NCBI: Difference between revisions
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[http://www.ncbi.nlm.nih.gov/ {{PAGENAME}}] is... | [http://www.ncbi.nlm.nih.gov/ {{PAGENAME}}] is... | ||
==Content== | ==Content== | ||
We have separate EcoliWiki pages for several parts of NCBI, including | |||
* [[Clusters_of_Orthologous_Groups_(COGs)]] | |||
* [[Conserved Domain Database (CDD)]] | |||
* [[Gene Expression Omnibus (GEO)]] | |||
* [[NCBI Short Read Archive]] | |||
==Using {{PAGENAME}}== | ==Using {{PAGENAME}}== | ||
===Browsing=== | ===Browsing=== | ||
Revision as of 19:45, 9 June 2009
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| Link/URL: | |
|---|---|
| What: |
National Center for Biotechnology Information |
| Who: |
National Library of Medicine, National Institutes of Health |
| Updates: | |
| Upcoming events: | |
| Web Services: | |
| edit table |
About NCBI
Add general information here NCBI is...
Content
We have separate EcoliWiki pages for several parts of NCBI, including
- Clusters_of_Orthologous_Groups_(COGs)
- Conserved Domain Database (CDD)
- Gene Expression Omnibus (GEO)
- NCBI Short Read Archive
Using NCBI
Browsing
Searching
Searching across databases can be done using Entrez. Alternatively, use the pull-down menu to specify searching within a specific database.
NCBI Entrez Protein: query by protein_id (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein&cmd=Retrieve&list_uids=1788157&dopt=GenPept)
NCBI PubMed: query by gene name OR b# AND Escherichia coli (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=PubMed&term=%28edd+OR+b1851%29+AND+escherichia+coli&tool=fuzzy&ot=%28edd+OR+b1851%29+AND+%27Escherichia+coli%27%29)
NCBI Entrez Gene: query by gene_id (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=graphics&list_uids=946362)
NCBI Entrez Genome: query by gene name (http://www.ncbi.nlm.nih.gov/genomes/altvik.cgi?gi=115&db=g&gene=edd)
Usage examples
Add links to additional pages describing success stories here.
Technology
Web Services/API
NCBI E-Utils web services can be used with Entrez databases
| Entrez Database | Primary ID | E-Utility Database Name | Example query |
|---|---|---|---|
|
3D Domains |
3D SDI |
domains |
|
|
Domains |
PSSM-ID |
cdd |
|
|
Genome |
Genome ID |
genome |
|
|
Nucleotide |
GI number |
nucleotide |
|
|
OMIM |
MIM number |
omim |
|
|
PopSet |
Popset ID |
popset |
|
|
Protein |
GI number |
protein |
|
|
ProbeSet |
GEO ID |
geo |
|
|
PubMed |
PMID |
pubmed |
|
|
Structure |
MMDB ID |
structure |
|
|
SNP |
SNP ID |
snp |
|
|
Taxonomy |
TAXID |
taxonomy |
|
|
UniGene |
UniGene ID |
unigene |
|
|
UniSTS |
UniSTS ID |
unists |
|
| edit table |
Discussion
References
See Help:References for how to manage references in EcoliWiki.