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Genes, Proteins and Literature Searching Ansuman Chattopadhyay, PhD Molecular Biology Information Services Health Sciences Library System University of.

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Presentation on theme: "Genes, Proteins and Literature Searching Ansuman Chattopadhyay, PhD Molecular Biology Information Services Health Sciences Library System University of."— Presentation transcript:

1 Genes, Proteins and Literature Searching Ansuman Chattopadhyay, 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 WorkshopsWebsite Software Licensing Bioinformatics Consultations http://www.hsls.pitt.edu/molbio

4 ED Green et al. Nature 470, 204-213 (2011) doi:10.1038/nature09764 Genomic achievements since the Human Genome Project

5 Growth of PubMed Citations Lu et al. Database (Oxford). 2011: baq036 240 K Breast Cancer 97K Schizophrenia 8.7K BRCA1 61K. p53 Feb 28 th 2012 http://www.hsls.pitt.edu/molbio

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

7 Topics Literature Informatics Search Engine for Life Sciences HSLS Mol Bio Information Service 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 Citations: 20 million Journals: 5200 Schizophrenia: 96,912 Schizophrenia gene: 7382 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 The U.S. National Library of Medicine's controlled vocabulary (thesaurus) Arranged in a hierarchical manner called the MeSH Tree Structures Updated annually

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. Anatomy B. Organisms C. Diseases D. Chemical and Drugs E. Analytical, Diagnostic and Therapeutic Techniques and Equipment F. Psychiatry and Psychology G. Biological Sciences H. Physical Sciences I. Anthropology, Education, Sociology and Social Phenomena J. Technology and Food and Beverages K. Humanities L. Information Science M. Persons N. Health Care V. Publication Characteristics Z. Geographic Locations http://www.hsls.pitt.edu/guides/genetics

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

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 Link to the video tutorial: http://media.hsls.pitt.edu/media/clres2705/mesh.swf Resources Mesh Browser : http://www.ncbi.nlm.nih.gov/mesh http://www.ncbi.nlm.nih.gov/mesh PubMed: http://www.ncbi.nlm.nih.gov/pubmed http://www.ncbi.nlm.nih.gov/pubmed

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 TermBooleanTermBooleanTerm# papers DengueANDOutbreaks823 Dengue *ANDOutbreaks746 DengueANDOutbreaksANDIndia123 Dengue*ANDOutbreaksANDIndia116 DengueANDOutbreaks/ statistics and numerical data ANDIndia7 Dengue*ANDOutbreaks/ statistics and numerical data ANDIndia7 http://www.hsls.pitt.edu/guides/genetics

33 Useful Links for MeSH MESH Browser: http://www.ncbi.nlm.nih.gov/mesh 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? 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/ 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.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 http://www.hsls.pitt.edu/molbio Find genes that are reported to be associated with the disease SCHIZOPHRENIA by searching PubMed Link to the video tutorial: http://media.hsls.pitt.edu/media/clres2705/scz.swf Resources PubMed Clinical Queries: http://www.ncbi.nlm.nih.gov/pubmed/clinical http://www.ncbi.nlm.nih.gov/pubmed/clinical

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 http://www.hsls.pitt.edu/molbio How to digest this?

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

44 Next-Generation Literature Search Tools

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

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

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

48 http://www.hsls.pitt.edu/molbio Find genes that are reported to be associated with the disease SCHIZOPHRENIA by using GoPubMed Link to the video tutorial: http://media.hsls.pitt.edu/media/clres2705/gopubmed.swf Resources GoPubMed: http://www.gopubmed.org/web/gopubmed/2?WEB10O00h00100090000 http://www.gopubmed.org/web/gopubmed/2?WEB10O00h00100090000

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

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

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

52 Latest Innovations in Literature Searching http://www.hsls.pitt.edu/molbio

53 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 http://www.ncbi.nlm.nih.gov/pubmed/15980585 http://www.hsls.pitt.edu/molbio

54 PubMed driven Web Tools http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search/ http://www.hsls.pitt.edu/molbio

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

56 Extract gene list from Literature http://www.hsls.pitt.edu/molbio http://www.quertle.info/

57 Questions for Quertle What genes cause Asthma? What cell lines are used in diabetes research? Which cell types are known to express EGFR? What animals are used in studies for diabetes? Which protein kinases activate TP53? http://www.hsls.pitt.edu/molbio

