Ontology meeting 2011-10-26

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Discussion notes


Protege/OWL training session

  • We need to find a place and time soon. The meeting has to be before the end of February.

TermGenie 1 Update

  • Chris

Discussion notes I

REGULATION OF TRANSCRIPTION IN RESPONSE TO

  • Dianna has submitted a bunch of SF requests for 'regulation of transcription in response to x' terms.

E.g. Reg of txn in response to acidity

  • They're currently all assigned to David. Please can we have a new TG template for these.
  • Looking into this further, existing terms of this syntax currently have 2 is_a relationships to the parents. Is this correct.... isn't transcription PART_OF the response?
response to stimulus ; GO:0050896
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with   detection of the stimulus and ends with a change in state or activity or the cell or organism.


Also: (revisiting our favourite topic from previous meetings):

REGULATION OF Y PROCESS BY REGULATION OF TRANSCRIPTION FROM RNA POLYMERASE II PROMOTER

Since we haven't been able to find a good solution for the XPs for these, could we have a template in TG to add these in with two is_a relations, and XPs to match the existing terms. Then we can fix them en-masse later, when we can capture primary regulation, secondary regulation, tertiary regulation etc ? It's a fudge, but would mean the annotators get an ID for their terms.

See positive regulation of gluconeogenesis by negative regulation of transcription from RNA polymerase II promoter ; GO:0035949, for an existing example.


Discussion notes II

CROSS-PRODUCTS

  • (Carrying this topic from previous agenda, as we'd like to hear Chris' feedback on it)

A plea for a re-cap on what information is needed to make a cross-product, in reference to the involved_in terms.

See http://sourceforge.net/tracker/?func=detail&aid=3396697&group_id=36855&atid=440764


Discussion notes III

Coming back to an earlier discussion: How are the 'regulation of' terms related, when the two parent processes are connected by a part_of relationship?

Clarification required for: https://sourceforge.net/tracker/?func=detail&aid=3317785&group_id=36855&atid=440764

  • Becky's closing response on the tracker sums this up. Note that the current behavior derives from the transitive_over assignment in the GO relations, i.e. regulates o part_of --> regulates. Cjm 13:46, 25 October 2011 (PDT)

When requesting a term 'regulation of pigment cell development', TG does not create a relationship between 'regulation of pigment cell development' and 'regulation of pigment cell differentiation'. Surely it should?

Or, the reasoner should be able to do it. Chris, is this the case?

  • It should. I can guarantee that TG1 will provide a complete classification, as it uses 3rd party reasoners that have been verified using mathematical proofs etc. The TG0 classification should always be correct, but may be incomplete for the transitive_over cases. Apologies for this. These can be classified more specifically in OE using the RBR, which is guaranteed to use transitive_over. Also when we switch to using Oort for the public releases, the public release is guaranteed complete. Cjm 13:49, 25 October 2011 (PDT)

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