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Professional Development Course 1 – Molecular Medicine June 07, 2011

Professional Development Course 1 – Molecular Medicine June 07, 2011. 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, 2011

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  1. Professional Development Course 1 – Molecular MedicineJune 07, 2011 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/guides/genetics

  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/guides/genetics

  5. June 07: Literature Informatics June 08: Genome Browsers

  6. Growth of PubMed Citations . p53 Lu et al. Database (Oxford). 2011; 2011: baq036 Feb 24, 2011 http://www.hsls.pitt.edu/guides/genetics

  7. Topics • PubMed query construction using Medical Subject Headings (MESH) terms • NextGen literature mining tools • Text similarity search engine for finding related articles, suitable journals for manuscript submission ..etc • Search engine for finding disease causing genes and disease causing SNPs • On line reference management tools • Post publication metrics 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: 91,997 Schizophrenia gene: 6664 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. MeSH Indexing http://www.hsls.pitt.edu/guides/genetics

  18. 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

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

  20. 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/molbiovideos/pubmedsearch1.swf http://www.hsls.pitt.edu/molbio

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

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

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

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

  29. 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 • Link to Wikipedia, Youtube videos, blogs etc on “medical subject heading”: • http://www.kosmix.com/topic/Medical_Subject_Headings? http://www.hsls.pitt.edu/guides/genetics

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

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

  32. 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/molbiovideos/pubmedsearch2.swf http://www.hsls.pitt.edu/molbio

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

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

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

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

  37. 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/molbiovideos/gopubmed.swf http://www.hsls.pitt.edu/molbio

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

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

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

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

  42. GoPubMed • Noteworthy links --- GoPubMed: exploring PubMed with the Gene Ontology. Doms A, Schroeder M., Nucleic Acids Res. 2005 Jul 1; 33 (Web Server issue): W783-6. http://www.ncbi.nlm.nih.gov/pubmed/15980585 --- Wiki, YouTube ,Blogs and Tweets: http://www.kosmix.com/topic/GoPubmed? http://www.hsls.pitt.edu/guides/genetics

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

  44. Search Engine Just for Human Genetics CDC HuGENavigator : http://hugenavigator.net/ http://www.hsls.pitt.edu/guides/genetics

  45. Find human genes that are reported to be • associated with the Asthma • Find human SNPs that are reported to be • associated with the Asthma • Resources • HugeNavigator: http://hugenavigator.net/HuGENavigator/home.do Link to the video tutorial: http://media.hsls.pitt.edu/media/molbiovideos/asthma.swf http://www.hsls.pitt.edu/molbio

  46. Search Engine Just for Human Genetics http://www.hsls.pitt.edu/guides/genetics

  47. Search Engine Just for Human Genetics CDC HuGENavigator : http://hugenavigator.net/ http://www.hsls.pitt.edu/guides/genetics

  48. GWAS Catalog • http://www.genome.gov/multimedia/illustrations/GWAS_2010_2nd.pdf http://www.hsls.pitt.edu/guides/genetics

  49. Search Engine Just for Human Genetics http://hugenavigator.net/HuGENavigator/huGEPedia.do http://www.hsls.pitt.edu/guides/genetics

  50. Search Engine Just for Human Genetics CDC HuGENavigator : http://hugenavigator.net/ http://www.hsls.pitt.edu/guides/genetics

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