58 A short video on Quertle Link to the video tutorial: http://media.hsls.pitt.edu/media/molbiovideos/quertle-ac0212.swf Resources Quertle: www.quertle.infowww.quertle.info

59 Search Engine for NIH funded research http://projectreporter.nih.gov/reporter.cfm http://www.hsls.pitt.edu/molbio

60 NIH Grant Applications to Gene List http://www.hsls.pitt.edu/molbio

61 PubMed MESHGoPubMed Quertle

62 Search Engine for finding Disease Causing Genes

63 Search Engine Just for Human Genetics CDC HuGENavigator : http://hugenavigator.net/http://hugenavigator.net/ http://www.hsls.pitt.edu/molbio

64  Find human genes reported to be associated with Asthma  Find human SNPs reported to be associated with Asthma Link to the video tutorial: http://media.hsls.pitt.edu/media/clres2705/asthma.swf Resources HugeNavigator: http://hugenavigator.net/HuGENavigator/home.do http://hugenavigator.net/HuGENavigator/home.do

65 GWAS Catalog http://www.ebi.ac.uk/fgpt/gwas/#timeseriestab http://www.hsls.pitt.edu/molbio

66 Search Engine Just for Human Genetics http://www.hsls.pitt.edu/molbio

67 Search Engine Just for Human Genetics CDC HuGENavigator : http://hugenavigator.net/http://hugenavigator.net/ http://www.hsls.pitt.edu/molbio

68 Search Engine Just for Human Genetics http://hugenavigator.net/HuGENavigator/huGEPedia.do http://www.hsls.pitt.edu/molbio

69 Search Engine Just for Human Genetics CDC HuGENavigator : http://hugenavigator.net/http://hugenavigator.net/ http://www.hsls.pitt.edu/molbio

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

71 Hands On Search PubMed and retrieve a list of genes that can serve as biomarkers for Alzheimer Disease

72 Software for Finding Similar Texts in Published Literature

73 Text-based Similarity Search Tools Search Box: http://www.hsls.pitt.edu/molbio

74 Text Similarity Search Tools eTBLAST http://etest.vbi.vt.edu/etblast3/ http://www.hsls.pitt.edu/molbio

75 Text Similarity Search Tools eTBLAST http://www.hsls.pitt.edu/molbio

76 Text Similarity Search Tools http://www.hsls.pitt.edu/molbio

77 Déjà Vu: a Database of Highly Similar Citations http://dejavu.vbi.vt.edu/dejavu/duplicate/ http://www.hsls.pitt.edu/molbio

78 Reference Management Tools http://www.hsls.pitt.edu/molbio

79 Automated email Notification Tool http://www.ncbi.nlm.nih.gov/sites/myncbi/ Save your searches at My NCBI and set up an email notification on new publication based on your search query http://www.hsls.pitt.edu/molbio

80 My NCBI 1 2 3 http://www.hsls.pitt.edu/molbio

81 My NCBI http://www.hsls.pitt.edu/molbio 4

82 My NCBI email Notification http://www.hsls.pitt.edu/molbio

83 Reference Management Tools Connotea CiteULike Mendaley Zotero online downloadable Scientific Research Papers Web pages EndNote Refworks http://www.hsls.pitt.edu/molbio

84 PDF Reader http://www.hsls.pitt.edu/molbio

85 NextGen PDF Reader: Utopia docs http://www.hsls.pitt.edu/molbio

86 Utopia Docs PMID: 22683712

87 READCUBE READCUBE MEDIA FILE MendeleyUtopia Docs

88 Search Engine for Life Scientists http://www.hsls.pitt.edu/molbio

89 Molecular Databases http://www.hsls.pitt.edu/molbio

90 Molecular Databases  Nucleic Acids Research : Annual databases IssueAnnual databases Issue  NAR: Annual Web Server IssueAnnual Web Server Issue  Oxford Journal : BioinformaticsBioinformatics  BioMedCentral: BMC Bioinformatics BioMedCentral: BMC Bioinformatics http://www.hsls.pitt.edu/molbio Growth of bioinformatics tools

91 Biomedical & Life Sciences Search Engines  OBRC : University of Pittsburgh http://www.hsls.pitt.edu/molbio/obrc  Bioinformatics.ca http://bioinformatics.ca/links_directory/  OReFil : University of Tokyo http://orefil.dbcls.jp/ http://www.hsls.pitt.edu/molbio

