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Modular environmental exposures ontology
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Perform gap analysis with MRE #6

Open cmungall opened 7 years ago

cmungall commented 7 years ago

Analysis of all MRE terms that can NOT be easily factored into DPs or mapped to ECTO.

I suggest we focus purely on the chemical set for now. Many of these are due to missing CHEBI IDs. The others are probably some trivial systematic thing.

Simple chemical

Dietary exposure

I think this may be a simple gap in the DPs

Prenatal/maternal

I think this may be a simple gap in the DPs

Occupational

I think this may be a simple gap in the DPs

Note - I couldn't find terms from just one ontology, and I couldn't find an ontology term for infrasound.

Procedures

Lower priority - should really have this in separate ontology

Other

cmungall commented 7 years ago

We'll also want to examine SubClassOfs that differ between the two (gulo?)

nicolevasilevsky commented 7 years ago

@cmungall I am finished reviewing all the simple chemical classes and have created tickets in Chebi where appropriate.

There are a few terms that exist already in Chebi (which I noted above), should I add those to this spreadsheet https://github.com/cmungall/environmental-conditions/blob/master/src/ontology/modules/dietary_exposure_to_chemical.csv ?

nicolevasilevsky commented 7 years ago

@cmungall And I have one question above (also noted above): do you think chemical element is the same as CHEBI:24431 chemical entity?

cmungall commented 7 years ago

Not dietary, put in exposure to chemical. Use TE if ready c.c . @doctorbud

On Jun 22, 2017 11:22, "Nicole Vasilevsky" notifications@github.com wrote:

@cmungall https://github.com/cmungall I am finished reviewing all the simple chemical classes and have created tickets in Chebi where appropriate.

There are a few terms that exist already in Chebi (which I noted above), should I add those to this spreadsheet https://github.com/cmungall/ environmental-conditions/blob/master/src/ontology/modules/ dietary_exposure_to_chemical.csv ?

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cmungall commented 7 years ago

In this context yes

On Jun 22, 2017 11:23, "Nicole Vasilevsky" notifications@github.com wrote:

@cmungall https://github.com/cmungall And I have one question above (also noted above): do you think chemical element is the same as CHEBI:24431 chemical entity?

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cmungall commented 7 years ago

Also request syns from chebi if appropriate

On Jun 22, 2017 16:46, "Chris Mungall" cjmungall@lbl.gov wrote:

Not dietary, put in exposure to chemical. Use TE if ready c.c . @doctorbud

On Jun 22, 2017 11:22, "Nicole Vasilevsky" notifications@github.com wrote:

@cmungall https://github.com/cmungall I am finished reviewing all the simple chemical classes and have created tickets in Chebi where appropriate.

There are a few terms that exist already in Chebi (which I noted above), should I add those to this spreadsheet https://github.com/cmungall/en vironmental-conditions/blob/master/src/ontology/modules/diet ary_exposure_to_chemical.csv ?

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nicolevasilevsky commented 7 years ago

@cmungall Oops, wrong spreadsheet, this is the correct one, yes? https://github.com/cmungall/environmental-conditions/blob/master/src/ontology/modules/exposure_to_chemical.csv @DoctorBud Can you help me get started using Table Editor?

nicolevasilevsky commented 7 years ago

@cmungall Ok- I'll add synonyms to my tickets on the chebi tracker

nicolevasilevsky commented 6 years ago

Note to self, need to add these terms via Table Editor:

nicolevasilevsky commented 6 years ago

@cmungall For the simple chemicals, all the term requests were filled in Chebi, and I added new terms to the csv for all of the chemicals listed above. Let me know the next steps.

For the other sections (dietary exposure, etc.) I am unsure what needs to be done, can you let me know if I need to do anything with those?

Thank you!

nicolevasilevsky commented 5 years ago

@cmungall to check all the boxes - do I need to add ontology terms and IDs to each respective csv file?

