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Professional Development Course 1 – Molecular Medicine June 07, 2012

Professional Development Course 1 – Molecular Medicine June 07, 2012. Ansuman Chattopadhyay , PhD Head, Molecular Biology Information Services Health Sciences Library System University of Pittsburgh ansuman@pitt.edu http://www.hsls.pitt.edu/guides/genetics.

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Professional Development Course 1 – Molecular Medicine June 07, 2012

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  1. Professional Development Course 1 –Molecular MedicineJune 07, 2012 AnsumanChattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of Pittsburgh ansuman@pitt.edu http://www.hsls.pitt.edu/guides/genetics

  2. Genomic achievements since the Human Genome Project ED Greenet al.Nature470, 204-213 (2011) doi:10.1038/nature09764

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

  4. Ansuman Chattopadhyay, 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

  5. June 07: Literature Informatics Bioinformatics Search Engines June 12: Genome Browsers June 14: Gene-Protein Knowledge Bases http://www.hsls.pitt.edu/molbio

  6. Topics • Literature Informatics • Comprehensive search: • MESH term based PubMed Search • PubMed special topics query • Next-generation literature search tools: • Gopubmed , EtBlast • GLAD4U, Quertle • HugeNavigator http://www.hsls.pitt.edu/guides/genetics

  7. Growth of PubMed Citations . p53 Lu et al. Database (Oxford). 2011; 2011: baq036 Feb 16, 2012 http://www.hsls.pitt.edu/guides/genetics

  8. Literature Informatics • What genes are reported to be associated with the disease SCHIZOPHRENIA? • Find published literature on DENGUE OUTBREAKS in India with statistical and numerical data on this outbreaks. http://www.hsls.pitt.edu/guides/genetics

  9. Literature Informatics Schizophrenia: 96,234 Schizophrenia gene: 7295 Citations: 20 million Journals: 5200 Dengue outbreaks in India: 302 Dengue outbreaks statistics India: 18 http://www.hsls.pitt.edu/guides/genetics

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

  11. PubMed Search • Am I getting the right things? Construct PubMed queries with MeSH terms using MeSH browser http://www.hsls.pitt.edu/guides/genetics

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

  13. 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

  14. 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

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

  16. MeSH Indexing PMD: 18045777 http://www.hsls.pitt.edu/guides/genetics

  17. Medical Subject Heading (MESH) http://www.hsls.pitt.edu/guides/genetics

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

  19. PubMed Search

  20. PubMed Search • Retrieve published articles on • Dengue outbreaks in India including • Statistical and numerical data on dengue outbreaks http://www.hsls.pitt.edu/guides/genetics

  21. PubMed Query Using MeSH http://www.ncbi.nlm.nih.gov/mesh http://www.hsls.pitt.edu/guides/genetics

  22. 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

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

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

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

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

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

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

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

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

  31. Useful Links for MeSH • MESH Browser: http://www.ncbi.nlm.nih.gov/mesh • 18 ways to improve your Pubmed searches by Carrie Iwema • http://goo.gl/B8rFf • Searching by using the MeSH Database. NCBI Handbook : • http://goo.gl/X4UAe http://www.hsls.pitt.edu/guides/genetics

  32. PubMed Query • What genes are reported to be associated with the disease SCHIZOPHRENIA ? • Topic-Specific PubMed Queries http://www.hsls.pitt.edu/guides/genetics

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

  34. 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

  35. Research on Optimal Search Strategies http://www.hsls.pitt.edu/guides/genetics

  36. Research on Optimal Search Strategies http://www.hsls.pitt.edu/guides/genetics

  37. PubMed Special Topic Queries http://www.hsls.pitt.edu/guides/genetics

  38. Search Filters http://www.hsls.pitt.edu/guides/genetics

  39. 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/guides/genetics

  40. PubMed Search Result Display How to digest this? http://www.hsls.pitt.edu/guides/genetics

  41. Next-Generation Literature Search Tools

  42. GoPubMed Display search results sorted into meaningful topics and subtopics http://www.hsls.pitt.edu/guides/genetics

  43. GoPubMed www.gopubmed.com http://www.hsls.pitt.edu/guides/genetics

  44. 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

  45. GoPubMed Search Result http://www.hsls.pitt.edu/guides/genetics

  46. GoPubMed Search Result Analysis http://www.hsls.pitt.edu/guides/genetics

  47. GoPubMed Search Result Analysis http://www.hsls.pitt.edu/guides/genetics

  48. Latest Innovations in Literature Searching http://www.hsls.pitt.edu/guides/genetics

  49. GoPubMed • Noteworthy links GoPubMed: exploring PubMed with the Gene Ontology. DomsA,Schroeder M., Nucleic Acids Res. 2005 Jul 1; 33 (Web Server issue):W783-6. http://www.ncbi.nlm.nih.gov/pubmed/15980585 http://www.hsls.pitt.edu/guides/genetics

  50. PubMed driven Web Tools http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search/

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