environmentontology / environmental-exposure-ontology Goto Github PK

As you can see, Nico and I are starting to migrate ECTO to odk and adding patterns that are a bit different from what was there originally. We are trying to be in alignment with PECO and ExO. There is still a lot of work to do. Feel free to take a look at the patterns in the dosdp-patterns directory (the others are just in reserve and may not be used). I would love some feedback.

I'm looking for a term for pm2.5 exposure. I found 'exposure to fine respirable suspended particulate matter' ECTO:0000113. It seems like this could be a match depending on how strictly "fine" is interpreted. Is this right?

I kind of understand (I think) what you are trying to get at with the term environmental condition. However, every term under it is a process (surgical process to be exact). This makes me wonder if what you really need a relation between exposure events and what you are calling 'exposure conditions'. Currently, what you are calling 'conditions' are really processes, and this can cause ambiguities down the line.

This wikidata query:

PREFIX wd: <http://www.wikidata.org/entity/> 
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wdt_cause: <http://www.wikidata.org/prop/direct/P828>
PREFIX wikibase: <http://wikiba.se/ontology#>
PREFIX p: <http://www.wikidata.org/prop/>
PREFIX p_route_of_administration: <http://www.wikidata.org/prop/P636>
PREFIX ps: <http://www.wikidata.org/prop/statement/>
PREFIX ps_route: <http://www.wikidata.org/prop/statement/P636>
PREFIX pq: <http://www.wikidata.org/prop/qualifier/>
PREFIX pq_symptoms: <http://www.wikidata.org/prop/qualifier/P780>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX bd: <http://www.bigdata.com/rdf#>
PREFIX RO: <http://purl.obolibrary.org/obo/RO_>
PREFIX upstream_positive: <http://purl.obolibrary.org/obo/RO_0002304>
PREFIX has_exposure_route: <http://purl.obolibrary.org/obo/RO_0002242>
PREFIX owl: <http://www.w3.org/2002/07/owl#>

CONSTRUCT {  
  ?cause rdfs:label ?causeLabel .
  ?exposure rdfs:label ?exposureLabel .
  ?symptom rdfs:label ?symptomLabel .
  ?route rdfs:label ?routeLabel .
  
  ?statement
    rdfs:label ?genLabel ;
    rdfs:subClassOf ?exposure ;
    rdfs:subClassOf [
      a owl:Restriction ;
      owl:onProperty has_exposure_route: ;
      owl:someValuesFrom ?route
    ] ;
    rdfs:subClassOf [
      a owl:Restriction ;
      owl:onProperty upstream_positive: ;
      owl:someValuesFrom ?symptom
    ] 

}
WHERE {
  ?exposure p_route_of_administration: ?statement .
  ?statement pq_symptoms: ?symptom .
  ?statement ps_route: ?route 
  bind(concat(?exposureLabel, " via ", ?routeLabel) AS ?genLabel) 
  SERVICE wikibase:label {
    bd:serviceParam wikibase:language "en" .
   }
}

doesn't succeed in binding genLabel - I assume because label service is called after the fact.

Replacing the service call with explicit rdfs:label clauses slows the query down too much

Wikidata has a lot of exposures associated with symptoms/disease. From NIOSH?

https://github.com/cmungall/environmental-conditions/tree/master/src/resources/wikidata

• gap analysis of wikidata exposure terms to ECTO
• gap analysis of wikidata symptoms to SYMP/HP
• include equivalence axioms between wd and OBO
• ingest!

cc @goodb @balhoff

The dbGAP Multi-Ethnic Study of Atherosclerosis and Air Pollution (MESA Air) captures
longitudinal data in support of investigating cardiovascular disease outcomes in response to air
pollution exposure. The study includes air pollutant, emission and exposure variables that are
well suited for semantic modeling via the Environmental and Exposure Ontology (ECTO).

consumed items that are not foods from UDN survey:

- [ ] exposure to consuming non-food item(s)

• exposure to consuming fiberglass (EOL)
• exposure to consuming pencils (??)
• exposure to consuming vapor rub (??)
• exposure to consuming paper/paper products (ENVO)
• exposure to consuming dirt (soil in ENVO)
• exposure to consuming painted surfaces (paint in ENVO)
• exposure to consuming metal, unknown type (OMIT?)
• exposure to consuming screws (NCIT, ??)
• exposure to consuming mud (ENVO)
• exposure to consuming fecal matter (UBERON)
• exposure to consuming sand (ENVO)
• exposure to consuming rocks (ENVO)
• exposure to consuming Styrofoam/foam/polystyrene (CHEBI)
• exposure to consuming crayons (??)
• exposure to consuming playdoh (??)
• exposure to consuming plants (flowers or grass) (PO, or ??)
• exposure to consuming fingernails (UBERON)
• exposure to consuming hair (UBERON)
• exposure to consuming cloth (ENVO)
• exposure to consuming plastic (ENVO)
• exposure to consuming glue/paste (glue)
• exposure to consuming coins (??)
• exposure to consuming cleansing cloths/baby wipes (??)

Food items (FOODON)

• exposure to consuming raw fish

Dietary behavior (EPR) (FOOD ON, can model specifics of these if we like?)
frequency of eating at: fast food restaurants, sit down restaurants, buffet restaurants, takeout restaurants, grocery stores (prepared food), cafeterias, vending machines, on-street vendors, other (gas station, quick mart, bakery)

consuming snacks
meal timing
Pgs. 20-25 EPR B are focused on FFQ type data. What do we want to do?

https://github.com/EnvironmentOntology/environmental-exposure-ontology/search?q=zeco&unscoped_q=zeco

Inferred parents in MRE:

https://github.com/cmungall/environmental-conditions/blob/eb59288ceb2421521fbbc22c85c8c1f8c0365d48/src/mapping/new-inf-mre.tsv#L3-L20

Are these all correct?

@mellybelly who should be the contact? @nicolevasilevsky?

I think GO needs to start using this and migrating exposure annotations away from GO, see geneontology/go-ontology#15848 (comment)

This was approved during the obo operations committee today. Please create the appropriate YAML files in https://github.com/OBOFoundry/purl.obolibrary.org.

Considering exposures to mother/fetus dyads here and trying to identify some route options we could use to describe fetal exposures:

Fetus is exposed to chemical (ex. Cocaine, exposure direct to fetus)
Amniotic fluid route (combo of oral and transdermal exposure to fetus)

• Infant can directly absorb/fluid passes through infant during first and second trimesters
• Following fetal skin keratinization, infant absorbs primarily through GI tract, consumption of amniotic fluid
• Harmful chemicals have been identified in amniotic fluid previously (ex. Cocaine, https://academic.oup.com/jat/article/21/2/97/684167)

Placenta route
-Maternal/fetal exchange of nutrients, water, gases, and waste substances
-Significant mediator to fetal chemical exposure, including environmental, supplement/drug exposure to mother, food based exposures etc.

