Replacing EFO is_about with proper RO properties

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Replacing EFO is_about with proper RO properties

dwelter
Dear obo-discuss hive-mind,

I'm in the process of reviewing options for replacing the catch-all object property is_about (IAO_0000136) in EFO with more meaningful properties. The main use cases I need to address are:
1. measurement is_about some chemical entity
This is our primary use case. We have numerous measurement subclasses representing the outcome of the quantification of a chemical entity in a sample. 

2. measurement is_about some disease 
Some measurements are linked to diseases, usually through the biomarker axiomatisation "measurement and (is_about some (disease and (has_role some biomarker)).

3. measurement is_about some biological process
These cases are for measurements that don't involve a chemical entity, usually behavioural measurements and memory measurements.

I suspect each of these cases requires a different property but none of the properties in RO quite seem to fit the bill.

Any suggestions would be most welcome.

Thanks
Dani Welter 
EFO developer at EBI

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Re: Replacing EFO is_about with proper RO properties

rrovetto
some ideas for consideration in-line below...

r/
Robert

On Fri, Jul 7, 2017 at 10:52 AM, <[hidden email]> wrote:

I'm in the process of reviewing options for replacing the catch-all object property is_about (IAO_0000136) in EFO with more meaningful properties. The main use cases I need to address are:
1. measurement is_about some chemical entity
This is our primary use case. We have numerous measurement subclasses representing the outcome of the quantification of a chemical entity in a sample. 

 
2. measurement is_about some disease 
Some measurements are linked to diseases, usually through the biomarker axiomatisation "measurement and (is_about some (disease and (has_role some biomarker)).


First, one of the relata is general: some disease type.
Second, this (particularly the axiomatization reference to a biomarker) seems to have an aspect of identification: the measurement identifies or marks the presence of a certain disease type. Given this, consider a pointer relation (for lack of a better phrase):
Third, given that measurement is a key aspect, consider relation terms using 'measurement'. 

RELATION IDEAS:
identifies, generically_identifies, approximately_identifies;
For numerical measurements... quantitatively_measures, generically_quantitatively_measures
IN USE: measurement generically-identifies disease (type/class)

Qualitatively incorporate uncertainty or a certain level of epistemological vagueness, by including a qualifier word in the relation term.
 
3. measurement is_about some biological process
These cases are for measurements that don't involve a chemical entity, usually behavioural measurements and memory measurements.

RELATION IDEAS: is_about_bioProcess, identifies_bioProcess, generically_identifies_bioProcess

 
I suspect each of these cases requires a different property but none of the properties in RO quite seem to fit the bill.


Consider also simply expandiing 'is_about':
is_about_disease, is_about_chemicalEntity, is_about_bioProcess



Any suggestions would be most welcome.

Thanks
Dani Welter 
EFO developer at EBI

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Re: Replacing EFO is_about with proper RO properties

Peter Robinson

​Hi Robert,

most biomarkers are not absolute diagnostic indicators of a disease but have predictive ability that depends on the marker, the test, and the prior probability of the disease in the tested individual. It would be interesting but probably very challenging to capture all of this across many areas of medicine. It might be useful to think of one or two concrete use cases and then try to figure out how much detail needs to go in new relations.

-Peter


Peter Robinson

Professor of Computational Biology

The Jackson Laboratory for Genomic Medicine

10 Discovery Drive

Farmington, CT 06032

860.837.2095 t | 860.990.3130 m

[hidden email]

www.jax.org

Robinson lab: https://robinsongroup.github.io/

The Jackson Laboratory: Leading the search for tomorrow's cures


From: [hidden email] <[hidden email]>
Sent: Sunday, July 9, 2017 4:53 PM
To: [hidden email]
Subject: Re: [Obo-discuss] Replacing EFO is_about with proper RO properties
 
some ideas for consideration in-line below...

r/
Robert

On Fri, Jul 7, 2017 at 10:52 AM, <[hidden email]> wrote:

I'm in the process of reviewing options for replacing the catch-all object property is_about (IAO_0000136) in EFO with more meaningful properties. The main use cases I need to address are:
1. measurement is_about some chemical entity
This is our primary use case. We have numerous measurement subclasses representing the outcome of the quantification of a chemical entity in a sample. 

 
2. measurement is_about some disease 
Some measurements are linked to diseases, usually through the biomarker axiomatisation "measurement and (is_about some (disease and (has_role some biomarker)).


First, one of the relata is general: some disease type.
Second, this (particularly the axiomatization reference to a biomarker) seems to have an aspect of identification: the measurement identifies or marks the presence of a certain disease type. Given this, consider a pointer relation (for lack of a better phrase):
Third, given that measurement is a key aspect, consider relation terms using 'measurement'. 

RELATION IDEAS:
identifies, generically_identifies, approximately_identifies;
For numerical measurements... quantitatively_measures, generically_quantitatively_measures
IN USE: measurement generically-identifies disease (type/class)

Qualitatively incorporate uncertainty or a certain level of epistemological vagueness, by including a qualifier word in the relation term.
 
3. measurement is_about some biological process
These cases are for measurements that don't involve a chemical entity, usually behavioural measurements and memory measurements.

RELATION IDEAS: is_about_bioProcess, identifies_bioProcess, generically_identifies_bioProcess

 
I suspect each of these cases requires a different property but none of the properties in RO quite seem to fit the bill.


Consider also simply expandiing 'is_about':
is_about_disease, is_about_chemicalEntity, is_about_bioProcess



Any suggestions would be most welcome.

Thanks
Dani Welter 
EFO developer at EBI

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