My only concern regarding AnnotationHub is offline use. I find that I'm more productive if I turn off the network interface altogether... Maybe I'm the only one. BiomaRt also scarred me a little.
--t > On Apr 7, 2016, at 8:34 AM, Vincent Carey <st...@channing.harvard.edu> wrote: > > > >> On Thu, Apr 7, 2016 at 11:24 AM, Tim Triche, Jr. <tim.tri...@gmail.com> >> wrote: >> Great! This is an awesome opportunity to move to ENSEMBL as a default ;-) >> (only half kidding, by the way) >> >> 1) BSGenome/2bit would be great -- I use this sometimes to generate fusion >> transcripts with defined breakpoints to supplement existing txomes >> >> 2) class name: don't change it >> >> 3) pre made packages: god yes. Try creating an ENSEMBL TxDb from a GTF on a >> laptop sometime! I am planning to try and help a bit in this respect with >> direct Reactome mappings of various ID types for downstream analysis so this >> is not just a feature request, I will help with it. > > I think this is a different concern. The TxDb infrastructure seems sound, > and EnsDb is useful too... but they are not well-harmonized; TxDb works > nicely with Gviz. I do think that we should have a richer collection of > interoperable transcript model sources packaged. But the OrganismDb > discipline, if I understand it correctly, only specifies links among diverse > annotation packages and helps with cross-package joins. > > An afterthought -- maybe the TxDb annotation package discipline will give way > to queries to AnnotationHub. OrganismDb instance construction would specify > AnnotationHub entities that comprise the instance and, on use, retrieve form > AnnotationHub whatever is not in the cache. > >> >> Thanks for picking this up. I and others use the organismdbi packages all >> the time and was wondering what would become of them now that Marc moved to >> Seattle Children's. It is great to hear that they will receive renewed >> attention because it is a really handy infrastructure. About all I could ask >> for is Drosophila, Danio, and Caenorhabditis organism packages ;-) >> >> Thank you, >> >> --t >> >> > On Apr 7, 2016, at 7:34 AM, Obenchain, Valerie >> > <valerie.obench...@roswellpark.org> wrote: >> > >> > BioC developers, >> > >> > After the release we plan to continue development the OrganismDb class >> > and packages. This email outlines some ideas for future direction. We're >> > interested in feedback on these points as well as other thoughts people >> > might have. >> > >> > ## Background >> > >> > The OrganismDb class is defined in the OrganismDbi package and consists >> > of a TxDb object and the combined mappings from GO.db and an OrgDb. It >> > supports the select() interface as well as several range-based >> > extractors such as exons(), transcripts(), etc. The idea was that given >> > a particular organism, a user would only need a single package to access >> > both system biology and transcripts-centric annotations. >> > >> > We currently have 3 OrganismDb packages >> > (http://www.bioconductor.org/packages/release/BiocViews.html#___OrganismDb). >> > These are light weight and don't contain any data themselves but instead >> > point to the GO.db, OrgDb and TxDb packages. >> > >> > ## Current issues >> > >> > - Support for sequence representation >> > >> > We've discussed incorporating an optional sequence component, maybe >> > BSgenome or 2bit or ... ? >> > >> > >> > - Class name >> > >> > OrganismDb is similar to OrgDb which could cause some confusion. We are >> > considering renaming ... here are a few ideas. Let us know what you >> > think or add your suggestion. >> > >> > OrganismDb (fine as is, leave it) >> > FullOrgDb >> > CrossDb >> > MultipleDb >> > >> > >> > - Package name >> > >> > The current names are not very descriptive: Homo.sapiens, Mus.musculus >> > and Rattus.norvegicus. We'd like to follow the naming convention used >> > in our BSgenome and TxDb packages which means including the source, >> > build and track from the TxDb as well as preceding with the class type. >> > >> > For example, the current 'Homo.sapiens' package would be renamed >> > 'OrganismDb.Hsapiens.UCSC.hg19.knownGene'. >> > >> > >> > - Pre-made packages >> > >> > Is it useful to supply pre-made packages or just increase awareness of >> > the helpers so users can make their own? Current helpers: >> > >> >> ?makeOrganism >> > ?makeOrganismDbFromBiomart ?makeOrganismDbFromTxDb >> > ?makeOrganismDbFromUCSC ?makeOrganismPackage >> > >> > NOTE: makeOrgansimPackage() will be renamed to makeOrganismDbPackage(). >> > >> > >> > Thanks. >> > Valerie >> > >> > >> > This email message may contain legally privileged and/or confidential >> > information. If you are not the intended recipient(s), or the employee or >> > agent responsible for the delivery of this message to the intended >> > recipient(s), you are hereby notified that any disclosure, copying, >> > distribution, or use of this email message is prohibited. If you have >> > received this message in error, please notify the sender immediately by >> > e-mail and delete this email message from your computer. 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