Fetal exposure secondary to maternal exposure
Example:
Fetus is exposed to uterine artery vasoconstriction d/t exposure to chemical (cocaine)
Fetus is exposed to blunt trauma during motor vehicle accident
Maternal/fetal route, Maternal route, ??
-Can be used to describe instances in which the impact of a chemical/ exposure is indirectly impacting the fetus, i.e. mediated by the mother
-I think this can be used for instances like the motor vehicle accident as well? But we will need to consider an appropriate “route” option for MVAs and other types of trauma items when talking about a free living human since we don’t really have a good option for that yet.

http://today.lbl.gov/2018/03/09/thirdhand-smoke-found-to-increase-lung-cancer-risk-in-mice/

Exposure through residues left on surfaces etc

UDN survey supplement free responses, may need to include in ECTO:

- [ ] exposure to vitamin supplements

NOTE: providing exposure to vitamins as chemicals from CHEBI, will include supplemental and food based forms.

• exposure to adult multivitamin supplements
• exposure to pediatric multivitamin supplements
• exposure to vitamin A supplements
  vitamin A
  beta-carotene
  retinyl palmitate
  all-trans-retinol
  all-trans-retinal
  11-cis-retinal
  all-trans-retinoic acid
  9-cis-retinoic acid
• exposure to vitamin D supplements (in calcium, revisit)
  vitamin D
  vitamin D2
  D3 vitamins
• exposure to vitamin E supplements (revisit)
  tocopherol
  (+)-alpha-tocopherol
  (-)-alpha-tocopherol
• exposure to vitamin K supplements
  vitamin K
  phylloquinone
  menaquinone
  menadione
• exposure to vitamin C supplements
  vitamin C
  L-ascorbic acid
  ascorbic acid
  sodium ascorbate
• exposure to vitamin B1 supplements/thiamin supplements
  thiamine
  thiamine hydrochloride
• exposure to vitamin B2 supplements/riboflavin supplements
  riboflavin
• exposure to vitamin B3 supplements/ niacin supplements
• exposure to vitamin B5 supplements/ pantothenic acid
• exposure to vitamin B6 supplements/ pyridoxine
• exposure to vitamin B7 supplements/biotin
• exposure to vitamin B9 supplements/folic acid
  folic acid
  5-methyltetrahydrofolate
• exposure to vitamin B12 supplements/cobalamin supplements
• B complex supplement

- [ ] exposure to mineral supplements

• exposure to calcium supplements
• exposure to potassium supplements
• exposure to potassium citrate supplements
• exposure to potassium chloride supplements
• exposure to potassium phosphate supplements
• exposure to phosphorus supplements
• exposure to iron supplements
• exposure to iodine supplements
• exposure to zinc supplements
• exposure to sodium bicarbonate supplements
• exposure to magnesium supplements
• exposure to selenium supplements
• exposure to chromium supplements

- [ ] exposure to phytochemical supplements

• exposure to adult supplemental nutrition beverages
• exposure to pediatric supplemental nutrition beverages
• exposure to poly-vi-sol with iron
• exposure to herbal laxatives
• exposure to fiber laxatives or fiber supplements
• exposure to supplemental protein shakes or powders
• exposure to fish oil supplements
• exposure to essential oil consumption
• exposure to lavender essential oil consumption
• exposure to peppermint essential oil consumption
• exposure to frankincense essential oil consumption
• exposure to lavender essential oil consumption
• exposure to garlic supplements
• exposure to ginger supplements
• exposure to “weight loss” supplements
• exposure to “anti-inflammatory” supplements
• exposure to “anti-oxidant” supplements
• exposure to “detoxification” supplements
• exposure to “estrogen balance” supplements
• exposure to “immune support” supplements
• exposure to “adaptogen” supplements
• exposure to “mitochondrial cocktail” supplements
• exposure to “phytoceramide” supplements
• exposure to “medical herb” supplements
• exposure to “hypothalamus stimulating” supplements
• exposure to “adrenal gland stimulating” supplements
• exposure to “thyroid gland stimulating” supplements
• exposure to “parotid gland stimulating” supplements
• exposure to glucosamine/chondritin supplements
• exposure to glutathione supplements
• exposure to melatonin supplements
• exposure to turmeric supplements
• exposure to flax seed / flax seed oil supplements
• exposure to goldenseal supplements
• exposure to St. John’s Wort supplements
• exposure to chia seed supplementation
• exposure to sesame seed oil supplementation
• exposure to Docosahexaenoic acid supplements
• exposure to Eicosapentaenoic acid supplements
• exposure to vinegar supplementation
• exposure to aloe vera supplements
• exposure to saw palmetto supplements
• exposure to charcoal supplementation
• exposure to cranberry suuplementation
• exposure to Echinacea supplements
• exposure to cinnamon supplements
• exposure to collagen supplements
• exposure to coconut oil supplementation
• exposure to betaine supplements
• exposure to probiotic supplements
• exposure to castor oil supplementation
• exposure to brewer’s yeast supplementation
• exposure to coenzyme Q10 supplements/co-Q10 supplements
• exposure to omega fatty acid supplements (omega 3, 6, and 9)
• exposure to elderberry supplements
• exposure to wheat
• exposure to soy /fermented soy
• exposure to valerian root supplements
• exposure to kefir/ fermented dairy
• exposure to burdock root tincture
• exposure to orange peel supplements
• exposure to boron supplements
• exposure to alpha lipoic acid supplements
• exposure to red yeast rice supplements
• exposure to shiitake maitake mushroom supplements
• exposure to sage tea/sage herbal tea
• exposure to oral hydrocortisone supplements
• exposure to topical hydroquinone
• exposure to uva ursi supplements
• exposure to “alkalizing” supplements/alkalizing agents
• exposure to serra peptase supplements
• exposure to rikkunshito supplements
• exposure to morinda citrifolia supplements
• exposure to astaxanthin supplements
• exposure to Acetylcarnitine/acetyl-L-carnitine,ALCAR, or ALC supplements
• exposure to acetylcysteine/N-acetylcysteine supplements
• exposure to carnitine/L-carnitine supplements
• exposure to creatine/creatine-monohydrate/L-creatine supplements
• exposure to arginine/L-arginine supplements
• exposure to lysine/L-lysine supplements
• exposure to mannose/D-mannose supplements
• exposure to citrulline/L-citrulline supplements
• exposure to taurine/L-taurine supplements
• exposure to tyrosine/L-tyrosine supplements
• exposure to uridine/uridine monophosphate supplements
• exposure to black cohosh supplements
• exposure to ginkgo biloba supplements
• exposure to ginseng supplements
• exposure to milk thistle supplements
• exposure to resveratrol supplements

There are number of developmental stage terms (e.g., blastula stage, embryo stage etc.). These should be grouped under a comment parent term, such as 'life cycle stage' (http://purl.obolibrary.org/obo/UBERON_0000105)

has stressor o has input subpropertyof: has stressor

So

has stressor some smoking and has input some nicotine

will classify under

has stressor some nictoine

E.g. nlm cde browser aggregates multiple CDEs

exposure CDEs:
https://cde.nlm.nih.gov/cde/search?q=exposure&page=1

Questionnaires often have Qs like "how often do you engage in vigorous activity"

vigorous is defined something like: lifting heavy objects, intense physical labor

Answers are grouped by daily, once a week etc.

We should import a physical activity ontology here.

cc @mateolan

One way to manage this is to say that if someone is the recipient of violence then they have been exposure to violence constructed using violent behavior in NBO. To say that someone is exposed to violence in their surroundings, we could construct a "violent environment" class in ENVO. Thoughts?

