search

OBOFoundry / OBOFoundry.github.io

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry
http://obofoundry.org
Other
163 stars 201 forks source link

Request prefix for MAxO #868

Closed LCCarmody closed 4 years ago

LCCarmody commented 5 years ago

Dear OBO-Discuss,

We are creating the Medical Action Ontology (MAxO), and we would a prefix and PURL in OBO.

Basic information:

-- Requested Prefix: MAXO Ontology Title: Medical Action Ontology Download link: https://github.com/monarch-initiative/MAxO/tree/master/src/ontology

Home page: https://github.com/monarch-initiative/MAxO

Contact e-mail: leigh.carmody@jax.org Mailing-list: Tracker link: https://github.com/monarch-initiative/MAxO/issues Description: MAxO is a domain ontology that provides a controlled vocabulary for that represents medical actions, procedures, therapies, interventions, and recommendations--especially important for rare diseases.

matentzn commented 5 years ago

Two weeks have passed and no comments have been given. As per OBO regulations, we just chase this ticket once more; @LCCarmody you can forward the original mail once more to the OBO mailing list with a comment like: "Reminder to comment on application of new Medical Action Ontology (MAXO)".

I am part of the OBO technical working group, but given my close involvement with MAXO, I would like others to make the call.

bpeters42 commented 5 years ago

Sorry for the late follow up. We are working on defining clearer criteria for handling purl requests. One potential concern is that it is not clear how your ontology relates to http://www.obofoundry.org/ontology/omrse.html and http://www.obofoundry.org/ontology/ogms.html. Would it be possible for you to collaborate with them, or at least re-use the terms they are covering?

Two other questions are:

Intended Use: Is your ontology serving the need of one or more specific projects? If so, please describe them. The OBO Foundry policy on documented users is described at http://obofoundry.org/principles/fp-009-users.html.

Data Source: Which resource, if any, was used to generate the ontology (e.g., NCBITaxon was created from the NCBI taxonomy resource; the Protein Ontology uses, in part, UniProtKB).

cmungall commented 5 years ago

I don't think there is any overlap with omrse which only deals with social entities.

There is maybe one class in OGMS that could be reused or at least xreffed to start: https://www.ebi.ac.uk/ols/ontologies/ogms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOGMS_0000090

I think there is most overlap with OBI, there is a pre-existing open ticket: https://github.com/monarch-initiative/MAxO/issues/30

bpeters42 commented 5 years ago

Thanks for pointing to that OBI ticket Chris. It looks like Maxo is not intending to be interoperable, so probably it should be outside of the OBO group.

On Tue, Jun 4, 2019 at 10:09 AM Chris Mungall notifications@github.com wrote:

I don't think there is any overlap with omrse which only deals with social entities.

There is maybe one class in OGMS that could be reused or at least xreffed to start:

https://www.ebi.ac.uk/ols/ontologies/ogms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOGMS_0000090

I think there is most overlap with OBI, there is a pre-existing open ticket: monarch-initiative/MAxO#30 https://github.com/monarch-initiative/MAxO/issues/30

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/OBOFoundry.github.io/issues/868?email_source=notifications&email_token=ADJX2IUCTWNIUWL2N4H3XP3PY2OWLA5CNFSM4HKF7PEKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODW5HXCQ#issuecomment-498760586, or mute the thread https://github.com/notifications/unsubscribe-auth/ADJX2IW2MV6A35DOWEXSCUTPY2OWLANCNFSM4HKF7PEA .

-- 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

LCCarmody commented 5 years ago

OGRE and OBI do have a handful of terms that could be useful, but the structure is very different than what we were planning to achieve. For new terms, we are trying to cross reference where we can and use terms from other ontologies (Including OBI, UBERON, FOODON, etc.) to help build the structure.

Our use is to develop a detailed ontology for medical actions used in disease, specifically rare disease. Our sources will be GeneReviews and PubMed and International Rare Diseases research consortium (IRDiRC) data. ClinGen representatives have also said they could supply us with specific references to clinical reports.

This ontology will (hopefully) be used for data mining efforts to identify and report medical actions (procedures, nutrition recommendations, and behavior modifications) for rare disease. It will be used in coordination with HPO and MONDO as a tool for gathering info.

Thanks.

-- Leigh Carmody, PhD Scientific Curator, Robinson Lab The Jackson Laboratory for Genomic Medicine Farmington, CT (860) 837-2040 leigh.carmody@jax.orgmailto:leigh.carmody@jax.org www.jax.orghttp://www.jax.org/

The Jackson Laboratory: Leading the Search for tomorrow’s cures

From: bpeters42 notifications@github.com Reply-To: "OBOFoundry/OBOFoundry.github.io" reply@reply.github.com Date: Tuesday, June 4, 2019 at 1:26 PM To: "OBOFoundry/OBOFoundry.github.io" OBOFoundry.github.io@noreply.github.com Cc: Leigh Carmody Leigh.Carmody@jax.org, Mention mention@noreply.github.com Subject: Re: [OBOFoundry/OBOFoundry.github.io] Request prefix for MAxO (#868)

Thanks for pointing to that OBI ticket Chris. It looks like Maxo is not intending to be interoperable, so probably it should be outside of the OBO group.

