Right, there are two things that need to be described: the annotation track
and the reference genome. The annotation track, if given a provider,
version and name, always (well at least in my experience) implies a
particular genome provider/version.

So:

TxDb.Hsapiens.myMart.64.ccds

Might work?

2011/11/4 Hervé Pagès <hpages@fhcrc.org>

> Hi Michael,
>
>
> On 11-11-03 06:36 PM, Michael Lawrence wrote:
>
>> We're actually using a patched version of makeTranscriptDbFromBiomart to
>> get models out of an internal biomart.  Patch is on its way to Marc.
>>
>> So it would be like: TxDb.Hsapiens.BioMart.hg19.**gneGenes?
>>
>
> This suggests that you have a Mart called "hg19" (see below why).
>
>
>
>> Seems weird to mix the technical mode of data retrieval into the name.
>>
>
> The naming scheme when 'Data source' is "BioMart" seems to be a little
> bit different. For example, if I use makeTranscriptDbFromBiomart() with
> biomart="ensembl" and dataset="hsapiens_gene_**ensembl", then I get:
>
>  > GenomicFeatures:::.**makePackageName(txdb)
>  [1] "TxDb.Hsapiens.BioMart.**ensembl.GRCh37.p5"
>
> Token #4 ("ensembl") is the name of the Mart. I'm a little bit
> surprised with token #5 though. I would have expected it to be
> the ensembl version (eventually followed by the reference genome)
> because one can always infer the reference genome from the ensembl
> version but not the other way around. In other words, if Ensembl
> makes 2 or more releases based on the same reference genome, our
> current naming scheme won't differentiate the 2 TxDb packages.
> Wouldn't it be better if we had something like:
>
>  TxDb.Hsapiens.BioMart.ensembl.**63
>  TxDb.Hsapiens.BioMart.ensembl.**64
>
> Anyway, back to your problem. Yes in your case the technical mode
> doesn't really matter so it's really up to you. Maybe being explicit
> about the reference genome (with *.UCSC.hg19.*) is more important
> than the technical mode?
>
> H.
>
>
>> Michael
>>
>> 2011/11/3 Hervé Pagès <hpages@fhcrc.org <mailto:hpages@fhcrc.org>>
>>
>>
>>    Hi Michael,
>>
>>
>>    On 11-11-02 08:58 PM, Michael Lawrence wrote:
>>
>>        What are the precise meanings of the tokens in the TxDb package
>>        names. In
>>        particular, is "UCSC" the genome provider or the annotation
>>        provider? In
>>        the official packages, those are one in the same, but if someone
>>        wanted to
>>        make a package for custom annotations on a UCSC genome?
>>
>>
>>    The pkg name is generated automatically by internal helper function
>>    GenomicFeatures:::.__**makePackageName(). This function extracts all
>> the
>>
>>    tokens from the txdb's metadata table. It looks like the 3rd token
>>    in the pkg name is extracted from the 'Data source' field and can only
>>    be "UCSC" or "BioMart", typically indicating whether the txdb was made
>>    with makeTranscriptDbFromUCSC() or makeTranscriptDbFromBiomart().
>>    The first function downloads annotations from the UCSC genome
>>    browser using rtracklayer. The 2nd one downloads them with biomaRt
>>    from whatever mart/dataset was specified.
>>
>>    For your custom annotations, the final name of the pkg will depend on
>>    what GenomicFeatures:::.__**makePackageName() finds in the metadata
>>
>>    table of your txdb, but, if 'Data source' is not "UCSC" or "BioMart",
>>    it seems that GenomicFeatures:::.__**makePackageName() will fail (and
>> not
>>
>>    in a very informative way I'm afraid). If I understand correctly, you
>>    are making your custom txdb object with a call to makeTranscriptDb()?
>>    If that's the case, make sure you provide enough information
>>    thru its 'metadata' argument. Maybe you could set 'Data source' to
>>    "UCSC" and use some kind of custom name for the table (which in your
>>    case is probably not a real UCSC "table"). This custom name will become
>>    the last token in the package name. So you would end up with something
>>    like:
>>
>>      TxDb.Hsapiens.UCSC.hg19.__**GenentechGenes
>>
>>
>>    This solution would have the advantage of having
>>    GenomicFeatures:::.__**makePackageName() work out-of-the-box.
>>
>>    But maybe it's confusing because it suggests that
>>    the txdb was made with makeTranscriptDbFromUCSC()? I hope
>>    it's not.
>>
>>    H.
>>
>>
>>        Thanks,
>>        Michael
>>
>>                [[alternative HTML version deleted]]
>>
>>        ______________________________**___________________
>>        Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.**org<Bioc-devel@r-project.org>
>> >
>>        mailing list
>>        https://stat.ethz.ch/mailman/_**_listinfo/bioc-devel<https://stat.ethz.ch/mailman/__listinfo/bioc-devel>
>>
>>        <https://stat.ethz.ch/mailman/**listinfo/bioc-devel<https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>> >
>>
>>
>>
>>    --
>>    Hervé Pagès
>>
>>    Program in Computational Biology
>>    Division of Public Health Sciences
>>    Fred Hutchinson Cancer Research Center
>>    1100 Fairview Ave. N, M1-B514
>>    P.O. Box 19024
>>    Seattle, WA 98109-1024
>>
>>    E-mail: hpages@fhcrc.org <mailto:hpages@fhcrc.org>
>>    Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>>    Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>>
>>
>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

	[[alternative HTML version deleted]]