• Look for poison control protocols, could potentially ask emergency room for this information
  Look at data structure and ask if we can pull it into the ontology
• Mother Risk - http://www.motherisk.org/
  Another source for exposure information
• https://www.cdc.gov/nceh/hsb/chemicals/ncrs.htm

@cboerkoel - please provide any additional information I may have missed.

Just a head's up that the SDGIO is dealing with "exposure" as defined by UN bodies. This is more along the lines of "assets exposed to risk". We had a crack at "exposure" as a process in the more general sense too.

'exposure process'=def. "A process which is causally within or downstream of another process whose direct or indirect effects cause one or more entities to realise one or more of their dispositions.
+ comment: "Consider that when "E died of exposure to P", E died as an outcome of the processes which were initiated by E's participation in P, in which E's dispositions to react to P (or its parts or participants) were realised."
+ editor note: "This class may be replaced by a class in EXO, pending a clarification on the scope of its meaning. Right now it is essentially the same as 'interaction'. https://github.com/SDG-InterfaceOntology/sdgio/issues/21"

at the moment we are only adding Sulfonylurea Antidiabetic Agent and not distinguishing 1st and 2nd generation sulfonylureas.
@matentzn

What's the difference?

There is an extra space in 'abdominal radiography related exposure'

The interacts_with_an_exposure stressor_via object property (http://purl.obolibrary.org/obo/exo.obo#interacts_with_an_exposure_stressor_via) needs to have a definition.

TERIS - Teratogen Information System
database designed to assist physicians or other healthcare professionals in assessing the risks of possible teratogenic exposures in pregnant women.
http://depts.washington.edu/terisdb/index.html
see http://depts.washington.edu/terisdb/samples/Betamethasone.htm
for sample record

REPROTOX https://reprotox.org/
Contains summaries on the effects of medications, chemicals, infections, and physical agents on pregnancy, reproduction, and development.
see sample entries here: https://reprotox.org/samples

MotherToBaby
Service of the non-profit Organization of Teratology Information Specialists, is dedicated to providing evidence-based information to mothers, health care professionals, and the general public about medications and other exposures during pregnancy and while breastfeeding.
https://mothertobaby.org/

Compiled list of medications indicated in UDN survey, includes both classes and individual medications:

- [ ] exposure to sedatives
Will focus on inclusion of the chemical components only, may include generic or brand name within synonyms

• exposure to sleeping pills
• exposure to barbiturates
• exposure to seconal
• exposure to quaaludes
• exposure to chloral hydrate
• exposure to advil pm
• exposure to ambien (zolpidem)
• exposure to klonopin (clonazepam)
• exposure to rozerem (ramelteon)
• exposure to trazodone (
• exposure to lunesta (Eszopiclone)
• exposure to donnatol (
• exposure to amitriptyline (
• exposure to benadryl pm (diphenhydramine)
• exposure to fioricet/fiorinal
• exposure to melatonin
• exposure to neurotonin (gabapentin)
• exposure to ibuprofen pm
• exposure to temazepam (restoril)
• exposure to mirtazipine (remeron)
• exposure to doxipin
• exposure to Zzzquil

- [ ] exposure to tranquilizers or anti-anxiety drugs

• exposure to librium (Chlordiazepoxide)
• exposure to muscle relaxants
• exposure to xanax (Alprazolam)
• exposure to ativan (lorazepam)
• exposure to guanfacine
• exposure to buspar (Buspirone)
• exposure to zoloft (Sertraline)
• exposure to lamictal (Lamotrigine)
• exposure to topamax (Topiramate)
• exposure to clonidine (
• exposure to baclofen
• exposure to citalopram (celexa)
• exposure to clobozam (onfi)
• exposure to clonazepam (klonopin)
• exposure to cyclobenzaprine (flexeril)
• exposure to trazodone
• exposure to cymbalta (Duloxetine)
• exposure to benzodiazepines
• exposure to effexor (venlafaxine)
• exposure to paroxetine (paxil)
• exposure to fluoxetine (prozac)
• exposure to hydroxyzine
• exposure to adderal
• exposure to valproic acid (depakote)
• exposure to valium, diastat (diazepam)
• exposure to SOMA (carisoprodol)
• exposure to metaxalone (skelaxin)
• exposure to escitalopram (lexapro)
• exposure to wellbutrin (bupropion)

- [ ] exposure to painkillers

• exposure to codeine
• exposure to darvon/propoxyphene (dextropropoxyphene)
• exposure to percodan/oxycontin (oxycodone)
• exposure to dilaudid (Hydromorphone)
• exposure to demerol (Meperidine)
• exposure to celebrex (Celecoxib)
• exposure to vioxx (Rofecoxib)
• exposure to hydrocodone (vicodin)
• exposure to morphine
• exposure to benzonatate
• exposure to aleve (naproxen)
• exposure to meloxicam
• exposure to norco/lortab (hydrocodone/acetaminophen)
• exposure to ziconotide (prialt)
• exposure to diclofenac/misoprostol (arthrotec)
• exposure to tussionex
• exposure to Acetaminophen / Oxycodone (percocet)
• exposure to tramadol (ultram)
• exposure to acetaminophen (dafalgan, paracetemol, tylenol)
• exposure to asprin/oxycodone (percodan)
• exposure to Diclofenac
• exposure to fentanyl
• exposure to Etodolac (Lodine)
• exposure to ibuprofen (motrin, nurofen)
• exposure to Ketorolac (toradol)
• exposure to pregabalin (lyrica)
• exposure to Sumatriptan (imitrex)
• exposure to Nortriptyline (pamelor)
• exposure to Amitriptyline
• exposure to Ketamine
• exposure to Hydrocodone / Ibuprofen (vicoprofen)

- [ ] exposure to stimulants

• exposure to Phenmetrazine (preludin)
• exposure to benzedrine
• exposure to methedrine/methamphetamine (desoxyn)
• exposure to Methylphenidate (ritalin/concerta ER/medikinet)
• exposure to uppers
• exposure to speed
• exposure to adderall
• exposure to dexmethylphenidate (focalin)
• exposure to Modafinil (provigil)
• exposure to Aripiprazole (abilify)
• exposure to Atomoxetine (strattera)
• exposure to Lisdexamfetamine (vyvanse)

- [ ] exposure to marijuana, grass or hash (smoke)

• exposure to cannabis
• exposure to CBD
• exposure to THC
• exposure to hemp extracted cannabinoids
• exposure to marijuana (edibles)
• exposure to marijuana (topical)
• exposure to marijuana (vaporized)
• exposure to marinol
• exposure to CBC

- [ ] exposure to cocaine

• exposure to crack
• exposure to crank
• exposure to coke

- [ ] exposure to hallucinogens

• exposure to ecstacy/MDMA
• exposure to LSD
• exposure to mescaline
• exposure to psilocybin
• exposure to PCP
• exposure to angel dust
• exposure to peyote
• exposure to acid

- [ ] exposure to inhalants or solvents

• exposure to amyl nitrite
• exposure to nitrous oxide
• exposure to glue
• exposure to toulene
• exposure to gasoline
• exposure to albuterol

