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NCBI Literature Databases: PubMed

Session #1, April 28, 2005Session #1, April 28, 2005Session #2, April 29, 2005Session #2, April 29, 2005 Ho Chi Minh City, VietNamHo Chi Minh City, VietNam

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The National Institutes of Health

Bethesda, MD

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The National Center for Biotechnology Information

• Created as a part of NLM in 1988– Establish public databases– Perform research in computational biology– Develop software tools for sequence analysis– Disseminate biomedical information

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Number of Users and Hits Per Day

0

50,000

100,000

150,000

200,000

250,000

300,000

350,000

400,000

450,000

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1997 1998 1999 2000 2001 2002 2003

Christmas &New Year’s

Days

NCBI, Currently averaging15,000,000 to 50,000,000

hits per day!

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PubMed Hits for March 2005

Saturday &Sunday ~6 million

hits/day

PubMed averages10,000,000 to 13,000,000

hits per day!

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Countries of Origin

U.S.U.S.(.com, .net, (.com, .net, .org,.org,

..govgov, .us), .us)40%40%

Japan 6%Italy 4%

Canada 3%

Germany 3%

United Kingdom3%

Netherlands 2%

Spain 2%

Brazil 2%Sweden 1%Switzerland 1%Belgium1%

OtherOther14%14%

U.S.U.S.(.com, .net, (.com, .net, .org,.org,

..govgov, .us), .us)40%40%

Japan 6%Italy 4%

Canada 3%

Germany 3%

United Kingdom3%

Netherlands 2%

Spain 2%

Brazil 2%Sweden 1%Switzerland 1%Belgium1%

OtherOther14%14%

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Literature Databases

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A part of the NCBI Bookshelf

Part 1. The Databases

Part 3. Querying and Linking the Data

Part 2. Data Flow and Processing

Part 4. User Support

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OMIM - A catalogue of genes involved with human disease processes - Detailed clinical and reference information - Curated and maintained by Johns Hopkins - Links to PubMed and sequence databases

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PubMed URL:

• http://www.ncbi.nlm.nih.gov/

• http://www.pubmed.gov/

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How to Query a Particular Database

(term1[tag delimiter] op term2[tag delimiter] op …)

tag delimiter = Entrez indexing field

op = AND, OR, NOT

Text WordJournalMeSH TermsAuthor

Boolean operators MUST be in ALL CAPS!

Examples oftag delimiters

term1 term2

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Sample PubMed QueryBrauninger a c-src kinase

Text WordJournalMeSH TermsAuthor

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Using Fields to Find RecordsAffiliationAll FieldsAuthorEC/RN NumberEntrez DateFilterGrant NumberIssueJournalLanguageMeSH DateMeSH Major TopicMeSH SubheadingMeSH TermsPaginationPharmacological ActionPublication DatePublication TypeSecondary Source IDSubstance NameText WordTitleTitle/AbstractVolume

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#1: thyroid peroxidase 340

#2: thyroid peroxidase AND human[orgn] 291

#3: thyroid peroxidase[title] AND human[orgn] 166

#4: #3 AND srcdb_refseq[prop] 5

#5: #3 AND srcdb_ddbj/embl/genbank[prop] 161

#6: #5 AND gbdiv_est[prop] 20

#7: #5 AND gbdiv_pri[prop] 141

#8: #7 AND biomol_genomic[prop] 25

#9: #7 AND biomol_mrna[prop] 116

Using Field Limits

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Complex searches you can do with Preview/Index

How many rat Unigene clusters contain at least one mRNA?

rat [organism]

Terms used (and indexed) in Entrez fieldscan be searched to gain useful information!

1) Select the UniGene database.2) Find all the rat records.3) Find those that have ≥ 1 mRNAs. (“not 0”)NOT

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Complex Queries with Preview/Index

NOT 0 [mRNA Count]

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EntrezEntrez

PopSet

Structure

PubMed

Books

3D Domains

Taxonomy

GEO/GDS

UniGene

Nucleotide

Protein Genome

OMIM

CDD/CDART

Journals

SNP

UniSTS

PubMed Central

Gene

HomoloGeneHomoloGene

Gene

NLM CatalogPubChem

BioAssaysCompounds

Substances

Cancer Chromosomes

GenSat GenomeProjects

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Other Advanced Queries

UniSTS: Markers on the Genethon map of human chromosome 12

Genethon [Map Name] AND human [organism] AND 12 [chromosome]

Nucleotide: Non-genomic sequences from the PLN division of Genbank

gbdiv_pln [properties] NOT biomol_genomic [properties]

Protein: RefSeq sequences with molecular weights of 80 to 100 kDa

srcdb_refseq [properties] AND 080000:100000 [Molecular Weight]

Structure: Structures of bacterial kinases with resolutions below 2 Å

Bacteria [organism] AND kinase AND 000.00:002.00 [resolution]

SNP: True SNPs that are uniquely mapped on the mouse genome

Snp [SNP Class] AND 1 [Map Weight] AND mouse [organism]

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“Global Entrez Query”

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NM_000249: PubMed

Books

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Books Link

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OMIM: Human Disease Genes

Conserved Domain

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Search Engines

• OAIster - http://www.oaister.org/

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Sources for Full Text

• Directory of Open Access Journals - http://www.doaj.org/

• Health Internetwork

• Institutional Archives e.g. http://archives.eprints.org/

• BioLine International - http://www.bioline.org.br/