search

EnvironmentOntology / environmental-exposure-ontology

Modular environmental exposures ontology
Other
32 stars 18 forks source link

NTRs: collection of COVID-19 related exposures #134

Open cmrn-rhi opened 4 years ago

cmrn-rhi commented 4 years ago

The CanCOGeN COVID-19 Ontology project requests your consideration on the integration of the following collection of human/organism exposure terms into ECTO.

New Term Requests Please refer to the “ECTO” tab in the following document: https://docs.google.com/spreadsheets/d/1FkC7p0vLbdoYoUgPMUhlvpHo26RqrP9FuUoXyQdrHGM/edit?usp=sharing

Consider this collection an initial draft - we are willing and able to reformat and make any other curation changes necessary to facilitate integration of these terms. We can also use ROBOT to generate an owl file for bulk integration if that’s more convenient.

Looking forward to your feedback.

cmrn-rhi commented 3 years ago

Hello ECTO team, Has anyone had a chance to consider this proposal?

diatomsRcool commented 3 years ago

I assume you are referring to the tab labeled "ECTO"? I think we can make this work. The most important piece will be identifying the elements we need to build the exposure term in ECTO. Maybe a new column for exposure stimulus ontology ID? We can help with this, if you like.

cmrn-rhi commented 3 years ago

Wonderful! Help from your team is definitely appreciated, especially "exposure stimulus" terms. I've tried to model other annotations similarly to what I have found in ECTO, but feel free to pick it apart and suggest alternatives.

I assume you are referring to the tab labeled "ECTO"?

That's the tab yes!

The most important piece will be identifying the elements we need to build the exposure term in ECTO. Maybe a new column for exposure stimulus ontology ID?

I've added now added an "exposure stimulus ontology ID" column and will begin trying to find matches (starting with classes already in ECTO).

diatomsRcool commented 3 years ago

Excellent. Would you like to let me know when I can take a look at the spreadsheet again?

cmrn-rhi commented 3 years ago

I'll be able to get the first pass on the "exposure stimulus ontology ID" column completed in the next day or two, so Monday at the latest. Either way I will let you know as soon as it's done.

cmrn-rhi commented 3 years ago

@diatomsRcool the spreadsheet (ECTO tab) is ready for your feedback. This link will provide you with the ability to comment, but if you'd prefer to edit the cells directly feel free to email me at cmrnrhi@student.ubc.ca and I can add you as an editor.

diatomsRcool commented 3 years ago

Excellent. The ENVO terms will be pretty straightforward. I would suggest getting the ENVO NTRs in sooner rather than later to get that discussion going. It looks like we'll have to import some new ontologies like GENEPIO, COVOC, and OPMI, which I'm not familiar with but we'll give it a try. COVOC isn't in OBO Foundry yet. Let's move forward by tackling some of this low-hanging fruit. I've got some ontology time on my calendar for Wed. I'll start adding new terms then.

cmrn-rhi commented 3 years ago

Wonderful, I agree that let's go with the low-hanging fruit first!

The ENVO NTRs are in progress and will be curated this week. We're in an ongoing process with ENVO of integrating new terms which is why several have been ID'd but won't be public until their next release. I don't know ENVOs exact time lines but I can keep you up to date on terms when they are released. Any terms that have ID's but aren't public yet are in italics and mentioned in the curator issues/comment column.

I was feeling uncertain about using COVOC as well. Instead I'll try connecting with IDO asap, and otherwise I can add terms we need to GenEpiO.

On Mon, Feb 8, 2021 at 6:02 AM diatomsRcool notifications@github.com wrote:

Excellent. The ENVO terms will be pretty straightforward. I would suggest getting the ENVO NTRs in sooner rather than later to get that discussion going. It looks like we'll have to import some new ontologies like GENEPIO, COVOC, and OPMI, which I'm not familiar with but we'll give it a try. COVOC isn't in OBO Foundry yet. Let's move forward by tackling some of this low-hanging fruit. I've got some ontology time on my calendar for Wed. I'll start adding new terms then.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/EnvironmentOntology/environmental-exposure-ontology/issues/134#issuecomment-775171176, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALTQODQBOM2OZSCNIXMFXQTS57VGBANCNFSM4RVDGKSA .

diatomsRcool commented 3 years ago

We just did a release with some of the "low hanging fruit". These terms should filter their way into OBO Foundry within 24 hrs.

cmrn-rhi commented 3 years ago

Thank you very much! Just to confirm, these are all the terms I was able locate the following the release in question:

Other updates:

diatomsRcool commented 3 years ago

confirmed. Will work on the highlighted terms

cmrn-rhi commented 3 years ago

After reviewing the discussion in https://github.com/EnvironmentOntology/environmental-exposure-ontology/issues/161, I was wondering whether you would prefer if I avoided recommended NCIT exposure stimuli for the time being?

diatomsRcool commented 3 years ago

I plan to use NCIT more, actually, for human-related things like exercise and homeless. For "exposure stimuli" I would suggest holding off. We should probably all use the COB term when it is available - unless you can't wait.

diatomsRcool commented 3 years ago

Oh, are there more terms to add? I guess the newly approved ones are green?

cmrn-rhi commented 3 years ago

I plan to use NCIT more, actually, for human-related things like exercise and homeless. For "exposure stimuli" I would suggest holding off. We should probably all use the COB term when it is available - unless you can't wait.

I'll leave the exposure stimuli travel (NCIT:C53462) and homeless (NCIT:C85868) as is then; however, if you think travel (or even homeless) will be appearing in COB in the future we can hold off for longer on that.

Oh, are there more terms to add? I guess the newly approved ones are green?

