NCBI Pub Med NCBI Literature Databases Pub Med
NCBI Pub. Med NCBI Literature Databases: Pub. Med Session #1, April 28, 2005 Session #2, April 29, 2005 Ho Chi Minh City, Viet. Nam
Bethesda, MD NCBI Pub. Med The National Institutes of Health
• 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 NCBI Pub. Med The National Center for Biotechnology Information
1997 1998 1999 2000 2001 2002 2003 NCBI, Currently averaging 15, 000 to 50, 000 hits per day! Christmas & New Year’s Days NCBI Pub. Med Number of Users and Hits Per Day
Pub. Med averages 10, 000 to 13, 000 hits per day! Saturday & Sunday ~6 million hits/day NCBI Pub. Med Hits for March 2005
NCBI Pub. Med Countries of Origin
NCBI Pub. Med Literature Databases
NCBI Pub. Med
Part 2. Data Flow and Processing Part 3. Querying and Linking the Data Part 4. User Support A part of the NCBI Bookshelf NCBI Pub. Med Part 1. The Databases
NCBI Pub. Med
NCBI Pub. Med
NCBI Pub. Med
NCBI Pub. Med OMIM - A catalogue of genes involved with human disease processes - Detailed clinical and reference information - Curated and maintained by Johns Hopkins - Links to Pub. Med and sequence databases
• http: //www. ncbi. nlm. nih. gov/ • http: //www. pubmed. gov/ NCBI Pub. Med URL:
![term 1 term 2 (term 1[tag delimiter] op term 2[tag delimiter] op = AND,](http://slidetodoc.com/presentation_image_h/0fc8952346b8ef14938b01238e628513/image-15.jpg "term 1 term 2 (term 1[tag delimiter] op term 2[tag delimiter] op = AND,")
term 1 term 2 (term 1[tag delimiter] op term 2[tag delimiter] op = AND, OR, NOT ¯Boolean operators MUST be in ALL CAPS! tag delimiter = Entrez indexing field Text Word Journal Me. SH Terms Author Examples of tag delimiters op …) NCBI Pub. Med How to Query a Particular Database
Brauninger a c-src kinase Text Word Journal Me. SH Terms Author NCBI Pub. Med Sample Pub. Med Query
Author EC/RN Number Entrez Date Filter Grant Number Issue Journal Language Me. SH Date Me. SH Major Topic Me. SH Subheading Me. SH Terms Pagination Pharmacological Action Publication Date Publication Type Secondary Source ID Substance Name Text Word Title/Abstract Volume NCBI Pub. Med Using Fields. Affiliation to Find Records All Fields
![NCBI Pub. Med Using Field Limits #1: thyroid peroxidase #2: thyroid peroxidase AND human[orgn]](http://slidetodoc.com/presentation_image_h/0fc8952346b8ef14938b01238e628513/image-18.jpg "NCBI Pub. Med Using Field Limits #1: thyroid peroxidase #2: thyroid peroxidase AND human[orgn]")
NCBI Pub. Med Using Field Limits #1: thyroid peroxidase #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] 5 161 20 141 25 116 340 291 166
Terms used (and indexed) in Entrez fields can be searched to gain useful information! How many rat Unigene clusters contain at least one m. RNA? 1) Select the Uni. Gene database. 2) Find all the rat records. 3) Find those that have ≥ 1 m. RNAs. (“not NOT 0”) rat [organism] NCBI Pub. Med Complex searches you can do with Preview/Index
![NCBI Pub. Med Complex Queries with Preview/Index NOT 0 [m. RNA Count]](http://slidetodoc.com/presentation_image_h/0fc8952346b8ef14938b01238e628513/image-20.jpg "NCBI Pub. Med Complex Queries with Preview/Index NOT 0 [m. RNA Count]")
NCBI Pub. Med Complex Queries with Preview/Index NOT 0 [m. RNA Count]
NLM Catalog Pub. Chem Compounds Bio. Assays Substances OMIM Pub. Med Central Journals 3 D Domains Books Structure Taxonomy CDD/CDART Entrez Protein NCBI Pub. Med The (ever expanding) Entrez System Genome Uni. STS Homolo. Gene SNP Uni. Gene GEO/GDS Gen. Sat Pop. Set Nucleotide Genome. Projects Cancer Chromosomes
![Nucleotide: Non-genomic sequences from the PLN division of Genbank gbdiv_pln [properties] NOT biomol_genomic [properties]](http://slidetodoc.com/presentation_image_h/0fc8952346b8ef14938b01238e628513/image-22.jpg "Nucleotide: Non-genomic sequences from the PLN division of Genbank gbdiv_pln [properties] NOT biomol_genomic [properties]")
Nucleotide: Non-genomic sequences from the PLN division of Genbank gbdiv_pln [properties] NOT biomol_genomic [properties] Protein: Ref. Seq sequences with molecular weights of 80 to 100 k. Da srcdb_refseq [properties] AND 080000: 100000 [Molecular Weight] SNP: True SNPs that are uniquely mapped on the mouse genome Snp [SNP Class] AND 1 [Map Weight] AND mouse [organism] Uni. STS: 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 000. 00: 002. 00 [resolution] NCBI Pub. Med Other Advanced Queries
NCBI Pub. Med “Global Entrez Query”
Books NCBI Pub. Med NM_000249: Pub. Med
Books Link NCBI Pub. Med
Conserved Domain NCBI Pub. Med OMIM: Human Disease Genes
• OAIster - http: //www. oaister. org/ NCBI Pub. Med Search Engines
• Directory of Open Access Journals http: //www. doaj. org/ • Health Internetwork • Institutional Archives e. g. http: //archives. eprints. org/ • Bio. Line International http: //www. bioline. org. br/ NCBI Pub. Med Sources for Full Text
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