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Include OORO data elements - Patient #37

Open andredekker opened 2 years ago

andredekker commented 2 years ago

To sync OORO and radont, we need to include the following OORO "Patient" concepts in radont

andredekker commented 2 years ago

Patient MRN, Anonymized Patient Identifier and Data Set Identifier are all Identifiers (IAO:002000) the way these should be used are in :identifier a IAO:identifier :identifier :denotes [ a person ] or :identifier :denotes [ a dataset ] To differentiate between the regular and anonymous identifiers ICO is used :identifier OBI is_specified_output_of [ a ICO: act of anonymizing]

andredekker commented 2 years ago

Birth is a process. The closes OBO term seems to be parturition (http://purl.obolibrary.org/obo/GO_0007567) "The reproductive process in which the parent is separated from its offspring either by giving birth to live young or by laying eggs." A birth occupies a temporal region (http://purl.obolibrary.org/obo/BFO_0000155). This temporal region may be zero dimensional which is the birth datetime. so to specify the birth of a person: :Andre RO:has_role :AndreBabyRole :AndreBabyRole a RoleOntology:Child :AndreBabyRole RO:realized_in :AndreBirth :AndreBirth a GO:parturition :AndreBirth BFO:occupies_temporal_region :AndreBirthDate :AndreBirthDate :stilltodetermine"1974-06-20"

andredekker commented 2 years ago

I can't find the concept of death and cause of death in OBO foundry -> going to ask Jonathan

andredekker commented 2 years ago

Race and ethnicity are considered an identity. Race: http://purl.obolibrary.org/obo/GSSO_008987 Ethnicity: http://purl.obolibrary.org/obo/GSSO_007232 Need to find the property to link a person to an identity

andredekker commented 2 years ago

Sex at birth is a fluid concept. Looking at GSSO and OORO what is meant is "sex for clinical use" http://purl.obolibrary.org/obo/GSSO_009428 Sex as defined in a specific medical and clinical context.

Bayesianworld commented 2 years ago

Another possible approach is to define a "life" and then use BFO temporal classes to define birth as beginning temporal boundary and death as the ending boundary. Then you just need to connect life to homo sapiens. Mark

From: Andre Dekker @.> Sent: Friday, November 19, 2021 10:42 AM To: aapm-bdsc-ontology-tg/radont @.> Cc: Subscribed @.***> Subject: Re: [aapm-bdsc-ontology-tg/radont] Include OORO data elements - Patient (Issue #37)

I can't find the concept of death and cause of death in OBO foundry -> going to ask Jonathan

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andredekker commented 2 years ago

OORO-Patient

andredekker commented 2 years ago

Reconsidered race and ethnicity and use OPMIs Population Group concept. In that thinking people consider themselves/are a member of a race or ethnic group. Issue in OORO is that they using FHIR and define other race and other ethnicity (not latina/hispanic) which FHIR themselves say are obsolote.

Current status: OORO-Patient

andredekker commented 2 years ago

Another possible approach is to define a "life" and then use BFO temporal classes to define birth as beginning temporal boundary and death as the ending boundary. Then you just need to connect life to homo sapiens. Mark … ____ From: Andre Dekker @.> Sent: Friday, November 19, 2021 10:42 AM To: aapm-bdsc-ontology-tg/radont @.> Cc: Subscribed @.***> Subject: Re: [aapm-bdsc-ontology-tg/radont] Include OORO data elements - Patient (Issue #37) I can't find the concept of death and cause of death in OBO foundry -> going to ask Jonathan — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#37 (comment)>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGU5EEUEQ2ILXVJXKA2OWY3UM2LBLANCNFSM5IGOAJOQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

I have spent some time again on birth, life and death but i don;t see a good way to model this. Per suggestion of Mark i looked at Life but that is not defined (properly) in OBO foundry ontologies. Parking it until I can discuss with @jonathanbona

andredekker commented 2 years ago

Current state (after talking to Jonathan). Not yet found the process of life. I guess there is a big discussion on when life starts....

OORO-Patient

jonathanbona commented 2 years ago

OGMS: life course might do the trick http://purl.obolibrary.org/obo/OGMS_0000092

On Thu, Jan 13, 2022 at 2:35 PM Andre Dekker @.***> wrote:

Current state (after talking to Jonathan). Not yet found the process of life. I guess there is a big discussion on when life starts....

