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EnvironmentOntology / environmental-exposure-ontology

Modular environmental exposures ontology
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Align with PomBase PECO #3

Open cmungall opened 7 years ago

cmungall commented 7 years ago

@mbrush @mah11

mah11 commented 7 years ago

PECO lives at https://github.com/pombase/fypo/blob/master/peco.obo

cmungall commented 7 years ago

(rough notes follow, will likely edit this...)

PECO top level

. http://purl.obolibrary.org/obo/PECO_0000001 ! phenotype condition
 % http://purl.obolibrary.org/obo/PECO_0000122 ! grouping growth timing * 
 % http://purl.obolibrary.org/obo/PECO_0000059 ! chemical added or excluded * 
 % http://purl.obolibrary.org/obo/PECO_0000238 ! grouping condition combinations * 
 % http://purl.obolibrary.org/obo/PECO_0000009 ! grouping growth medium * 
 % http://purl.obolibrary.org/obo/PECO_0000132 ! grouping experimental environment *

chemicals

 % http://purl.obolibrary.org/obo/PECO_0000059 ! chemical added or excluded
  % http://purl.obolibrary.org/obo/PECO_0000120 ! grouping absent * 
  % http://purl.obolibrary.org/obo/PECO_0000011 ! grouping limited * 
  % http://purl.obolibrary.org/obo/PECO_0000109 ! grouping excess *

Currently ECTO just has exposure to presence of chemicals. But realistically we're talking about above normal levels, not trace amounts? E.g if I eat Himalayan table salt, there are trace amounts of polonium. But I wouldn't say I was exposed to polonium. It would have to be some significant amount.

medium

 % http://purl.obolibrary.org/obo/PECO_0000009 ! grouping growth medium
  % http://purl.obolibrary.org/obo/PECO_0000275 ! competitive culture * 
  % http://purl.obolibrary.org/obo/PECO_0000102 ! agar plates * 
  % http://purl.obolibrary.org/obo/PECO_0000080 ! grouping rich medium * 
  % http://purl.obolibrary.org/obo/PECO_0000213 ! non-fermentable carbon sources medium * 
  % http://purl.obolibrary.org/obo/PECO_0000013 ! grouping - defined medium * 
  % http://purl.obolibrary.org/obo/PECO_0000103 ! liquid culture *

out of scope for ECTO, should be in OBI?

growth

 % http://purl.obolibrary.org/obo/PECO_0000122 ! grouping growth timing
  % http://purl.obolibrary.org/obo/PECO_0000216 ! growth <24 hrs * 
  % http://purl.obolibrary.org/obo/PECO_0000265 ! >6 hrs in nitrogen starvation * 
  % http://purl.obolibrary.org/obo/PECO_0000125 ! growth to exponential phase * 
  % http://purl.obolibrary.org/obo/PECO_0000237 ! growth >48 hrs * 
  % http://purl.obolibrary.org/obo/PECO_0000217 ! growth >24 hrs * 
  % http://purl.obolibrary.org/obo/PECO_0000124 ! growth to late exponential phase * 
  % http://purl.obolibrary.org/obo/PECO_0000123 ! growth to stationary phase *

again more of an OBI thing

environment

 % http://purl.obolibrary.org/obo/PECO_0000132 ! grouping experimental environment
  % http://purl.obolibrary.org/obo/PECO_0000005 ! standard temperature * 
  % http://purl.obolibrary.org/obo/PECO_0000134 ! anaerobic environment * 
  % http://purl.obolibrary.org/obo/PECO_0000140 ! in vitro * 
  % http://purl.obolibrary.org/obo/PECO_0000215 ! low pH * 
  % http://purl.obolibrary.org/obo/PECO_0000129 ! high pH * 
  % http://purl.obolibrary.org/obo/PECO_0000227 ! permissive temperature * 
  % http://purl.obolibrary.org/obo/PECO_0000202 ! chilled cells * 
  % http://purl.obolibrary.org/obo/PECO_0000228 ! semi-permissive temperature * 
  % http://purl.obolibrary.org/obo/PECO_0000141 ! in vivo * 
  % http://purl.obolibrary.org/obo/PECO_0000004 ! high temperature * 
  % http://purl.obolibrary.org/obo/PECO_0000006 ! low temperature * 
  % http://purl.obolibrary.org/obo/PECO_0000135 ! semi-aerobic environment * 
  % http://purl.obolibrary.org/obo/PECO_0000229 ! nonpermissive temperature *
cmungall commented 4 years ago

note PECO ID space is now taken by what was EO