OBO Core Disease - Githubissues

Documenting in this ticket 'disease' term history, usage

Below, I have outlined how 'disease' has been defined in the DO since 2006, then revised in 2010-2012, to be orthogonal with OGMS. I have included links to the source documents: google docs, archives of files.

I also had a look at BioPortal, to get a view of how the term - URI - definition has been re-used for new ontologies.

Cheers, Lynn

Under the Disease Ontology Project: archived in SF: http://sourceforge.net/p/diseaseontology/ 2005: DiseaseOntology2 release -- prior to upper level re-structuring 2007 DiseaseOntology3 release 2006-08-28. DO3v30.obo 2006-08-28 DOID:4 Disease --> root of DO tree, upper level branches defined 2006-11-05 Revision 20 DOID:4 Disease, defined: A disease is an enduring pattern of abnormal functioning, or abnormal localization of normal functioning, and / or abnormal localization of constituents of the human body, or a normal physiological response to an environmental insult, which without intervention, would lead to an evolving set of signs and symptoms.

In 2008: The DO received an R01 (Warren Kibbe and Lynn Schriml), formed an advisory board. The definition of disease in the DO, was discussed with the advisory board and (see notes from 2010, 2011 and 2012, below) These discussions included Barry Smith and Alan Ruttenburg (DO Advisory board members).

         These discussions are documented in the following Google docs

Discussion of Definition of Disease

  as we came to consensus, the outcome of the discussions was recorded in this google doc: 
      [Definition of Disease(https://docs.google.com/document/d/1N_A6kJb3UmrYwzRIwj99Bzb-YGY7OpaGzM9AxP8dptk/edit)

DO 'disease' definition in 2011-2012: A disease is a pattern of abnormal functioning, or abnormal localization of normal functioning, and / or abnormal localization of constituents when compared to other members of that species.

Barry created OGMS, OBO Foundry page and defined disease as: A disposition to undergo pathological bodily processes that exists in an organism because of one or more disorders in that organism.

The initial versions of OGMS are found in the archived Google code ohms directory OGMS (OBO) v0.1 darted Jul 27, 2009 with disease defined as: [Term] id: ID:0000031 name: disease def: "A disposition (i) to undergo pathological processes that (ii) exist in an organism because of one or more disorders in that organism." [http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf] comment: Examples: Epilepsy as a disease that disposes to the occurence of seizures (pathological process) due to an underlying abnormality in the neuronal circuitry of the brain (phyisical basis). is_a: ID:0000009 ! disposition created_by: agoldfain creation_date: 2009-06-23T11:21:20Z

--> This definition was published in Toward an Ontological Treatment of Disease and Diagnosis (2009) [PDF(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/pdf/amia-s2009-116.pdf)]

Barry suggested aligning the DO 'disease' definition with the OGMS definition.

--> During these discussions, Barry, in OGMS had devised a new disease definition, which the DO

The four of us, Warren, Barry, Alan and myself, upon further discussion, revised the DO definition of disease, to be orthogonal with the new OGMS definition of disease.

The DO definition of disease became: A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. Reference: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf

Use - Re-Use of 'term', URI, definitions: I thought it would be informative to take a look at how these have been implemented:

Querying BioPortal, query results -- there is quite a bit of variation in how the term 'disease' is represented. In some cases the URI has been re-used with the DO or OGMS definition, in other cases there is a new URI, with the same definition.

the purl the term disease, the DO - OGMS definitions, showing the diversity of 'disease' usage/definition across ontologies.

Google doc

Hi @lschriml. I think maybe when you say that the DO definition was revised to be orthogonal with the OGMS definition, you mean that it was revised to be consistent with it. They look the same to me.

Since they are the same, it seems like we need to merge them into one term with a single ID.

Hello Ramona, The DO originally had a different definition for ‘disease’, we worked with Barry and others (documented in the GitHub ticket), to make a new DO definition that all were happy with. This was before OGMS. This definition was then subsequently used by OGMS. Cheers, Lynn

Sent from my iPhone

On Jul 28, 2019, at 6:12 PM, Ramona Walls notifications@github.com wrote:

Hi @lschriml. I think maybe when you say that the DO definition was revised to be orthogonal with the OGMS definition, you mean that it was revised to be consistent with it. They look the same to me.

