On Apr 7, 2016, at 8:34 AM, Vincent Carey <stvjc at channing.harvard.edu> wrote:
On Thu, Apr 7, 2016 at 11:24 AM, Tim Triche, Jr. <tim.triche at 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.Obenchain at 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:
?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. Thank you.