genes, proteins and literature searching ansuman chattopadhyay, phd molecular biology information...

Genes, Proteins and Literature Searching

Ansuman Chattopadhyay, PhDMolecular Biology Information ServicesHealth Sciences Library SystemUniversity of [email protected]

mailto:[email protected]

Molecular Biology Information Service

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


http://www.hsls.pitt.edu/

HSLS Molecular Biology Information Service

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Bioinformatics Consultations

http://www.hsls.pitt.edu/molbio


ED Green et al. Nature 470, 204-213 (2011) doi:10.1038/nature09764

Genomic achievements since the Human Genome Project

Growth of PubMed Citations

Lu et al. Database (Oxford). 2011: baq036

240 K

• Breast Cancer

97K • Schizophrenia

8.7K • BRCA1

61K. p53

Feb 28th 2012




Research Lifecycle




http://goo.gl/shGsH

Topics

Literature Informatics

Search Engine for Life Sciences

HSLS Mol Bio Information Service




Learn how to

.. find the most appropriate literature

.. mine the literature

.. manage your collected information

.. browse the scientific papers





Comprehensive search: MESH term based PubMed Search PubMed special topics query

Next-generation literature search tools: GoPubMed, eTBlast Quertle HuGE Navigator Utopia Docs





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





Citations: 20 millionJournals: 5200

Schizophrenia: 96,912Schizophrenia 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. 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



MeSH Indexing


Source: NLM


MeSH Indexing



PubMed Search

Retrieve published articles

on Dengue outbreaks in India

including Statistical and numerical data on dengue

outbreaks



PubMed Query Using MeSH http://www.ncbi.nlm.nih.gov/mesh


http://www.ncbi.nlm.nih.gov/mesh



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• PubMed: http://www.ncbi.nlm.nih.gov/pubmed


http://media.hsls.pitt.edu/media/clres2705/mesh.swf


http://www.ncbi.nlm.nih.gov/pubmed

PubMed Query Using MeSH



Building a PubMed Query



Building PubMed QueriesTerm Boolean Term Boolean Term # papers

Dengue AND Outbreaks 823

Dengue * AND Outbreaks 746

Dengue AND Outbreaks AND India 123

Dengue* AND Outbreaks AND India 116

Dengue AND Outbreaks/statistics and numerical data

AND India 7

Dengue* AND Outbreaks/statistics and numerical data

AND India 7



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-s

earches/ 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.kosmix.com/topic/Medical_Subject_Headings?

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/

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helppubmed&part=pubmedhelp

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helppubmed&part=pubmedhelp


PubMed Query

What genes are reported to be associated with the disease SCHIZOPHRENIA ?

Topic-Specific PubMed Queries



Topic-Specific PubMed Querieshttp://www.nlm.nih.gov/bsd/special_queries.html


http://www.nlm.nih.gov/bsd/special_queries.html



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://media.hsls.pitt.edu/media/clres2705/scz.swf

http://www.ncbi.nlm.nih.gov/pubmed/clinical

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 digestthis?


Data Mining-Knowledge Discovery

http://www.hsls.pitt.edu/molbiohttp://www.hsls.pitt.edu/molbio



Next-Generation Literature Search Tools

PubMed based Tools


Lu et al. Database (Oxford). 2011; 2011: baq036

http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search/




Latest Innovations in Literature Searching

GoPubMed Display search results sorted into meaningful topics and subtopics



GoPubMed


www.gopubmed.com


http://www.gopubmed.com/


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://media.hsls.pitt.edu/media/clres2705/gopubmed.swf

http://www.gopubmed.org/web/gopubmed/2?WEB10O00h00100090000

GoPubMed Search Result



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. 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


PubMed driven Web Tools





PubMed based Tools


Lu et al. Database (Oxford). 2011; 2011: baq036





Extract gene list from Literature


http://www.quertle.info/



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:http://media.hsls.pitt.edu/media/molbiovideos/quertle-ac0212.swf

