NTRs: collection of COVID-19 related exposures

[cmrn-rhi]

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]

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

[diatomsRcool]

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]

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]

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

[cmrn-rhi]

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]

@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]

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]

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 ***@***.***> 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 <#134 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALTQODQBOM2OZSCNIXMFXQTS57VGBANCNFSM4RVDGKSA> .

[diatomsRcool]

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]

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

• abattoir exposure ECTO_1000033
• exposure to farm ECTO_1000034
• exposure to hospital ECTO_1000035
• exposure to laboratory ECTO_1000036
• exposure to office ECTO:1000037

Other updates:

• All the ENVO requests have been made and ID'd but I'm not sure when the final review and release will be. I'm keeping an eye on things and will inform you as soon as it occurs.
• Any exposure stimulus terms that are available to work with presently have been highlighted in the spreadsheet (bold text, green highlight) but no rush as the majority of exposure stimuli are still pending.
• I intend to have an GenEpiO related exposure stimuli added around mid-April (will follow-up once they are added and released).

[diatomsRcool]

confirmed. Will work on the highlighted terms

[cmrn-rhi]

After reviewing the discussion in #161, I was wondering whether you would prefer if I avoided recommended NCIT exposure stimuli for the time being?

[diatomsRcool]

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]

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