[Bioc-devel] Feedback on OrganismDb development
Obenchain, Valerie
Valerie.Obenchain at roswellpark.org
Fri Apr 8 23:33:57 CEST 2016
Hi,
It sounds like we have agreement on these points:
- Add support for sequences
- Keep the OrganismDb name
- Do provide pre-built packages
I'm not sure we got much weigh in on the package name. I tend towards a
more descriptive name. This post (to me) is an example of the confusion
that can come from a very general name:
https://support.bioconductor.org/p/80612/
These areas could use some development:
- More support for Ensembl-based tracks:
I don't think we're moving to ENSEMBL as a default (sorry Tim!) but we
can provide more Ensembl-centric TxDbs.
- Role of AnnotationHub:
We have thought of storing the sqlite dbs in AnnotationHub and creating
an OrganismDb on the fly. There is the issue of working off-line that
Tim brought mentioned. We plan to do some testing with this after the
release.
- Better advertise the useful operations one can do with OrganismDb such
as seqinfo, seqlengths, symbol translations etc.
Tim and Ludwig, you asked for a few specific organisms. In devel we now
have TxDbs for all mentioned except ecoli and arabidopsis so you can
make your own OrganismDb with makeOrganismPackage(). I'm planning to
send out a summary email to bioc-devel out that highlights the new Txdbs
and other changes to the annotation in 3.3.
Thanks for the feedback.
Valerie
On 04/07/2016 08:38 AM, Tim Triche, Jr. wrote:
> 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 <stvjc at channing.harvard.edu
> <mailto:stvjc at channing.harvard.edu>> wrote:
>
>>
>>
>> On Thu, Apr 7, 2016 at 11:24 AM, Tim Triche, Jr.
>> <tim.triche at gmail.com <mailto: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
>> <mailto: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:
>> >
>> >> ?makeOrganism
>> > ?makeOrganismDbFromBiomart ?makeOrganismDbFromTxDb
>> > ?makeOrganismDbFromUCSC ?makeOrganismPackage
>> >
>> > NOTE: makeOrgansimPackage() will be renamed to
>> makeOrganismDbPackage().
>> >
>> >
>> > Thanks.
>> > Valerie
>> >
>> >
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