[image: OORO-Patient] https://user-images.githubusercontent.com/2337314/149405117-1fbc645c-c5ce-4be3-b3f0-feeeb3a31dec.gif

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andredekker commented 2 years ago

To consider. Perhaps we should look more at death stage and neonate stage (UBERON). These are planned processes that people participate in

Bayesianworld commented 2 years ago

I like Jonathan's OGMS class (since it mirrors my original idea 🙂 ). It has the advantage that both "process" and "process boundary" are obo classes so that birth (or even conception if you are so inclined) and death can be defined as boundaries of life process. Mark

From: Andre Dekker @.> Sent: Thursday, January 13, 2022 12:42 PM To: aapm-bdsc-ontology-tg/radont @.> Cc: Mark H. Phillips @.>; Comment @.> Subject: Re: [aapm-bdsc-ontology-tg/radont] Include OORO data elements - Patient (Issue #37)

To consider. Perhaps we should look more at death stage and neonate stage (UBERON). These are planned processes that people participate in

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Bayesianworld commented 2 years ago

This is a detour from weighty subjects such as life and death, but I am wondering what the best property is to associate a process, e.g. radiation induced pathology, and it measurement/label, e.g. an IAO type object for the term used to describe said adverse event. None of the BFO terms seem to apply. I was thinking of Andre's use of OBI approach for "weight" but that doesn't seem to apply so easily since in that case "weight" is a quality of a person, whereas here we are trying to measure or label a biological process.

Mark

From: Jonathan Bona @.> Sent: Thursday, January 13, 2022 12:42 PM To: aapm-bdsc-ontology-tg/radont @.> Cc: Mark H. Phillips @.>; Comment @.> Subject: Re: [aapm-bdsc-ontology-tg/radont] Include OORO data elements - Patient (Issue #37)

OGMS: life course might do the trick http://purl.obolibrary.org/obo/OGMS_0000092

On Thu, Jan 13, 2022 at 2:35 PM Andre Dekker @.***> wrote:

Current state (after talking to Jonathan). Not yet found the process of life. I guess there is a big discussion on when life starts....

[image: OORO-Patient] https://user-images.githubusercontent.com/2337314/149405117-1fbc645c-c5ce-4be3-b3f0-feeeb3a31dec.gif

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andredekker commented 2 years ago

Added birth and death and also cause of death OORO-Patient

andredekker commented 2 years ago

Added "Age At Date of Death" following OBI standards. OORO-Patient I have a question for @jonathanbona : I have to link the age measurement assay to the death , otherwise we cannot express that this is age at death. I have now selected "happens during" as the (RO) relation and pointed this from the age assay to the zero-dimensional time region (moment when the death stage starts). There are a few concerns however. One is the the age assay does not really happen at that moment, e.g. you can determine at any time (after death). And also "happens during" a zero-d time region is illogical. But I could not find something better. Any ideas?

jonathanbona commented 2 years ago

How about linking the age measurement datum to the moment of death via the "is about" relation?

andredekker commented 2 years ago

So something like this @jonathanbona : OORO-Patient

jonathanbona commented 2 years ago

Yes, but the 'is about' link should be from the age measurement datum to the death stage instead, because the domain of 'is about' is information content entity, and no process is an information content entity.

andredekker commented 2 years ago

Oh - i see it is from assay - my fault

andredekker commented 2 years ago

Corrected: OORO-Patient

andredekker commented 2 years ago

I think I am almost ready to close this issue. I added the final OORO element (Cause of Death Attributable to Treatment) in the below graph and sent it out to Chuck Mayo for some input.

@jonathanbona : Although not strictly necessary, the classes and properties in the below graph (all OBO) would ideally be added to rto.owl. Do you want met to do it - or is that something you have a good and quick procedure running on?

Will start working on the next OORO elements.

