[Bioc-devel] Feedback on OrganismDb development

Ludwig Geistlinger Ludwig.Geistlinger at bio.ifi.lmu.de
Fri Apr 8 10:45:38 CEST 2016

Dear Valerie,

Thank you for the update.

1) Class name: I'd definitely prefer the exisiting naming over the three
other suggestions you gave.

2) Pre-made packages: Yes, I think it would be great to have such packages
available for well-established Bioc model organisms, i.e. as returned by
AnnotationForge::available.db0pkgs(), or at the very least for

ecoli (Escherichia.coli)
yeast (Saccharomyces.cerevisiae)
arabidopsis (Arabidopsis.thaliana)
fly (Drosophila.melanogaster)
zebrafish (Danio.rerio)
worm (Caenorhabditis.elegans)

(in addition to the exisiting 3 for human, mouse and rat)

Thx & Best,

Dipl.-Bioinf. Ludwig Geistlinger

Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München

Tel.: 089-2180-4067
eMail: Ludwig.Geistlinger at bio.ifi.lmu.de

> 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
> - 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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