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Literature Informatics August 20 , 2013

Literature Informatics August 20 , 2013. Ansuman Chattopadhyay , PhD Head, Molecular Biology Information Service Health Sciences Library System University of Pittsburgh ansuman@pitt.edu http://www.hsls.pitt.edu/molbio. Ansuman Chattopadhyay , Ph.D. ansuman@pitt.edu. 1990-1996

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Literature Informatics August 20 , 2013

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  1. Literature InformaticsAugust 20, 2013 AnsumanChattopadhyay, PhD Head, Molecular Biology Information Service Health Sciences Library System University of Pittsburgh ansuman@pitt.edu http://www.hsls.pitt.edu/molbio

  2. AnsumanChattopadhyay, Ph.D. ansuman@pitt.edu • 1990-1996 • University of Nebraska-Lincoln • PhD. in Biochemistry • Protein synthesis initiation in eukaryotic system • 1997-2001 • Vanderbilt University School of Medicine, Nashville • Research Fellow • Epidermal Growth Factor (EGF) mediated signal transduction • 2001-2002 • Cellomics Inc., Pittsburgh • Knowledge Engineer • 2002- 2006 • Information Specialist in Molecular Biology and Genetics • HSLS, University of Pittsburgh • 2006- Present • Head, Molecular Biology Information Service • HSLS, University of Pittsburgh http://www.hsls.pitt.edu/molbio

  3. Carrie L Iwema, PhD, MLS, AHIP iwema@pitt.edu • 1993-2001 • SUNY Upstate Medical University, Syracuse • PhD in Neuroscience • Specificity of connectivity in the mammalian olfactory system • 2001-2005 • Yale University School of Medicine, New Haven • Postdoctoral Fellow • Development & regeneration in the mammalian olfactory system • 2004-2006 • Southern Connecticut State University, New Haven • Masters in Library Science • 2006- 2007 • Johns Hopkins Medical Institutions, Welch Medical Library, Baltimore • Basic Science Librarian • 2007- Present • University of Pittsburgh, Health Sciences Library System, Pittsburgh • Information Specialist in Molecular Biology http://www.hsls.pitt.edu/molbio

  4. HSLS Molecular Biology Information Service http://www.hsls.pitt.edu/molbio

  5. Today’s Agenda • 10 am to 12 pm Genes, Proteins and Literature Searching • 1pm to 3 pm NCBI Resources - Genetic Variations Databases 3pm to 3:30 pmQ A Session

  6. Literature Informatics http://www.hsls.pitt.edu/guides/genetics

  7. Learn how to .. find the most appropriate literature .. mine the literature .. manage your collected information .. browse scientific papers http://www.hsls.pitt.edu/molbio

  8. Topics • Introduction • Intuitive PubMed Search • Next-Generation Literature Search Tools • Reference Management • PDF Reader http://www.hsls.pitt.edu/molbio

  9. Literature Informatics • Comprehensive search: • MESH term based PubMed Search • PubMed special topics query • Next-generation literature search tools: • GoPubMed, eTBlast • Quertle • HuGE Navigator • Utopia Docs http://www.hsls.pitt.edu/molbio

  10. Introduction

  11. Genomic achievements since the Human Genome Project http://www.hsls.pitt.edu/molbio

  12. Progress in Genomics 1990 2003 2013 Time Technology 6-8 year 3-4 months 2-3 days Time 1B 10-50 M 4-6 K Cost Source: Eric Green; HGP10 Symposium

  13. DNA Sequencing Cost http://www.hsls.pitt.edu/molbio

  14. Big DATA Biology Multi-Gene System-wide High-throughput Multi-Institution Single Gene Single Protein Single lab Big Science Small Science

  15. Growth of PubMed Citations . p53 Lu et al. Database (Oxford). 2011: baq036 Aug 20th 2013 http://www.hsls.pitt.edu/molbio

  16. Searching PubMed http://www.hsls.pitt.edu/molbio

  17. Find published literature with statistical and numerical data on DENGUE OUTBREAKS in India. • What genes are reported to be associated with the disease SCHIZOPHRENIA? http://www.hsls.pitt.edu/molbio

  18. Schizophrenia: 96,912 Schizophrenia gene: 7382 Citations: 20 million Journals: 5200 Dengue outbreaks in India: 329 Dengue outbreaks statistics India: 21 http://www.hsls.pitt.edu/molbio

  19. Challenges • Am I getting everything / the right things? • How to digest this? http://www.hsls.pitt.edu/guides/genetics

  20. Medical Subject Headings (MeSH) http://www.hsls.pitt.edu/guides/genetics

  21. MeSH Vocabulary • Headings • over 24,000 representing concepts found in the biomedical literature (Body Weight, Kidney, Radioactive Waste) • Subheadings • attached to headings to describe a specific aspect of a concept (adverse effects , metabolism, diagnosis, therapy) • Supplementary Concept Records • over 172,000 terms in a separate chemical thesaurus -updated weekly (cordycepin , valspodar , tacrolimus binding protein 4) • Publication Types (Letter, Review, Randomized Controlled Trial) http://www.hsls.pitt.edu/guides/genetics