On Tue, Jun 4, 2019 at 10:09 AM Chris Mungall notifications@github.com wrote:

I don't think there is any overlap with omrse which only deals with social entities.

There is maybe one class in OGMS that could be reused or at least xreffed to start:

https://www.ebi.ac.uk/ols/ontologies/ogms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOGMS_0000090

I think there is most overlap with OBI, there is a pre-existing open ticket: monarch-initiative/MAxO#30 https://github.com/monarch-initiative/MAxO/issues/30

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/OBOFoundry.github.io/issues/868?email_source=notifications&email_token=ADJX2IUCTWNIUWL2N4H3XP3PY2OWLA5CNFSM4HKF7PEKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODW5HXCQ#issuecomment-498760586, or mute the thread https://github.com/notifications/unsubscribe-auth/ADJX2IW2MV6A35DOWEXSCUTPY2OWLANCNFSM4HKF7PEA .

-- 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 GitHubhttps://github.com/OBOFoundry/OBOFoundry.github.io/issues/868?email_source=notifications&email_token=AGG4AQBADDN3Q37TZVBDYX3PY2QSFA5CNFSM4HKF7PEKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODW5JC7I#issuecomment-498766205, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AGG4AQGJNCC6GREHV2JOVWTPY2QSFANCNFSM4HKF7PEA.

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

mellybelly commented 5 years ago

@bpeters42, I would not say that is true, quite the contrary. I can see your concerns though, let me try to address them.

First, I think it is important to recognize that MAxO is not like NCBITaxon nor PRO (both of which have all or most of their content auto-generated from an upstream database), so perhaps I don't understand the source question exactly. There isn't any other source other than information captured from the literature and other sources.

Second, there is very little overlap with any current OBO ontology, and where a few terms exist, they can be reused, xref'd, included in the new OBO-core if they are not already, and/or be used in logical defs (as per above example using OBI 'assay'.

OGMS has ~10 procedure in total terms that could be of use, but has an odd structure. (i.e., the term, ‘clinical history taking’, is a child ‘health care process assay’. We could reuse these terms or xref, however, this structure does not work for MAXO to address our use cases.

Finally, I think it is important that the OBO library can evolve to support different use cases, which might mean some ontologies with different classification strategies, and/or their convergence and evolution.

bpeters42 commented 5 years ago

Sorry, my second comment was needlessly aggressive. Apologies especially to you Leigh - I did not realize that this is a new world for you, and it was unfair for me to assume you were aware of the policies and principles.

Some clarifications: I wrote the first comment together with 10+ people on the OBO call, so this was not just me. As I wrote, we are trying to improve the information requested from ALL PURL submission requests. The two points about 'Intended Use' and 'Data Source' are not at all asked because there is a particular concern for MAXO. We just reviewed what other information can be helpful in deciding on PURL requests.

The second comment, which was overly aggressive, was triggered by this sentence in the ticket on overlap to OBI: https://github.com/monarch-initiative/MAxO/issues/30

"the hierarchies of the ontologies [...] including NCIt and OBI, do not reflect the clean groupings we are looking for now with MAXO"

This triggered me, as I might imagine some of you might be triggered by someone saying they want to create a new ontology needing anatomy terms, but they do not want to take them from any of the existing anatomy ontologies because they are not 'clean'.

Yes, interoperability is hard. And it is perfectly reasonable to not want to be interoperable for an ontology that is intended for in house use. But then there is also no need to work within the OBO group, and confuse ontology users that already are struggling with overlapping ontologies.

I hope this is more constructive.

matentzn commented 5 years ago

@bpeters42 I 100% agree with the sentiment on interoperability :) I see this to be my primary responsibility on this project to ensure that MAxO is interoperable with related ontologies and that we adhere to the OBO foundry principles. While I gather my rebuttal arguments, do I understand it correctly that your primary concern is the interoperability issue (OGMS, OBI, NCIT alignments)?

Without designing a final argument yet, just to give some prima facie peace of mind:

Thanks again!

mellybelly commented 5 years ago

thanks @matentzn. Given the degree of interoperability work that Monarch has accomplished in aligning ontologies in the OBO library, or for use in OBO library, should also count for some credibility and demonstration of commitment towards that ;-).

cmungall commented 5 years ago

Thanks Nico, just to add two things:

bpeters42 commented 5 years ago

Thanks for the response Nico. The biopsy example is a good case in point: OBI has a very similar design pattern, also based on UBERON for 'specimen from organism'.

http://www.ontobee.org/ontology/OBI?iri=http://purl.obolibrary.org/obo/OBI_0600005

Looking at it, we are probably mis-using 'derives from'. Working jointly on this rather than having multiple overlapping and incompatible sets of terms is exactly what we need to work on together.