My other questions are:

cmungall commented 5 years ago

On Fri, Jan 11, 2019 at 12:47 PM Nicole Vasilevsky notifications@github.com wrote:

@cmungall https://github.com/cmungall to check all the boxes - do I need to add ontology terms and IDs to each respective csv file?

yes. in some cases new yamls will be required

My other questions are:

  • what ontologies should I use? Are there certain ontologies that should be prioritized? Looks like the Food Ontology has some terms for dietary exposure. NCIt probably has a lot of terms we can use as well.

ideally not an ad-hoc mix, in general each pattern should use a single ontology for each slot

  • many of these terms do not currently exist in an ontology, like chemical residue. Should I make new term requests to other ontologies?

yes

nicolevasilevsky commented 5 years ago

@cmungall thanks for the clarifications, I'll work on finishing this up.

nicolevasilevsky commented 5 years ago

@cmungall I am confused by the content in the CSV files. For example, prenatal.csv has cause and cause label headers in column C and D - what does that mean? I don't want to override the existing data, but this isn't formatted like the exposure_to_chemical.csv, which has stressor and stressor label, with corresponding CHEBI IDs and labels.

cmungall commented 5 years ago

The strings don't matter to long as they match the variables declared in the yaml. We may want to unify these to be tidy but the end user doesn't see

nicolevasilevsky commented 5 years ago

Ok, I added the CHEBI IDs and labels to dietary_exposure_to_chemical.csv. I committed directly to master, let me know if you prefer if I do PRs instead.

cmungall commented 5 years ago

Whatever if fastest for you right now

On Tue, Jan 15, 2019 at 1:03 PM Nicole Vasilevsky notifications@github.com wrote:

Ok, I added the CHEBI IDs and labels to dietary_exposure_to_chemical.csv. I committed directly to master, let me know if you prefer if I do PRs instead.

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nicolevasilevsky commented 5 years ago

Note- I didn't add ECTO IDs in these files above, because I didn't know which ID to start with

Questions: Do you have any recommendations as to where I should make terms requests for:

cmungall commented 5 years ago

On Tue, Jan 15, 2019 at 2:27 PM Nicole Vasilevsky notifications@github.com wrote:

Note- I didn't add ECTO IDs in these files above, because I didn't know which ID to start with

There is a make target for filling these. It may be hard for you to replicate the environment but help is coming here - can Anne help with this?

Questions: Do you have any recommendations as to where I should make terms requests for:

  • maternal famine
  • infrasound

ENVO

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nicolevasilevsky commented 5 years ago

For the procedures, some of the terms are in NCIT, but the anatomical radiograph are not, although there is radiograph, and we could post-compose with an Uberon term. Should I create a csv file for these terms too?

cmungall commented 5 years ago

yes and yaml

On Tue, Jan 15, 2019 at 2:31 PM Nicole Vasilevsky notifications@github.com wrote:

For the procedures, some of the terms are in NCIT, but the anatomical radiograph are not, although there is radiograph, and we could post-compose with an Uberon term. Should I create a csv file for these terms too?

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nicolevasilevsky commented 5 years ago

I created yaml files for procedure exposure: https://github.com/EnvironmentOntology/environmental-exposure-ontology/blob/master/src/patterns/exposure_via_procedure.yaml

https://github.com/EnvironmentOntology/environmental-exposure-ontology/blob/master/src/patterns/exposure_via_procedure_in_anatomy.yaml

nicolevasilevsky commented 5 years ago

for the procedure exposures- is 'radioactivity' a procedure? In NCIt, it is classified as a Physical Phenomenon or Property.

cmungall commented 5 years ago

tou can be exposed to radioactivity outside of procedures

On Tue, Jan 15, 2019 at 4:04 PM Nicole Vasilevsky notifications@github.com wrote:

for the procedure exposures- is 'radioactivity' a procedure? In NCIt, it is classified as a Physical Phenomenon or Property.

