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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

2 Molecular Biology Information Service

3 HSLS Molecular Biology Information Service WorkshopsWebsite Software Licensing Bioinformatics Consultations

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

5 Growth of PubMed Citations Lu et al. Database (Oxford). 2011: baq K Breast Cancer 97K Schizophrenia 8.7K BRCA1 61K. p53 Feb 28 th 2012

6 Research Lifecycle

7 Topics Literature Informatics Search Engine for Life Sciences HSLS Mol Bio Information Service

8 Literature Informatics

9 Literature Informatics Learn how to.. find the most appropriate literature.. mine the literature.. manage your collected information.. browse the scientific papers

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

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?

12 Searching PubMed

13 Literature Informatics Citations: 20 million Journals: 5200 Schizophrenia: 96,912 Schizophrenia gene: 7382 Dengue outbreaks in India: 329 Dengue outbreaks statistics India: 21

14 Challenges Am I getting everything / the right things? How to digest this?

15 PubMed Search Am I getting the right things?  Construct PubMed queries with MeSH terms using MeSH browser

16 Medical Subject Headings (MeSH) 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)

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

19 MeSH Indexing Source: NLM

20 MeSH Indexing

21 MeSH Indexing

22 PubMed Search  Retrieve published articles on  Dengue outbreaks in India including  Statistical and numerical data on dengue outbreaks

23 PubMed Query Using MeSH

24 Find articles on “Dengue outbreaks in India” by searching PubMed using MeSH terms Link to the video tutorial: Resources Mesh Browser : PubMed:

25 PubMed Query Using MeSH

26 PubMed Query Using MeSH

27 Building a PubMed Query

28 Building a PubMed Query

29 Building a PubMed Query

30 Building a PubMed Query

31 Building a PubMed Query

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

33 Useful Links for MeSH MESH Browser: Link to Wikipedia, Youtube videos, blogs etc on “medical subject heading”:  18 ways to improve your Pubmed searches by Carrie Iwema  searches/ searches/ Searching by using the MeSH Database. NCBI Handbook :  =pubmedhelp#pubmedhelp.Searching_by_using_t =pubmedhelp#pubmedhelp.Searching_by_using_t

34 PubMed Query  What genes are reported to be associated with the disease SCHIZOPHRENIA ?  Topic-Specific PubMed Queries

35 Topic-Specific PubMed Queries

36 Find genes that are reported to be associated with the disease SCHIZOPHRENIA by searching PubMed Link to the video tutorial: Resources PubMed Clinical Queries:

37 Research on Optimal Search Strategies

38 PubMed Special Topic Queries

39 Search Filters

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]))

41 Topic-Specific PubMed Queries

42 PubMed Search Result Display How to digest this?

43 Data Mining- Knowledge Discovery

44 Next-Generation Literature Search Tools

45 PubMed based Tools Lu et al. Database (Oxford). 2011; 2011: baq036 /

46 Latest Innovations in Literature Searching GoPubMed Display search results sorted into meaningful topics and subtopics

47 GoPubMed

48 Find genes that are reported to be associated with the disease SCHIZOPHRENIA by using GoPubMed Link to the video tutorial: Resources GoPubMed:

49 GoPubMed Search Result

50 GoPubMed Search Result Analysis

51 GoPubMed Search Result Analysis

52 Latest Innovations in Literature Searching

53 GoPubMed Noteworthy links GoPubMed: exploring PubMed with the Gene Ontology. Doms A,Schroeder M., Nucleic Acids Res Jul 1; 33 (Web Server issue):W

54 PubMed driven Web Tools

55 PubMed based Tools Lu et al. Database (Oxford). 2011; 2011: baq036 /

56 Extract gene list from Literature

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?

58 A short video on Quertle Link to the video tutorial: Resources Quertle:

59 Search Engine for NIH funded research

60 NIH Grant Applications to Gene List

61 PubMed MESHGoPubMed Quertle

62 Search Engine for finding Disease Causing Genes

63 Search Engine Just for Human Genetics CDC HuGENavigator :

64  Find human genes reported to be associated with Asthma  Find human SNPs reported to be associated with Asthma Link to the video tutorial: Resources HugeNavigator:

65 GWAS Catalog

66 Search Engine Just for Human Genetics

67 Search Engine Just for Human Genetics CDC HuGENavigator :

68 Search Engine Just for Human Genetics

69 Search Engine Just for Human Genetics CDC HuGENavigator :

70 Find Disease Causing SNPs What SNPs are associated with “Schizophrenia”?

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:

74 Text Similarity Search Tools eTBLAST

75 Text Similarity Search Tools eTBLAST

76 Text Similarity Search Tools

77 Déjà Vu: a Database of Highly Similar Citations

78 Reference Management Tools

79 Automated Notification Tool Save your searches at My NCBI and set up an notification on new publication based on your search query

80 My NCBI

81 My NCBI 4

82 My NCBI Notification

83 Reference Management Tools Connotea CiteULike Mendaley Zotero online downloadable Scientific Research Papers Web pages EndNote Refworks

84 PDF Reader

85 NextGen PDF Reader: Utopia docs

86 Utopia Docs PMID:

87 READCUBE READCUBE MEDIA FILE MendeleyUtopia Docs

88 Search Engine for Life Scientists

89 Molecular Databases

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 Growth of bioinformatics tools

91 Biomedical & Life Sciences Search Engines  OBRC : University of Pittsburgh  Bioinformatics.ca  OReFil : University of Tokyo

92 Peptide Sequence >nxp|NX_P |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 Search for bioinformatics Resources Locate online tools that predict phosphorylation sites in a protein sequence. Link to the video tutorial: Resources Search.HSLS.MolBio :

94 Life Sciences Search Engine

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

97 Summary  Setup 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

98 Links MESH Database: PubMed Special Topic Queries: GoPubMed: CDC HuGENavigator : Novoseek: etBLAST: déjà vu: MyNCBI: CiteUlike: Publish or Perish: OBRC:

99 Thank you! Any questions? Ansuman Chattopadhyay


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