Download Linking literature to data in the life sciences

Data Publication
COASP 2012
Publications
Europe PubMed Central
26 million abstracts
2.2 million full text articles
Citation networks
Database links
Text-mining
2006
2011
2012
2016?
How many open access articles in UKPMC?
PubMed (995K)
UKPMC (18%,182K)
OA (9.6%, 96K)
Managing the public data ecosystem
3
Research
articles
Unstructured
Data
2
1
2
Big Data:
Deposition
Primary
1
Big Data:
Curated
Annotation
Literature citation from data
(data annotation)
Links from Literature to Databases
•
•
•
•
•
•
•
•
•
800 K
370 K
110 K
Proteins
Nucleotides
OMIM
Chemicals
Structure
Clinical reviews
Protein families
Protein-protein interactions
Gene expression experiments
Database crosslinks
Bibliography from P25106
Data citation from literature
(provenance)
Text Mining in UKPMC (2.2 million articles)
Semantic Type
Unique Terms
Articles
Annotations
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
Accession No.
Accession numbers stories:
data citation in OA articles
Senay Kafkas
Jee-Hyub Kim
Annotation of accession numbers (OA)
100
100
90
90
80
80
70
publisher-annotated
70
60
60
50
50
40
40
30
30
20
20
10
10
0
0
~10,000 articles
text-mined
>25,000 articles
• Névéol A, Wilbur WJ, Lu Z (2012) Improving links between literature and biological data with text mining: a case study with
GEO, PDB and MEDLINE. Database 2012:bas026 (PMC3371192)
• Névéol A, Wilbur WJ, Lu Z (2011) Extraction of data deposition statements from the literature: a method for automatically
tracking research results. Bioinformatics 27, 3306-3312 (PMC3223368)
Efficacy of Accession number tagging (OA)
Most text-mined tags
Most publisher tags
Most articles
bmc genomics
• plos one
• plos one
bmc evolutionary biology
• nucleic acids research
acta crystallographica section e:
the journal of cell biology
bmc genomics
british journal of cancer
virology journal
bmc evolutionary biology
bmc microbiology
the journal of cell biology
plos pathogens
bmc bioinformatics
bmc plant biology
environmental health perspectives
• nucleic acids research
the journal of experimental medicine
bmc bioinformatics
the journal of cell biology
the journal of experimental medicine
critical care
the journal of biological chemistry
virology journal
• emerging infectious diseases
bmc molecular biology
bmc microbiology
bmc bioinformatics
• emerging infectious diseases
BMC Genomics:
PLoS One:
1,484 TM tags*,
4,226 TM tags*,
4,337 articles
42,888 articles
Why is this important? Implications
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
That we can perform this analysis at all highlights a benefit of Open Access
AY387398: needle in a haystack
Unstructured data
Articles with supplemental data (UKPMC)
%
• 235,000 articles (50K+ in 2011)
• 718, 511 files
• 459 extensions
• 0.8 TB (1200 CDs)
•
(However most data in ~60 extension types)
Pub Year
Managing the public data ecosystem
Research
articles
provenance
analysis
Unstructured
Data
reuse
Structured links
Big Data:
Deposition
Primary
Big Data:
Curated
Annotation
•
•
•
•
Open
Citable
Discoverable
Reusable
People
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•
•
•
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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