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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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binding standard def rewrite? #1425

Closed gocentral closed 9 years ago

gocentral commented 20 years ago

Our standard def for 'binding' terms is currently "Interacting selectively with ...". At the Bar Harbor meeting, we decided to remove the link between binding and enzyme activity terms, as (to quote from the meeting minutes, action item 17) "Binding is only a parent when stable binding occurs.". Would it be worth altering the standard binding def to take this into account, eg. "Interacting selectively and stably with ..."?

Answers on a postcard to SourceForge, please!

Reported by: girlwithglasses

Original Ticket: "geneontology/ontology-requests/1428":https://sourceforge.net/p/geneontology/ontology-requests/1428

gocentral commented 20 years ago

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That seems like a sensible idea to me.

Jen

Original comment by: jenclark

gocentral commented 20 years ago

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Suggestion from John Garavelli (source of much wisdom in this matter): we might like to add something to take into account covalent vs noncovalent binding.

Was there ever a suggestion about adding covalent binding as a term?

Original comment by: girlwithglasses

gocentral commented 20 years ago

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Relevant interactions imply both specificity and stability whether binding is covalent (enzymes) or non-covalent (DNA- protein, protein-protein). So, having the two attributes sounds sensible, although perhaps a bit redundant for those working on molecular interactions. Non-specific binding (rather low specificity characterized by weak energetics) can be monitored and one may think about having specific/non- specific binding as terms, much like having covalent/non- covalent binding terms However, I think this might create complications. I'm pleased with the definition as it is now, which to me describes an interaction specific to that particular molecule/system (not just enzymes).

Original comment by: vpetri

gocentral commented 20 years ago

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Isn't 'stable binding' a bit meaningless? Do we not need to be a bit tighter about what we mean?

Original comment by: jl242

gocentral commented 20 years ago

Original comment by: girlwithglasses