Literature-Data Integration in the Life Sciences

Lisbon, Oct 2nd 2012

Publications and Data Sources

26 million abstracts

2.3 million full text articles

Citation networksDatabase linksText-mining

20122006 2011 2016?

Europe PubMed Central

How many open access articles in UKPMC?PubMed (995K)

UKPMC (18%,182K)

OA (9.6%, 96K)

Total: 489,000 OA articles

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Figure 2. Growth of key resources

• Big data• Thematic data• Public data• Archived data

• Two petabytes of data• Scales to 7 pbs raw disk 

•Majority is DNA

Literature citation from datavs

Data referal from literature

PMC336623 Extended to several other biological data types

Literature citation from data

• Proteins• Nucleotides• OMIM• Chemicals• Structure• Clinical reviews• Protein families• Protein-protein interactions• Gene expression experiments

800 K

370 K

110 K

Semantic Type Unique Terms Articles Annotations

Accession No. 233,017 66,356 387,787

Chemical 76,712 1,694,385 83,923,066

Disease 171,692 1,768,214 57,821,871

Gene/Protein 227,318 1,310,382 77,189,022

GO Terms 32,664 1,832,294 65,061,579

Organism 180,637 1,713,280 70,832,222

Data referral from literature: text mining

2.3 million articles

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publisher-annotated text-mined

Annotation of accession numbers (OA)

~10,000 articles >25,000 articles

BMC Genomics: 1,484 TM tagged, 4,337 articles (1135 tagged)PLoS One: 4,226 TM tagged, 42,888 articles

Senay Kafkas and Jee-Hyub Kim

Scientific:Linking articles that cite the same data

Citation:Data Citation as measure of impact (Thomson: Data citation index)

Context of data citation: submission, reuse, analysis

Operational:Services for publishers to improve Accession number tagging

Editorial policies and adherence

Extension of NLM DTD

Lessons learned for considering unstructured data

Why is this important? Implications

That we can perform this analysis at all highlights a benefit of Open Access

Case Study of an FP7-funded article (1)

Case Study of an FP7-funded article (2)

Europe PubMed Central content map

Abstract Full text

Databases

Extractedterms

UnstructuredDatasets

Citingarticles

Citingarticles

AY387398: needle in a haystack

Europe PubMed Central and Institutional Repositories:content matching

Number of article IDs

OpenAIRE plus

**Coming soon: RESTful interface for data linked to articles

People

• Paula Buttery• Andrew Caines• Norman Cobley• Yuci Gou• Senay Kafkas• Jyothi Katuri• Oliver Kilian• Jee-Hyub Kim• Nikos Marinos• Jo McEntyre• Xingjun Pi• Philip Rossiter

• Rebholz Group• Peter Stoehr

• University of Manchester• British Library

• OpenAIRE/OpenAIRE Plus

• NCBI, NLM