Search on MEDLINE
The triage function is an essential element of the curation system directly integrated into the CovidTriage, but also available through a special API developed on HTTP GET/POST protocols. This service provides a ranked list of MEDLINE documents for a keyword-centric curation request.
The base URL is :
subject parameter is mandatory as it specifies the name of the researched entity.
The following parameters are available :
- axis : to define the section of the thesaurus used for the curation, default is ALL (to match any concept from COVoc, regardless of its axis)
- 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. "COVOC:0010013,COVOC:0030019" respectively to exclude the occurrences of "interaction" and "marijuana" from the scoring)
- requested : to define the maximum number of retrieved citations, default is 50 and maximum is 1000
Regardless of the selected axis, the CovidTriage search is always based on the controlled vocabulary available on github.
If the default axis is not wanted, one or more of the following section can be set (separated by a comma):
- Biological / Medical vocabulary
- Cell Line
- Clinical Trial
- Conceptual Entity
- Disease and Syndrom
- Protein and Genome
The following URL provides a list of publications corresponding to the keyword "pangolin", ranked for their relevance to the curation of MEDLINE using the Biological / Medical vocabulary.
http://candy.hesge.ch/CovidTriageService/webservice/ranking/MEDLINE/json?subject=pangolin&axis=Biological / Medical vocabulary
The output is provided in JSON format :
"abstract":"An outbreak of coronavirus disease 2019 (COVID-19) caused by [...].",
"title":"Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak.",
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-CovidTriage search engine, depending of the curation query
You can contact us for questions specifically relating to this service.