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

Molecular Biology Information Service

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

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

Research Lifecycle

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

Literature Informatics

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

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

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?

Searching PubMed

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

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

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

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

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)

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

MeSH Indexing Source: NLM

MeSH Indexing

MeSH Indexing

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

PubMed Query Using MeSH

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

PubMed Query Using MeSH

PubMed Query Using MeSH

Building a PubMed Query

Building a PubMed Query

Building a PubMed Query

Building a PubMed Query

Building a PubMed Query

Building PubMed Queries TermBooleanTermBooleanTerm# papers DengueANDOutbreaks823 Dengue *ANDOutbreaks746 DengueANDOutbreaksANDIndia123 Dengue*ANDOutbreaksANDIndia116 DengueANDOutbreaks/ statistics and numerical data ANDIndia7 Dengue*ANDOutbreaks/ statistics and numerical data ANDIndia7

Useful Links for MeSH MESH Browser: Link to Wikipedia, Youtube videos, blogs etc on “medical subject heading”:  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

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

Topic-Specific PubMed Queries

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

Research on Optimal Search Strategies

PubMed Special Topic Queries

Search Filters

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]))

Topic-Specific PubMed Queries

PubMed Search Result Display How to digest this?

Data Mining- Knowledge Discovery

Next-Generation Literature Search Tools

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

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

GoPubMed

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

GoPubMed Search Result

GoPubMed Search Result Analysis

GoPubMed Search Result Analysis

Latest Innovations in Literature Searching

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

PubMed driven Web Tools

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

Extract gene list from Literature

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?

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

Search Engine for NIH funded research

NIH Grant Applications to Gene List

PubMed MESHGoPubMed Quertle

Search Engine for finding Disease Causing Genes

Search Engine Just for Human Genetics CDC HuGENavigator :

 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:

GWAS Catalog

Search Engine Just for Human Genetics

Search Engine Just for Human Genetics CDC HuGENavigator :

Search Engine Just for Human Genetics

Search Engine Just for Human Genetics CDC HuGENavigator :

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

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

Software for Finding Similar Texts in Published Literature

Text-based Similarity Search Tools Search Box:

Text Similarity Search Tools eTBLAST

Text Similarity Search Tools eTBLAST

Text Similarity Search Tools

Déjà Vu: a Database of Highly Similar Citations

Reference Management Tools

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

My NCBI

My NCBI 4

My NCBI Notification

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

PDF Reader

NextGen PDF Reader: Utopia docs

Utopia Docs PMID:

READCUBE READCUBE MEDIA FILE MendeleyUtopia Docs

Search Engine for Life Scientists

Molecular Databases

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

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

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

Search for bioinformatics Resources Locate online tools that predict phosphorylation sites in a protein sequence. Link to the video tutorial: Resources Search.HSLS.MolBio :

Life Sciences Search Engine

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.

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

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

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

Thank you! Any questions? Ansuman Chattopadhyay