[XMLPipeDB-developer] loose ends for various species profiles

[Kam D. <kda...@lm...>]

Hi,

Testing is up-to-date for seven of our ten released species.  Here is a recap:

1.  No issues with gmb2b61/gmb2b62:  Vibrio cholerae, Pseudomonas 
aerugenosa, Salmonella typhimurium.

2.  Very minor issue with export wizard that I'd like to see cleaned 
up:  Staphylococcus aureus, Helicobacter pylori, Mycobacterium tuberculosis.

In the first screen of the Export to GenMAPP wizard, there is a 
drop-down menu to select the species.  To the right of that drop-down 
menu, there is a text description that says "This profile customizes 
the GenMAPP Builder export for Genus species data loaded from a 
UniProt XML file."

The words "Genus species" need to be replaced with the actual name of 
the species, like "Mycobacterium tuberculosis".

For the Mycobacterium tuberculosis profile, this change needs to be 
made to replace "Genus species" with "Mycobacterium 
tuberculosis".  I've attached a screenshot so you can see what I'm 
talking about.

For Staphyolococcus aureus, the "A" in "aureus" has mistakenly been 
capitalized.  Would you change it to a lower case "a"?  (Only the 
genus name is capitalized as in Staphylococcus; the species name 
"aureus" is not.)

For Helicobacter pylori, two things need to be changed.  First, 
"Helicobacter pylori" needs to replace "Genus species" in the text.

Second, there are actually two choices in the drop-down menu.  The 
other choice is Campylobacter pylori, which is a synonym for the 
correct species name, Helicobacter pylori.  Can we get rid of this 
alternate choice entirely?  I believe if someone chooses it, they 
will not get the customizations that we made to the profile.

3.  Mycobacterium smegmatis and Mycobacterium tuberculosis both have 
TallyEngine issues.  I don't want to pursue these right now, but I 
just want to make note of them.  For smegmatis, ther are 4 extra 
RefSeq and GeneIds in the TallyEngine counts than there should 
be.  Since it is not affecting the gdb, I'm going to let it slide 
right now, but eventually it would be nice to know what is going on here.

For tuberculosis, the issues are larger; OrderedLocus is being 
counted twice and none of the four counts generated match each other 
or the gdb.  It also looks like there are also 4 extra RefSeq and 
GeneIds in the TallyEngine counts here than the gdb.

Like I said, I'd like to see us tackle the issues listed above in (2) 
first.  Tomorrow, I'm going to document what is going on with P. 
falciparum, E. coli, and A. thaliana since I think they all have 
serious export issues.

Thanks,
Kam