Announcement: sparqlprog, a pack for federated logic programming over SPARQL endpoints

Announce Pack
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Hi all,

I would like to announce something I have been working on for a while, a way of executing logic program queries over a SPARQL endoint. This is similar to Samer Abdallah’s sparkle, but extends on it a number of ways.

You can get it from:

The basic idea is that you can write logic programs, and so long as you stay within a specified subset (essentially datalog) and leverage the use of the semweb rdf/3 and related predicates, then you can make normal prolog queries that are compiled down to SPARQL and executed remotely.

For example, we can write:

has_shared_band_member(B1,B2,A) :-
      rdf(A,dbo:associatedBand,B1),
      rdf(A,dbo:associatedBand,B2),
      B1\=B2.

And ask has_shared_band_member(dbr:Deep_Purple, OtherBand, SharedMember)

It’s also possible freely mix execution within the prolog engine and remote execution on the SPARQL server in a way that avoids the impedance mismatches of an imperative language.

I want to credit Sam Neaves for the ideas here, nicely described in Reactome Pengine: a web-logic API to the Homo sapiens reactome

And because Prolog is sometimes a hard sell, there is a Python wrapper, plus some example Jupyter notebooks: sparqlprog-python. (A sparqlprog service can easily be run via Docker, communication is via Pengines).

I’m going to be working on this as part of a Biohackathon in Japan the first week of September. There is a not currently very active sparqlprog gitter room which I promise to monitor during this week, if others want to join me remotely! (Will Byrd of “The Reasoned Schemer” and miniKanren fame will also be at the hackathon).

–
Chris Mungall, PhD
Department Head, Molecular Ecosystems Biology, Lawrence Berkeley National Laboratory
717 Potter Street,
Berkeley, CA 94710


(510) 486 4170

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