- [ ] exposure to heroine

OTHERS NOTED

• exposure to enteregam
• exposure to anticonvulsants
• exposure to Levetiracetam (keppra)
• exposure to Oxcarbazepine (trileptal)
• exposure to topiramate
• exposure to infant formula
• exposure to neocade
• exposure to proton pump inhibitors
• exposure to prevacid
• exposure to rantidine (zantac)
• exposure to antiviral medications
• exposure to antibiotic medications
• exposure to vancomycin
• exposure to levofloxacin (Levaquin)
• exposure to erythromycin
• exposure to anti-histamines
• exposure to digestive enzymes
• exposure to citalopram
• exposure to anti-eczema medications (topical)
• exposure to Cetirizine (Zyrtec)
• exposure to fexofenadine (Allegra)
• exposure to levocetirizine (Xyzal)
• exposure to loratadine (Claritin, Alavert)
• exposure to anticholinergic medications
• exposure to ACE inhibitors
• exposure to lisinopril
• exposure to anti-emetic medications
• exposure to reglan
• exposure to Megestrol acetate (megace)
• exposure to mylicon
• exposure to bean-o
• exposure to corticosteroids
• exposure to steroids
• exposure to bethanechol
• exposure to naltrexone
• exposure to desmopressin
• exposure to statins
• exposure to ditropan
• exposure to vastatin
• exposure to Rivaroxaban (xarelto)
• exposure to lactulose
• exposure to bicitra
• exposure to senna
• exposure to Cyproheptadine (periactin)
• exposure to Ondansetron (zofran)
• exposure to Trihexyphenidyl
• exposure to Zonisamide (zonegran)
• exposure to Acyclovir
• exposure to Omeprazole (prilosec)
• exposure to panzytrat
• exposure to Phenobarbital
• exposure to lacosamide (vimpat)
• exposure to Carbamazepine (tegretol)
• exposure to hydrocortisone
• exposure to Phytonadione (konakion)
• exposure to prednisone
• exposure to budesonide
• exposure to Triamcinolone acetonide
• exposure to rifaximin

Per the EPR survey, responses are categorized as either listing currently used medications or classifying medications intended to treat certain systems:
Cardiovascular health:

• Abnormal Heart Rhythm (Arrhythmia or
  Atrial Fibrillation [A-fib])
• Angina (Chest Pain)
• Blood Thinners
• Coronary Heart Disease
• Heart Failure (Congestive Heart Failure)
• Hypercholesterolemia (High Cholesterol)
• Hypertension (High Blood Pressure)
• Stroke or Transient Ischemic Attack (TIA) or Mini Stroke

Endocrine Health

• Diabetes (High Blood Sugar)
• Thyroid Disease/Condition

Mental Health

• Anxiety
• Depression

Respiratory Health

• Asthma
• Chronic Bronchitis or Emphysema (COPD)

Other Conditions

• Acid Reflux or Gasteroesophageal Reflux Disease
• Chronic pain
• Insomnia or sleep disorders

Reproductive Health

• Birth Control
• Hormone Replacement Therapy (HRT)

A number of definitions appear to be generated programmatically. In these cases, it is helpful to add an annotation to say which script and/or design pattern generated the definition.

When we say exposure to {caesium, lead, mercury, copper, ...} do we mean

• exposure to X molecular entity
• exposure to X ions
• exposure to some compound with X as a part
• exposure to X isotopes

etc

it seems safest to opt for the most general (X molecular entity), and if we need more specific subforms, add more specific classes.

some examples:

    is_a CHEBI:33676 ! d-block molecular entity
     is_a CHEBI:33673 ! zinc group molecular entity
      is_a CHEBI:25196 ! mercury molecular entity ***
       is_a CHEBI:25706 ! organomercury compound
        is_a CHEBI:22648 ! arylmercury compound
        is_a CHEBI:25193 ! mercuribenzoate
        is_a CHEBI:25194 ! mercuribenzoic acid
        is_a CHEBI:33255 ! alkylmercury compound
        is_a CHEBI:39152 ! mercury difulminate
        is_a CHEBI:59445 ! chlormerodrin
       is_a CHEBI:35113 ! elemental mercury
        is_a CHEBI:16170 ! mercury(0)
        is_a CHEBI:25197 ! mercury cation
       is_a CHEBI:36561 ! mercury coordination entity
        is_a CHEBI:28216 ! methylmercury chloride
        is_a CHEBI:31823 ! mercury dichloride
        is_a CHEBI:33050 ! dimercury dichloride
        is_a CHEBI:33210 ! dimercury diacetate
        is_a CHEBI:33211 ! mercury diacetate
        is_a CHEBI:36569 ! triiodomercurate(1-)
        is_a CHEBI:36573 ! mercury dicyanide
        is_a CHEBI:36574 ! diamminemercury(2+)
        is_a CHEBI:36576 ! tetraiodomercurate(2-)
        is_a CHEBI:36577 ! tetrakis(thiocyanato)mercurate(2-)
        is_a CHEBI:49639 ! mercury dibromide
        is_a CHEBI:49659 ! mercury diiodide
        is_a CHEBI:49727 ! (acetyloxy)mercury(1+)

    is_a CHEBI:33674 ! s-block molecular entity
     is_a CHEBI:33296 ! alkali metal molecular entity
      is_a CHEBI:37128 ! caesium molecular entity ***
       is_a CHEBI:33988 ! caesium hydroxide
       is_a CHEBI:37130 ! caeside
       is_a CHEBI:60270 ! caesium ion
        is_a CHEBI:49547 ! caesium(1+)
       is_a CHEBI:63039 ! caesium chloride

may not be sufficient to classify radioactive isotopes

@mbrush @mah11

ECTO needs to contain classes that will be useful for others modeling immune responses. The latest release has a pattern for exposure to organism. I would like to keep this pattern for other use cases, but this is likely not sufficient for the immunity use case. For example, someone could be exposed to a cat without being exposed to toxoplasmodium. Someone could be exposed to toxoplasmodium without developing an infection. Then someone could be exposed to an infected person or be infected themselves. I could use some help thinking through this to arrive at a suite of patterns that satisfies use cases.
@bpeters42

src/Makefile:
make: *** No rule to make target ecto-edit.obo', needed by ecto-core.owl'. Stop.

src/resources/wikidata/Makefile:
make: *** No rule to make target hazard-all.obo', needed by combined.obo'. Stop.

Any idea why I have the errors? Thanks.

proposed new MRE links based on ECTO

https://github.com/cmungall/environmental-conditions/blob/eb59288ceb2421521fbbc22c85c8c1f8c0365d48/src/mapping/new-inf-mre.tsv#L29-L47

In this case the mapping from MRE to ECTO is probably wrong.

ECTO:

MRE:

MRE:0000173 ! Exposure to inorganic compound *** [DEF: "Being exposed to a compound that is not organic, i.e.,that does not contain carbon."]

Here compound is likely used in the sense of two or more elements. The ECTO/CHEBI usage is more general, encompassing elements.

There is no CHEBI class for 'inorganic compound'

https://en.wikipedia.org/wiki/Inorganic_compound has a whole discussion on different usages

New term: exposure to personal care or consumer product chemicals.
Parent: exposure to chemical with application.
Definition: A exposure event involving the interaction of an exposure receptor to a personal care or consumer product chemical. Exposure may be through a variety of means, including through the air or surrounding medium, or through ingestion.

