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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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transcription obsoletion messages #8843

Closed gocentral closed 9 years ago

gocentral commented 13 years ago

I notice that from the transcription overhaul, there is alway an informative comment for curators which terms to use as replacement, but there is no comment for all users of GO in the from "this term was made obsolete becasue...." Should these be added? see

http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0016566 http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0017163

The part about annotation transfer is relevant only until all of the gene products annotated to the term have been re assigned, and from this point the reason for obsoletion ids the most important piece of information attached to an obsolete term

Thanks

Val

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/8631

gocentral commented 13 years ago

Original comment by: jl242

gocentral commented 13 years ago

Original comment by: rebeccafoulger

gocentral commented 13 years ago

Original comment by: krchristie

gocentral commented 13 years ago

Original comment by: mah11

gocentral commented 13 years ago
  1. This group of obsoleted MF terms:

* GO:0003701 - RNA polymerase I transcription factor activity

already included this comment:

This term was obsoleted because it is essentially identical to a Process term, i.e. it is defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism.

For these, I have added this parenthetical expression to be clearer that you can use the consider tags to find the equivalent BP term.

"(specifically the Biological Process term which has been selected as a term to consider for reannotation)"

  1. This group of MF terms related to general/nonspecific/basal vs specific transcription:

* GO:0003704 - specific RNA polymerase II transcription actor activity

This group of MF terms related to general/nonspecific/basal vs specific transcription were the only ones that started with the comment about "To transfer all annotations without review, ...". For these, I have added this comment:

"This term was obsoleted because "general/nonspecific/basal" transcription vs "specific" transcription were determined not to be separable, distinct process. Thus, terms trying to distinguish "general/nonspecific/basal" transcription from "specific" transcription were removed from both the Molecular Function and the Biological Process ontologies. In addition, this Molecular Function term was defined only in terms of the process it acts in and it does NOT convey any information about the molecular nature of the function or whether the function is based on binding DNA, on interacting with other proteins, or some other mechanism."

Original comment by: krchristie

gocentral commented 13 years ago

Original comment by: krchristie