ncbi pubmed ncbi literature databases: pubmed session #1, april 28, 2005 session #2, april 29, 2005...
TRANSCRIPT
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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 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
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150,000
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250,000
300,000
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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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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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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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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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edThe (ever expanding) Entrez System
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]