1. NCBI Literature Databases: PubMed
Session #1, April 28, 2005 Session #2, April 29, 2005
Ho Chi Minh City, VietNam

2. The National Institutes of Health
Bethesda, MD

3. 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

4. Number of Users and Hits Per Day
NCBI, Currently averaging
15,000,000 to 50,000,000
hits per day!
The number refers to NCBI, the bulk of the hits and users just uses PubMed
Christmas &
New Year’s Days

5. Sunday ~6 million hits/day
PubMed Hits for March 2005
PubMed averages
10,000,000 to 13,000,000
hits per day!
graph_hits.png
Bar chart shows data from last month
Line graphs show historical data for comparisons:
 2 months ago (thick solid line); 3 months ago (solid line); 4 months ago (dashed line); 5 months ago (dotted line)
Saturday &
Sunday ~6 million hits/day

6. Countries of Origin

7. Literature Databases

9. A part of the NCBI Bookshelf
Part 2. Data Flow and Processing
Part 1. The Databases
Part 3. Querying and Linking the Data
Part 4. User Support
A part of the NCBI Bookshelf

13. 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

14. PubMed URL:

15. How to Query a Particular Database
term1 term2
(term1[tag delimiter] op term2[tag delimiter] op …)
op = AND, OR, NOT
Boolean operators MUST be in ALL CAPS!
With the exception of PubMed, boolean operators must be in all CAPS, but since so many users do not follow this convention in PubMed, lower case and upper case boolean operators are both accepted.
tag delimiter = Entrez indexing field
Text Word
Journal
MeSH Terms
Author
Examples of
tag delimiters

16. Sample PubMed Query Brauninger a c-src kinase Text Word Journal
MeSH Terms
Author
Brauninger a (author name) & c-src kinase (name of protein)
Click on “Details” to show the actual Entrez query structure.
Order of word identification…..
1. Organism classification (Cancer = crab)
2. Journal name (jmb = journal of molecular biology)
3. Key word list (MESH terms)
4. Author name (“last name” “first initial”)

17. Using Fields to Find Records
Affiliation
All Fields
Author
EC/RN Number Entrez Date
Filter
Grant Number
Issue
Journal
Language
MeSH Date
MeSH Major Topic
MeSH Subheading
MeSH Terms
Pagination
Pharmacological Action
Publication Date
Publication Type
Secondary Source ID
Substance Name
Text Word
Title Title/Abstract
Volume

18. Using Fields to Find Records
Accession
All Fields
Author
EC/RN Number
Feature Key
Filter
Gene Name
Issue
Journal
Keyword
Modification Date
Organism
Page Number
Primary Accession
Properties
Protein Name
Publication Date
SeqID String
Sequence Length
Substance Name
Text Word
Title
Volume
Most useful search field [Organism]:
human[orgn] …or… bacteria[orgn]
Useful search terms in [Properties] field:
srcdb: “source database” ( srcdb_genbank[prop] )
gbdiv: “genbank division” ( gbdiv_est[prop] )
biomol: “biomolecular type” ( biomol_mrna[prop] )

19. Using Field Limits #1: thyroid peroxidase 340
#2: thyroid peroxidase AND human[orgn]
#3: thyroid peroxidase[title] AND human[orgn]
#4: #3 AND srcdb_refseq[prop]
#5: #3 AND srcdb_ddbj/embl/genbank[prop]
#6: #5 AND gbdiv_est[prop]
#7: #5 AND gbdiv_pri[prop]
#8: #7 AND biomol_genomic[prop]
#9: #7 AND biomol_mrna[prop]

20. Complex searches you can do with Preview/Index
Terms used (and indexed) in Entrez fields
can be searched to gain useful information!
How many rat Unigene clusters contain at least one mRNA?
Select the UniGene database.
Find all the rat records.
Find those that have ≥ 1 mRNAs. (“not 0”)
NOT
rat [organism]

21. Complex Queries with Preview/Index
NOT 0 [mRNA Count]

22. Batch Downloads

23. Batch Downloads: FASTA and GI list

24. The (ever expanding) Entrez System
PubChem
NLM Catalog
Entrez
PopSet
Structure
PubMed
Books
3D Domains
Taxonomy
GEO/GDS
UniGene
Nucleotide
Protein
Genome
OMIM
CDD/CDART
Journals
SNP
UniSTS
PubMed Central
Gene
HomoloGene
Protein
Sequence/Structure
Compounds
BioAssays
Genome
Sequence/Structure
Substances
Literature
Organism
Expression
Sequence
Nucleotide
HomoloGene
Based on key word searching (MESH terms, author names, gene names, accession or gi numbers, or just recognized patterns in the records).
15 database are included….
Gene
GenSat
GenomeProjects
Cancer Chromosomes

25. Other Advanced Queries
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 : [Molecular Weight]
SNP: True SNPs that are uniquely mapped on the mouse genome
Snp [SNP Class] AND 1 [Map Weight] AND mouse [organism]
UniSTS: Markers on the Genethon map of human chromosome 12
Genethon [Map Name] AND human [organism] AND 12 [chromosome]
Structure: Structures of bacterial kinases with resolutions below 2 Å
Bacteria [organism] AND kinase AND : [resolution]

26. “Global Entrez Query”

27. NM_000249: PubMed
Books

28. Books Link

29. OMIM: Human Disease Genes
Conserved Domain

30. Search Engines
OAIster -

31. Sources for Full Text
Directory of Open Access Journals -
Health Internetwork
Institutional Archives e.g.
BioLine International -