annotation extension (col 16) or NTR?

[gocentral]

I am going through my annotation extensions in order to define the relationships I have used.

I wonder if all of the extensions which are within an ontology should actually be hardcoded into the ontology in some way....

here is an example: /GO="aspect=P; term=chromosome passenger complex localization to kinetochore; GOid=GO:0072356; evidence=IMP; annotation_extension=dependent_on(GO:0072355); db_xref=PMID:20929775; date=20101115" /GO="aspect=P; term=histone H3-T3 phosphorylation; GOid=GO:0072355; evidence=IDA; db_xref=PMID:20929775; annotation_extension=involved_in(GO:0072356); date=20101115"

here, I wanted to capture the fact that chromosome passenger complex localization to kinetochore was dependent on histone H3-T3 phosphorylation (this is a conserved mechanism, I think, but there may be different modifications for localizations to different regions which it is useful to capture.....)

so I guess the term here would be histone H3-T3 phosphorylation involved in chromosome passenger complex localization to kinetochore does this sound reasonable?

Val

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/8438

[gocentral]

here is another example /GO="aspect=P; term=chromosome condensation; GOid=GO:0030261; evidence=IMP; db_xref=PMID:11792803; annotation_extension=dependent_on(GO:0043987); date=20090707"

this would proably be clearer as histone H3 S10 phosphorylation involved in chromosome condensation?

Original comment by: ValWood

[gocentral]

anotehr example which could be ontology encoded /GO="aspect=P; term=positive regulation of proteasomal ubiquitin-dependent protein catabolic process; GOid=GO:0032436; annotation_extension=during(GO:0071456); evidence=IGI; db_xref=PMID:18418381;

positive regulation of proteasomal ubiquitin-dependent protein catabolic process during response to hypoxia

Original comment by: ValWood

[gocentral]

also see SF 3303022

https://sourceforge.net/tracker/?func=detail&aid=3303022&group\_id=36855&atid=440764

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

I think this can close, I am pretty sure I got these terms recently via the term genie?

Val

Original comment by: ValWood

[gocentral]

not all of 'em are in ... I'm doing the rest later today m

Original comment by: mah11

[gocentral]

added in TermGenie:

id: GO:2000775 name: histone H3-S10 phosphorylation involved in chromosome condensation

id: GO:2000776 name: histone H4 acetylation involved in response to DNA damage stimulus

id: GO:2000777 name: positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia

now I can close it :) m

Original comment by: mah11

[gocentral]

• labels: --> New term request
• status: open --> closed-accepted

Original comment by: mah11

[gocentral]

• milestone: --> PomBase

Original comment by: mah11