Extract PMID supporting a relation

[maximeDelmas]

Context

Currently, only the number of articles supporting the relation is displayed on the interface, in the column papers

Desired behaviour

As a user I would be able to extract the complete list of PMID that are supporting the relation

Solutions ?

Even if the complete list of PMID associated to each association is not stored in the SQL database (as it would involve a massive load of data), the information is encoded in the KG and could be extracted using SPARQL requests.

• We could create URLs containing the SPARQL request allowing to extract PMIDs related to a specific PubChem/CheBI/ChemOnt-MeSH association as a GET/POST http request. This url could be added in a new column of the result table.

• The request could also be part of the pre-filled SPARQL requests.

[maximeDelmas]

For the URL part, I will start to work on it. The idea is to provide a link to an http request that will send a request to the SPARQL endpoint to get the PMIDs associated to an assocition in the result table.
I think that for heavily supported associations (>1000 articles) we should set a limit in the number of articles returned when using the web interface as the SPARQL request can be really long. I will start to test some http requests.

To get all the PMID the user should use the SPARQL endpoint with the pre-filled SPARQL request. But, we have to discuss on how to implement pre-filled SPARQL request in the Virtuoso SPARQL endpoint with @ofilangi in a meeting soon.

[maximeDelmas]

Requests with ChEBI and ChemOnt can be very long, more than 5 minutes, which is incompatible with a request of the web interface ...

For PubChem - MeSH, it is more reasonable as the engine does not have to go through the chemical ontology...

I would also propose to pre-compute all the PMID sets, and if we can't store them in the database, we could provide the files on the ftp.

[maximeDelmas]

When specifying graphs using FROM attributes, it seems to increase requests' speed

Maybe we do not need the limit 1000 also