This comes from the CDC Report on Human Exposure to Environmental Chemicals (https://www.cdc.gov/exposurereport/pdf/FourthReport_UpdatedTables_Volume2_Mar2018.pdf). This is part of a class at Oregon State University. cc: @putmantime

I am unable to open ecto-edit.obo in Protégé, I get an error that says: Level: ERROR Time: 1515454262730 Message: An error occurred whilst loading the ontology at Could not load imported ontology: Cause: /Users/vasilevs/git/environmental-exposure-ontology/src/ontology/imports/ncbitaxon_import.owl (No such file or directory). Cause: {}. Any thoughts on how to troubleshoot?

See geneontology/go-ontology#12523

The desired hierarchy might look like:

• change in nutrient level
  • change in calory level
    • reduction in calories
      • restriction in calories (reduction that does not cause malnutrition or starvation)
      • reduction in calories leading to starvation

The basic pattern would be {change,increase,decrease} {nutrition,calory}. We would get elemental roles or defined classes for the latter from the food ontology.

I think we should avoid overloading is_a and treat starvation/malnutrition as disjoint conditions with caused_by axioms linking to the reduction hierarchy (or the increased hierarchy, for overnutrition)

cc @pbuttigieg @mateolan

Hi! Combing through the UDN survey info, and below are some of the exposures indicated within the survey that we do not currently have modeled in ECTO. Will continue to update this ticket.

Chemicals/Mixtures: (most all substances currently included from chebi terms)

• exposure to hydrochloric acid
• exposure to sulfuric acid
• exposure to phosphoric acid
• exposure to acetic acid
• exposure to nitric acid
• exposure to alkalies (including sodium hydroxide, magnesium hydroxide, calcium hydroxide, and potassium hydroxide)
• exposure to alcohols (including, methanol, ethanol)
• exposure to isopropanol/propan-2-ol
• exposure to butanol
• exposure to aluminum (and aluminum oxide)
• exposure to ammonia
• exposure to arsenic atom
  ** do we need other kinds of arsenic specifically modeled
• exposure to asbestos
• exposure to benzene
• exposure to xylene
• exposure to toluene
• exposure to toluene diisocyanate (TDI)
  ** both 2, 4 and 2, 6 forms and meta, all added
• exposure to chromium atom
• exposure to chromate(2-)
• exposure to ethylene dichloride
• exposure to formaldehyde
• exposure to mercury atom
  ** any other forms?
• exposure to chloroform
• exposure to chloroprene
• exposure to ketones
• exposure to methylene chloride/dichloromethane
• exposure to methylene bis(4phenyl isocyanate)/diphenylmethane-4,4'-diisocyanate
• exposure to beryllium atom
• exposure to cadmium atom
• exposure to carbon tetrachloride/tetrachloromethane
• exposure to carbon dioxide
• exposure to carbon monoxide
• exposure to nitrous oxide/dinitrogen oxide
• exposure to ozone
• exposure to lead atom
• exposure to barium atom
• exposure to talc
• exposure to polybrominated biphenyls (currently have polybrominated biphenyl ether from chebi)
• exposure to bisphenol A (BPA)
• exposure to dichlorobenzene
• exposure to ethylbenzene
• exposure to ethylene dibromide/1,2-dibromoethane
• exposure to ethylene dichloride/1,2-dichloroethane
• exposure to coal tar pitch/
• exposure to nickel atom
• exposure to vinyl chloride/chloroethane
• 2-methoxyethanol, 2-ethoxyethanol, AND 2-butoxyethanol (glycol ethers)
• polychlorobiphenyl, other PCBs we want??
• exposure to styrene
• exposure to phosgene
• exposure to phenol
• exposure to manganese atom
• exposure to silica powder/silicon dioxide
• exposure to tetrochloroethene/perchloroethylene
• exposure to trichloroethylene/trichloroethene
• exposure to sodium hypochlorite (bleach)
• exposure to chlorine atom
• exposure to triclosan
• polymers
• exposure to solvent
• sodium carbonate (common degreaser product)
• sodium silicate (common in detergents)
• EDTA(2-) (common solvent)
• white glue (polyvinyl acetate)
• exposure to hexane
• exposure to heptane
• rubber particle
• neoprene/chloroprene
• epichlorohydrin (another name for epoxy resin)
• urethane,
• exposure to polyurethane polymer
• polyethylene polymer
• exposure to methyl ethyl ketone/butanone
• alpha-pinene (major component to turpentine)
• beta-pinene (major component to turpentine)
• exposure to iodine atom
• exposure to acetone
• N,N-diethyl-m-toluamide (DEET, common in bug spray)
• Cyfluthrin (common in bug spray)
• citronellol (component of citronella)
• citronellal (component of citronella)
• geraniol (component of citronella)

Will require consideration for a new env. material class (mixture):

• exposure to citronella (in NCBITaxon and DRON, contains citronellol, citronellal, and geraniol)
• exposure to enamel (enameling hobby), only in NCIT
• exposure to depleted uranium (not certain we have specific term), putting in uranium atom for now
• exposure to bug spray, flea/tick medication, pest control chemicals
• exposure to hand sanitizer, DRON has options for specific ones
• exposure to steel (stainless or carbon), OMIT term,
• exposure to mold treatment fumes (identify common components)
• exposure to paint thinner/remover (i.e. mineral spirits or turpentine), NCIT term only needs a new term
• exposure to metals/heavy metals or metal fibers (may need to describe what metals are considered heavy to then create individual exposures, we do have metal dust)
• exposure to naptha (no identifiable term, mizture of items)
• exposure to paint primer (typically has synthetic resin, solvent, and additives including polyethylene)
• polymides/nylons (category, no clear examples)
• cyanoacrylates (poly(butyl 2-cyanoacrylate) polymer??)
• ethylene-vinyl acetate (available in DRON, not in CHEBI)
• epoxy (multiple types?)
• latex ?? (mixture)
• rubber cement (mixture, an adhesive made from elastic polymers (typically latex) mixed in a solvent such as acetone, hexane, heptane or toluene )
• sodium tripolyphosphate (common in degreasers)
• exposure to industrial adhesives or glues (glue in ENVO)
• degreaser (can look further for more in this category)
• exposure to glycol ethers (CATEGORY, we do not have)
• exposure to polychlorinated biphenyls (CATEGORY)
• exposure to nontoxic child craft paint (we do not have)
• exposure to ink (we do not have) (India ink, inkjet printer, gel ink, fountain pen ink, toner, soy ink, pharmaceutical ink)
• exposure to photo development chemicals (we do not have)
• exposure to cabinet stain (we do not have)
• exposure to cleaner (industrial or household) (we do not have)
• exposure to dyes (hair, leather, textile, paper)
• resins (category, includes epoxy, vinylester, and polyester resins) has NCIT term
• epoxy resins (category, includes glycidyl epoxy and non-glycidyl epoxy)
• glycidyl epoxy (category, includes glycidyl-ether, glycidyl-ester, and glycidyl-amine)
• non-glycidyl epoxy (category, includes aliphatic or cycloaliphatic epoxy resins)
• wallpaper paste (mixture)
• exposure to paint or varnish (we do not have) (nail varnish, shellac, wood stain, resin varnish, , lacquer, acrylic, oil based, luminescent)
• chlorinated napthalenes, is there a specific one we want? not listed
• ethyl fumigants, specific options to add?
• exposure to pool maintenance chemicals

Other stuff:

• exposure to biological agents (bacteria, virus, mold), available within NCIT and ExO, want separate terms for each piece? Those are in NCIT mostly

