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larisa-soldatova / EXACT

an ontology for biomedical protocols
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EXACT2 and BFO/OBI #2

Open Public-Health-Bioinformatics opened 6 years ago

Public-Health-Bioinformatics commented 6 years ago

I'm wondering if the EXACT2 curation team has any plans to formally move the ontology into OBOFoundry? We were just discussing in the OBI telecon the need for an ontology that focuses on experimental or manufacturing procedures. We have requests for "scooping" (https://github.com/obi-ontology/obi/issues/902) and "pouring" (https://github.com/obi-ontology/obi/issues/901), the latter of which I see EXACT2 already has. OBI could potentially directly house these processes but they apply much more broadly than in just biomedical processes. So I was wondering if a) you take on new terms, b) if they would have a purl that OBOFoundry hosted, c) underlying this, what the curation picture is for EXACT2, as it looks inactive for a few years? (Ideally, EXACT2 terms would have identifiers like http://purl.obolibrary.org/obo/EXACT2_1234567 to fit the form of most other ontologies there.)

An alternative is for OBI to consider bringing in all the "experimental action" items that you have in EXACT2, under "planned process" (http://www.ontobee.org/ontology/OBI?iri=http://purl.obolibrary.org/obo/OBI_0000011) or more particularly, "material process" ? I would favour generalizing them a bit to be some kind of "intervention process" or "protocol process" that applies to protocols, whether they be experimental or manufacturing procedures. (OBI is discussing what to calve off into a more general BFO component ontology.)

Public-Health-Bioinformatics commented 6 years ago

I should note that I am equally interested in drawing upon a more general material handling process ontology for our FoodOn.org ontology, which at moment has a variety of processes that are mostly more food-centric, but which really needs something similar to an experimental proceedure vocabulary when it comes time to provide a proper way of describing recipes, which is a future plan!

larisa-soldatova commented 6 years ago

Hi Damion, CC: Fatima

Thank you for contacting us regarding the EXACT work and your suggestions. You are right, we should keep EXACT generic, and we should submit it to OBO and get PURLs.

I hope to do this fairly soon.

To answer your questions:

a) you take on new terms,

Yes.

b) if they would have a purl that OBOFoundry hosted,

We will do that

c) underlying this, what the curation picture is for EXACT2, as it looks inactive for a few years? (Ideally, EXACT2 terms would have identifiers like http://purl.obolibrary.org/obo/EXACT2_1234567 to fit the form of most other ontologies there.)

A bit of background:

We continue working on EXACT, but due to the funding constrains it is mostly withing Fatima's PhD study (see CC). As the result we drifted more towards clinical procedures, as per her thesis: https://github.com/fatibaba/EXACT-med

We added many new terms to EXACT, but had to rename the new version for clinical procedures as OCL-SOP (an ontology for clinical standard operating procedures).

Wa are happy to keep OCL-SOP as a separate (even if a closely related) resource, and have EXACT as a generic ontology describing experimental actions.

There is no any formal curation process yet, but I can see that we need to put one in place. Meanwhile, if you can send Fatima and myself a request for inclusion terms, we will handle it.

Thank you, Larisa

On Tue, Jul 10, 2018 at 5:05 AM, Damion Dooley notifications@github.com wrote:

I'm wondering if the EXACT2 curation team has any plans to formally move the ontology into OBOFoundry? We were just discussing in the OBI telecon the need for an ontology that focuses on experimental or manufacturing procedures. We has a request for "scooping" (obi-ontology/obi#902 https://github.com/obi-ontology/obi/issues/902) and "pouring" ( obi-ontology/obi#901 https://github.com/obi-ontology/obi/issues/901), the latter of which I see EXACT2 already has. OBI could potentially directly house these processes but they apply much more broadly than in just biomedical processes. So I was wondering if a) you take on new terms, b) if they would have a purl that OBOFoundry hosted, c) underlying this, what the curation picture is for EXACT2, as it looks inactive for a few years? (Ideally, EXACT2 terms would have identifiers like http://purl.obolibrary.org/obo/EXACT2_1234567 to fit the form of most other ontologies there.)

An alternative is for OBI to consider bringing in all the "experimental action" items that you have in EXACT2, under "planned process" ( http://www.ontobee.org/ontology/OBI?iri=http://purl. obolibrary.org/obo/OBI_0000011) or more particularly, "material process" ? I would favour generalizing them a bit to be some kind of "intervention process" or "protocol process" that applies to protocols, whether they be experimental or manufacturing procedures. (OBI is discussing what to calve off into a more general BFO component ontology.)

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Public-Health-Bioinformatics commented 6 years ago

This is encouraging news! I will check in with other OBI people about possible ways forward, but the generic EXACT sounds attractive. I appreciate the BFO/OBI/IAO work you have done so far in EXACT. It seems that to get it into OBOFoundry some more curation work is needed? I would have to be cautious in waiting to see the converted version in OBOFoundry before making a final decision to reference it and send term requests.

