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Term request: 'code set' #5

Closed CDowland closed 4 years ago

CDowland commented 4 years ago

I am submitting a term request for code set, as a child of document, with the following annotations:

Definition: A document that is a collection of identifiers that has been created to identify and annotate core ideas of a specified domain, and where the intention of its creators is that the identifiers have a one-to-one correspondence with entities in reality outside the aggregate.

Comment: Does not imply absence vs. presence of any taxonomy

Comment: Does not imply that identifiers denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities (e.g., SNOMED and even various OBO ontologies have identifiers that identify entities in all three categories).

Comment: The identifiers do not denote each other.

Comment: Each identifier is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation.

When there is no such string, it is almost always because the identifiers take the form of human language words. For example, a “sex” or “gender” code set could have identifiers “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).

Comment: For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).

Comment: Many code sets are created for a specific purpose in addition to merely identifying and annotating core ideas of a specified domain.

Comment: For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.

mbrochhausen commented 4 years ago

I am not sure this class should be created in PNO. Was that what we agreed upon in the Aim 4 meeting?

On Wed, Apr 15, 2020 at 1:10 PM Clint Dowland notifications@github.com wrote:

I am submitting a term request for code set, as a child of document, with the following annotations:

Definition: A document that is a collection of identifiers that has been created to identify and annotate core ideas of a specified domain, and where the intention of its creators is that the identifiers have a one-to-one correspondence with entities in reality outside the aggregate.

Comment: Does not imply absence vs. presence of any taxonomy

Comment: Does not imply that identifiers denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities (e.g., SNOMED and even various OBO ontologies have identifiers that identify entities in all three categories).

Comment: The identifiers do not denote each other.

Comment: Each identifier is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation.

When there is no such string, it is almost always because the identifiers take the form of human language words. For example, a “sex” or “gender” code set could have identifiers “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).

Comment: For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).

Comment: Many code sets are created for a specific purpose in addition to merely identifying and annotating core ideas of a specified domain.

Comment: For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.

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CDowland commented 4 years ago

Yes, submitting this term request to PNO is the plan that came out of the Aim 4 meeting. Is there another ontology that you think would be a more appropriate home for this class?

mbrochhausen commented 4 years ago

I do think it fits better into IAO.

On Wed, Apr 15, 2020 at 1:43 PM Clint Dowland notifications@github.com wrote:

Yes, submitting this term request to PNO is the plan that came out of the Aim 4 meeting. Is there another ontology that you think would be a more appropriate home for this class?

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CDowland commented 4 years ago

On one hand, I can see why you would say that, as the sort of document described in the definition would indeed be an information artifact ("a dependent continuant or its bearer that is created as the result of one or more intentional processes").

On the other hand, a defining trait of the document is that it is a collection of identifiers, and identifier is a PNO class.

Perhaps a further reason to favor PNO is that since the PNO class identifier is not currently imported into IAO, and has no equivalent there, putting code set in IAO would result in its being in an ontology in which one of the key terms in its definition is not defined anywhere in that ontology.

mbrochhausen commented 4 years ago

IAO should have imported as part of the ZIP code work. So, that doesn't provide a reason.

I think it clearly belongs in IAO. I would be interesting to get Bill's take.

If we agree, I can make Jie implement the changes.

Best, Mathias

On Wed, Apr 15, 2020 at 2:14 PM Clint Dowland notifications@github.com wrote:

On one hand, I can see why you would say that, as the sort of document described in the definition would indeed be an information artifact ("a dependent continuant or its bearer that is created as the result of one or more intentional processes").

On the other hand, a defining trait of the document is that it is a collection of identifiers, and identifier is a PNO class.

Perhaps a further reason to favor PNO is that since the PNO class identifier is not currently imported into IAO, and has no equivalent there, putting code set in IAO would result in its being in an ontology in which one of the key terms in its definition is not defined anywhere in that ontology.

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sjbost commented 4 years ago

Hi Clint,

Do you want to ask Bill’s opinion via email or would you prefer to add it to the agenda for next week’s Aim 4 meeting?

Best, Sarah

Sarah Bost, MSLS | Research Coordinator Department of Health Outcomes and Biomedical Informatics University of Florida 352-294-8424 | sarah.bost@ufl.edumailto:sarah.bost@ufl.edu

From: Mathias Brochhausen notifications@github.com Reply-To: ProperNameOntology/proper-name-ontology reply@reply.github.com Date: Wednesday, April 15, 2020 at 2:37 PM To: ProperNameOntology/proper-name-ontology proper-name-ontology@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [ProperNameOntology/proper-name-ontology] Term request: 'code set' (#5)

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IAO should have imported as part of the ZIP code work. So, that doesn't provide a reason.

I think it clearly belongs in IAO. I would be interesting to get Bill's take.

If we agree, I can make Jie implement the changes.

Best, Mathias

On Wed, Apr 15, 2020 at 2:14 PM Clint Dowland notifications@github.com wrote:

On one hand, I can see why you would say that, as the sort of document described in the definition would indeed be an information artifact ("a dependent continuant or its bearer that is created as the result of one or more intentional processes").

On the other hand, a defining trait of the document is that it is a collection of identifiers, and identifier is a PNO class.

Perhaps a further reason to favor PNO is that since the PNO class identifier is not currently imported into IAO, and has no equivalent there, putting code set in IAO would result in its being in an ontology in which one of the key terms in its definition is not defined anywhere in that ontology.

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hoganwr commented 4 years ago

IAO should have imported what? (as part of the ZIP code work). If you mean the class 'identifier', then why can't it import 'code set', too?

What is the plan going forward for PNO/IAO? If the plan is to discontinue further PNO development then I understand the issue. Otherwise I am really confused. It was quite clear that we were going to put code set into PNO.

mbrochhausen commented 4 years ago

My apologies for missing that we had decided on that in the last Aim 4 meeting.

Since we have 2 votes in favor, I am planning to add the class by Monday, April 20. If anyone as further objects, please make those known before the end of the week.

Just for clarification: my current plan is to maintain and develop PNO independently from IAO (albeit for the time being using the IAO namespace). Of course, If the emerging PNO community felt otherwise, this would be a discussion to be had.

On Wed, Apr 15, 2020 at 3:32 PM Bill Hogan notifications@github.com wrote:

IAO should have imported what? (as part of the ZIP code work). If you mean the class 'identifier', then why can't it import 'code set', too?

What is the plan going forward for PNO/IAO? If the plan is to discontinue further PNO development then I understand the issue. Otherwise I am really confused. It was quite clear that we were going to put code set into PNO.

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mbrochhausen commented 4 years ago

resolved by commit https://github.com/ProperNameOntology/proper-name-ontology/commit/4deaba5e86dd627746d41ce73cb98adc821dfaaa