Requires ENVO terminology:

• asphalt (ENVO)
• exposure to fiberglass dust (fibrous glass dust in ENVO)
• exposure to rock dust (we do have rock from ENVO, included mineral dust and other options)
• exposure to wood dust (we do not have, did include wood and treated wood)
• exposure to brick dust (we do have slate dust + mineral dust in ENVO, both included)
• exposure to brick
• exposure to mortar (none, included various plaster terms)
• exposure to radiation from xray, radioactive materials, electromagnetic fields (radiation general ENVO, electromagnetic radiation ENVO)
• exposure to vehicle exhaust (frequent) including diesel (NCIT has only)
• exposure to plastic fumes (used plastic pollution, fumes is also NCIT term)

Indoor environment:

• Exposure to a(n) Air conditioner (only option in ENVO, no specific types)
• Exposure to a(n) Central air conditioning
• Exposure to a(n) window or wall unit air conditioning
• Exposure to a(n) portable unit air conditioning
  ** currently, no household stove, dryer, or oven related terms
• Exposure to a(n) Wood burning stove/range
• Exposure to a(n) electric stove
• Exposure to a(n) Gas Stove or Oven
• Exposure to a(n) Propane stove
• Exposure to a(n) Gas Clothes Dryer
• Exposure to a(n) Humidifier (only in NCIT)
• Exposure to a(n) Wood burning Fireplace (artificial logs?)
• Exposure to a(n) Gas Fireplace
• Exposure to a(n) Kerosene Heater (heater in NCIT)
• Exposure to a(n) Coal Burning Fireplace (currently have fossil fuel term from chebi)
• Exposure to a(n) Coal Stove (currently have fossil fuel term from chebi)
• Exposure to a(n) Central Heating System (powered by gas, electricity, fuel oil/kerosene, coal, wood, solar, other)
• exposure to HEPA filter in residence
• exposure to vaccuming in residence

Irregular environment exposures: ** an odd mix of quite specific items, rec for more universal terms

• exposure to environmental copper (living near copper mine), using copper atom and will adjust route as necessary

• exposure to chromium, route water (chrome 6 hexavalent chromium in water supply) (using chromium atom)

• exposure to iron, route water (high iron in well water)

• exposure to electric substation (living near electric substation, included power plants of various energy sources)

• exposure to pesticide

• insecticides,

• rodenticides,

• herbicides,

• fertilizers,

• fungicides (includes

• ethyl dibromide/1,2-dibromoethane

• exposure to PFOS, route water (using perfluorooctane-1-sulfonic acid)

• exposure to PFOC, route water (in water near home. also in fish population from rivers) did they actually mean PFOAs?? (adding perfluorooctanoic acid)

• exposure to extreme temperatures (did add extreme heat, may need to req extreme cold)

• exposure to extreme weather (a variety of additions provided)

• exposure to extreme noise

• exposure to methyl tert butyl ether (gasoline additive in well water)

• exposure to well water (community or private) (have included underground water)

• exposure to city/town water (drinking, showering, bathing)

• exposure to filtered water/water filtering system (water(processed) from FOODON?)

• exposure to bottled water (look for FOOD ON term)

• exposure to rain water or cistern

• exposure to river, lake, or pond water

• exposure to consuming holy water (consider FOODON term?)

• exposure to fumes (general or nondescript air content, also from fires, and from living near methamphetamine lab)

• exposure to radon atom

• exposure to farm animals/cattle, or pet animals (dogs, cats, small furry animals?)

• exposure to water damage at the home (leaks, broken pipes, flooding)

• exposure to fresh water source (swimming, not consumption, we have pool options here, what is the goal of this term?)

• exposure to an animal/vector bite (cat, dog, monkey, insect, tick, other)

• exposure to environmental allergens

Occupational/hobby exposures:

• exposure to auto or boat repair chemicals/solvents (we have general solvent) from vehicles (we do not have), includes brake fluid, transmission fluid, motor oil, and hydraulic fluid
  ** ENVO has a motor vehicle term,
• smog (ENVO term)
• exposure to airplane exhaust
• exposure to woodworking chemicals, furniture re-furnishing
• exposure to combustion gases
• exposure to textile fibers/dust
• exposure to welding, welding fumes, soldering (we do have welding occupations, may consider welding hobbies like jewelry making or stained glass)
• exposure to soldering materials (eutectin/tin lead alloy, tin sinc alloy, lead silver alloy, cadmium silver alloy, flux, solder paste, solder wire, rosin)
• exposure to coal dust and coal
• exposure to coal mining (need to add ENVO:01001440, environmental condition?)
• exposure to mining (need to add, ENVO:01001437) Can include mine drainage as well
• exposure to clay or clay dust, ceramics
• exposure to pottery glaze( (mixture of components)
• exposure to unexploded ordinance
• exposure to leather crafting
• exposure to fishing using lead weights or sinkers

Lifestyle exposures:

• exposure to poverty (all SES inquired about, for childhood and current)
• exposure to education (all levels, for individual and parents/caregiver)
• exposure to food insecurity
• exposure to living near an industrial plant
• exposure to living near a manufacturing facility
• exposure to living near agricultural fields, orchards, farm (or current residence on ag land past/present, or in close proximity)
• exposure to traffic while driving (various levels of traffic)
• exposure to a heavily traveled road near residence
• exposure to animal waste lagoon
• exposure to bus station/truck depot
• exposure to commercial airport
• exposure to dry cleaner
• exposure to gas station
• exposure to golf course
• exposure to greenhouse or commercial nursery
• exposure to gardening, yard work, lawn care
• exposure to hazardous waste site
• exposure to high-tension power lines
• exposure to incinerator
• exposure to landfill/garbage dump
• exposure to leather tannery
• exposure to military base
• exposure to oil refinery
• exposure to poultry processing plant
• exposure to power generation plant, coal, gas, petroleum/oil, nuclear
• exposure to factory
• exposure to ecigarettes, cigarettes, cigars, chewing tobacco etc. (we have smoking terms)
• exposure to alcoholic beverages (we have ethanol (added) and alcohol terms)
• exposure to intoxication
• exposure to incarceration or imprisonment
• exposure to candles or incense
• exposure to international travel or domestic travel (survey does inquire what country or state)
• exposure to regional living location (southeast, midwest, southwest, new england, mid-atlantic)
• exposure to potential contamination from Chernobyl (food)
• exposure to secondhand smoke (in residence, car, work)
• exposure to hand food and mouth disease
• exposure to jet fuel
• exposure to methyl bromide (parent and child)
• exposure to swimming in a pool
• exposure to stachybotrys mycotoxin
• exposure to carpet in the residence
• exposure to plastic or vinyl flooring in the residence/work (pergo, linoleum, laminate)
• exposure to wall material in the residence/work (cloth, fiber wallpaper, plastic)
• exposure to household remodeling (i.e. new carpet, painting, new flooring, wall papering)
• exposure to workplace remodeling (i.e. new carpet, painting, new flooring, wall papering, water damage replacement)
• exposure to enclosed garage on the residence (parked automobiles within garage?)
• exposure to crawl space/basement in the residence (gas powered devices in the residence?)
• exposure to rental or purchased residence, type of housing (i.e. townhouse)
• exposure to personal protective equipment (gloves, face mask, respirator, eye wear, lab coat, apron, other protective clothing) may include a hat with brim/sunglasses/sunscreen during leisure sun exposure
• exposure to sunlight
• exposure to sunburn/skin rash (radiation burn, first degree burn)
• exposure to artificial tanning, tanning booth
• exposure to sunlamp
  ** In EPR, there are some "lifestyle" exposures related to stress that are not very categorical, but we should likely consider some lifestyle or occupational stress terminology (expo survey part B pg 12)

