Question: Genecards v3 access
0
gravatar for Daniel Brewer
8.9 years ago by
Daniel Brewer1.9k
Daniel Brewer1.9k wrote:
Hello, Just wondering if there was a way to interrogate genecards v3 from within bioconductor/R? Thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}
cancer • 1.8k views
ADD COMMENTlink modified 8.9 years ago by Sean Davis21k • written 8.9 years ago by Daniel Brewer1.9k
Answer: Genecards v3 access
1
gravatar for Sean Davis
8.9 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Mon, Sep 13, 2010 at 6:56 AM, Daniel Brewer <daniel.brewer@icr.ac.uk>wrote: > Hello, > > Just wondering if there was a way to interrogate genecards v3 from > within bioconductor/R? > > Hi, Dan. Are you aware of an API for querying and returning structured data from GeneCards? As far as I know, the information is limited to HTML results to online queries. Also, I am not aware of batch query capabilities for that site (well, they are limited to 100 genes/day, so I don't count that as batch). What information were you interested in getting from GeneCards? It might be possible to get that information via other resources like biomaRt, NCBI, UCSC, or the annotation packages. Sean [[alternative HTML version deleted]]
ADD COMMENTlink written 8.9 years ago by Sean Davis21k
Hi Dan, I don't know if it is quite what you are looking for or not, but there are a set of custom annotation packages based on the GeneCards database which are maintained by Francesco Ferrari. You can see them listed on the annotation page here: http://www.bioconductor.org/packages/release/data/annotation/ Marc On 09/13/2010 04:14 AM, Sean Davis wrote: > On Mon, Sep 13, 2010 at 6:56 AM, Daniel Brewer <daniel.brewer at="" icr.ac.uk="">wrote: > > >> Hello, >> >> Just wondering if there was a way to interrogate genecards v3 from >> within bioconductor/R? >> >> >> > Hi, Dan. > > Are you aware of an API for querying and returning structured data from > GeneCards? As far as I know, the information is limited to HTML results to > online queries. Also, I am not aware of batch query capabilities for that > site (well, they are limited to 100 genes/day, so I don't count that as > batch). > > What information were you interested in getting from GeneCards? It might be > possible to get that information via other resources like biomaRt, NCBI, > UCSC, or the annotation packages. > > Sean > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 8.9 years ago by Marc Carlson7.2k
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