Ontology meeting 2013-07-25

Attendees:

Minutes: Paola

Hydrogen Production Follow-up

Trudy got back about the suggested changes (see [1]) they're suggesting we still make it 'hydrogen biosynthesis' as a child of 'small molecule biosynthesis' because it's analogous to formate biosynthesis etc. I see their point, but do we need to distinguish between making big things from small pieces v/s recycling from other components?

Logical definitions for GO terms referring to 'roles' in ChEBI

We need to discriminate between terms we want to define in GO vs. terms we 'care less' about - terms we can map to the ChEBI roles.

Examples of terms we lack logical defs. for so far are listed in email thread ('Logical defs. for 'role' chemical terms').

Propagating via positive and negative regulation

Do we want to have this property chain, or could the asserted links not always be safe - or could they involve loss of information?

Continues from last week: Updates on ongoing work

• RHEA - https://www.ebi.ac.uk/panda/jira/browse/GO-191 (Chris)
• Binding to domains and interpro: https://www.ebi.ac.uk/panda/jira/browse/GO-144

Two directories in /scratch with initial work. Look at go-rhea-xref-cardinality.rpt, there are 75 one-to-many (about
half relate to NAD(P)H). Demo by Chris in Protege with file /scratch/rhea/mf-merged.owl.  May not need a Rhea link for
every reaction.

Website updates

Can we revisit our strategy for updating the ontology docs? [2]