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Repository for the Plant Experimental Conditions Ontology
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CHEBI roles #98

Open marieALaporte opened 7 years ago

marieALaporte commented 7 years ago

I am checking the exposure-chebi.tsv file for the patterns.

Should we make a separate file for the eo/peco classes that map to a chebi role? and have separate yaml file for those with a nested definition or something like that?

@austinmeier @cmungall @cooperl09

cmungall commented 7 years ago

Yes, roles are potentially problematic. How many are there?

On 6 Jun 2017, at 10:34, Marie-Angélique Laporte wrote:

I am checking the exposure-chebi.tsv file for the patterns.

Should we make a separate file for the eo/peco classes that map to a chebi role? and have separate yaml file for those with a nested definition or something like that?

@austinmeier @cmungall @cooperl09

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marieALaporte commented 7 years ago

Only a few. 10 to be exact. Here the list:

http://purl.obolibrary.org/obo/CHEBI_27027=micronutrient, http://purl.obolibrary.org/obo/CHEBI_33281=antimicrobial agent, http://purl.obolibrary.org/obo/CHEBI_25944=pesticide, http://purl.obolibrary.org/obo/CHEBI_37845=growth hormone, http://purl.obolibrary.org/obo/CHEBI_24527=herbicide, http://purl.obolibrary.org/obo/CHEBI_24127=fungicide, http://purl.obolibrary.org/obo/CHEBI_33287=fertilizer, http://purl.obolibrary.org/obo/CHEBI_22676=auxin, http://purl.obolibrary.org/obo/CHEBI_23530=cytokinin, http://purl.obolibrary.org/obo/CHEBI_24852=insecticide

marieALaporte commented 7 years ago

@cmungall shall we make a DP for them ? Something like for the fertilizer:

'plant treatment' 
  and 'has exposure stimulus'
    some ('chemical entity' and 'has role' some 'fertilizer')
cmungall commented 7 years ago

Perfect. In GO we precoordinated classes like this, as we couldn't handle the nesting. Here it's OK (but may be a bit before we can handle in AmiGO).

Be careful with the nutrient branch of CHEBI, it's human-specific. You may get odd inferences for micronutrient.

I think we need our own mini plant nutrient role ontology (or chemical-with-nutrient-role ontology)

cmungall commented 8 months ago

was this fixed?