Ontology meeting 2013-07-25

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Attendees: Paola, David, Harold, Heiko, Tanya, Jane, Becky

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?

AI: Jane will go ahead with MENGO's suggestion. They provided other fermentation terms that they'd want under there. Jane will add a comment saying that those terms might move elsewhere in the future.


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').

Resolution: the discrimination should be on this basis: terms we want to define in GO with respect to GO biological processes should have logical defs. referring to GO terms; other terms can have logical defs. referring to a ChEBI role term. The latter can be considered placeholders, we can change them to refer to GO if we add related process terms in GO.

AI: Paola to add xps for terms that can safely refer to ChEBI roles (e.g., 'xenobiotic catabolic process').

As for the logical definitions that we want to refer to GO, we need Chris, so discussion is bumped to next week.


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?

Discussion: it's not always satisfactory to have that chain of links asserted; we lose information about whether regulation is direct or indirect...

We may revisit the idea of 'indirectly_regulates'. We also need to play more with tests. David presented the LEGO example of glycolysis.

AI: Ask Paul Thomas to provide the full example file??


Continues from last week: Updates on ongoing work

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.

Chris not on the call, so bump to next week.


Website updates

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

David put his outline in Dropbox some time ago, and Chris added suggestions.

Resolution: For each ontology documentation page (e.g. Molecular Function), let's do a very short 'public face' page, plus an 'editorial face' page with more in it.