See #5 and https://www.wikidata.org/wiki/Q21167876

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

• MRE:0000098 Exposure to gas TICKETED ebi-chebi/ChEBI#3337
• MRE:0000100 Exposure to 2,2',4'-tribromodiphenyl ether TICKETED ebi-chebi/ChEBI#3338
• MRE:0000102 Exposure to endocrine-disrupting chemical TICKETED ebi-chebi/ChEBI#3339
• MRE:0000105 Exposure to chemical element
  CHEBI:24431 chemical entity, this is in the csv file
• MRE:0000107 Exposure to metalloid TICKETED ebi-chebi/ChEBI#3340
• MRE:0000130 Exposure to volatile organic compound TICKETED ebi-chebi/ChEBI#3212, New term was added to CHEBI, see CHEBI:134179, need to add to csv
• MRE:0000143 Exposure to 1,3-dichloropropane TICKETED ebi-chebi/ChEBI#3341
• MRE:0000144 Exposure to 1,4-dichloropropane TICKETED https://github.com/monarch-initiative/Medically-Relevant-Exposome/issues/3 Confirmed with Peter that this is a typo and it is referring to CHEBI:28618 - 1,4-dichlorobenzene. This is in the csv file
• MRE:0000159 Exposure to m-/p-xylene m-xylene is in chebi: CHEBI:28488 - m-xylene, and p-xylene is in Chebi too: CHEBI:27417 - p-xylene, this is in the csv file
• MRE:0000161 Exposure to polybrominated diphenyl ether TICKETED ebi-chebi/ChEBI#3213 Term was added to Chebi, see CHEBI:134094, need to add to csv
• MRE:0000162 Exposure to 2,4,4'-tribromodiphenyl ether TICKETED ebi-chebi/ChEBI#3342
• MRE:0000164 Exposure to 2,3',4,4'-tetrabromodiphenyl ether TICKETED ebi-chebi/ChEBI#3343
• MRE:0000165 Exposure to 2,2',3,4,4'-pentabromodiphenyl ether TICKETED ebi-chebi/ChEBI#3344
• MRE:0000167 Exposure to 2,2',4,4',6-pentabromodiphenyl ether TICKETED ebi-chebi/ChEBI#3345
• MRE:0000171 Exposure to 2,2',3,3',4,4',5,5',6,6'-decabromodiphenyl ether TICKETED ebi-chebi/ChEBI#3346
• MRE:0000172 Exposure to 2,2',4,4',5,5'-hexabromobiphenyl TICKETED ebi-chebi/ChEBI#3347
• MRE:0000176 Exposure to ethyl paraben TICKETED ebi-chebi/ChEBI#3214 this term has been added to chebi, see CHEBI:31575 - ethylparaben, this is in the csv file
• MRE:0000178 Exposure to n-propyl paraben TICKETED ebi-chebi/ChEBI#3214 this term has been added to chebi, see CHEBI:32063 - propylparaben, this is in the csv file
• MRE:0000179 Exposure to inorganic acid TICKETED ebi-chebi/ChEBI#3348
• MRE:0000184 Exposure to perfluorinated compound TICKETED ebi-chebi/ChEBI#3215 this term has been added to chebi, see CHEBI:134091 - perfluorinated compound, need to add to csv file
• MRE:0000185 Exposure to perfluorobutane sulfonic acid this term exists: CHEBI:132446 - perfluorobutanesulfonic acid, need to add to csv file
• MRE:0000189 Exposure to perfluorohexane sulfonic acid this term exists: CHEBI:132448 - perfluorohexanesulfonic acid, need to add to csv file
• MRE:0000192 Exposure to perfluorooctane sulfonamide TICKETED ebi-chebi/ChEBI#3349
• MRE:0000204 Exposure to arsenocholine TICKETED ebi-chebi/ChEBI#3216 This term was added to chebi, see CHEBI:134092, need to add to csv file
• MRE:0000208 Exposure to trimethylarsine oxid TYPO TICKETED https://github.com/monarch-initiative/Medically-Relevant-Exposome/issues/2 this term exists: CHEBI:27131 - trimethylarsine oxide, need to add to csv file
• MRE:0000087 Exposure to organochloride pesticide TICKETED ebi-chebi/ChEBI#3211 This term was added to chebi, see CHEBI:38656, this term is in the csv file
• MRE:0000218 Exposure to chlorofluorocarbon compound TICKETED ebi-chebi/ChEBI#3217 This term was added to chebi, see CHEBI:134024, this term is in the csv file
• MRE:0000219 Exposure to dioxin compound TICKETED ebi-chebi/ChEBI#3218 This term was added to chebi, see CHEBI:36682, need to add to csv

Dietary exposure

I think this may be a simple gap in the DPs

• MRE:0000002 Dietary exposure
• MRE:0000011 Dietary exposure to a chemical residue
• MRE:0000012 Dietary aflatoxin exposure
• MRE:0000013 Dietary antimony exposure
• MRE:0000014 Dietary arsenic exposure
• MRE:0000015 Dietary cadmium exposure
• MRE:0000016 Dietary mercury exposure
• MRE:0000017 Dietary exposure to food additive
• MRE:0000018 Dietary exposure to low-calorie sweetener
• MRE:0000019 Dietary exposure to preservative
• MRE:0000020 Dietary exposure to color additive
• MRE:0000021 Dietary exposure to flavor enhancer
• MRE:0000022 Dietary exposure to bisphenol A
• MRE:0000023 Dietary exposure to deoxynivalenol
• MRE:0000024 Dietary exposure to emulsifier
• MRE:0000025 Dietary exposure to monosodium glutamate
• MRE:0000026 Dietary exposure to disodium guanylate

Prenatal/maternal

I think this may be a simple gap in the DPs

• MRE:0000001 Prenatal exposure
• MRE:0000003 Diagnostic medical exposure
• MRE:0000004 Radiological exposure
• MRE:0000005 Diagnostic radiological examination
• MRE:0000006 Interventional radiological procedure
• MRE:0000007 Radiograph
• MRE:0000008 Chest radiograph
• MRE:0000009 Exposure to infectious agent
• MRE:0000010 Exposure to airborne pollution
• MRE:0000092 Prenatal air pollutant exposure
• MRE:0000093 Prenatal polycyclic aromatic hydrocarbon exposure
• MRE:0000094 Prenatal medication exposure
• MRE:0000095 Prenatal exposure to maternal famine TICKETED EnvironmentOntology/envo#655
• MRE:0000038 Maternal cigarette use
• MRE:0000039 Maternal alcohol use
• MRE:0000040 Maternal marijuana use
• MRE:0000041 Maternal opiate use
• MRE:0000042 Maternal cocaine use
• MRE:0000043 Maternal methamphetamine use

