The CALBC RDF Triple store: retrieval over large literature content

Transcription

1 The CALBC RDF Triple store: retrieval over large literature content Samuel Croset, Christoph Grabmüller, Chen Li, Silverstras Kavaliauskas, Dietrich Rebholz-Schuhmann 10 th December 2010, Berlin EBI is an Outstation of the European Molecular Biology Laboratory.

2 Outline Motivation Integrating multiple resources CALBC Corpus LexEBI Public databases Querying the Triple Store

3 Outline Motivation Integrating multiple resources CALBC Corpus LexEBI Public databases Querying the Triple Store

4 Why representing scientific literature in RDF? Scientific literature: Primary data resource reporting novel scientific findings Text-mining: Biological entities recognition Population of biomedical databases through curators RDF representation: Standardization of the content extracted Exploitation of the literature in the Semantic Web

5 Outline Motivation Integrating multiple resources CALBC Corpus LexEBI Public databases Querying the Triple Store

6 CALBC Corpus Collaborative Annotation of a Large Biomedical Corpus 4 Project partners Medline abstract related to Immunology annotated Harmonization Silver Standard Corpus I (SSCI) Challenge Participants annotate SSCI Harmonization with best results Silver Standard Corpus II (SSCII)

7 CALBC Corpus Advantages of the CALBC Corpus: Large-scale corpus 4 semantic types: Gene-Protein, Diseases, Chemicals and Species Generated in a purely automatic way Highly reproducible

8 CALBC in RDF dc:date k/rebholz/core/cor pus_calbc 92 calbc:isin calbc:hassentence Seshadri, M S dc:creator Varkey, K dc:identifier <urn:issn: > Hepatitis B surface antigen (HBsAg) positive polyarteritis nodosa. A report of two cases and review of literature dc: calbc:

9 CALBC in RDF calbc:hasstartposition calbc:ispartof calbc:hasendposition calbc: 46 A calbc:isentitytype CHED calbc:haslabel prostaglandin s

10 Outline Motivation Integrating multiple resources CALBC Corpus LexEBI Public databases Querying the Triple Store

11 LexEBI BioThesaurus: Complete term repository for the biomedical domain LexEBI XML Features: Frequency count for the occurrence of the term in British National Corpus (BNC) or in MEDLINE Disambiguation Mapping to original resource (URI) Normalization

12 LexEBI in RDF 16 :isin W8 k/rebholz/core/cor pus_lexebi :species :hasvariant A :FrequencyInMedline 30 : < A :hasvariant :istype :SurfaceForm True :istype :FrequencyInMedline :SurfaceForm ftsj Orthographic Ribosomal large subunit methyltransferas e E

13 Outline Motivation Integrating multiple resources CALBC Corpus LexEBI Public databases Querying the Triple Store

14 Uniprot Human RDF <Unigene uniprot:unigene uniprot:chebi <ChEBI <HGNC <Specie uniprot:ispartof uniprot:hgnc uniprot:classifiedwith <GO uniprot: uniprot:... <GeneCards uniprot:genecards uniprot:ensemble <UniProt uniprot:hasinteraction uniprot:citations <Medline <Ensemble

15 Uniprot RDF <Unigene uniprot:unigene uniprot:chebi <ChEBI Array Express and uniprot: Chebi... on the way <HGNC <Specie uniprot:ispartof uniprot:hgnc uniprot:classifiedwith <GO uniprot: <GeneCards uniprot:genecards uniprot:ensemble <UniProt uniprot:hasinteraction uniprot:citations <Medline <Ensemble

16 Outline Motivation Integrating multiple resources CALBC Corpus LexEBI Public databases Querying the Triple Store

17 Querying the Triple Store 16 uniprot:q21ww8 uniprot:hasinteraction <UniProt calbcsentence: calbc:ispartof lexebi:hasvariant uniprot:classifiedwith <GO term calbc:hasannotation calbc:hasstartposition A calbc:hasendposition A lexebi:frequencyinmedline lexebi:surfaceform calbc:haslabel calbc:isentitytype ftsj pubmed: PRGE

18 Use cases Normalization of CALBC named entities Disambiguation of CALBC named entities Term collocation at the sentence level e.g. Evidence for Gene Disease association Checking consistency of bioinformatics resources from literature

19 Thank you for your attention