Hi everyone, I am currently in the process of making a R package which implements some of my work and in order to make it faster and more reliable, I am planning to make a custom annotation package with a custom schema (although this would be based on existing schema). Are their any guidelines for creating such annotation packages? I couldn't see anything on BioC. In all I am planning on creating this package and releasing it and was wondering if there was a code review process implemented for any new packages? I have found the current guidelines for R packages and was wondering if there were anything similar for BioC. Many thanks in advance, Nathan Harmston

Hi Nathan, If you plan to make a custom annotation package you should read the SQLForge.pdf vignette that you can find in the AnnotationDbi package. You can find the information here: http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html Since the annotation packages are automatically generated using this code, we haven't needed a complex review process for those. But you should contact me if you have any further questions about submitting them to bioconductor, Marc Nathan Harmston wrote: > Hi everyone, > > I am currently in the process of making a R package which implements > some of my work and in order to make it faster and more reliable, I am > planning to make a custom annotation package with a custom schema > (although this would be based on existing schema). Are their any > guidelines for creating such annotation packages? I couldn't see > anything on BioC. > > In all I am planning on creating this package and releasing it and was > wondering if there was a code review process implemented for any new > packages? I have found the current guidelines for R packages and was > wondering if there were anything similar for BioC. > > Many thanks in advance, > > Nathan Harmston > > _______________________________________________ > 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 > >

following up slightly on what Marc Carlson already said, in general schema that are close, but not identical to the ones that are provided now are problematic as they tend to lead to confusion and make it difficult for package authors to accommodate them, so please do one of these three things: 1) use the standard schema, 2) discuss needed changes with us (on bioc-devel though) as there are almost surely some changes that might benefit all and we can see if changes to the existing schema are possible (not this close to the release though - any changes would only make it into 2.4) 3) use something completely different, with a very different naming convention best wishes Robert Nathan Harmston wrote: > Hi everyone, > > I am currently in the process of making a R package which implements > some of my work and in order to make it faster and more reliable, I am > planning to make a custom annotation package with a custom schema > (although this would be based on existing schema). Are their any > guidelines for creating such annotation packages? I couldn't see > anything on BioC. > > In all I am planning on creating this package and releasing it and was > wondering if there was a code review process implemented for any new > packages? I have found the current guidelines for R packages and was > wondering if there were anything similar for BioC. > > Many thanks in advance, > > Nathan Harmston > > _______________________________________________ > 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org