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#191 Term Enrichment: species as background set?

open
Seth Carbon
None
8
2010-01-28
2009-09-09
Jane Lomax
No

In the term enrichment tool, you can choose as a background set from a list of DBs. This doesn't work for an e.g. human data-set because there is no DB exactly corresponding to human (UniProtKB contains many other species too).

Can we make the background sets by species?

Discussion

  • Seth Carbon
    Seth Carbon
    2009-09-09

    It would be an extra join, so might make things a bit slower, but we'd have to see.

    Given that, I'm not sure of why we're doing things the way we are now anyways. Would you remember the original rational for using source instead of species?

     
  • Jane Lomax
    Jane Lomax
    2009-09-09

    I don't think speed is that critical (within reason!) for the term enrichment tool - being able to select the appropriate background is certainly more important.

    I was under the impression that there was some technical reason we had to use source instead of species as background? I can't think of any other reason you'd do it this way...

     
  • Jane Lomax
    Jane Lomax
    2009-09-09

    Oh, btw, Emily has a test data set for the term enrichment tool - I'll get her to send it to us.

     
  • Seth Carbon
    Seth Carbon
    2009-09-09

    I was under the impression that there was some other reason, but it may just be an artefact of past API restrictions (a lot of TE is now custom code).

    The speed is an issue (if there is one, we'll find out) for more than just time reasons--people's browsers might timeout and cause an error at their end; I remember that we had to do a lot of speed tweaking after TE first came out because of this. Looking at it right now though, it looks like it would be relatively easy to slip something in for species directly.

    (For the second part--cool!)

     
  • Jane Lomax
    Jane Lomax
    2010-01-28

    We've just had another request in to gohelp wondering why they can't use TE for human, so I've upped the priority of this again...please please can we get this fixed?

     
  • Jane Lomax
    Jane Lomax
    2010-01-28

    • priority: 7 --> 8