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Locating Gene/Protein Information January 11, 2011

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  1. Locating Gene/Protein InformationJanuary 11, 2011 AnsumanChattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of Pittsburgh ansuman@pitt.edu http://www.hsls.pitt.edu/molbio

  2. Objectives • Generate a gene list • Mine gene/protein information http://www.hsls.pitt.edu/molbio

  3. Topics • Literature Informatics • Gene / Protein Information Gateways • Search Engine for MolBio/ Bioinformatics Databases and Software http://www.hsls.pitt.edu/molbio

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

  5. http://www.hsls.pitt.edu/guides/genetics

  6. Literature Informatics Which genes/proteins are reported to be associated with the disease - Schizophrenia? Citations: 19 million Journals: 5200 Schizophrenia: 86,384.. 96234 Schizophrenia gene: 5851…7295 http://www.hsls.pitt.edu/guides/genetics

  7. Challenges in Literature Search • Am I getting everything? • Too much Information.. How to digest? A list with citations http://www.hsls.pitt.edu/guides/genetics

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

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

  10. 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

  11. 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

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

  13. MeSH Indexing Genes/Chemicals MeSH Terms http://www.hsls.pitt.edu/guides/genetics

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

  15. 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

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

  17. Useful links for MESH • MESH Browser: http://www.ncbi.nlm.nih.gov/mesh • Link to Wikipedia, Youtube videos, blogs etc on “medical subject heading”: • http://www.kosmix.com/topic/Medical_Subject_Headings? • 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

  18. 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

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

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

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

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

  23. 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

  24. PubMed Search Result Display http://www.hsls.pitt.edu/guides/genetics

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

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

  27. 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

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

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

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

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

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

  33. Literature to Gene List • GLAD4U • http://bioinfo.vanderbilt.edu/glad4u/ http://www.hsls.pitt.edu/guides/genetics

  34. Gene list to common functions http://www.hsls.pitt.edu/guides/genetics

  35. Literature to Gene list http://www.quertle.info/ http://www.hsls.pitt.edu/guides/genetics

  36. NIH Grant Applications to Gene List http://www.hsls.pitt.edu/guides/genetics

  37. Curated Molecular Databases http://www.hsls.pitt.edu/guides/genetics

  38. Molecular Databases • Nucleic Acids Research : Annual databases Issue • NAR: Annual Web Server Issue • Oxford Journal : Bioinformatics • BioMedCentral: BMC Bioinformatics Growth of bioinformatics tools http://www.hsls.pitt.edu/guides/genetics

  39. Growth of Molecular Databases 2011: 1330 2008: 1078 Source: Nodal Point Blog http://www.hsls.pitt.edu/guides/genetics

  40. GWA Studies Catalog http://www.hsls.pitt.edu/guides/genetics

  41. GWA Studies Catalog http://www.genome.gov/gwastudies/ http://www.hsls.pitt.edu/guides/genetics

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

  43. 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/clres2705/asthma.swf http://www.hsls.pitt.edu/molbio

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

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

  46. Search Engine Just for Human Genetics http://hugenavigator.net/HuGENavigator/huGEPedia.do 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. Find Disease Causing SNPs http://hugenavigator.net/HuGENavigator/gWAHitStartPage.do What SNPs are associated • with “Schizophrenia”? http://www.hsls.pitt.edu/guides/genetics

  49. Hands-On exercise on lit search • Which proteins are related to Alzheimer’s disease? • Where/who are the leading centers and scientists for liver transplantation? • Which hormones are Autistic Disorder associated with? http://www.hsls.pitt.edu/guides/genetics

  50. Gene/Protein Information Mining http://www.hsls.pitt.edu/guides/genetics