Ontology meeting 2011-09-28
Report
Discussion notes
Discussion notes - I
(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
- A plea for a re-cap on what information is needed to make a cross-product.
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
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?
Discussion notes - IV
- Can we add 'HAS_PART' relationships between function and process terms? E.g. for 'x process via y function' terms or biochemical pathways?
- Stems from this SF item: [1]
Discussion notes - V
- ChEBI stuff
- diff file
- ACTION: David and Tanya will look through the diff file and generate a user-friendly file of suggested errors/missing links in ChEBI
- new compounds to add
- ACTION: Chris to generate a block of stanzas for the new terms to paste directly into goche, and an additional set of intermediate is_a terms to go through manually
- diff file
Task List