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nicolevasilevsky commented 5 years ago

agreed. currently radioactivity doesn't fit with any of the current patterns, but is that okay? Does everything need to be created via a pattern? Radioactivity is a class in NCIt but I don't see it in ENVO. Or should I make a NTR to ENVO?

nicolevasilevsky commented 5 years ago

actually, there is a pattern for exposure to radiation - that covers it, yes? https://github.com/EnvironmentOntology/environmental-exposure-ontology/blob/master/src/patterns/exposure_to_radiation.yaml

cmungall commented 4 years ago

@diatomsRcool - it looks like this analysis may need to be redone as ECTO IDs were deleted between when we did it and now?

laurenechan commented 4 years ago

@cmungall @diatomsRcool @nicolevasilevsky and I spoke today, and it sounds like we have some discrepancies with some of the legacy terms from this issue and some of the newer developed terms. We do think we have a plan for managing the identifiers for duplicate and stand alone terms from both the old and new sets. There are some terms that were added to ECTO that use CHEBI terms from above for the patterns and these have since been removed out of ECTO, but there is a saved file that exists with all of this data. Current version of ECTO contains duplicate/overlapping terms with new IDs. Our plan is to: 1) Reconcile "old" and "new" terms and their associated IDs to evaluate duplicates 2) We can obsolete and merge terms with duplicates. Mondo imports ECTO terms for various diseases, would it be disruptive to Mondo if we deprecated the "old"/original ECTO terms and replace them with the new IDs? The rationale for keeping the new IDs is that @diatomsRcool has created specific ID ranges for each of the new patterns currently being used.

We noticed that some of the terms from patterns have not been classified as we'd expect in ECTO and we are also reviewing the ENVO hierarchy to ensure we are using the correct ENVO terms. For example, 'exposure to brick', 'brick' is a child of 'environmental feature' whereas we want it as a child of 'environmental material' and therefore we should use the ENVO class 'brick material' instead which is a child of 'environmental material' in ENVO.

cmungall commented 4 years ago

Sounds good

Don't worry too much about Mondo, Nicole can coordinate replacing the IDs. If you use replaced_by we can use robot repair to do this.

Ideally we'd have a cross-OBO mechanism for forewarning of obsoletions, there is a ticket in one of the trackers about this, e.g. omo:scheduled_for_obsoletion_on

On Tue, May 19, 2020 at 2:07 PM Lauren notifications@github.com wrote:

@cmungall https://github.com/cmungall @diatomsRcool https://github.com/diatomsRcool @nicolevasilevsky https://github.com/nicolevasilevsky and I spoke today, and it sounds like we have some discrepancies with some of the legacy terms from this issue and some of the newer developed terms. We do think we have a plan for managing the identifiers for duplicate and stand alone terms from both the old and new sets. There are some terms that were added to ECTO that use CHEBI terms from above for the patterns and these have since been removed out of ECTO, but there is a saved file that exists with all of this data. Current version of ECTO contains duplicate/overlapping terms with new IDs. Our plan is to:

  1. Reconcile "old" and "new" terms and their associated IDs to evaluate duplicates
  2. We can obsolete and merge terms with duplicates. Mondo imports ECTO terms for various diseases, would it be disruptive to Mondo if we deprecated the "old"/original ECTO terms and replace them with the new IDs? The rationale for keeping the new IDs is that @diatomsRcool https://github.com/diatomsRcool has created specific ID ranges for each of the new patterns currently being used.

We noticed that some of the terms from patterns have not been classified as we'd expect in ECTO and we are also reviewing the ENVO hierarchy to ensure we are using the correct ENVO terms. For example, 'exposure to brick', 'brick' is a child of 'environmental feature' whereas we want it as a child of 'environmental material' and therefore we should use the ENVO class 'brick material' instead which is a child of 'environmental material' in ENVO.

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nicolevasilevsky commented 4 years ago

Sounds good, @cmungall. I think this is the ticket: https://github.com/information-artifact-ontology/ontology-metadata/issues/32

This ticket is still open, but looks like this annotation property is available in IAO: http://purl.obolibrary.org/obo/IAO_0006012 scheduled for obsoletion on or after

@laurenechan let me know when you've identified the terms to keep and which to obsolete and I'll help you with next steps.

We'd need to import the annotation property into ECTO, and add this to all the terms we want to obsolete.

