[BioC] webbioc chicken

Nianhua Li nli at fhcrc.org
Wed Feb 21 04:06:55 CET 2007

Hi, Jane,

AnnBuilder has been extended for chicken last year, but the annotation coverage
was not good:

I just created a chicken annotation package for R 2.5. All the source data
(Affymetrix, Entrez, GO, KEGG) were download on Aug, 2006. So, the source data
version is consistent with other annotation data packages on bioc 1.9 and 2.0.
You can find it at
The data coverage is still not very good. We extract gene name (nomenclature
name) and cytogenetic map from Entrez Gene. Unfortunately, those information is
missing for chicken in the source.

Quality control information for  chicken
Date built: Created: Tue Feb 20 17:28:51 2007

Number of probes: 38535
Probe number missmatch: None
Probe missmatch: None
Mappings found for probe based rda files:
         chickenACCNUM found 37846 of 38535
         chickenCHRLOC found 6718 of 38535
         chickenCHR found 22902 of 38535
         chickenENTREZID found 23306 of 38535
         chickenENZYME found 184 of 38535
         chickenGENENAME found 0 of 38535
         chickenGO found 11342 of 38535
         chickenMAP found 0 of 38535
         chickenPATH found 305 of 38535
         chickenPMID found 7647 of 38535
         chickenREFSEQ found 23050 of 38535
         chickenSUMFUNC found 0 of 38535
         chickenSYMBOL found 23302 of 38535
         chickenUNIGENE found 13617 of 38535
Mappings found for non-probe based rda files:
         chickenENZYME2PROBE found 88
         chickenGO2ALLPROBES found 3247
         chickenGO2PROBE found 1848
         chickenORGANISM found 1
         chickenPATH2PROBE found 60
         chickenPFAM found 18588
         chickenPMID2PROBE found 2672
         chickenPROSITE found 13449

hope this is helpful


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