[Bioc-devel] Feedback on OrganismDb development

Obenchain, Valerie Valerie.Obenchain at roswellpark.org
Fri Apr 8 23:48:17 CEST 2016 

On 04/08/2016 02:34 PM, Obenchain, Valerie wrote:
> 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/

By 'use some development' I mean we have them on the TODO to work on
after the release.

Valerie
>
>
> 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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