intermine.bio2rdf.org : A QLever SPARQL endpoint

intermine.bio2rdf.org : A QLever SPARQL endpoint

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  intermine.bio2rdf.org A QLever SPARQLendpoint for InterMine databases François Belleau ISMB 2024 BOSC 12 July 2024
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  2 Contents • InterMine project •Semantic Web concepts • Data transformation process from REST to RDF • InterMine SPARQL endpoint demo • Concluding remarks
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   InterMine isan open source data warehouse system, licensed under the LGPL 2.1. It is used to create databases of biological data accessed by sophisticated web query.  InterMine includes a user-friendly web interface that works 'out of the box' and can be easily customised.  InterMine makes it easy to integrate multiple data sources into a single data warehouse.  There is 19 InterMine databases are available. https://en.wikipedia.org/wiki/InterMine InterMine Project 3
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  FlyMine query : Pathwayidentifier and name for the selected gene with FlyMine 4 https://www.flymine.org/flymine
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  InterMine : ProgrammingAPI available 5
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   Semantic Webis an extension of the World Wide Web that create a web of data where machines can understand the meaning and relationships between things.  RDF provides a standard way to represent information in the form of triples: (subject, predicate, object).  SPARQL is a query language specifically designed for retrieving and manipulating data stored in RDF format in a triplestore. Semantic Web concepts 6
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  20 years ofSemantic web in Life Science evolution 7 ISMB 2005 ISMB 2008 Linked Data 2005 2014 Linked Data 2024 for life science Linked Data 2009
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  SPARQL endpoints today…andmany more 8 https://www.genome.jp/sparql/linkdb https://disease-ontology.org/do-kb/sparql https://sparql.uniprot.org/ https://id.nlm.nih.gov/mesh/query https://query.wikidata.org/ https://rdfportal.org/dataset/pdbj UniProt MeSH Kegg DO PDP Wikipedia
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  InterMine SPARQL endpointsare missing. 9
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  MO-LD project :InterMine RDF conversion first attempt 10 https://github.com/mo-ld DÉRASPE, Maxime, BINKLEY, Gail, BUTANO, Daniela, et al. Making linked data SPARQL with the InterMine biological data warehouse. In : CEUR Workshop Proceedings. Rheinisch-Westfaelische Technische Hochschule Aachen* Lehrstuhl Informatik V, 2016.
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  • Data transformationprocess from REST to RDF 11 http://es.kibio.science QLever triplestore DB collection : • FlyMine • WormMine • YeastMine http://intermine.bio2rdf.org SPARQL endpoints - QLever UI • intermine-linkml-classe • intermine-linkml-field • intermine-DB-relation • Intermine-DB-object Python InterMine REST API • DB-relation.nt.gz • DB-object.nt.gz qlever index intermine2linkml.py intermine2os.py elasticdump https://huggingface.co/datasets/bio2rdf/intermine json_gz2nt_gz.py • DB-relation.ndjson.gz • DB-object.ndjson.gz • linkml-DB.yaml linkml2es.py
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  http://intermine.bio2rdf.org:7000 12
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  Show the Pathwayidentifier(s) and name for the selected gene 13 SPARQL query InterMine query
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  14 Concluding remarks • SemanticWeb as evolved with new technologies : • JSON-LD (https://json-ld.org/) • LinkML (https://linkml.io/) • QLever triplestore (https://qlever.cs.uni- freiburg.de) • Converting JSON from REST API to RDF is a simple approach • Future works : • Other InterMine SPARQL endpoints will be added • We will explore SPARQL query generation with LLM
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  15 Acknowlegments • Collaborators • GosMicklem (Cambridge University) • Deepak Unni (SIB, Swiss Institute of Bioinformatics) • Arnaud Droit (ADLab) • Funding • BioHackathon 2023 organizers • BOSC 2024 Organizing Committee
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  1 1 http://intermine.bio2rdf.org:7000 https://huggingface.co/datasets/bio2rdf/intermine Try it Get dataand scripts [email protected]