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Locating Gene/Protein Information September 26, 2013

Locating Gene/Protein Information September 26, 2013. Ansuman Chattopadhyay , PhD Head, Molecular Biology Information Services Health Sciences Library System University of Pittsburgh ansuman@pitt.edu http://www.hsls.pitt.edu/molbio. Topics. Literature Informatics

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Locating Gene/Protein Information September 26, 2013

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  1. Locating Gene/Protein InformationSeptember 26, 2013 AnsumanChattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of Pittsburgh ansuman@pitt.edu http://www.hsls.pitt.edu/molbio

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

  3. 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

  4. 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

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

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

  7. 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

  8. 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

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

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

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

  12. 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

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

  14. 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

  15. 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

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

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

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

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

  20. 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

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

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

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

  24. 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

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

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

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

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

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

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

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

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

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

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

  35. 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

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

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

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

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

  40. 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

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

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

  45. Find Disease Causing SNPs http://hugenavigator.net/HuGENavigator/gWAHitStartPage.do What SNPs are associated • with “Schizophrenia”? http://www.hsls.pitt.edu/guides/genetics

  46. 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

  47. Search Engine for Bioinformatics Tools http://www.hsls.pitt.edu/guides/genetics

  48. Biomedical and Life Sciences Search Engines • OBRC : University of Pittsburgh http://www.hsls.pitt.edu/guides/genetics/obrc • Vadlo http://vadlo.com/ • OReFil : University of Tokyo http://orefil.dbcls.jp/ http://www.hsls.pitt.edu/guides/genetics

  49. Search.HSLS.MolBio http://www.hsls.pitt.edu/molbio http://www.hsls.pitt.edu/guides/genetics

  50. Search.HSLS.MolBio • Integrated search system • Databases & Software • Articles on Databases & Software • Genes/Proteins • Pathways • Protocols • Seminar/Talks Videos • Recommended Articles • Tabbed browsing • Clustered search results http://www.hsls.pitt.edu/guides/genetics

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