Ontology meeting 2011-10-26: Difference between revisions

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Clarification required for: https://sourceforge.net/tracker/?func=detail&aid=3317785&group_id=36855&atid=440764
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. [[User:Cjm|Cjm]] 13:46, 25 October 2011 (PDT) cjm
* 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. [[User:Cjm|Cjm]] 13:46, 25 October 2011 (PDT) cjm


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?
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?

Revision as of 16:47, 25 October 2011

Report

Discussion notes


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) cjm

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?


Task List