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Innovations in Literature Informatics: Insights from the Molecular Biology Information Service

Join us for a comprehensive exploration of literature informatics with experts Ansuman Chattopadhyay, PhD, and Carrie L. Iwema, PhD, at the University of Pittsburgh. This session covers effective literature searching strategies for molecular biology, protein synthesis, and genetic research. Attendees will learn to utilize advanced tools, including intuitive PubMed searches and next-generation literature search methodologies. The workshop aims to enhance your ability to find, manage, and utilize scientific literature for research. Engage with peers and enhance your informational skills in the biomedical field.

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Innovations in Literature Informatics: Insights from the Molecular Biology Information Service

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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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