  22. MeSH Tree Structure • A. AnatomyB. OrganismsC. DiseasesD. Chemical and DrugsE. Analytical, Diagnostic and • Therapeutic Techniques and EquipmentF. Psychiatry and PsychologyG. Biological SciencesH. Physical SciencesI. Anthropology, Education, • Sociology and Social PhenomenaJ. Technology and Food and BeveragesK. Humanities L. Information Science M. Persons N. Health CareV. Publication Characteristics Z. Geographic Locations http://www.hsls.pitt.edu/guides/genetics

  23. MeSH Indexing Source: NLM http://www.hsls.pitt.edu/guides/genetics

  24. MeSH Indexing http://www.hsls.pitt.edu/guides/genetics

  25. MeSH Indexing http://www.hsls.pitt.edu/guides/genetics

  26. Find published literature with statistical and numerical data on DENGUE OUTBREAKS in India.

  27. PubMed Query Using MeSH http://www.ncbi.nlm.nih.gov/mesh http://www.hsls.pitt.edu/molbio

  28. Find articles on “Dengue outbreaks in India” by searching PubMed using MeSH terms • Resources • Mesh Browser : http://www.ncbi.nlm.nih.gov/mesh • PubMed: http://www.ncbi.nlm.nih.gov/pubmed Link to the video tutorial: http://media.hsls.pitt.edu/media/clres2705/mesh.swf http://www.hsls.pitt.edu/molbio

  29. PubMed Query Using MeSH http://www.hsls.pitt.edu/guides/genetics

  30. PubMed Query Using MeSH http://www.hsls.pitt.edu/guides/genetics

  31. Building a PubMed Query http://www.hsls.pitt.edu/guides/genetics

  32. Building a PubMed Query http://www.hsls.pitt.edu/guides/genetics

  33. Building a PubMed Query http://www.hsls.pitt.edu/guides/genetics

  34. Building a PubMed Query http://www.hsls.pitt.edu/guides/genetics

  35. Building a PubMed Query http://www.hsls.pitt.edu/guides/genetics

  36. Building PubMed Queries http://www.hsls.pitt.edu/guides/genetics

  37. Useful Links for MeSH • MESH Browser: http://www.ncbi.nlm.nih.gov/mesh • 18 ways to improve your Pubmed searches by Carrie Iwema • http://bitesizebio.com/2008/03/05/18-ways-to-improve-your-pubmed-searches/ • Searching by using the MeSH Database. NCBI Handbook : • http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helppubmed&part=pubmedhelp#pubmedhelp.Searching_by_using_t http://www.hsls.pitt.edu/guides/genetics

  38. What genes are reported to be associated with the disease SCHIZOPHRENIA?

  39. Topic-Specific PubMed Queries http://www.nlm.nih.gov/bsd/special_queries.html http://www.hsls.pitt.edu/guides/genetics

  40. Find genes that are reported to be associated with the disease SCHIZOPHRENIA by searching PubMed • Resources • PubMed Clinical Queries: http://www.ncbi.nlm.nih.gov/pubmed/clinical Link to the video tutorial: http://media.hsls.pitt.edu/media/clres2705/scz.swf http://www.hsls.pitt.edu/molbio

  41. PubMed Special Topic Queries http://www.hsls.pitt.edu/molbio

  42. Search Filters http://www.hsls.pitt.edu/molbio

  43. PubMed Search Filter: Medical Genetics • ("schizophrenia"[MeSH Terms] OR "schizophrenia"[All Fields]) AND (("genetics, medical"[MeSH Terms] OR ("genetics"[All Fields] AND "medical"[All Fields]) OR "medical genetics"[All Fields] OR ("medical"[All Fields] AND "genetics"[All Fields])) OR ("genotype"[MeSH Terms] OR "genotype"[All Fields]) OR "genetics"[Subheading] AND ("genetics"[Subheading] OR "genetics"[All Fields] OR "genetics"[MeSH Terms])) http://www.hsls.pitt.edu/molbio

  44. Topic-Specific PubMed Queries

  45. PubMed Search Result Display How to digest this? http://www.hsls.pitt.edu/molbio

  46. Data Mining- Knowledge Discovery http://www.hsls.pitt.edu/molbio http://www.hsls.pitt.edu/molbio

  47. Next-Generation Literature Search Tools GoPubMed Quertle

  48. Latest Innovations in Literature Searching • GoPubMed Display search results sorted into meaningful topics and subtopics http://www.hsls.pitt.edu/molbio

  49. GoPubMed www.gopubmed.com http://www.hsls.pitt.edu/molbio

  50. Find genes that are reported to be associated with the disease SCHIZOPHRENIA by using GoPubMed • Resources • GoPubMed: http://www.gopubmed.org/web/gopubmed/2?WEB10O00h00100090000 Link to the video tutorial: http://media.hsls.pitt.edu/media/clres2705/gopubmed.swf http://www.hsls.pitt.edu/molbio

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