PAMGO conference calls: Difference between revisions
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=='''PAMGO Conference Call-February 15 2008'''== | =='''PAMGO Conference Call-February 15 2008'''== | ||
''' | ''' update on association files submitted to GOC''': | ||
gene_association.PAMGO_Atumefaciens.gz | gene_association.PAMGO_Atumefaciens.gz | ||
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these part_of relationships with a new relationship type called | these part_of relationships with a new relationship type called | ||
'regulates'. We are now in a position to make this replacement" | 'regulates'. We are now in a position to make this replacement" | ||
See entire e-mail: | |||
Most of the modulation/regulation terms have a is_a relationship to parents | |||
Few with part_of relationships, which should still be fine if "part_of" is replaced with "regulates" | |||
See examples: | |||
'''Induction and Upregulation terms''' | '''Induction and Upregulation terms''' | ||
Induction and | Induction and Up-regulation of........ are currently child terms of positive regulation. Should this be merged into positive | ||
regulation? | regulation? Many of the induction and upregulation terms are synonyms of their respective "positive regulation" parent terms | ||
anyway. | |||
See examples: | |||
'''Changing wording in some host terms''' | '''Changing wording in some host terms''' | ||
Will put a list on the wiki soon for your comments | |||
| Line 40: | Line 46: | ||
'''Report''' | '''Report''' | ||
Use of PAMGO terms by virulence community-Michelle | Use of PAMGO terms by virulence community-Michelle | ||
'''PAMGO workshop July 14-16 2008''' | |||
Please print out attached brochure and distribute at meetings/conferences you plan on attending before July | |||
We need to attract a diverse group of people this year. | |||
Revision as of 15:57, 14 February 2008
PAMGO Conference Call-February 15 2008
update on association files submitted to GOC:
gene_association.PAMGO_Atumefaciens.gz
gene_association.PAMGO_Oomycetes.gz
Update on association files for:
P. syringae
Erwinia
M. grisea
GOC announcement: Regulation terms
"For some time now, the GO content developers have been aware that
regulatory processes are not necessarily integral to the processes (as
previously indicated by the use of the 'part_of' relation) that they
regulate. Nevertheless, regulatory processes have been represented as
part_of the processes they regulate. We have long intended to replace
these part_of relationships with a new relationship type called
'regulates'. We are now in a position to make this replacement"
See entire e-mail:
Most of the modulation/regulation terms have a is_a relationship to parents
Few with part_of relationships, which should still be fine if "part_of" is replaced with "regulates"
See examples:
Induction and Upregulation terms
Induction and Up-regulation of........ are currently child terms of positive regulation. Should this be merged into positive
regulation? Many of the induction and upregulation terms are synonyms of their respective "positive regulation" parent terms
anyway.
See examples:
Changing wording in some host terms
Will put a list on the wiki soon for your comments
Mini Reviews
Report
Use of PAMGO terms by virulence community-Michelle
PAMGO workshop July 14-16 2008
Please print out attached brochure and distribute at meetings/conferences you plan on attending before July
We need to attract a diverse group of people this year.
Others
PAMGO Conference Call-November 15 2007
Test set of annotations sent to Chris Mungall (GOC) File:PAMGO test assoc.xls
New "Properties" column in the association file
Updated Evidence Code documentation. http://www.geneontology.org/GO.evidence.shtml New children codes under ISS (still under review)
Topic for discussion: Hypersensitive response (HR) and Programmed cell death (PCD) tree
See "PAMGO SUMMARY_2007" for Candace's proposal on this subject