92 Peptide Sequence >nxp|NX_P00533-1|EGFR|Epidermal growth factor receptor|Iso 1 MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEV VLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALA VLSNYDANKTGLKELPMRNLQEILHGAVRFSNNPALCNVESIQWRDIVSSDFLSNMSMDF QNHLGSCQKCDPSCPNGSCWGAGEENCQKLTKIICAQQCSGRCRGKSPSDCCHNQCAAGC TGPRESDCLVCRKFRDEATCKDTCPPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYV VTDHGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFK NCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAF ENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKL FGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCN LLEGEPREFVENSECIQCHPECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVM GENNTLVWKYADAGHVCHLCHPNCTYGCTGPGLEGCPTNGPKIPSIATGMVGALLLLLVV ALGIGLFMRRRHIVRKRTLRRLLQERELVEPLTPSGEAPNQALLRILKETEFKKIKVLGS GAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGI CLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAA RNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSY GVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPK FRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQ QGFFSSPSTSRTPLLSSLSATSNNSTVACIDRNGLQSCPIKEDSFLQRYSSDPTGALTED SIDDTFLPVPEYINQSVPKRPAGSVQNPVYHNQPLNPAPSRDPHYQDPHSTAVGNPEYLN TVQPTCVNSTFDSPAHWAQKGSHQISLDNPDYQQDFFPKEAKPNGIFKGSTAENAEYLRV APQSSEFIGA

93 http://www.hsls.pitt.edu/molbio Search for bioinformatics Resources Locate online tools that predict phosphorylation sites in a protein sequence. Link to the video tutorial: http://media.hsls.pitt.edu/media/Search%20Bioinfo%20Resoursec.swf Resources Search.HSLS.MolBio :

94 Life Sciences Search Engine http://www.hsls.pitt.edu/molbio/ http://www.hsls.pitt.edu/molbio

95 Hands on (a) Locate two online databases on microRNA targets, and report their URLs. (b) Identify one database that store all HIV inhibiting siRNA data and cite its URL. (c) Cite a paper offering a step-by-step guide for analyzing ChIP-seq data.

96 Summary Construct a comprehensive PubMed query:  MESH Browser Retrieve gene/protein/disease information straight from a PubMed search :  GoPubmed,  Find suitable journals for manuscript submission, etc…  eTBLAST Find disease causing genes and disease causing SNPs:  HUGENavigator_ Geneprospector, Phenopedia, GWASIntegrator http://www.hsls.pitt.edu/guides/genetics

97 Summary  Setup email alert for new publications  My NCBI  Store articles online  CiteULike  Analyze popularity of a published article  Post Publication Metrics  Search for databases and software  OBRC http://www.hsls.pitt.edu/guides/genetics

98 Links MESH Database: http://www.ncbi.nlm.nih.gov/meshhttp://www.ncbi.nlm.nih.gov/mesh PubMed Special Topic Queries: http://www.nlm.nih.gov/bsd/special_queries.html http://www.nlm.nih.gov/bsd/special_queries.html GoPubMed: http://www.gopubmed.comhttp://www.gopubmed.com CDC HuGENavigator : http://hugenavigator.net/http://hugenavigator.net/ Novoseek: http://www.novoseek.comhttp://www.novoseek.com etBLAST: http://etest.vbi.vt.edu/etblast3/http://etest.vbi.vt.edu/etblast3/ déjà vu: http://dejavu.vbi.vt.edu/dejavu/duplicate/http://dejavu.vbi.vt.edu/dejavu/duplicate/ MyNCBI: http://www.ncbi.nlm.nih.gov/sites/myncbi/http://www.ncbi.nlm.nih.gov/sites/myncbi/ CiteUlike: http://www.citeulike.org/ http://www.citeulike.org/ Publish or Perish: http://www.harzing.com/pop.htmhttp://www.harzing.com/pop.htm OBRC: http://www.hsls.pitt.edu/guides/genetics/obrchttp://www.hsls.pitt.edu/guides/genetics/obrc http://www.hsls.pitt.edu/guides/genetics

99 Thank you! Any questions? Ansuman Chattopadhyay ansuman@pitt.edu http://www.hsls.pitt.edu/guides/genetics

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