[Bioc-devel] [BioC] homology package question

Sean Davis sdavis2 at mail.nih.gov
Wed Apr 18 23:12:47 CEST 2007

James W. MacDonald wrote:
> Hi Nianhua,
> Nianhua Li wrote:
>> Hi, James,
>> The source file of mmuhomology is  
>> ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/hmlg.ftp (download on 02/28/2007)
>> and the description is
>> ftp://ftp.ncbi.nih.gov/pub/HomoloGene/README-old
>> According to the description, the 4th and 7th column of hmlg.ftp are Entrez Gene
>> ID, the 5th and 8th column are internal HomoloGene ID. If you look at the
>> hmlg.ftp file, even the current one, you can find that the internal HomoloGene
>> ID is the same as Entrez Gene ID for most of the case. That's why
>> mmuhomologyHGID2LL and mmuhomologyLL2HGID look identical. 
> Odd. I wonder if they no longer even check to see if the data are 
> correct. I checked several of the IDs, and AFAIK they really are Entrez 
> Gene IDs, and they really are not HomoloGene IDs.
> Anyway, it's really easy to get the mappings from biomaRt so that might 
> be the direction to point people until we start using an updated source 
> of these data.
Moved over to bioc-devel....

Just a thought and it is not my decision to make, but should the 
homology packages be part of the release at all if they can't be updated 


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