Perform gap analysis with MRE #6
Comments
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We'll also want to examine SubClassOfs that differ between the two (gulo?) |
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@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 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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Not dietary, put in exposure to chemical. Use TE if ready c.c . @DoctorBud
…On Jun 22, 2017 11:22, "Nicole Vasilevsky" ***@***.***> 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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In this context yes
…On Jun 22, 2017 11:23, "Nicole Vasilevsky" ***@***.***> 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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Also request syns from chebi if appropriate
…On Jun 22, 2017 16:46, "Chris Mungall" ***@***.***> wrote:
Not dietary, put in exposure to chemical. Use TE if ready c.c . @DoctorBud
On Jun 22, 2017 11:22, "Nicole Vasilevsky" ***@***.***>
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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@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 |
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@cmungall Ok- I'll add synonyms to my tickets on the chebi tracker |
…with-MRE added new CHEBI terms, addresses #6
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Note to self, need to add these terms via Table Editor:
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exposure to gas molecular entity exposure to 2-bromophenyl 2,4-dibromophenyl ether addresses EnvironmentOntology#6
exposure to endocrine disruptor addresses EnvironmentOntology#6
exposure to 4-bromophenyl 2,4-dibromophenyl ether exposure to 2,4-dibromophenyl 3,4-dibromophenyl ether addresses EnvironmentOntology#6
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yes and yaml
…On Tue, Jan 15, 2019 at 2:31 PM Nicole Vasilevsky ***@***.***> 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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I created yaml files for procedure exposure: |
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for the procedure exposures- is 'radioactivity' a procedure? In NCIt, it is classified as a Physical Phenomenon or Property. |
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tou can be exposed to radioactivity outside of procedures
…On Tue, Jan 15, 2019 at 4:04 PM Nicole Vasilevsky ***@***.***> wrote:
for the procedure exposures- is 'radioactivity' a procedure? In NCIt, it
is classified as a Physical Phenomenon or Property.
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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? |
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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 |
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@diatomsRcool - it looks like this analysis may need to be redone as ECTO IDs were deleted between when we did it and now? |
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@cmungall
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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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. <Cls>
omo:scheduled_for_obsoletion_on <xsd:date>
…On Tue, May 19, 2020 at 2:07 PM Lauren ***@***.***> 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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Sounds good, @cmungall. I think this is the ticket: This ticket is still open, but looks like this annotation property is available in IAO: @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. |
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There are some terms in here that are checked as being added, but I can't find in ECTO. Is exposure to organophosphorus herbicide the same as exposure to organophosphorus compound? exposure to toxic waste 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. |
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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? |
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@diatomsRcool who are these questions for? |
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@nicolevasilevsky partially for me - so I don't forget. Although if you know any answers feel free. |
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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. |
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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
<monarch-initiative/MAxO#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
…
-
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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Where are we with this? All checks are ticked, but Lauren has a separate spreadsheet...? |
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A full account I think is here: https://docs.google.com/spreadsheets/d/129U_YTAfWPt5I6Hjs6gE7te4EcpP7R0bhPj9sbHWdV4/edit#gid=1641348924 |
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not sure how to read the spreadsheet - how do we know when we are done here? |
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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.
The most impactful thing you can do to move this forward is to find someone to deal with EnvironmentOntology/envo#1399. |
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I have to do an envo PR for this.... |
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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
<EnvironmentOntology/envo#1399>.
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@cmungall please
I have created a pipeline to generate the subset. |
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Relevant issues and PR requests are below |
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
CHEBI:24431 chemical entity, this is in the csv file
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
NTR: infrasound envo#656
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
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