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Genes, Proteins and Literature Searching

Genes, Proteins and Literature Searching

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Genes, Proteins and Literature Searching

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  1. Genes, Proteins and Literature Searching AnsumanChattopadhyay, PhD Molecular Biology Information Services Health Sciences Library System University of Pittsburgh ansuman@pitt.edu

  2. Molecular Biology Information Service http://www.hsls.pitt.edu/guides/genetics

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

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

  5. Growth of PubMed Citations . p53 Lu et al. Database (Oxford). 2011: baq036 Feb 28th 2012 http://www.hsls.pitt.edu/molbio

  6. Research Lifecycle http://www.hsls.pitt.edu/molbio

  7. Topics http://www.hsls.pitt.edu/guides/genetics

  8. Literature Informatics http://www.hsls.pitt.edu/guides/genetics

  9. Literature Informatics Learn how to .. find the most appropriate literature .. mine the literature .. manage your collected information .. browse the scientific papers http://www.hsls.pitt.edu/molbio

  10. 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

  11. Literature Informatics • 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

  12. Searching PubMed http://www.hsls.pitt.edu/molbio

  13. Literature Informatics 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

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

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

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

  17. 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

  18. 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

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

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

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

  22. 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

  23. PubMed Query Using MeSH http://www.ncbi.nlm.nih.gov/mesh http://www.hsls.pitt.edu/molbio

  24. 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

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

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

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

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

  33. 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

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

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

  36. 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

  37. Research on Optimal Search Strategies http://www.hsls.pitt.edu/molbio

  38. PubMed Special Topic Queries http://www.hsls.pitt.edu/molbio

  39. Search Filters http://www.hsls.pitt.edu/molbio

  40. 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

  41. Topic-Specific PubMed Queries

  42. PubMed Search Result Display How to digest this? http://www.hsls.pitt.edu/molbio

  43. Data Mining- Knowledge Discovery http://www.hsls.pitt.edu/molbio http://www.hsls.pitt.edu/molbio

  44. Next-Generation Literature Search Tools

  45. PubMed based Tools http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search/ Lu et al. Database (Oxford). 2011; 2011: baq036 http://www.hsls.pitt.edu/molbio

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

  47. GoPubMed www.gopubmed.com http://www.hsls.pitt.edu/molbio

  48. 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

  49. GoPubMed Search Result http://www.hsls.pitt.edu/molbio

  50. GoPubMed Search Result Analysis http://www.hsls.pitt.edu/molbio