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obi-ontology / obi

The Ontology for Biomedical Investigations
http://obi-ontology.org
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Replace obsolete GO 'core promoter binding' #1215

Closed jamesaoverton closed 11 months ago

jamesaoverton commented 4 years ago

GO has replaced 'core promoter binding' http://purl.obolibrary.org/obo/GO_0001047 with 'core promoter sequence-specific DNA binding' http://purl.obolibrary.org/obo/GO_0001046

'core promoter binding' was defined as "Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors."

'core promoter sequence-specific DNA binding' is defined as "Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region. The core promoter is composed of the transcription start site and binding sites for the RNA polymerase and the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon."

According to Ontobee it looks like we just use 'core promoter binding' in OBI to define 'promoter activity detection by reporter gene assay' http://purl.obolibrary.org/obo/OBI_0000913

@rvita @bpeters42 Can we replace 'core promoter binding' with 'core promoter sequence-specific DNA binding'?

turbomam commented 4 years ago

whoa, I have no idea how that got in there. I'll check to see if I really need it

jamesaoverton commented 4 years ago

@turbomam Sorry, I don't understand your comment. I added this import four years ago for use in an assay for IEDB. But now it's obsolete, so we need to update it.

turbomam commented 4 years ago

yeah, I should have read the whole post. Sorry about that.

jamesaoverton commented 4 years ago

We're going to use "core promoter sequence-specific DNA binding".