I'm going to pitch this list of items that you probably already have in mind just to see if we have a similar vision?

Would it be too much to ask to convert the term identifiers to an EXACT_1234567 format in preparation for an OBOFoundry version? (I presume you have some existing systems that are using your current identifiers?) I would be willing to do the term id conversion myself for the 241 classes and 17 individuals. It is a way to encourage a multilingual view of the ontology content, and it would allow mixing of different ontology short identifiers in databases without necessarily needing namespace prefix. Its not enforced in OBOFoundry but it is encouraged.

Also, to anticipate your terms coming up in a large lookup service like OLS or Ontobee where visually one may need a few more cues about what type of thing a term is, would you be open to providing slightly longer labels for the experimental actions, like "aliquot process", "centrifuge process" etc. to distinguish them from the nouns they could be confused with?

I had a question about "optional descriptor of experimental action". I'm wondering if the issue of "optional" components can be resolved by using "min 0" or "max 1" cardinality e.g. "process subClassOf 'has proposition' min 0 period" instead of 'has proposition some '(optional) period'. Was there a logic engine compatibility issue with OWL flavour that precluded this?

Public-Health-Bioinformatics commented 6 years ago

p.s. about ENVO_03000043, scratch that. As mentioned earlier it seems bringing OBI "material processing" http://purl.obolibrary.org/obo/OBI_0000094 into EXACT, would provide a more natural generic home for your current experimental actions?

ddooley commented 6 years ago

Have any further decisions about the shape of EXACT been finalized? (BTW, I am the new incarnation of "ghost", as that account has been turned into the public-health-bioinformatics github organization).

Cheers,

Damion

ddooley commented 5 years ago

I wanted to follow up on this ... I think I can contribute if that is desired, along the above lines, to the Exact2 ontology. Do you have a status report?

larisa-soldatova commented 5 years ago

Hi Damion,

CC: Fatima

Thank you for following up. Fatima, my PhD student (see CC), following your request changed URLs in EXACT

(w3id.org/EXACT) http://w3id.org/EXACT2 some time ago.

Please check if that fits the purpose. Please contact us if something further is necessary.

Kind regards,

Larisa

On Tue, Apr 2, 2019 at 10:38 PM Damion Dooley notifications@github.com wrote:

I wanted to follow up on this ... I think I can contribute if that is desired, along the above lines, to the Exact2 ontology. Do you have a status report?

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ddooley commented 5 years ago

Where is the new Exact2? The links above don't quite seem to work at moment. Thx,

ddooley commented 5 years ago

Any update on this?
Regards, Damion

larisa-soldatova commented 5 years ago

Hi Damion, CC: Fatima

I hoped that Fatima would respond to your email and explain about EXACT. The last what I heard from her about this is that she changed IRI from w3id.org/EXACT2

to w3id.org/EXACT http://w3id.org/EXACT2

Does that work for you? Otherwise please advise what should we do.

Thank you and sorry that this takes so long, Larisa

On Wed, Apr 10, 2019 at 4:12 PM Damion Dooley notifications@github.com wrote:

Any update on this? Regards, Damion

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fatibaba commented 5 years ago

Where is the new Exact2? The links above don't quite seem to work at moment. Thx,

Hi Damion,

Apologies for the late response. I received an email of your last conversation with Larisa but for some reason, I didn't realize it was a thread here until now so I didn't see your question.

the correct link for EXACT2 is actually w3id.org/EXACT and the latest version with the new terms is in a new ontology I am working on for my PhD (as Larisa mentioned earlier) which is here w3id.org/OCL-SOP

Kind regards, Fatima

ddooley commented 5 years ago

It would be helpful to have a link from the current EXACT readme that points to your new work.

I'm starting to feel that it would be too difficult to interact with this work as an open source curation supported project. The w3id.org/OCL-SOP site shows code that hasn't been adjusted for 2 years, suggesting that none of the updates mentioned above are live. We need to reuse an ontology that is undergoing more frequent iterative updates - on the order of months rather than years. I understand why this isn't easy to attain.

It will be great to read about your research though. Laboratory SOP / protocol / process is a key part of analysis that a number of our projects need capturing, and its important to be able to show stakeholders how it can be done using ontology. I've shown collegues the Exact2 paper examples and they are much appreciated.

Regards, Damion

larisa-soldatova commented 5 years ago

Damion, I can commit to regular maintenance of EXACT if there is interest in using it. This work is dear to me and I wish it to be of some use to others.

There was no need for frequent updates of EXACT so far. Fatima was working on a version for clinical protocols as a part of her PhD study. Here is a bit about her work: http://ceur-ws.org/Vol-2050/ODLS_paper_4.pdf

If you can state what is required for this: 'to interact with this work as an open source curation supported project", then I hope I can follow it.