OORO-Patient

andredekker commented 2 years ago

Here is a list of URIs I used, grouped by source ontology

Homo Sapiens NBCITaxon:9609

patient role OBI:0000093 has representation OBI:0002815 is_specified_output_of OBI:0000312 Hospital OBI:0000844 age measurement assay OBI:0001158 age measurement datum OBI:0001167 has specified output OBI:0000299 has specified input OBI:0000293 has value specification OBI:0001938 is_specified_output_of OBI:0000312 has specified value OBI:0002135 scalar value specification OBI:0001931 specifies value of OBI:0001927

has role RO:0000087 has quality RO:0000086 member of RO:0002350 member of RO:0002350 has participant RO:0000057 participates in RO:0000056 starts with RO:0002224 has disposition RO:0000091 realizes RO:0000056 has quality RO:0000086

sex for clinical use GSSO:009428

female PATO:0000383 male PATO:0000384 age PATO:0000011

Race NCIT:C16495 American Indian or Alaska Native NCIT:C41259 Asian NCIT:C41260 Black or African American NCIT:C16352 Native Hawaiian or Other Pacific Islander NCIT:C41219 White NCIT:C41261 Other race NCIT:C104495 Ethnic Group NCIT:C16495 Hispanic or Latino NCIT:C17459 Not Hispanic or Latino NCIT:C41222

Identifier IAO:0020000 denoted by IAO:0000235 assigning a centrally registered identifier IAO:0000574 given name IAO:0020016 denoted by IAO:0000235 family name IAO:0020017 has measurement unit label IAO:0000039 is quality measurement of IAO:0000221 is about IAO:0000136

act of anonymizing ICO:0000217

time unit UO:0000003

cause of death status OPMI:0000543 neonate stage UBERON:007221 (import from OPMI) death stage UBERON:0000071 (import from OPMI)

one-dimensional temporal region BFO:0000038 occupies temporal region BFO:0000155 zero-dimensional temporal region BFO:0000148 disposition BFO:0000091

Treatment OGMS:0000090

Bayesianworld commented 2 years ago

Hi Andre, Have all of these been properly imported? Mark

From: Andre Dekker @.> Sent: Saturday, May 21, 2022 5:21 AM To: aapm-bdsc-ontology-tg/radont @.> Cc: Mark H. Phillips @.>; Comment @.> Subject: Re: [aapm-bdsc-ontology-tg/radont] Include OORO data elements - Patient (Issue #37)

Here is a list of URIs I used, grouped by source ontology

Homo Sapiens NBCITaxon:9609

patient role OBI:0000093 has representation OBI:0002815 is_specified_output_of OBI:0000312 Hospital OBI:0000844 age measurement assay OBI:0001158 age measurement datum OBI:0001167 has specified output OBI:0000299 has specified input OBI:0000293 has value specification OBI:0001938 is_specified_output_of OBI:0000312 has specified value OBI:0002135 scalar value specification OBI:0001931 specifies value of OBI:0001927

has role RO:0000087 has quality RO:0000086 member of RO:0002350 member of RO:0002350 has participant RO:0000057 participates in RO:0000056 starts with RO:0002224 has disposition RO:0000091 realizes RO:0000056 has quality RO:0000086

sex for clinical use GSSO:009428

female PATO:0000383 male PATO:0000384 age PATO:0000011

Race NCIT:C16495 American Indian or Alaska Native NCIT:C41259 Asian NCIT:C41260 Black or African American NCIT:C16352 Native Hawaiian or Other Pacific Islander NCIT:C41219 White NCIT:C41261 Other race NCIT:C104495 Ethnic Group NCIT:C16495 Hispanic or Latino NCIT:C17459 Not Hispanic or Latino NCIT:C41222

Identifier IAO:0020000 denoted by IAO:0000235 assigning a centrally registered identifier IAO:0000574 given name IAO:0020016 denoted by IAO:0000235 family name IAO:0020017 has measurement unit label IAO:0000039 is quality measurement of IAO:0000221 is about IAO:0000136

act of anonymizing ICO:0000217

time unit UO:0000003

cause of death status OPMI:0000543 neonate stage UBERON:007221 (import from OPMI) death stage UBERON:0000071 (import from OPMI)

one-dimensional temporal region BFO:0000038 occupies temporal region BFO:0000155 zero-dimensional temporal region BFO:0000148 disposition BFO:0000091

Treatment OGMS:0000090

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andredekker commented 2 years ago

No. I asked @jonathanbona to see if he wants to do it or I should.

jonathanbona commented 2 years ago

yes, I should be able to get to this in the next few days

On Sun, May 22, 2022 at 1:06 AM Andre Dekker @.***> wrote:

No. I asked @jonathanbona https://github.com/jonathanbona to see if he wants to do it or I should.

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