neXtA5 services
Annotations service
This service aims to provide the so-called triplets {subject – relation – object} for annotation.
It directly interrogates the BioMed database and fetches the annotations generated by neXtA5 depending of the requested PMID/axis .
The base URL is :
http://candy.hesge.ch/neXtA5/webservice/publicationStatements/json?
Parameters
The following parameters are available :
- publicationSource : Selected literature (PMID|PMCID)
- publicationId : Identifier of the publication, depending on the publicationSource (can be a list with comma "," as separator)
- axis : Dimension for the curation (DISEASE|GO_BP|GO_CC|GO_MF|INTERACTION), default is DISEASE
- gene : Focus of the curation
Example
The following URL provides the complete set of diseases annotations related to the kinase IRAK4 in PMID 24030499.
http://candy.hesge.ch/neXtA5/webservice/publicationStatements/json?publicationSource=PMID&publicationId=24030499&axis=GO_BP&gene=IRAK4
Output
The output is provided in JSON format :
{
"data": {
"gene": "IRAK4",
"annotations": [{
"proposedObject": {
"name": "interferon production",
"id": "GO:0001816"
},
"passage": "Innate immune interleukin-1 receptor-associated kinase 4 exacerbates viral myocarditis by reducing CCR5(+) CD11b(+) monocyte migration and impairing interferon production.",
"proposedRelation": {
"name": "causes disease",
"id": ""
},
"proposedEco": {
"name": "",
"id": ""
},
"position": 0
}, ...],
"axis": "GO_BP",
"publicationId": "24030499",
"error": ""
},
"success": true
}
Output fields for each document are :
- "gene" : subject of the annotation triplet
- "proposedObject" : object of the annotation triplet ("name" describe the concept found in the text and "id" normalized it depending on a specific thesaurus)
- "passage" : sentence in the document where the concept was mapped
- "proposedRelation" : characterize the relation between the subject and the object of the annotation
- "proposedEco" : ECO (evidence code) found in the text
- "position" : appearance of this evidence in the text
- "axis" : remind the requested axis
- "publicationId" : remind the requested identifier of the publication
- "error" : short description of the error when the requested annotation is not available
Getting Help
You can contact us for questions specifically relating to this service.
