Literature Informatics

Beyond PubMed: Next Generation Literature Searching

Carrie Iwema, PhD, MLS 24 th August 2011

Growth of PubMed citations from 1986 to 2010 Lu, Database 2011 HSLS, U.Pitt

Information Overload?

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GoPubMed:

“searching is now sorted”

Ontology-based literature searching – Medical Subject Headings (MeSH) • Hierarchical vocabulary for biomedical and health-related topics – Gene Ontology (GO) • Controlled vocabulary for molecular biology topics 4 filter categories: • What • Who • Where • When

Statistics!

Related search engines: • Go3R • GoGene • GoWeb Developed by Transinsight GmbH

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GoPubMed

http://www.gopubmed.org

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LigerCat:

“Literature & Genomics Resource Catalog” • Search articles/journals/genes • Explore tag clouds • Craft queries to PubMed • View Publication History

http://ligercat.ubio.org/

Developed by the Biology of Aging project at MBLWHOI Library

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Pubget:

“Find papers

fast

.”

• • • • The search results ARE the papers—PDFs!

Synched w/home institution journal subscriptions Customizable “latest issues” journal list Easily browse your favorite journals

PaperPlane

http://pubget.com/site/help/paper_plane Developed by Pubget

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Pubget

http://pubget.com

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eTBLAST:

text similarity-based search engine Uses natural language processing, keyword weighting, and sentence alignment to search MEDLINE (and more) for query-similar text.

Uses: – Find an expert – Find a journal – View publication history – Identify implicit keywords Developed by UT Southwestern Computational Biology Group, serviced by Virginia Bioinformatics Institute eTBLAST team

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eTBLAST

http://etest.vbi.vt.edu/etblast3/

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Deja Vu:

database of highly similar & duplicate citations • • • Offshoot of eTBLAST Identifies articles from Medline exhibiting similar if not identical text Plagiarism buster!

Classifications: – Distinct – Duplicate – Erratum – Sanctioned – No abstract – Unverified Developed by UT Southwestern Computational Biology Group, serviced by Virginia Bioinformatics Institute eTBLAST team

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Deja Vu

http://dejavu.vbi.vt.edu/dejavu

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Why They’re Cool…

•

GoPubMed—

•

LigetCat—

•

Pubget—

•

eTBLAST—

•

Deja Vu—

Statistics!

Word Clouds!

PDFs!

Text Similarity!

Plagiarism Buster!

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Systems Ranking search results

RefMed Quertle MedlineRanker MiSearch Hakia SemanticMEDLINE MScanner

eTBLAST

PubFocus Twease Anne O’Tate

Clustering results into topics

McSyBi

GoPubMed

ClusterMed XplorMed

Extracting and displaying semantics and relations

MedEvi EBIMed CiteXplore MEDIE PubNet

Improving search interface and retrieval experience

iPubMed

PubGet

BabelMeSH HubMed askMEDLINE SLIM PICO PubCrawler

Year Major features

2010 2009 2009 2009 2008 2008 2008

2007

2006 2005 Featuring multi-level relevance feedback for ranking Allowing searches with concept categories Finding relevant documents through classification Using implicit feedback for improving ranking Powered by Hakia’s proprietary semantic search technology Powered by cognition’s proprietary search technology Finding relevant documents through classification

Finding documents similar to input text

Sorting by impact factor and citation volume Query expansion with relevance ranking technique 2008 2007

2005

2004 2001 Clustering by important words, topics, journals, authors, etc.

Clustering by MeSH or UMLS concepts

Clustering by MeSH or GO terms

Clustering by MeSH, title/abstract, author, affiliation, or date Clustering by extracted keywords from abstracts 2008 2007 2006 2006 2005 Providing textual evidence of semantic relations in output Displaying proteins, GO annotations, drugs and species EBI’s tool for integrating biomedical literature and data Extracting text fragments matching queried semantics Visualizing literature-derived network of bio-entities 2010

2007

2006 2006 2005 2005 2004 1999 Allow fuzzy search and approximate match

Retrieving results in PDFs

Multi-language search interface Export data in multiple format; visualization; etc Converting questions into formulated search as PICO Slider interface for PubMed searches Search with patient, intervention, comparison, outcome Alerting users with new articles based on saved searches

/ http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search HSLS, U.Pitt

Lu Z Database 2011

Video Tutorials

• Searching using MESH terms: http://media.hsls.pitt.edu/media/clres2705/mesh.swf

• Pubmed Clinical Queries: http://media.hsls.pitt.edu/media/clres2705/scz.swf

• GoPubmed : http://media.hsls.pitt.edu/media/clres2705/gopubmed.swf

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Thanks for your attention.

Good luck searching!

Carrie Iwema, PhD, MLS Information Specialist in Molecular Biology Health Sciences Library System University of Pittsburgh [email protected]