Extrac’ng pa,erns of database and so3ware usage from the bioinforma’cs literature Geraint Duck, Goran Nenadic, Andy Brass, David L. Robertson and Robert Stevens The University of Manchester, UK h,p://www.cs.man.ac.uk/~duckg/ h,p://bionerds.sourceforge.net/networks/
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ECCB 2014: Extracting patterns of database and software usage from the bioinformatics literature
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Extrac'ng pa,erns of database and so3ware usage from the bioinforma'cs literature
Geraint Duck, Goran Nenadic, Andy Brass, David L. Robertson and Robert
Stevens
The University of Manchester, UK h,p://www.cs.man.ac.uk/~duckg/ h,p://bionerds.sourceforge.net/networks/
Introduc'on
• Methods are fundamental to science – Judgement – Replica'on – Extension
• Methods in bioinforma'cs: – In silico: Data and tools – Workflows
• Objec've representa'on • Sharing and reuse
2
Bioinforma'cs
• Resource focused domain: “Resourceome” – Our research suggests:
• Around 200,000 unique resources in the literature • Over 4 million men'ons • … and s'll growing!
• Resource/method search and selec'on… – Best-‐prac'ce – Common-‐prac'ce
• What are the main pa,erns in bioinforma'cs resources, and associated methods? 3
Approach
• Use bioinforma'cs literature (to answer this ques'on)
• Extract database and so3ware men'ons • Combine resources to form pairs • Combine pairs to forms pa,erns – Common-‐prac'ce – Method?
4
PHYLIPClustalW
ModellerBLAST PROCHECK
Document Collec'on
• PubMed Central open-‐access full-‐text ar'cles • Bioinforma2cs[MeSH] • 22,376 ar'cles • 67 journals • 3 journals were > 50% of total documents