Resources

• Quertle: www.quertle.info


http://media.hsls.pitt.edu/media/molbiovideos/gquertle-ac0212.swf


Search Engine for NIH funded research http://projectreporter.nih.gov/reporter.cfm


http://projectreporter.nih.gov/reporter.cfm


NIH Grant Applications to Gene List



PubMed

MESH GoPubMed Quertle

Search Engine for finding

Disease Causing Genes

Search Engine Just for Human GeneticsCDC HuGENavigator : http://hugenavigator.net/


http://hugenavigator.net/



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://media.hsls.pitt.edu/media/clres2705/asthma.swf

http://hugenavigator.net/HuGENavigator/home.do

GWAS Catalog http://www.ebi.ac.uk/fgpt/gwas/#timeseriestab


http://www.ebi.ac.uk/fgpt/gwas/


Search Engine Just for Human Genetics



Search Engine Just for Human Geneticshttp://hugenavigator.net/HuGENavigator/huGEPedia.do


http://hugenavigator.net/HuGENavigator/huGEPedia.do


Find Disease Causing SNPs

What SNPs are associated with “Schizophrenia”?

http://hugenavigator.net/HuGENavigator/gWAHitStartPage.do


http://hugenavigator.net/HuGENavigator/gWAHitStartPage.do


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

eTBLASThttp://etest.vbi.vt.edu/etblast3/


http://etest.vbi.vt.edu/etblast3/



eTBLAST



Déjà Vu: a Database of Highly Similar Citationshttp://dejavu.vbi.vt.edu/dejavu/duplicate/


http://dejavu.vbi.vt.edu/dejavu/duplicate/


Reference Management Tools



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




My NCBI1

23



My NCBI


4


My NCBI email Notification



Reference Management Tools

Connotea

CiteULike

Mendaley

Zotero

online

downloadable

Scientific Research Papers

Web pages

EndNoteRefworks



PDF Reader




NextGen PDF Reader: Utopia docs



Utopia DocsPMID: 22683712

READCUBE

READCUBE MEDIA FILE

Mendeley Utopia Docs

Search Engine for Life Scientists



Molecular Databases



Molecular Databases

Nucleic Acids Research : Annual databases Issue NAR: Annual Web Server Issue Oxford Journal : Bioinformatics BioMedCentral: BMC Bioinformatics


Growth of bioinformatics tools

http://nar.oxfordjournals.org/content/vol36/suppl_1/index.dtl

http://nar.oxfordjournals.org/content/vol35/suppl_2/index.dtl

http://bioinformatics.oxfordjournals.org/

http://www.biomedcentral.com/bmcbioinformatics/

http://www.biomedcentral.com/bmcbioinformatics/


Biomedical & Life Sciences Search Engines

OBRC : University of Pittsburgh

http://www.hsls.pitt.edu/molbio/obrc

Bioinformatics.cahttp://bioinformatics.ca/links_directory/

OReFil : University of Tokyo

http://orefil.dbcls.jp/


http://www.hsls.pitt.edu/guides/genetics/obrc

http://bioinformatics.ca/links_directory/



http://orefil.dbcls.jp/


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


Search for bioinformatics ResourcesLocate 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 :


http://media.hsls.pitt.edu/media/Search%20Bioinfo%20Resoursec.swf

Life Sciences Search Enginehttp://www.hsls.pitt.edu/molbio/


http://www.hsls.pitt.edu/molbio/


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 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



Links MESH Database: http://www.ncbi.nlm.nih.gov/mesh PubMed Special Topic Queries:

http://www.nlm.nih.gov/bsd/special_queries.html GoPubMed: http://www.gopubmed.com CDC HuGENavigator : http://hugenavigator.net/ Novoseek: http://www.novoseek.com etBLAST: http://etest.vbi.vt.edu/etblast3/ déjà vu: http://dejavu.vbi.vt.edu/dejavu/duplicate/ MyNCBI: http://www.ncbi.nlm.nih.gov/sites/myncbi/ CiteUlike: http://www.citeulike.org/ Publish or Perish: http://www.harzing.com/pop.htm OBRC: http://www.hsls.pitt.edu/guides/genetics/obrc



http://www.nlm.nih.gov/bsd/special_queries.html

http://www.gopubmed.com/


http://www.novoseek.com/

http://etest.vbi.vt.edu/etblast3/

http://dejavu.vbi.vt.edu/dejavu/duplicate/


http://www.citeulike.org/

http://www.harzing.com/pop.htm

http://www.hsls.pitt.edu/guides/genetics/obrc


Thank you!Any questions?

Ansuman [email protected]


mailto:[email protected]


genes, proteins and literature searching ansuman chattopadhyay, phd molecular biology information...

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