global alignment and collaboration jo mcentyre @jomcentyre
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Global Alignment and Collaboration
Jo McEntyre
@jomcentyre
www.europepmc.org
www.ebi.ac.uk
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About EMBL-EBI
• Part of the European Molecular Biology Laboratory
• International, non-profit research institute
• Europe’s hub for biological data services and research
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Science is global
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2. Discoverability through structured datastructured data is one of the true
enablers of life science
- Discovery of homology between genes across species
- Predicting function based on protein folds
• Structured data can be cross-analysed, compared by algorithm, and encourages development of new products and tools
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Osteoarthritis
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Data Ecosystem Unstructured/
semi-structured
Structured
Added Value
LiteratureOntologies Metadata
Citations & Links• ORCIDs• DOIs, ROIs• PIDs
Algorithms• Text and data mining• Analytical tools
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A stable, freely available, shared repository
Europe PMC
• Abstracts: 30 million
• Full-text articles: 3 million
• Article citation counts• Grants• ORCIDs • Semantic annotation• Data citations• Data integration
Europe PMC is a member of the PMC International Collaboration.
Supports OA mandates of 26 European funders of life science research
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Europe PMC content
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The scent of information
It's healthy to remember that users are selfish, lazy, and ruthless in applying their cost-benefit analysesInformation Foraging: by JAKOB NIELSEN, June 30, 2003 http://www.nngroup.com/articles/information-scent/
• Data placement: where people will find it • Scent alone is not scientific …
“retaining files and being prepared to share them” ≠ accessible data
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Data Citation Principles
• Data as legitimate, citable products of research
• Attribution and credit• Cited as evidence for a claim• Unique identification• Access• Persistence• Specificity and verifiability
(provenance)• Interoperability and flexibility
https://www.force11.org/datacitation
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BioStudyEBI
BioStudies database for unstructured data
Study
Publications
Ontologies
Data files
Other DBs
Metadata
Other DBs
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PIDs build infrastructure for scientific discovery and credit systems
Reused from: seier+seier, Flickr
Reused from: Images Money, Flickr
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(1) Europe PMC and
Use of the claiming tool• ~400K article claims• ~ 21K unique ORCIDs
Incorporation into Europe PMC• 1.2M unique articles in Europe
PMC linked to ORCIDs (cf. PubMed 12K)
An integrated encyclopedia of DNA elements in the human genome.(PMID:22955616 PMCID:PMC3439153)
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A network of repositories
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Cross Disciplinary Integration
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Elixir: An international distributed infrastructure for
• Data
• Standards
• Tools
• Compute
• Training
• Industry
Alignment with BD2K (NIH)