Since they are the same, it seems like we need to merge them into one term with a single ID.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

I think Ramona was just picking up on the word 'orthogonal', which would imply that DO and OGMS have fundamentally different definitions of disease. As Lynn goes on to explain, that does not seem to be the case, so the use of the word in the first email was likely just an oversight by Lynn (which happens to me all the time, so no judgement)

On Sun, Jul 28, 2019 at 6:34 PM lschriml notifications@github.com wrote:

Hello Ramona, The DO originally had a different definition for ‘disease’, we worked with Barry and others (documented in the GitHub ticket), to make a new DO definition that all were happy with. This was before OGMS. This definition was then subsequently used by OGMS. Cheers, Lynn

Sent from my iPhone

On Jul 28, 2019, at 6:12 PM, Ramona Walls notifications@github.com wrote:

Hi @lschriml. I think maybe when you say that the DO definition was revised to be orthogonal with the OGMS definition, you mean that it was revised to be consistent with it. They look the same to me.

Since they are the same, it seems like we need to merge them into one term with a single ID.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/Experimental-OBO-Core/issues/19?email_source=notifications&email_token=ADJX2ITFWW2DW6GHVOTMFDTQBYNGJA5CNFSM4HH3SSVKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD27H62Y#issuecomment-515800939, or mute the thread https://github.com/notifications/unsubscribe-auth/ADJX2IQIJUA2V3MOO42HYALQBYNGJANCNFSM4HH3SSVA .

-- Bjoern Peters Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

Good point. Synergy is good :)

Sent from my iPhone

On Jul 28, 2019, at 6:53 PM, bpeters42 notifications@github.com wrote:

I think Ramona was just picking up on the word 'orthogonal', which would imply that DO and OGMS have fundamentally different definitions of disease. As Lynn goes on to explain, that does not seem to be the case, so the use of the word in the first email was likely just an oversight by Lynn (which happens to me all the time, so no judgement)

On Sun, Jul 28, 2019 at 6:34 PM lschriml notifications@github.com wrote:

Hello Ramona, The DO originally had a different definition for ‘disease’, we worked with Barry and others (documented in the GitHub ticket), to make a new DO definition that all were happy with. This was before OGMS. This definition was then subsequently used by OGMS. Cheers, Lynn

Sent from my iPhone

On Jul 28, 2019, at 6:12 PM, Ramona Walls notifications@github.com wrote:

Hi @lschriml. I think maybe when you say that the DO definition was revised to be orthogonal with the OGMS definition, you mean that it was revised to be consistent with it. They look the same to me.

Since they are the same, it seems like we need to merge them into one term with a single ID.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/Experimental-OBO-Core/issues/19?email_source=notifications&email_token=ADJX2ITFWW2DW6GHVOTMFDTQBYNGJA5CNFSM4HH3SSVKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD27H62Y#issuecomment-515800939, or mute the thread https://github.com/notifications/unsubscribe-auth/ADJX2IQIJUA2V3MOO42HYALQBYNGJANCNFSM4HH3SSVA .

-- Bjoern Peters Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

Thanks, Lynn and exactly, Bjoern. I just wanted to make sure I wasn’t missing something in my sleep deprived state following and early morning flight.

Enviado de Buffalo

On Jul 28, 2019, at 6:54 PM, lschriml notifications@github.com wrote:

Good point. Synergy is good :)

Sent from my iPhone

On Jul 28, 2019, at 6:53 PM, bpeters42 notifications@github.com wrote:

I think Ramona was just picking up on the word 'orthogonal', which would imply that DO and OGMS have fundamentally different definitions of disease. As Lynn goes on to explain, that does not seem to be the case, so the use of the word in the first email was likely just an oversight by Lynn (which happens to me all the time, so no judgement)

On Sun, Jul 28, 2019 at 6:34 PM lschriml notifications@github.com wrote:

Hello Ramona, The DO originally had a different definition for ‘disease’, we worked with Barry and others (documented in the GitHub ticket), to make a new DO definition that all were happy with. This was before OGMS. This definition was then subsequently used by OGMS. Cheers, Lynn

Sent from my iPhone

On Jul 28, 2019, at 6:12 PM, Ramona Walls notifications@github.com wrote:

Hi @lschriml. I think maybe when you say that the DO definition was revised to be orthogonal with the OGMS definition, you mean that it was revised to be consistent with it. They look the same to me.

Since they are the same, it seems like we need to merge them into one term with a single ID.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/Experimental-OBO-Core/issues/19?email_source=notifications&email_token=ADJX2ITFWW2DW6GHVOTMFDTQBYNGJA5CNFSM4HH3SSVKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD27H62Y#issuecomment-515800939, or mute the thread https://github.com/notifications/unsubscribe-auth/ADJX2IQIJUA2V3MOO42HYALQBYNGJANCNFSM4HH3SSVA .

-- Bjoern Peters Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread. — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

OBOFoundry / COB

OBO Core Disease #19