Increased/decreased chemical concentration in location #973
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| pattern_name: abnormallyDecreasedConcentrationOfChemicalEntityInLocation | ||
| pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedConcentrationOfChemicalEntityInLocation.yaml | ||
| description: "An abnormal decrease in concentration of a chemical, like sodium, in a location, like the blood." | ||
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| classes: | ||
| decreased concentration: PATO:0001163 | ||
| abnormal: PATO:0000460 | ||
| chemical: CHEBI:24431 | ||
| independent continuant: BFO:0000004 | ||
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| relations: | ||
| inheres_in: RO:0000052 | ||
| has_modifier: RO:0002573 | ||
| has_part: BFO:0000051 | ||
| part_of: BFO:0000050 | ||
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| annotationProperties: | ||
| exact_synonym: oio:hasExactSynonym | ||
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| vars: | ||
| chemical: "chemical" | ||
| location: "'independent continuant'" | ||
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| name: | ||
| text: "abnormally decreased %s concentration in %s" | ||
| vars: | ||
| - chemical | ||
| - location | ||
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| def: | ||
| text: "An abnormally decreased concentration of %s in %s." | ||
| vars: | ||
| - chemical | ||
| - location | ||
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| equivalentTo: | ||
| text: "'has_part' some ('decreased concentration' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))" | ||
| vars: | ||
| - chemical | ||
| - location | ||
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| contributors: | ||
| - https://orcid.org/0000-0002-3528-5267 | ||
| - https://orcid.org/0000-0002-9611-1279 | ||
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| pattern_name: abnormallyIncreasedConcentrationOfChemicalEntityInLocation | ||
| pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyIncreasedConcentrationOfChemicalEntityInLocation.yaml | ||
| description: "An abnormal increase in concentration of a chemical, like sodium, in a location, like the blood." | ||
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There was a problem hiding this comment. Could you please ask the curators for two or three phenotype examples when using the more general "level"-pattern (as in abnormallyIncreasedLevelOfChemicalEntityInLocation) would miss distinguishing some phenotypes that are based on concentration measurements from other types (e.g. total amount) of measurements? |
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| classes: | ||
| increased concentration: PATO:0001162 | ||
| abnormal: PATO:0000460 | ||
| chemical: CHEBI:24431 | ||
| independent continuant: BFO:0000004 | ||
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| relations: | ||
| inheres_in: RO:0000052 | ||
| has_modifier: RO:0002573 | ||
| has_part: BFO:0000051 | ||
| part_of: BFO:0000050 | ||
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| annotationProperties: | ||
| exact_synonym: oio:hasExactSynonym | ||
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| vars: | ||
| chemical: "chemical" | ||
| location: "'independent continuant'" | ||
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| name: | ||
| text: "abnormally increased %s concentration in %s" | ||
| vars: | ||
| - chemical | ||
| - location | ||
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| def: | ||
| text: "An abnormally increased concentration of %s in %s." | ||
| vars: | ||
| - chemical | ||
| - location | ||
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| equivalentTo: | ||
| text: "'has_part' some ('increased concentration' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))" | ||
| vars: | ||
| - chemical | ||
| - location | ||
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| contributors: | ||
| - https://orcid.org/0000-0002-3528-5267 | ||
| - https://orcid.org/0000-0002-9611-1279 | ||
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@seger
Could you please ask the curators for some phenotype examples when using the more general "level"-pattern (as in abnormallyDecreasedLevelOfChemicalEntityInLocation) would miss distinguishing some phenotypes that are based on concentration measurements?
We need to provide examples of justified cases for this template.
It may be confusing that some phenotype categories that use the
abnormallyDecreasedLevelOfChemicalEntityInLocation or the
abnormallyIncreasedLevelOfChemicalEntityInLocation
patterns are based on concentration measurements.
However, as @sbello noted, the term "level" (used as a synonym of PATO "amount") has been intended to include both "concentration" and non-concentration-type amount qualities (like "total amount"). The meaning of "level" in uPheno is removed from the strict primary measurement type (concentration- or other measurement). When the quantitative observation/measurement is interpreted, the original dimensions are lost and, the phenotype is interpreted on a relative scale that includes abnormally decreased or abnormally increased (and compared to a reference).
See for example the EQs for these phenotype terms:
Technically all of these phenotypes are based on concentration measurements. It is not typically feasible to measure (quickly and in a non-invasive way) the total amount of sodium in the blood of mouse and human, so we do not loose any granularity by using the more general "level" pattern (as far as I know).
I think there could be justified cases for the more specific "concentration" patterns, but we need two or three examples in the description of this pattern so that we can help curators decide how and when to use it.