And on looking more closely into the terms you guys have, I was actually wondering if an attempt has been made to contact the OGMS folks and work completely within OGMS? It is an open development team, and they can definitely need help and input. It would be great for the community to have these things be done right, once.

On Wed, Jun 5, 2019 at 10:20 AM Chris Mungall notifications@github.com wrote:

Thanks Nico, just to add two things:

  • Nerves should always be in the PNS by definition, I will convince David and Melissa :-)

  • When you say "If the semantical disagreement is too large, but the terms still appear to relate closely, we add xrefs," -- this is sensible, but there should also be a (possibly reciprocal) ticket to the external ontology tracker, so the semantic challenges are transparent and can be commented on by all. This is often long running (e.g the various GO-CL, CHEBI-PRO, etc ones) but at least it is there. The ticket on maxo about obi is a start but it would be good to have maxo editors have comment on the obi tracker about some things they are struggling with.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/OBOFoundry.github.io/issues/868?email_source=notifications&email_token=ADJX2ISPXKUT3QMUXSWP22DPY7YXPA5CNFSM4HKF7PEKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXANJCY#issuecomment-499176587, or mute the thread https://github.com/notifications/unsubscribe-auth/ADJX2IX2PH2E2AAVP6KYKEDPY7YXPANCNFSM4HKF7PEA .

-- 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

matentzn commented 5 years ago

Ok, I think I understand your concerns. Let me see whether I can hash out a plan for mutual stimulation and cross-fertilisation and run it by the other parties involved. I can see us at the very least share design patterns, but if this is not enough to pass OBO foundry thresholds (and I like high thresholds), we will probably continue to evolve MaxO a bit more outside of the OBO umbrella (of course fully in line with OBO foundry principles, because they are all sensible) and re-apply once we have internally clarified our conceptual relationship with OGMS and OBI. And then re-apply! :) Thanks for the gate-keeping and the pointers to related ontologies; I will see what I can do! :)

mellybelly commented 5 years ago

(off topic) should there be a place for coordinating cross-ontology issues? If there is already (beyond what we do by necessity), perhaps that would be a good way to address and document some of these challenges and questions and improve the OBO library overall?

cstoeckert commented 5 years ago

Thanks all for the interesting discussion about how MAxo can fit into the OBO Foundry. This discussion highlights the difficulties of new ontology requests even when coming from OBOF working group members! I agree with Melissa’s comment regarding coordinating cross-ontologies issues; maybe these can be highlighted as part of the OBO Core (https://github.com/OBOFoundry/Experimental-OBO-Core). Regarding MAxo, I think we want to recognize the intent and willingness to follow OBO Foundry principles including reusability and interoperability so am happy to move ahead with the request. We can (and should) still continue to argue and debate design patterns! But for MAxo and other new ontology requests, agreeing on those should not be a barrier as long as there is the willingness to work together.

cmungall commented 4 years ago

so it seems like we are OK to add this?

mellybelly commented 4 years ago

We still don't seem to have a PURL. Can someone approve this request?

If the answer is no that is fine, we can use a different PID but it would be good to know. It IS our intention to follow OBO best practices; integration, coordination, and differences of modeling are an important, but orthogonal issue imho.

zhengj2007 commented 4 years ago

@mellybelly Hi Melissa, after the request prefix is approved, two configuration files need to be generated for new ontology registration and purl setting up. The maxo.md file need to be created under https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology directory for prefix registration. The maxo.yml file need to be created under https://github.com/OBOFoundry/purl.obolibrary.org/tree/master/config directory for purl setting up.

According to OBO Foundry operation committee meeting discussion, we prefer the prefix submitters to add two files using pull request. Please let me know if you have any questions or need help on making two configuration files.

cmungall commented 4 years ago

Luckily maxo was generated using the ODK, so you have the files in place:

https://github.com/monarch-initiative/MAxO/tree/master/src/metadata

You should review these and submit as PRs. Or perhaps you could do this Jie?

Still a bit tedious but getting easier!

On Tue, Feb 11, 2020 at 12:01 PM jie zheng notifications@github.com wrote:

@mellybelly https://github.com/mellybelly Hi Melissa, after the request prefix is approved, two configuration files need to be generated for new ontology registration and purl setting up. The maxo.md file need to be created under https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology directory for prefix registration. The maxo.yml file need to be created under https://github.com/OBOFoundry/purl.obolibrary.org/tree/master/config directory for purl setting up.

According to OBO Foundry operation committee meeting discussion, we prefer the prefix submitter to add two files using pull request. Please let me know if you have any questions or need help on making two configuration files.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/OBOFoundry.github.io/issues/868?email_source=notifications&email_token=AAAMMOOZXWLTOHXVPKBYMIDRCL7X3A5CNFSM4HKF7PEKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELN3I6Y#issuecomment-584823931, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOJM64DX63YYEDTXGBTRCL7X3ANCNFSM4HKF7PEA .

zhengj2007 commented 4 years ago

@cmungall I'd prefer that MAXO developers take care of it.

matentzn commented 4 years ago

Did it.