Yes, the terms with exposure stimuli highlighted green are ready to go. Sorry if it it's not very clear. There is a legend at the top of the sheet under the headers that I try to put all cell formatting information under but I'll also be sure to clearly describe which terms are ready in future updates.

diatomsRcool commented 3 years ago

As of now, all the terms highlighted in green have been added to the staging files. EXCEPT for homeless.

laurenechan commented 2 years ago

Hi @cmrn-rhi , just wanted to revisit this issue. Did all of your needs get figured out on this ticket or did you still have outstanding pieces you were looking for? Thanks!

cmrn-rhi commented 2 years ago

Hi @laurenechan, unfortunately there still are some standing requests that need resolving - but that is mostly due to awaiting the release of "exposure stimuli" term requests in other ontologies. We have requested an update on the status of those terms. I will also review and stream-line what remains of this request this week.

cmrn-rhi commented 2 years ago

We're meeting with ENVO to confirm the release of the relevant "exposure stimulus" ontology terms early September. In the meantime I have revisiting all the terms in the request to simplify the table, make the annotations more in line with the terms we've been provided so far, and see if I can find alternate exposure stimulus terms for the non-ENVO ones still pending. Hope to have this done in the next day or two, will update once ready.

cmrn-rhi commented 2 years ago

Sorry for the delay, we're still waiting on the release of the ENVO terms (ETD September 2022) but I've made a new worksheet revising the existing term requests to try to make them easier to process for ECTO curators: https://docs.google.com/spreadsheets/d/1iTt9TjUxuc0WsM4Ts7hu1MLsclXY_J1UTFSECIU6LHQ/edit?usp=sharing

Thank you for your time and patience. Hopefully we'll be able to get this finished up in the next month or so. In the future we'll make smaller term request batches!

laurenechan commented 2 years ago

Hi @cmrn-rhi we are starting to get into things that are a little complex here, we would love to see if you had time to meet with our curation team to find an approach that gets the terms you need in the most useful fashion. We would love to hear more about your use case specifically, I will send a follow up email with you and @diatomsRcool so we can find a time to meet. Thanks!!

laurenechan commented 2 years ago

@cmungall @matentzn

Hi!! Speaking with @cmrn-rhi this morning, we are wondering about if you have input on some particular terms being requested. The use case for these terms is alignment of survey data with ontology terms, with questions like ' have you been exposed to anyone with a confirmed COVID-19 case' and if someone says 'yes' they have technically been "exposed" but that doesn't mean that they get sick or that if they got COVID that the case came from that exposure incident. We were looking at the 'exposure stimulus' definitions and it includes the statement that an exposure stimulus 'causally effects an organism', which in this case we do not know for sure if there would be any causal effect from being exposed to a person with COVID (e.g., cannot confirm resulting illness). Any thoughts on how we might include these terms or terms with a similar sentiment for the use case in ECTO?

exposure to human confirmed COVID-19 case exposure to human patient contact exposure to human probable COVID-19 case exposure to human acute respiratory illness exposure to human with fever and/or cough exposure to human recent traveler

cmungall commented 2 years ago

this would lead to an explosion - is it possible to post-compose?

diatomsRcool commented 2 years ago

and....this also pushes up against immunological exposures - might be out of scope for ECTO

cmrn-rhi commented 2 years ago

this would lead to an explosion - is it possible to post-compose?

I am very pro post-composing and happy to go in that direction.

and....this also pushes up against immunological exposures - might be out of scope for ECTO

Do you know of any domain ontologies that try to work on "immunological exposures"?

wdduncan commented 2 years ago

@cmrn-rhi I emailed some folks who were/are associated with the infectious disease ontology (IDO). But, I never heard anything in response. Also, it looks like IDO has not been updated in 5 years. So, using IDO may not be the best route here.

OBI also has the term environmental exposure to infectious agent. Maybe sub-typing that term would suite some (maybe all?) your needs?

cmrn-rhi commented 2 years ago

@wdduncan yeah, I emailed them (specifically the covid-19-ido) regarding this work in 2021 and also did not hear back.

Thank you for the OBI recommendation - I'll bring it up with the team on my end and take it from there. I've greyed them out on the worksheet so we can just proceed with the other terms. There are some "ready-to-go" (highlighted yellow), but unfortunately the bulk of them have exposure stimuli still sitting in envo-edit.owl. I will keep an eye out for the next ENVO release and notify this thread so hopefully we can get those other terms complete and this issue closed :)

ddooley commented 1 year ago

Any updates, and plan of action here?

diatomsRcool commented 1 year ago

As far as I know we are looking at the spreadsheet periodically and adding terms to ECTO as soon as they are added to other ontologies. Is that not going to work anymore?

cmrn-rhi commented 1 year ago

@diatomsRcool that does work for us, but some of the terms in the sheet have been labelled as ready for ECTO curation for over a year now and if they have been added to ECTO we weren't notified. I'll do another round of "ready" updates right now (I am overdue in this responsibility) as it looks like some/many of those pending ENVO terms have finally be released.

Also, when it comes to the composite "Exposure Stimulus" terms are those acceptable or should we be finding/requesting a single concept so those terms can be complete?

cmrn-rhi commented 1 year ago

Sorry, and to clarify I am still pro "post-compose". E.g. I will change "exposure to human confirmed COVID-19 case" to "exposure to human confirm case", but that still leaves me listing two exposure stimuli for that term request: "confirmed diagnosis" [OPMI:0000614] and "human patient role" [OMRSE:00000030]

cmrn-rhi commented 1 year ago

OK, all but two terms are ready to go if ECTO approves!

cmrn-rhi commented 1 month ago

@diatomsRcool is there anything more I can do to help?

diatomsRcool commented 1 month ago

Apologies, the student that was working on this graduated. Can you point me to the terms that need adding?