NCBI
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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 |
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Contents
About NCBI
NCBI is the National Center for Biotechnology Information at the National Libraries of Medicine at the NIH.
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 <protect>
| 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 |
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Discussion
References
See Help:References for how to manage references in EcoliWiki.
