Question: annotation data packages in BioC1.9
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gravatar for Nianhua Li
13.0 years ago by
Nianhua Li870
Nianhua Li870 wrote:
Hi, I would like to briefly summarize the changes of annotation data packages in release 1.9. ================== Package Statistics ================== genome annotation packages: 8 CDF packages: 301 probe data packages: 279 annotation packages: 330 Among the above 918 packages, 206 CDF, 206 probe and 206 annotation packages are provided by Molecular and Behavioral Neuroscience Institute of University of Michigan. ============ New Packages ============ Annotation data for codelink chips from GE healthcare, contributed by Diego Diez adme16cod ADME Rat 16-Assay Bioarray Annotation Data h10kcod CodeLink UniSet Human I Bioarray (~10 000 human genes) Annotation Data h20kcod CodeLink UniSet Human 20k I Bioarray Annotation Data hi16cod CodeLink Human Inflammation 16 Bioarray Annotation Data hwgcod CodeLink Human Whole Genome Bioarray (~55 000 human genes) Annotation Data m10kcod CodeLink UniSet Mouse I Bioarray (~10 000 mouse gene targets) Annotation Data m20kcod CodeLink UniSet Mouse 20k I Bioarray Annotation Data mi16cod CodeLink Mouse Inflammation 16 Bioarray Annotation Data mwgcod CodeLink Mouse Whole Genome Bioarray (~36 000 mouse gene targets) Annotation Data r10kcod CodeLink UniSet Rat I Bioarray (~10 000 rat gene targets) Annotation Data ri16cod CodeLink Rat Inflammation 16 Bioarray Annotation Data rwgcod CodeLink Rat Whole Genome Bioarray (~34 000 rat gene targets) Annotation Data Annotation data for chips from RNA/MRC, contributed by Simon de Bernard hs25kresogen RNG_MRC Human Pangenomic 25k Set Annotation Data (hs25kresogen) mm24kresogen RNG_MRC Mouse Pangenomic 24k Set Annotation Data (mm24kresogen) ==================== Deprecated Packages ==================== prt440acdf and prt440scdf ================================ Major Changes in Annotation Data ================================ All the LOCUSID environments (e.g. hgu95av2LOCUSID, GOLOCUSID2GO) in annotation packages are deprecated, and ENTREZID environments (e.g. hgu95av2ENTREZID, GOENTREZID2GO) are provided as replacements. ========================================== Bug Fix and Minor Changes in Annotation Data ========================================== ** Fixed data parsing problem in GENENAME environments in annotation packages. (bug report: http://article.gmane.org/gmane.science.biology.informatics.conductor/1 0076) ** Fixed data parsing problem in MAP environments in annotation packages. Here is an example: > get("40653_at", hgu95av2MAP) in older version: [1] "1q43|1q23.1 according to Sierra (Genomics 79" [2] " 177" [3] " 2002) [AFS]" now: [1] "1q43" [2] "1q23.1 according to Sierra (Genomics 79, 177, 2002) [AFS]" ** Update on ath1121501 and ag: ** add ENTREZID environment for compatible with GoHyperG (bug report: http://article.gmane.org/gmane.science.biology.informatics.conductor/9 715) ** add GENENAME environment (feature request: http://article.gmane.org/gmane.science.biology.informatics.conductor/8 984 and http://article.gmane.org/gmane.science.biology.informatics.conductor/4 793) ** change data source of PubMed annotation (feature request: http://article.gmane.org/gmane.science.biology.informatics.conductor/7 945) ** add KEGG pathway annotation to PATH environment, move AraCyc pathway annotation to ARACYC environment ** change source of probe to gene mapping, now use TAIR ** add MULTIHIT environment when one probe maps to multiple genes cheers nianhua
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