[BioC] homology package question

[Nianhua Li]

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. 

I think we should update the homology packages in the near future to use another
source data because the README file on this site says:

"The old HomoloGene FTP file formats (hmlg.ftp and hmlg.trip.ftp) are now
deprecated.  They will be produced for the time being, to make the
transition to the new file formats smoother, but will be discontinued 
as of Jan. 1, 2007."

But we don't have time to make the changes for this release. Sorry...

best

nianhua