Literature Informatics

Beyond PubMed: Next Generation

Literature Searching

Carrie Iwema, PhD, MLS24th August 2011

Growth of PubMed citations from 1986 to 2010

Lu, Database 2011

HSLS, U.Pitt

Information Overload?

HSLS, U.Pitt

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

GoPubMed: “searching is now sorted”

Developed by Transinsight GmbH

4 filter categories:

• What• Who• Where• When

Related search engines:

• Go3R• GoGene• GoWeb

Statistics!

HSLS, U.Pitt

http://www.gopubmed.org

GoPubMed

HSLS, U.Pitt

LigerCat: “Literature & Genomics Resource Catalog”

Developed by the Biology of Aging project at MBLWHOI Library

• Search articles/journals/genes• Explore tag clouds• Craft queries to PubMed• View Publication History

HSLS, U.Pitt

http://ligercat.ubio.org/

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

PaperPlanehttp://pubget.com/site/help/paper_plane

Developed by Pubget

HSLS, U.Pitt

http://pubget.com

Pubget

HSLS, U.Pitt

eTBLAST: text similarity-based search engine

Uses:– Find an expert– Find a journal– View publication history– Identify implicit

keywordsDeveloped by UT Southwestern Computational Biology

Group, serviced by Virginia Bioinformatics Institute eTBLAST team

Uses natural language processing, keyword weighting, and sentence alignment to search MEDLINE (and

more) for query-similar text.

HSLS, U.Pitt

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

HSLS, U.Pitt

Deja Vu: database of highly similar & duplicate citations

Classifications:– Distinct– Duplicate– Erratum

– Sanctioned

– No abstract

– Unverified

• Offshoot of eTBLAST• Identifies articles from Medline

exhibiting similar if not identical text

• Plagiarism buster!

Developed by UT Southwestern Computational Biology Group, serviced by Virginia Bioinformatics Institute

eTBLAST team

HSLS, U.Pitt

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

HSLS, U.Pitt

Why They’re Cool…

• GoPubMed— Statistics!

• LigetCat— Word Clouds!

• Pubget— PDFs!

• eTBLAST— Text Similarity!

• Deja Vu— Plagiarism Buster!

HSLS, U.Pitt

Systems Year Major featuresRanking search results

 RefMed 2010 Featuring multi-level relevance feedback for ranking Quertle 2009 Allowing searches with concept categories MedlineRanker 2009 Finding relevant documents through classification MiSearch 2009 Using implicit feedback for improving ranking Hakia 2008 Powered by Hakia’s proprietary semantic search technology SemanticMEDLINE 2008 Powered by cognition’s proprietary search technology MScanner 2008 Finding relevant documents through classification eTBLAST 2007 Finding documents similar to input text PubFocus 2006 Sorting by impact factor and citation volume Twease 2005 Query expansion with relevance ranking technique

Clustering results into topics Anne O’Tate 2008 Clustering by important words, topics, journals, authors, etc. McSyBi 2007 Clustering by MeSH or UMLS concepts GoPubMed 2005 Clustering by MeSH or GO terms

 ClusterMed 2004 Clustering by MeSH, title/abstract, author, affiliation, or date

 XplorMed 2001 Clustering by extracted keywords from abstractsExtracting and displaying semantics and relations

 MedEvi 2008 Providing textual evidence of semantic relations in output EBIMed 2007 Displaying proteins, GO annotations, drugs and species CiteXplore 2006 EBI’s tool for integrating biomedical literature and data MEDIE 2006 Extracting text fragments matching queried semantics PubNet 2005 Visualizing literature-derived network of bio-entities

Improving search interface and retrieval experience iPubMed 2010 Allow fuzzy search and approximate match PubGet 2007 Retrieving results in PDFs BabelMeSH 2006 Multi-language search interface HubMed 2006 Export data in multiple format; visualization; etc askMEDLINE 2005 Converting questions into formulated search as PICO SLIM 2005 Slider interface for PubMed searches PICO 2004 Search with patient, intervention, comparison, outcome PubCrawler 1999 Alerting users with new articles based on saved searches

Lu

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2011

HSLS, U.Pitt

http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search /

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

HSLS, U.Pitt

Thanks for your attention.

Good luck searching!Carrie Iwema, PhD, MLS

Information Specialist in Molecular Biology

Health Sciences Library SystemUniversity of Pittsburgh

iwema@pitt.edu