Patterns for axiomatisation of transcription factor activities

[dosumis]

From @dosumis on August 28, 2015 9:56

We currently have patterns like this:

• molecular_function that ('has part' some 'nucleic acid binding') and ('part of' some 'regulation of transcription, DNA-templated')
• molecular_function and ('part of' some 'regulation of nucleic acid-templated transcription') and ('has part' some 'RNA polymerase core enzyme binding')

But these patterns are not safe. It is not necessarily the case that being part of a regulatory process entails being a regulator of the regulated process. This pattern probably arose from implementation of the general MF part_of BP pattern. In this case, it would be better to directly assert MF regulation of BP. But which relation to use?

Perhaps directly activates:

Current def: "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q."

But see notes from 2015-07-23 eds meeting on defining directly postively regulates.

CC @cmungall @ukemi

Copied from original issue: geneontology/go-ontology#12033

[dosumis]

From @cmungall on August 28, 2015 16:16

I think 'directly activates' is correct here, even if we have a more general direct regulation parent that is not restricted to activities

[dosumis]

From @ukemi on August 28, 2015 17:5

It fits the definition of directly activates.

[dosumis]

This issue was moved to geneontology/molecular_function_refactoring#23