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

From GO Wiki
Jump to: navigation, search
m (Obsoleting the BP 'regulation of molecular activity' branch)
m (Obsoleting the BP 'regulation of molecular activity' branch)
 
Line 108: Line 108:
  
 
* Discussion  
 
* Discussion  
** to move those as GO-CAM as 'causally upstream of or within'
+
** Proposal is to move those as GO-CAM as 'causally upstream of or within'
 
** Paul: We need to understand the semantics  
 
** Paul: We need to understand the semantics  
 
** Guidance we can give to curators: use 'has input' and include the substrate  
 
** Guidance we can give to curators: use 'has input' and include the substrate  

Latest revision as of 09:43, 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)
    • No action needed ?? Pascale to check
  • '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
  • Would be biologically more accurate NOT to have them
  • Might solve the is_a o regulation transitivity issue ?

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

  • 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

By group:

  • UniProt : 2134
  • BHF-UCL : 1066
  • MGI : 821
  • RGD : 454
  • SGD : 312
  • FlyBase : 275
  • ARUK-UCL : 261
  • AgBase : 217
  • Reactome : 194
  • dictyBase : 166
  • ParkinsonsUK-UCL : 162
  • CAFA : 115
  • WB : 114
  • PomBase : 98
  • TAIR : 94
  • CACAO : 84
  • PINC : 80
  • ZFIN : 80
  • EcoCyc : 67
  • HGNC-UCL : 58
  • PseudoCAP : 41
  • SynGO : 41
  • MTBBASE : 30
  • CGD : 26
  • AspGD : 23
  • Alzheimers_University_of_Toronto : 18
  • GOC : 16
  • ComplexPortal : 15
  • GeneDB : 9
  • DFLAT : 8
  • GO_Central : 6
  • UniProtKB : 6
  • DIBU : 5
  • HGNC : 4
  • GDB : 3
  • EcoliWiki : 2
  • JCVI : 2
  • SynGO-UCL : 2
  • PAMGO_MGG : 1
  • PAMGO_VMD : 1
  • Discussion
    • Proposal is to move those as GO-CAM as 'causally upstream of or within'
    • Paul: We need to understand the semantics
    • Guidance we can give to curators: use 'has input' and include the substrate
    • Use GP2term relation: x acts upstream of (-/+) or a child some MF has_input [substrate]
    • ACA activity enabled by ACA1 _positively regulates_ PKA activity, has input PKA1
    • Try to stay away from 'BP Regulation of MF activity'

To confirm & revisit

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