Difference between revisions of "Ontology meeting 2020-07-13"

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m (Obsoleting the BP 'regulation of molecular activity' branch)
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** 3 experimental evidence used in manual assertion
 
** 3 experimental evidence used in manual assertion
 
** 2 high throughput mutant phenotypic evidence used in manual assertion
 
** 2 high throughput mutant phenotypic evidence used in manual assertion
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 +
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People still make those annotations:
 +
2000 8
 +
2001 6
 +
2002 29
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2003 109
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2004 68
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2005 140
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2006 255
 +
2007 274
 +
2008 286
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2009 351
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2010 468
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2011 756
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2012 427
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2013 511
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2014 609
 +
2015 575
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2016 524
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2017 541
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2018 712
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2019 365
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2020 97
  
 
* Would be biologically more accurate NOT to have them
 
* Would be biologically more accurate NOT to have them

Revision as of 07:42, 13 July 2020

Conference Line

See calendar for details

Agenda

Retiring gorel relations

(from June 29 call):

  • 'acts on population of' -> added to RO; need to update logical definitions that use this relation (cell population proliferation children and some homeostasis terms)
  • 'exists during' -> replace with 'existence overlaps' but with a modified definition?
    • X existence overlaps y iff the connected temporal region T1 in which the continuant X exists overlaps the connected temporal region during which y occurs
    • 'exists during' is currently only used in annotation extensions, but 'existence overlaps' could perhaps be used in logical definitions of some CC terms, e.g. mitotic spindle?

Obsoleting the BP 'regulation of molecular activity' branch

  • Those are 'single-step processes', ie molecular functions
  • Many annotations !
    • 39290 similarity evidence used in manual assertion
    • 29453 biological aspect of ancestor evidence used in manual assertion
    • 15480 evidence used in automatic assertion
    • 6521 experimental evidence
    • 5973 sequence orthology evidence used in manual assertion
    • 3811 sequence similarity evidence used in manual assertion
    • 3519 direct assay evidence used in manual assertion
    • 2498 mutant phenotype evidence used in manual assertion
    • 465 author statement supported by traceable reference used in manual assertion
    • 447 genetic interaction evidence used in manual assertion
    • 63 author statement without traceable support used in manual assertion
    • 62 curator inference used in manual assertion
    • 44 physical interaction evidence used in manual assertion
    • 40 sequence alignment evidence used in manual assertion
    • 13 match to sequence model evidence used in manual assertion
    • 8 expression pattern evidence used in manual assertion
    • 3 experimental evidence used in manual assertion
    • 2 high throughput mutant phenotypic evidence used in manual assertion


People still make those annotations: 2000 8 2001 6 2002 29 2003 109 2004 68 2005 140 2006 255 2007 274 2008 286 2009 351 2010 468 2011 756 2012 427 2013 511 2014 609 2015 575 2016 524 2017 541 2018 712 2019 365 2020 97

  • Would be biologically more accurate NOT to have them
  • Might solve the is_a o regulation transitivity issue ?

ie for example: - kinase activity is_a ATPase --> we dont want to have: regulation of kinase activity is a regulation of ATPase But not having those terms at all would avoid the problem

Other Business

https://github.com/geneontology/go-ontology/projects/1 (no new ticket to discuss?)

Minutes should be recorded on individual tickets and in individual projects