sivarajankumar / phenotype-ontologies

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acidemia vs acidosis confusion #7

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago
Elk says

Acidosis = acidosis = acidemia

HP:

Acidosis is a condition in which there is excessive acid in the body fluids.

has_part some 
    ('increased concentration'
     and ('inheres in' some blood)
     and (towards some acid))

"Acidemia" is an exact synonym

MP:

a pathological state characterized by an increase in the hydrogen ion 
concentration in tissues and blood caused by an decrease in the concentration 
of alkaline compounds, or by a increase in the concentration of acidic 
compounds or carbon dioxide to the body fluids

has_part some 
    ('increased concentration'
     and (towards some acid)
     and ('inheres in' some blood)
     and ('inheres in part of' some artery))

acidemia is a distinct class, def: "increased concentration of H-ion in the 
blood or a fall below normal in pH in the arterial blood"

Analysis:

(acidosis) The HP text def is straightforward, but the logical definition is 
too specific for the text (blood -> bodily fluid)

(acidosis) The MP test def is more verbal and brings in aetiology. The logical 
definition is probably too specific for the text ("arterial blood"). Not clear 
what the intended location here?

Suggestion:

(acidosis) Standardize on a simple def, e.g. the HP one. Include aetiology and 
additional text after period. Make the logical def use bodily fluid in both.

(acidemia) keep MP as is; weaken HP exact syn to related.

Original issue reported on code.google.com by cmung...@gmail.com on 3 Feb 2014 at 2:32

GoogleCodeExporter commented 8 years ago
Slight correction to the above - the 3-ary equivalence is due to lexical 
matching, not reasoning. Doesn't affect recommended course of action.

Original comment by cmung...@gmail.com on 3 Feb 2014 at 2:39

GoogleCodeExporter commented 8 years ago
Additional notes: in MP, acidemia is under abnormal blood pH regulation, 
whereas is under the more general non-blood-specific acidosis, supporting the 
above

Original comment by cmung...@gmail.com on 3 Feb 2014 at 2:43

GoogleCodeExporter commented 8 years ago
This issue was closed by revision r433.

Original comment by cmung...@gmail.com on 3 Feb 2014 at 2:45

GoogleCodeExporter commented 8 years ago
Implemented the above for equivalence axioms with commit 433, still to resolve 
syns/text defs

Original comment by cmung...@gmail.com on 3 Feb 2014 at 2:46

GoogleCodeExporter commented 8 years ago
From Peter:

Clinically these terms are used nearly interchangeably, since you get acidemia 
if you have acidosis and only almost always measures acidosis via the blood. 
There is more of a mechanistic touch to the acidosis terms ("metabolic 
acidosis"), and this is an inference which is in principle so certain 
clinically that it is regarded as a phenotypic feature. The wikipedia entry is 
correct

The term acidemia describes the state of low blood pH, while acidosis is used 
to describe the processes leading to these states. Nevertheless, the terms are 
sometimes used interchangeably.

http://en.wikipedia.org/wiki/Acidosis

This might be a good suggestion of how to define the terms, one based on the 
actual observation, the other based on the inferred abnormal process.

Original comment by cmung...@gmail.com on 3 Feb 2014 at 4:18

GoogleCodeExporter commented 8 years ago
See also:
https://en.wikipedia.org/wiki/Metabolic_acidosis

Original comment by cmung...@gmail.com on 3 Feb 2014 at 4:27