstract/MED/15892892#geneRif_356408_P36159", # ann_link "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.", # exact "source": "http://europepmc.org/articles/MED/15892892", # ext_id "isPartOf": "Abstract" #section }
,
creator (string, optional):
Provider of the annotation
,
id (string, optional):
Link back to the specific sentence of the article that contains the annotation
,
memberOf (string, optional):
Field populated only for accession numbers or resource names annotations. It indicates the database name the annotations are belonging to.
,
target (string, optional):
For named entity annotations (i.e. provided by Europe PMC) it represents the portion of the article where the annotation is contained: "target": { "id": "http://europepmc.org/articles/MED/21494379#europepmc_1-1", # ann_link "source": "http://europepmc.org/articles/MED/21494379", # ext_id "isPartOf": "Title", # section "selector": { "type": "TextQuoteSelector", "exact": "Fluoride", "prefix": "", "suffix": " concentration of some brands of ferment" } }. For sentence based annotations (i.e. provided by HES-SO / SIB Text Mining for Elixir, NaCTeM, IntAct) it represents the URI of the database resource the annotation is referring to. For annotations containing Gene Disease relationships (i.e. provided by Open Targets Platform and DisGeNET) represents the URI of both gene and disease the annotation is referring to : "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" } ] # tags }.
,
type (string, optional):
Type of the resource
} ArticleResult {
annotations (Array[Annotation], optional):
Annotations contained in this article
,
extId (string, optional):
Identifier of the article connected with the domain specified by the source field (i.e. if SOURCE=MED it will be the PubMed ID or if SOURCE=PMC it will be a number representing the pmcid)
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.
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
}
}