SIBiLS-Disprot services

Document triage service

The triage function is an essential element of the curation system directly integrated into the disprotGUI, but also available through a special API developed on a HTTP POST protocol. This service provides a ranked list of MEDLINE documents for a gene-centric curation request.

The base URL is :

http://candy.hesge.ch/disprot/webservice/ranking/json?

Parameters

gene parameter is mandatory as it specifies the name of the researched entity.

The following parameters are available :

• axis : to define the thesaurus used for the curation (1|2|3|4), default is 1
• dateMin : the publication dates prior to this year will be excluded from the search, default is 2000
• dateMax : the publication dates next to this year will be excluded from the search, default is 2020
• excludedConcept : to list the identifiers of the non-relevant concept to filter out of the ranking strategy (e.g. "C2916,C9305" respectively to exclude the occurrences of "Carcinoma" and "Cancer" from the scoring)
• requested : to define the maximum number of retrieved citations, default is 100 and maximum is 2000

Thesaurus

Regardless of the selected axis, the thesaurus is always based on the ontology available on DisProt :

• 1 matches only the preferred forms
• 2 also covers synonyms
• 3 includes MeSH synonyms related to the DisProt concepts
• 4 is completed with additional concepts proposed by experts

Example

The following URL provides a list of publications corresponding to the kinase PAGE4, ranked for their relevance to the Biological Process curation.

http://candy.hesge.ch/disprot/webservice/ranking/json?gene=PAGE4&axis=3

Output

The output is provided in JSON format :

[ { "abstract":"The cancer/testis antigens (CTAs) are [...].", "title":"The cancer/testis antigen prostate-associated gene 4 (PAGE4) is a highly intrinsically disordered protein.", "neXtA5Score":74.7, "pubDate":2011, "publicationId":"21357425", "statements":7 }, ... ]

Output fields for each document are :

• "publicationId" : the identifier of the retrieved publication
• "title" : the title of the publication
• "abstract" : the abstract of the publication
• "pubDate" : the publication year
• "statements" : the number of annotations found in the text
• "neXtA5Score" : the score provided by the SIBiLS-Disprot search engine, depending of the curation query

Processing full-texts

The triage service can also be applied to full-texts from PubMed Central. To query this collection, the base URL is :

http://candy.hesge.ch/disprot/webservice/ranking/PMC/json?

E.g. http://candy.hesge.ch/disprot/webservice/ranking/PMC/json?gene=PAGE4&axis=3

Getting Help

You can contact us for questions specifically relating to this service.