I can help you with obsoleting/merging the classes, and we'll add 'term replaced by' annotations.

diatomsRcool commented 3 years ago

There are some terms in here that are checked as being added, but I can't find in ECTO. exposure to urea-based herbicide

Is exposure to organophosphorus herbicide the same as exposure to organophosphorus compound? Is exposure to nitrile herbicide the same as exposure to nitrile?

exposure to toxic waste exposure to anticoagulant rodenticide exposure to noise exposure to nuclear medicine

Is it important to have all the different radiography terms? Why not just exposure to radiography?

I don't understand the significant of the exposure being occupational.

diatomsRcool commented 3 years ago

There are exposures listed under the prenatal/maternal header that do not list anything about prenatal/maternal in the label. Are these prenatal/maternal exposures?

nicolevasilevsky commented 3 years ago

@diatomsRcool who are these questions for?

diatomsRcool commented 3 years ago

@nicolevasilevsky partially for me - so I don't forget. Although if you know any answers feel free.

laurenechan commented 2 years ago

Matching of MRE terms to ECTO terms is largely done with some lingering issues that I am dealing with here...

Here is my checklist: https://docs.google.com/spreadsheets/d/17IyJ4DMVBOzslDb5sdZwjma0hOrrbwbSRi6d2gJKUZg/edit?usp=sharing

The bigger issue is whether we are interested in creating a new sociology ontology (sociontology) or can we continue to use NCIT/NBO for these needs? Addictive substance use/abuse are using NBO in many cases, and we have other patterns that use NCIt like those that include physical activity. We may also be interested in these for the use cases of sleep, social environments, and resource availability etc.

cmungall commented 2 years ago

On Mon, Dec 6, 2021 at 3:12 PM Lauren @.***> wrote:

Matching of MRE terms to ECTO terms is largely done with some lingering issues that I am dealing with here...

-

MAxO term requests: monarch-initiative/MAxO#256 https://github.com/monarch-initiative/MAxO/issues/256

thanks

  • Can we discuss what Radioactive Contamination is? I think I need some more details prior to being able to create a suitable ECTO term

    do we need a distinction between contamination/exposure

  • MRE:0000001 Prenatal exposure: is it suitable to consider this covered by the 'maternal' route now included in ExO? This is not really a particular exposure to anything, but we are able to model a variety of stimuli using this route

seems ok

-

MRE:0000056 Occupational exposure to bactericide: can we use exposure to antibacterial agent?

I think so

-

some additional ChEBI requests need to be made to satisfy the needs of specific herbicide/rodenticide types (will follow up this week)

great

  • a request to ENVO is needed for toxic waste and noise exposure (will follow up this week)

  • we are waiting for acceptance of the 'famine' term in ENVO prior to creating a maternal famine term

I approved https://github.com/EnvironmentOntology/envo/pull/1211

-

Here is my checklist: https://docs.google.com/spreadsheets/d/17IyJ4DMVBOzslDb5sdZwjma0hOrrbwbSRi6d2gJKUZg/edit?usp=sharing

The bigger issue is whether we are interested in creating a new sociology ontology (sociontology) or can we continue to use NCIT/NBO for these needs? Addictive substance use/abuse are using NBO in many cases, and we have other patterns that use NCIt like those that include physical activity. We may also be interested in these for the use cases of sleep, social environments, and resource availability etc.

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cmungall commented 7 months ago

Where are we with this?

All checks are ticked, but Lauren has a separate spreadsheet...?

matentzn commented 7 months ago

A full account I think is here: https://docs.google.com/spreadsheets/d/129U_YTAfWPt5I6Hjs6gE7te4EcpP7R0bhPj9sbHWdV4/edit#gid=1641348924

cmungall commented 6 months ago

not sure how to read the spreadsheet - how do we know when we are done here?

matentzn commented 6 months ago

These are the remaining ones:

Please comment on these in the spreadsheet if you see how we can create them, or if we indeed should.

