Re: [XMLPipeDB-developer] Leishmania IDs

[John D. N. D. <do...@lm...>]

Hi  Kam,

Sounds good, thanks for the updates and details.  I'll put the queries together then work on a new versions of the profiles (new profile in the case of infantum).

I had ended my office hours a few minutes early due to an 11am meeting in UHall.  But that's over now :)

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University


> On Feb 25, 2014, at 11:41 AM, Kam Dahlquist <kda...@lm...> wrote:
> 
> Hi Dondi,
> 
> Here's a rundown of what we talked about yesterday with regards to 
> the Leishmania major IDs and some explanations:
> 
> 1.  LmjF##.#### This form is "old" according to GeneDB; we are going 
> to keep it because it is used in our microarray data.
> 
> 2.  LMJF.##.####  This form is the "official" new form according to 
> GeneDB.  Thus we need it.
> 
> 3.  LMJF_##_#### This form actually appears in UniProt records 
> although it is not in our microarray data or GeneDB.  We are going to 
> keep it because it's used by UniProt so somebody out there might be 
> using it, too. (We just figured this out this morning.)
> 
> 4.  "straggler IDs"  These are not of the above three forms, but are 
> coming from UniProt.  They are synonyms of other genes that have one 
> of the above three forms.  We are automatically capturing them with 
> our code, so we are going to just keep them instead of trying to weed 
> them out.  It's possible that somebody out there is using them since 
> they are in UniProt.  Dondi, if you would construct a query to find 
> out which UniProt records have these extra IDs, that would be 
> great.  We just want it for our documentation.
> 
> In summary, we are going to have triplicates of all the IDs with 
> forms 1, 2, and 3, + some extra number of stragglers in our 
> OrderedLocusNames table.
> 
> Let's make sure that we are capturing IDs from both the Ordered Locus 
> tag and the ORF tag (I think that's what you've been doing, but I 
> just wanted to make sure).  You might be converting IDs to one of 
> these forms, could you let us know what conversions you are doing so 
> we can have that for our documentation?
> 
> Kevin is right now in the process of documenting ID forms for 
> Leishmania infantum.  Right off the bat, it looks like we are going 
> to have the same forms of 1, 2, and 3, except the prefix will be LinJ 
> instead of LmjF.  Also, it looks like the IDs are appearing under the 
> ORF tag instead of the OrderedLocus tag (an export with a generic 
> profile turned up 0 OrderedLocus IDs), but we'd better capture from 
> both tags, just in case.
> 
> Also, we are fast-tracking the creation of an L. infantum gdb because 
> it turns out that the vast majority of IDs from the microarray data 
> are to L. infantum instead of L. major.  Once we have an infantum 
> gdb, we can create the combined gdb.  The next step would be a 
> further customization that relates the L. major IDs to the L. infantum IDs.
> 
> Finally, in the microarray data, each gene has duplicate spots 
> (duplicate rows).  Ideally, we would like to average the log fold 
> changes for these as technical replicates before doing the 
> statistics.  I think I have a script in Matlab that Dr. Fitzpatrick 
> wrote for me to split my yeast data.  I'm going to try  it on the 
> Leishmania data to see if it works.  If so, we would not need an 
> additional script to split the data.
> 
> Best,
> Kam
> 
> 
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