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Biomedical Data

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Material Information

Title:
Biomedical Data
Series Title:
Big Data, Little Data: Having it All A Research Data & Data Management 2013 Workshop
Physical Description:
Presentation slides
Language:
English
Creator:
Garcia-Milian, Rolando
Publisher:
George A. Smathers Libraries, University of Florida
Place of Publication:
Gainesville, FL
Publication Date:

Notes

Abstract:
Presentation slides by resource expert presenter at the Big Data, Little Data Workshop on Oct. 3, 2013.
General Note:
Data Management / Curation Task Force Materials ( DMCTF Materials )

Record Information

Source Institution:
University of Florida
Holding Location:
University of Florida
Rights Management:
Applicable rights reserved.
System ID:
AA00017906:00005

MISSING IMAGE

Material Information

Title:
Biomedical Data
Series Title:
Big Data, Little Data: Having it All A Research Data & Data Management 2013 Workshop
Physical Description:
Presentation slides
Language:
English
Creator:
Garcia-Milian, Rolando
Publisher:
George A. Smathers Libraries, University of Florida
Place of Publication:
Gainesville, FL
Publication Date:

Notes

Abstract:
Presentation slides by resource expert presenter at the Big Data, Little Data Workshop on Oct. 3, 2013.
General Note:
Data Management / Curation Task Force Materials ( DMCTF Materials )

Record Information

Source Institution:
University of Florida
Holding Location:
University of Florida
Rights Management:
Applicable rights reserved.
System ID:
AA00017906:00005


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Biomedical Databases & Tools Rolando Garcia Milian Rolando.milian@ufl.edu Biomedical & Health Information Services Department Health Sciences Center Library October 3, 2013

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Problem Rapid Growth of Biomedical data GenBank Statistics http://www.ncbi.nlm.nih.gov/genbank/genbankstats 2008/ 0.00 0.50 1.00 1.50 2.00 2.50 3.00 3.50 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 Millions Samples Submitted to Gene Expression Omnibus Database Compiled from GEO historic data http://www.ncbi.nlm.nih.gov/geo/summary/?type=history

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Compiled by from PubMed http://www.ncbi.nlm.nih.gov/pubmed 0.00 5.00 10.00 15.00 20.00 25.00 1940 1950 1960 1970 1980 1990 2000 2010 2020 Millions Number of Records in PubMed Biomedical Literature Problem Growth of the Biomedical Literature H uge volume ( PubMed 23132342 citations) High diversity High quality (peer review) Users overwhelmed by long list of search results 1/3 of Pubmed queries result in 100 or more citations ( Islamaj 2009)

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Querying the biomedical literature becomes more difficult Medical Subject Headings Filters Boolean operators Problem Querying the Biomedical Literature

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Alternative Mining Tools for the Biomedical Literature Main gene query Protein/gene associated Synonym Medical terminology

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Based on Universal Medical Language System Repository of semantic predications (subject predicate object triples ) 57.6 million predications from all of PubMed citations ( Rindflesch 2011) Alternative Mining Tools for the Biomedical Literature

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Alternative Mining Tools for the Biomedical Literature Linked to Entrez Gene database

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Workshop Novel Online Tools for Mining the Biomedical Literature

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Case 1 Few Results in the Biomedical Literature Searching for novel genes

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Case 2 Few Results in the Biomedical Literature Searching for side effects of drugs: Cerebyx respiratory failure

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P henotypic information can be used to infer molecular interactions and hinting at new uses of marketed drugs ( Campillos 2008) Case 2 Few Results in the Biomedical Literature

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Freely Available Up To Date Discovery Tools National Center for Biotechnology Information, USA European Bioinformatics Institute, UK

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Proprietary Tools

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Annotation/ Visualization Tools Genome Browsers

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Workshop Introduction to Genome Browsers

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References Campillos M*, Kuhn M*, Gavin AC, Jensen LJ, Bork P. Drug target identification using side effect similarity. Science. 2008 Jul 11;321(5886):263 6. http://www.ncbi.nlm.nih.gov/pubmed/18621671 Islamaj Dogan R, Murray GC, Nvol A, Lu Z. (2009) Understanding PubMed user search behavior. Database (Oxford) http://www.ncbi.nlm.nih.gov/pubmed/ 20157491 Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002 Jun;12(6):996 1006. http://www.ncbi.nlm.nih.gov/pubmed/12045153 Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P. A side effect resource to capture phenotypic effects of drugs. Mol Syst Biol. 2010;6:343. Epub 2010 Jan 19. http://sideeffects.embl.de/drugs/56338/ Rindflesch T.C. et al. (2011) Semantic MEDLINE: An advanced information management application for biomedicine. Information Services & Use, 31, 15 21. http://lhncbc.nlm.nih.gov/system/files/pub lhncbc 2011 109. pdf

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Data Resources Data Management Resources, UF Libraries: http://library.ufl.edu/datamgmt Surveys on Your Needs UF Research Data Needs Assessment: http:// bit.ly/UFdatasurvey Big Data, Little Data Workshop Evaluation: http://bit.ly/dataeval