subject_id subject_label comment
MRE:0000236 Exposure to electroplating fumes No term in ENVO
MRE:0000252 Exposure to soldering fumes No term in ENVO
MRE:0000253 Exposure to lead solder No term in ENVO
MRE:0000254 Exposure to non-lead solder No term in ENVO
MRE:0000258 Occupational exposure to gasoline fumes No term in ENVO
MRE:0000074 Occupational exposure to toxic waste No term in ENVO
MRE:0000089 Exposure to noise No term in ENVO
MRE:0000090 Occupational noise exposure No term in ENVO
MRE:0000220 Exposure to road traffic noise No term in ENVO
MRE:0000221 Exposure to aircraft noise No term in ENVO
MRE:0000250 Passive smoking at home No term in ENVO
MRE:0000251 Passive smoking in the workplace No term in ENVO
MRE:0000144 Exposure to 1,4-dichloropropane No term in CHEBI
MRE:0000217 Exposure to environmentally persistent free radicals No term in ENVO
MRE:0000229 Crack cocaine use No term in CHEBI
MRE:0000081 Radioactive contamination Missing ECTO term
MRE:0000086 Helicobacter pylori infection Missing ECTO term
MRE:0000035 Passive smoking Missing ECTO term
MRE:0000255 Pneumatic drilling Missing ECTO term
MRE:0000001 Prenatal exposure This should be a proper ecto term (not ExO:0000159)
MRE:0000239 Use of chewing tobacco Same id as 'Exposure to smokeless tobacco

The most impactful thing you can do to move this forward is to find someone to deal with https://github.com/EnvironmentOntology/envo/issues/1399.

diatomsRcool commented 6 months ago

I have to do an envo PR for this....

cmungall commented 6 months ago

The PR should be straightforward, see my advice in the linked issue (I could do this PR in 5 mins just need to find the time)

crack is interesting. Not chebi. I'd put in ENVO along with other materials. But there is an argument for DRON. Also an argument that these are really behavior terms. use != exposure != exposure to use. And maybe not everything in ECTO should be axiomatized...

On Fri, Jan 12, 2024 at 8:13 AM Nico Matentzoglu @.***> wrote:

These are the remaining ones:

Please comment on these in the spreadsheet if you see how we can create them, or if we indeed should. subject_id subject_label comment MRE:0000236 Exposure to electroplating fumes No term in ENVO MRE:0000252 Exposure to soldering fumes No term in ENVO MRE:0000253 Exposure to lead solder No term in ENVO MRE:0000254 Exposure to non-lead solder No term in ENVO MRE:0000258 Occupational exposure to gasoline fumes No term in ENVO MRE:0000074 Occupational exposure to toxic waste No term in ENVO MRE:0000089 Exposure to noise No term in ENVO MRE:0000090 Occupational noise exposure No term in ENVO MRE:0000220 Exposure to road traffic noise No term in ENVO MRE:0000221 Exposure to aircraft noise No term in ENVO MRE:0000250 Passive smoking at home No term in ENVO MRE:0000251 Passive smoking in the workplace No term in ENVO MRE:0000144 Exposure to 1,4-dichloropropane No term in CHEBI MRE:0000217 Exposure to environmentally persistent free radicals No term in ENVO MRE:0000229 Crack cocaine use No term in CHEBI MRE:0000081 Radioactive contamination Missing ECTO term MRE:0000086 Helicobacter pylori infection Missing ECTO term MRE:0000035 Passive smoking Missing ECTO term MRE:0000255 Pneumatic drilling Missing ECTO term MRE:0000001 Prenatal exposure This should be a proper ecto term (not ExO:0000159) MRE:0000239 Use of chewing tobacco Same id as 'Exposure to smokeless tobacco

The most impactful thing you can do to move this forward is to find someone to deal with EnvironmentOntology/envo#1399 https://github.com/EnvironmentOntology/envo/issues/1399.

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matentzn commented 6 months ago

@cmungall please

I have created a pipeline to generate the subset.

diatomsRcool commented 6 months ago

Relevant issues and PR requests are below https://github.com/mcwdsi/dron/issues/22 https://github.com/EnvironmentOntology/envo/pull/1486 https://github.com/ebi-chebi/ChEBI/issues/4468