Occupational

I think this may be a simple gap in the DPs

• MRE:0000052 Occupational exposure to herbicide
• MRE:0000053 Occupational exposure to insecticide
• MRE:0000054 Occupational exposure to fungicide
• MRE:0000055 Occupational exposure to rodenticide
• MRE:0000056 Occupational exposure to bactericide
• MRE:0000057 Occupational exposure to carbamate insecticide
• MRE:0000058 Occupational dust exposure
• MRE:0000059 Occupational aerosol exposure
• MRE:0000060 Occupational mineral dust exposure
• MRE:0000061 Occupational metallic dust exposure
• MRE:0000062 Occupational fibrous dust exposure
• MRE:0000063 Occupational fibrous glass dust exposure
• MRE:0000064 Maternal heroin use
• MRE:0000066 Occupational exposure to Paraquat
• MRE:0000067 Occupational exposure to Diquat
• MRE:0000068 Occupational exposure to urea-based herbicide
• MRE:0000069 Occupational exposure to isoproturon
• MRE:0000070 Occupational exposure to organophosphorus herbicide
• MRE:0000071 Occupational exposure to anilofos
• MRE:0000072 Occupational exposure to gluphosphate - I think this is a typo and should be glyphosate
• MRE:0000073 Occupational exposure to nitrile herbicide
• MRE:0000074 Occupational exposure to toxic waste
• MRE:0000075 Occupational exposure to anticoagulant rodenticide
• MRE:0000090 Occupational noise exposure
• MRE:0000091 Occupational exposure to infrasound TICKETED
  EnvironmentOntology/envo#656
• MRE:0000049 Occupational exposure to pesticide

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

• MRE:0000027 Nuclear medicine procedure
• MRE:0000028 Cervical spine radiograph
• MRE:0000029 Pelvis radiograph
• MRE:0000030 Skull radiograph
• MRE:0000031 Intravenous pyelogram TICKETED: NCI-Thesaurus/thesaurus-obo-edition#47
• MRE:0000033 Positron emission tomography scan
• MRE:0000078 Exposure to ultrasonography
• MRE:0000080 Exposure to radioactivity

Other

• MRE:0000048 Tobacco pipe smoking
• MRE:0000051 Alcohol use
• MRE:0000077 Angiography
• MRE:0000081 Radioactive contamination
• MRE:0000085 Human papilloma virus infection
• MRE:0000089 Exposure to noise

Wikidata has various classes of use under hazard

In particular, chemical hazards link to exposure routes and phenotypes, e.g. strychnine exposure - this seems to come from CSC NIOSH

try this query

SELECT ?cause ?chebiId ?causeLabel ?exposure ?exposureLabel ?symptom ?symptomLabel ?route ?routeLabel WHERE {
  ?exposure p:P636 ?statement .
  ?statement pq:P780 ?symptom .
  ?statement ps:P636 ?route .
  ?exposure wdt:P828 ?cause .
  ?cause wdt:P683 ?chebiId .
  SERVICE wikibase:label {
    bd:serviceParam wikibase:language "en" .
   }
}

This query would eventually be integrated into dipper (see monarch-initiative/dipper#363 for discussion on wikidata statement model), but for now in exploratory phase it's useful to see what data WD has info on exposures on.

inferred superclasses for exposure to ethylparaben:

are these correct?

they all come from CHEBI:

Our role pattern is 'has exposure stimulus' some ('chemical entity' and 'has role' some %s), so if CHEBI says that C has role R, then an exposure to C will be classified as an exposure "to" R. Is this right in all cases? Let's look.

• phytoestrogen - explanation comes from CHEBI, seems to be correct (Note MRE did not have this link).
• antimicrobial food preservative - seems dubious. Even though ethylparaben is used for this purpose sometimes, if the exposure is in the context of cosmetics use seems odd to classify this way.

I think we need to distinguish between

1. classification by potentially realized roles, or rigid roles: 'has exposure stimulus' some ('chemical entity' and 'has role' some %s)
2. classification by roles that actually realized: 'has exposure stimulus' some ('chemical entity' and 'has role' some (%s and realized-by some process))

E.g.

• any exposure to ethylparaben is an exposure to a potential antimicrobial food preservative
• an exposure to ethylparaben used as a cosmetic is an exposure to a potential antimicrobial food preservative, but not an exposure to a chemical with a antimicrobial food preservative role that is actually realized

Should we always name these 2 classes, to avoid confusion, and for maximum precision? Also a 3rd class for when we know the role is not realized?

If we follow this pattern for 'hormone', we would have exposures to chemicals with potential hormone roles, and exposures to chemicals with realized hormone roles. The former is what most people would query by. For example, we would expect BPA to come back in a query for xenestrogen, whether or not it actually realized this role in any given exposure. Of course it's hard to determine whether in any given exposure the role is realized, so the existence of the subclass may seem odd.

It may be simplest in the short term to continue to use the uncommitted version (1), but for some cases, specifically those roles involving some kind of human intention, we make more specific subclasses.

To align with BFO / OBO core, exposure event should be a subtype of BFO:process (see #57).
In ecto.owl (http://purl.obolibrary.org/obo/ecto/releases/2019-09-20/ecto.owl), exposure event is a top level term.

from Bjoern:

Many of exposures, in particular experimental ones such as administration
of a compound to an animal model, changes in bedding, etc. are covered in
OBI or in OBI scope. There are also classes in OBI for unplanned exposures
not really in scope, but we needed to include them as a placeholder to keep
definitions consistent and there wasn't always a natural home for them
(e.g. travel to an endemic area of Malaria; living in the same household as
an active TB case, naturally occuring infection). Randi presented that work
at ICBO, and we are actively looking to coordinate these exposure terms
across ontologies.

This is great, I think many of these are complementary to what we may have.

So at a very minimum, I would beg you to include OBI in the list of
ontologies you are including in your considerations. Better yet, I would
ask you to coordinate this work with us, minimally at the higher level.
(administered exposure / naturally occurring exposure / inferred exposure).

Our plan in ECTO was to be neutral about intentionality. Biologically an exposure to X is an exposure to X. ECTO is already somewhat ridiculously compositional, and to have {admininstered,natural} exposure to {C} via {Route} could get too unwieldy.

Was this what you had in mind?

Related to #6

ECTO's classification is based entirely on CHEBI and our OWL defs. MRE is manual.

In have aligned ECTO and MRE, and compared classifications:

• potential new edges for MRE based on ECTO
• missing edges in ECTO based on MRE

I will break down the categories here:

• organochlorine compounds - #11
• phytoestrogens - #10
• inorganic compounds - #13

More to be added later

http://eelst.cs.unibo.it/apps/LODE/source?url=https://tw.rpi.edu/chear.rdf

The occurrent branch of `ecto.owl (http://purl.obolibrary.org/obo/ecto/releases/2019-09-20/ecto.owl) does not include BFO:process.

Currently these classes appear to be doing the same kind of work. Why is there a distinction? They seem to be the same thing.

2019-09-20 18:52:56,509 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: http://purl.obolibrary.org/obo/ENVO_3100011 == http://purl.obolibrary.org/obo/ENVO_09200021
2019-09-20 18:52:56,510 ERROR org.obolibrary.robot.ReasonOperation - Equivalence: http://purl.obolibrary.org/obo/ENVO_01001483 == http://purl.obolibrary.org/obo/ENVO_00010504

They seem to be equivalent.. Why?