Biohackathon 2015

Europe PubMed Central and Linked Data

Jee-Hyub Kim0000-0002-0359-2887

Nagasaki 13 Sep 2015

Contents

● Europe PubMed Central● Linking Literature● Mining Identifiers● Publishing Mined Identifiers on RDF● Web Annotation Data Model● Use Case for Database Curation

Europe PubMed Central

● Europe PMC is a literature database○ Abstracts: 30 million PubMed, Agricola and patent

records, updated daily○ Full text articles: over 3 million full text articles, of

which over 900,000 are free to read and reuse, updated daily

Services in Europe PMC

● RESTful web service:○ http://europepmc.org/RestfulWebService○ Text-mined terms, metadata, full text

● ORCID article claiming tool● Embassy Cloud for 3rd party contents providers● BioJS literature module: http://biojs.io/d/biojs-vis-

pmccitation● RSS

Linking Literature

● Europe PMC provides various types of linking methods○ By external links: to any URL (e.g., database,

Wikipedia, press release, etc.)○ By text mining

■ Biological entities■ Identifiers (e.g., accession numbers)

○ By ORCID (article claims)● 24 external links providers, 1 ORCID, 9 cross-reference

DBs, 20 DB identifiers, 6 named entity types

Linking Examples

To By Relation REST API

Wikipedia Provider Mention labsLinks

Publons Provider Review labsLinks

UniProt Curator Citation databaseLinks

ORCID Provider Author search

EFO Named entity tagger

Recognition textMinedTerms

PDB Accession number tagger

Mention textMinedTerms

Mining Identifiers in Free Text

● Motivation○ Started for cross-linking with EBI databases○ Data citation, impact analysis○ Now, moving for linked data

● We use patterns from identifiers.org and link back to it.● A IE problem: ID matching + NER for resource names● Some ambiguities

○ PDB: 4min○ OMIM and ERC funding id: both 6-digit numbers○ Resource name variations: UniProt, Swiss-Prot, etc.

Mentioned in Europe PMC articles

Identifiers in Literature

DatabasesENA, PDB, ArrayExpress, UniProt, RefSNP, OMIM, PFam, RefSeq, Ensembl, InterPro, Bioproject, Biosample, EMDB, PXD, EGA, TreeFam

Funding resourcesEuropean Research Council

OntologiesGO, UniProt, EFO, ChEBI, NCBI Taxonomy, UMLS

Clinical TrialsNCT, EudraCT

Digital Repositories (Dryad, figshare, etc.)Data DOI

Identifiers in Different ResourcesArticles (978,605) Patents 2014 (266,192) Wiki pages (15,346,290)

db # articles db # patents db # pagesena/genbank/

ddbj 23,295ena/genbank/

ddbj 4,074 pdb 4,265

pdb 15,544 uniprot 1,387 omim 2,226

nct 13,006 pdb 1,093 uniprot 1,712

refsnp 10,168 refseq 1,002 refseq 1,643

refseq 6,551 refsnp 322 ensembl 1,402

omim 5,093 omim 254 go 1,351

uniprot 2,865 pfam 115 pfam 582

go 1,900 ensembl 97 interpro 560

arrayexpress 1,832 interpro 46ena/genbank/

ddbj 396

Publishing Identifiers on RDF

● Goals○ More connectivity○ More provenance for each linking

■ PMCID, sentence, section label, etc.○ Links to share and comment (e.g., hypothes.is)

● Challenges:○ How to model? Web Annotation Data Model.○ dealing with nearly a billion annotations generated

automatically in a large scale

Web Annotation Data Model

● Built on the top on RDF● Annotations as resources● To provide a standard description mechanism for

sharing annotations between systems● For more general purpose use

○ Not only for text mining○ For example, YouTube video comments (by people),

image annotation, etc.○ W3C Working Draft

Core Annotation Framework

● Typically an Annotation has a single Body, which is the comment or other descriptive resource, and a single Target that the Body is somehow "about".

● The Body provides the information which is annotating the Target.

● This "aboutness" may be further clarified or extended to notions such as classifying or identifying.

Text-Mining RDF Service

● Running on EBI RDF Platform● Stores 1,563,241,810 triples text-mined from 400,746

Open Access articles in Europe PubMed Central.● Provides

○ for each article, all the annotations linking to ontologies/databases

○ with contexts:■ sentences■ section information

Use Case for Database Curation

● Given an database identifier, provides sentence-level information for database curation.○ Show all the articles where a PDB accession number

3NSS is mentioned.○ Show all the annotations with each its label in

PMC3382907.○ Show all the articles where inflammatory bowel

disease (C0021390) is mentioned.● http://wwwdev.ebi.ac.uk/rdf/services/textmining/sparql

Plans for BioHackathon 2015

● Integration with other SPAQL endpoints

● Interoperability with other formats used in text-mining community○ e.g., BioC, UIMA

● Produce more links on RDF

References

Europe PMC Consortium. Europe PMC: a full-text literature database for the life sciences and platform for innovation. Nucleic Acids Res. 2015 Jan;43(Database issue) D1042-8. doi:10.1093/nar/gku1061. PMID: 25378340; PMCID: PMC4383902.

Kafkas Ş, Kim JH, McEntyre JR. Database citation in full text biomedical articles. PLoS One. 2013;8(5) e63184. doi:10.1371/journal.pone.0063184. PMID: 23734176; PMCID: PMC3667078.

Juty N, Le Novère N, Laibe C. Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Res. 2012 Jan;40(Database issue) D580-6. doi:10.1093/nar/gkr1097. PMID: 22140103; PMCID: PMC3245029.