Question: entrez gene summary
0
gravatar for Amit Kumar Kashyap
6.9 years ago by
Amit Kumar Kashyap50 wrote:
Hello All , I have a list of genes (HUGO gene symbols ) or Entrez IDs . I would like to get the entrez gene summaries for those genes. Does any one know if there is R package exits by which I get obtain entrez gene summary. e.g http://www.ncbi.nlm.nih.gov/gene/1 I would like to extract summary part from this page. Thanks Cheers ! - Amit [[alternative HTML version deleted]]
• 1.8k views
ADD COMMENTlink modified 6.9 years ago by David Westergaard280 • written 6.9 years ago by Amit Kumar Kashyap50
Answer: entrez gene summary
0
gravatar for David Westergaard
6.9 years ago by
David Westergaard280 wrote:
Dear Amit, You can retrieve the XML record by making use the Entrez Programming Utilities. This is descirbed at http://www.ncbi.nlm.nih.gov/books/NBK25499/. Looking through the page, they give an example of how to retrieve the XML record for a gene: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=2& retmode=xml. You can probably retrieve the XML record using Curl, wget or similar, and then parse it using an XML parser in your favorite language. Best, David 2012/7/24 Amit Kumar Kashyap <amitonbiochem at="" gmail.com="">: > Hello All , > > I have a list of genes (HUGO gene symbols ) or Entrez IDs . I would like to > get the entrez gene summaries for those genes. > > Does any one know if there is R package exits by which I get obtain entrez > gene summary. > e.g > http://www.ncbi.nlm.nih.gov/gene/1 > > I would like to extract summary part from this page. > > > > Thanks > > Cheers ! > - Amit > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 6.9 years ago by David Westergaard280
Or if you are satisfied with specific fields like the gene name, you could just use one of the annotation packages: library(org.Hs.eg.db) symbols = c( "A1BG", "A2M", "A2MP1") select(org.Hs.eg.db, keys=symbols, cols=c("GENENAME"), keytype="ALIAS") Marc On 07/24/2012 09:57 AM, David Westergaard wrote: > Dear Amit, > > You can retrieve the XML record by making use the Entrez Programming > Utilities. This is descirbed at > http://www.ncbi.nlm.nih.gov/books/NBK25499/. Looking through the page, > they give an example of how to retrieve the XML record for a gene: > http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id= 2&retmode=xml. > You can probably retrieve the XML record using Curl, wget or similar, > and then parse it using an XML parser in your favorite language. > > Best, > David > > 2012/7/24 Amit Kumar Kashyap<amitonbiochem at="" gmail.com="">: >> Hello All , >> >> I have a list of genes (HUGO gene symbols ) or Entrez IDs . I would like to >> get the entrez gene summaries for those genes. >> >> Does any one know if there is R package exits by which I get obtain entrez >> gene summary. >> e.g >> http://www.ncbi.nlm.nih.gov/gene/1 >> >> I would like to extract summary part from this page. >> >> >> >> Thanks >> >> Cheers ! >> - Amit >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 6.9 years ago by Marc Carlson7.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 234 users visited in the last hour