search

proco-ontology / PROCO

PROCO: A formal ontology in the domain of process chemistry
9 stars 2 forks source link

Use original STATO term for rate #16

Open schaferw opened 2 years ago

schaferw commented 2 years ago

Comment from OBO submission

• [ ] You define http://purl.obolibrary.org/obo/PROCO_0000232 which seems identical to http://purl.obolibrary.org/obo/STATO_0000071. Any reason? Schaferw> Apologies – I thought we answered this before. There is no reason except our inexperience at he beginning of the endeavor and the fact that reaction rate is much more related to a chemistry ontology than a statistical one. The STATO term is directly referenced and accredited in the term. We have many other general OBO terms imported into PROCO under their original identifier/URL.

cmungall commented 2 years ago

The correct thing to do here is to open an issue on the STATO tracker to ask them to cede it if you intend to keep it.

There should only be a single "reaction rate" concept in OBO. It seems this belongs more in the chemistry domain than the statistics domain, but this should be resolved by involving others in the discussion.

An additional complication here is that both stato and proco concepts refer to information entities. However, there could also be a concept that is a subclass of PATO rate, which is a characteristic. My personal opinion is that including shadow information concepts for "X" and "X rate" across ontologies is a huge mistake, but this view is not shared by others in OBO. However, I think it is consensus that if you DO make shadow information concepts then this MUST be reflected in the name/label. I.e the information concept should be "reaction rate datum" and it SHOULD be axiomatized using a standard design pattern that relates it to the "real" reaction rate.

The use of these information entities brings in an additional complication - how do you decide what is in CHEMINF vs PROCO?

schaferw commented 2 years ago

Thanks for the comment. We will reach out to STATO.

From: Chris Mungall @.> Sent: Tuesday, August 9, 2022 9:21 AM To: proco-ontology/PROCO @.> Cc: Schafer, Wes A @.>; Author @.> Subject: Re: [proco-ontology/PROCO] Use original STATO term for rate (Issue #16)

EXTERNAL EMAIL– Use caution with any links or file attachments.

The correct thing to do here is to open an issue on the STATO tracker to ask them to cede it if you intend to keep it.

There should only be a single "reaction rate" concept in OBO. It seems this belongs more in the chemistry domain than the statistics domain, but this should be resolved by involving others in the discussion.

An additional complication here is that both stato and proco concepts refer to information entities. However, there could also be a concept that is a subclass of PATO rate, which is a characteristic. My personal opinion is that including shadow information concepts for "X" and "X rate" across ontologies is a huge mistake, but this view is not shared by others in OBO. However, I think it is consensus that if you DO make shadow information concepts then this MUST be reflected in the name/label. I.e the information concept should be "reaction rate datum" and it SHOULD be axiomatized using a standard design pattern that relates it to the "real" reaction rate

— Reply to this email directly, view it on GitHubhttps://github.com/proco-ontology/PROCO/issues/16#issuecomment-1209374753, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQTWPT5AUTI22ULBN36TQOLVYJLNRANCNFSM5T63MGCQ. You are receiving this because you authored the thread.Message ID: @.**@.>> This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD https://www.msd.com/contact-us/.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

schaferw commented 2 years ago

With regard to the PATO rate, we have attempted to be fully BFO compliant and have defined rates as process profiles.

From: Chris Mungall @.> Sent: Tuesday, August 9, 2022 9:21 AM To: proco-ontology/PROCO @.> Cc: Schafer, Wes A @.>; Author @.> Subject: Re: [proco-ontology/PROCO] Use original STATO term for rate (Issue #16)

EXTERNAL EMAIL– Use caution with any links or file attachments.

The correct thing to do here is to open an issue on the STATO tracker to ask them to cede it if you intend to keep it.

There should only be a single "reaction rate" concept in OBO. It seems this belongs more in the chemistry domain than the statistics domain, but this should be resolved by involving others in the discussion.

An additional complication here is that both stato and proco concepts refer to information entities. However, there could also be a concept that is a subclass of PATO rate, which is a characteristic. My personal opinion is that including shadow information concepts for "X" and "X rate" across ontologies is a huge mistake, but this view is not shared by others in OBO. However, I think it is consensus that if you DO make shadow information concepts then this MUST be reflected in the name/label. I.e the information concept should be "reaction rate datum" and it SHOULD be axiomatized using a standard design pattern that relates it to the "real" reaction rate

— Reply to this email directly, view it on GitHubhttps://github.com/proco-ontology/PROCO/issues/16#issuecomment-1209374753, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQTWPT5AUTI22ULBN36TQOLVYJLNRANCNFSM5T63MGCQ. You are receiving this because you authored the thread.Message ID: @.***> This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD https://www.msd.com/contact-us/.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.