Question: KEGG pathway IDs ,issing
0
gravatar for Daniel Brewer
10.6 years ago by
Daniel Brewer1.9k
Daniel Brewer1.9k wrote:
Dear list, I am fiddling around with KEGG.db and KEGGSOAP and I am finding that some of the networkd in KEGG.db are not available through the KEGGSOAP API. FOr example, hsa05030 : Amyotrophic lateral sclerosis (ALS) When I search for the name on the KEGG website I get a different number e.g. hsa05014. Is this because the KEGG.db annotation package is old? > sessionInfo() R version 2.8.1 (2008-12-22) i386-apple-darwin8.11.1 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] KEGG.db_2.2.5 org.Hs.eg.db_2.2.6 RSQLite_0.7-1 [4] DBI_0.2-4 AnnotationDbi_1.4.3 Biobase_2.2.2 [7] KEGGSOAP_1.16.0 SSOAP_0.4-6 RCurl_0.94-1 [10] XML_2.3-0 reshape_0.8.2 plyr_0.1.5 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}}
annotation cancer keggsoap • 485 views
ADD COMMENTlink modified 10.6 years ago by Marc Carlson7.2k • written 10.6 years ago by Daniel Brewer1.9k
Answer: KEGG pathway IDs ,issing
0
gravatar for Marc Carlson
10.6 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi Daniel, Yes. We rebuild all of the annotation packages for each new release (which happens twice a year). The new KEGG.db has the term you found and will be available in a matter of days as part of the new release. Marc Daniel Brewer wrote: > Dear list, > > I am fiddling around with KEGG.db and KEGGSOAP and I am finding that > some of the networkd in KEGG.db are not available through the KEGGSOAP > API. FOr example, > > hsa05030 : Amyotrophic lateral sclerosis (ALS) > > When I search for the name on the KEGG website I get a different number > e.g. hsa05014. > > Is this because the KEGG.db annotation package is old? > > >> sessionInfo() >> > R version 2.8.1 (2008-12-22) > i386-apple-darwin8.11.1 > > locale: > en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] KEGG.db_2.2.5 org.Hs.eg.db_2.2.6 RSQLite_0.7-1 > [4] DBI_0.2-4 AnnotationDbi_1.4.3 Biobase_2.2.2 > [7] KEGGSOAP_1.16.0 SSOAP_0.4-6 RCurl_0.94-1 > [10] XML_2.3-0 reshape_0.8.2 plyr_0.1.5 > > Thanks > > Dan > >
ADD COMMENTlink written 10.6 years ago by Marc Carlson7.2k
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