Kind regards, Larisa

On Thu, Apr 11, 2019 at 4:08 PM Damion Dooley notifications@github.com wrote:

It would be helpful to have a link from the current EXACT readme that points to your new work.

I'm starting to feel that it would be too difficult to interact with this work as an open source curation supported project. The w3id.org/OCL-SOP site shows code that hasn't been adjusted for 2 years, suggesting that none of the updates mentioned above are live. We need to reuse an ontology that is undergoing more frequent iterative updates - on the order of months rather than years. I understand why this isn't easy to attain.

It will be great to read about your research though. Laboratory SOP / protocol / process is a key part of analysis that a number of our projects need capturing, and its important to be able to show stakeholders how it can be done using ontology. I've shown collegues the Exact2 paper examples and they are much appreciated.

Regards, Damion

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ddooley commented 5 years ago

Well, my 2 bits then ... its a marketing conundrum. People won't demonstrate an interest in reusing it until the repository demonstrates certain characteristics conducive to reuse. So a bit more investment up front is required. The open source part is partly covered in having the EXACT and EXACT-med sites live, but a number of issues remain.

A solution is to clarify in development vs release versions. I like the ontology development kit, https://github.com/INCATools/ontology-development-kit, which has a folder structure with /src/ontology/[ontology name]-edit.owl where draft work is done, which can then occasionally be published/released to /[ontology name].owl . Other advantages are that it sets up an import scheme which isolates the terms being imported into one or more import files, which can then be refreshed with new definition/axiom content. (Addendum: it does this with a Makefile command line tool that can also be set up to do reasoner tests on the ontology).

That aside, I'll need to see the latest version to know if its close to that wish-list I was hoping for.

There is one other competitive part that needs a solution - the general process ontology mission. Exact has many parts of a general process ontology, but others are casting about to develop or adapt one too - some are turning to PO2 for example in food science, which also has its access problems (closed publication, similar term reuse and naming & maintenance structure issues). So explaining EXACT's ambitions with respect to a general process ontology would be important. And that brings us to the curation model - another avenue to success would be to demonstrate a multi-lab/agency/researcher curation team. Reaching that level of chain-reaction.

Hope that helps?

larisa-soldatova commented 5 years ago

Damion,

Thank you very much for your '2 bits', it is very helpful. You are right: the work on EXACT was publication driven. But I want to see it being used, and I will follow your advise on making it more usable.

I also like your suggestion for including to it more general processes. You are most welcome to join us to be a part our small EXACT team, If you are interested. I am thinking of making an open call to invite more researchers to this work.

I will update you how we are progressing with your suggestions.

Thank you again, Larisa

On Thu, Apr 11, 2019 at 6:36 PM Damion Dooley notifications@github.com wrote:

Well, my 2 bits then ... its a marketing conundrum. People won't demonstrate an interest in reusing it until the repository demonstrates certain characteristics conducive to reuse. So a bit more investment up front is required. The open source part is partly covered in having the EXACT and EXACT-med sites live, but a number of issues remain.

  • You mentioned for example that "following your request changed URLs in EXACT". This is not visible in EXACT on the live site; and if done it seems we have a forking problem where EXACT-med hasn't implemented this live either, leading to an issue of users not knowing where to go to get a consolidated latest version? It seems EXACT-med doesn't import EXACT, which suggests one supersedes and leaves to its own devices the other?
  • Is there an issue of wanting to publish before releasing the corresponding ontology? If so this is counter to reuse scenarios where term requests are acted on before publication cycles. An unworkable situation.
  • Having a single latest version EXACT site which is actively monitored for issues is an important marketing piece. A scenario where months go by before response is a strong disincentive.
  • If you have too many requests coming in, that is a problem of success!

A solution is to clarify in development vs release versions. I like the ontology development kit, https://github.com/INCATools/ontology-development-kit, which has a folder structure with /src/ontology/[ontology name]-edit.owl where draft work is done, which can then occasionally be published/released to /[ontology name].owl . Other advantages are that it sets up an import scheme which isolates the terms being imported into one or more import files, which can then be refreshed with new definition/axiom content.

That aside, I'll need to see the latest version to know if its close to that wish-list I was hoping for.

There is one other competitive part that needs a solution - the general process ontology mission. Exact has many parts of a general process ontology, but others are casting about to develop or adapt one too - some are turning to PO2 for example in food science, which also has its access problems (closed publication, similar term reuse and naming & maintenance structure issues). So explaining EXACT's ambitions with respect to a general process ontology would be important. And that brings us to the curation model - another avenue to success would be to demonstrate a multi-lab/agency/researcher curation team. Reaching that level of chain-reaction.

Hope that helps?

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ddooley commented 5 years ago

Ok. I'll contact you off-line about some possibilities re. a general process ontology.