A number of anthropogenic and other terms for our GenEpiO

[Public-Health-Bioinformatics]

At moment GenEpiO has some terms that would best be moved into ENVO. Below is a list of terms we're currently using, along with commented out items which we'd created placeholders for and which we thought you'd like moved over to ENVO to get ENVO id's ?. I presume we need to provide a definition for each of these? How should we do the submissions?

# http://purl.obolibrary.org/obo/ #    agricultural - crop
http://purl.obolibrary.org/obo/ENVO_00000042 #    agricultural - drainage canal
http://purl.obolibrary.org/obo/ENVO_00000140 #    agricultural - drainage ditch
# http://purl.obolibrary.org/obo/    edit #    drain
# http://purl.obolibrary.org/obo/ # edit    agricultural - storage - feed
# http://purl.obolibrary.org/obo/ # edit    agricultural - storage - manure

http://purl.obolibrary.org/obo/ENVO_00003040 #    animal - housing - built
# http://purl.obolibrary.org/obo/ # edit    animal - housing - built - closed
# http://purl.obolibrary.org/obo/ # edit    animal - housing - built - open
# http://purl.obolibrary.org/obo/ # edit    animal - litter / cage / bedding
# http://purl.obolibrary.org/obo/ # edit    animal - petting zoo

http://purl.obolibrary.org/obo/ENVO_00000073 #    building
http://purl.obolibrary.org/obo/ENVO_00003864 #    building - bakery
...
http://purl.obolibrary.org/obo/ENVO_00002272 #    building - waste treatment plant
# http://purl.obolibrary.org/obo/ # edit    building - abattoir or meat processing
# http://purl.obolibrary.org/obo/ # edit    building - agricultural fair
# http://purl.obolibrary.org/obo/edit #    building - dairy processing
# http://purl.obolibrary.org/obo/edit #    building - daycare
# http://purl.obolibrary.org/obo/edit #    building - fish processing
# http://purl.obolibrary.org/obo/ # edit    building - long term care facility
# http://purl.obolibrary.org/obo/  #edit    building - residential
# http://purl.obolibrary.org/obo/  #edit    building - restaurant
# http://purl.obolibrary.org/obo/  #edit    campground
# http://purl.obolibrary.org/obo/  #edit    social gathering 
# http://purl.obolibrary.org/obo/  #edit    vehicle

http://purl.obolibrary.org/obo/ENVO_01000252 #    water - lake
http://purl.obolibrary.org/obo/ENVO_01000048 #    water - ocean
http://purl.obolibrary.org/obo/ENVO_01000253 #    water - river
http://purl.obolibrary.org/obo/ENVO_01000002 #    water - well
...
http://purl.obolibrary.org/obo/ENVO_00002018 #    water - waste water - sewage
# http://purl.obolibrary.org/obo/ # edit    water - waste water - industrial
# http://purl.obolibrary.org/obo/    edit #    sewage - raw sewage
# http://purl.obolibrary.org/obo/ # edit (not necessarily Private)    water - pool
# http://purl.obolibrary.org/obo/  #    water - canal
# http://purl.obolibrary.org/obo/  #edit    water - hot-tub / jacuzzi spa
# http://purl.obolibrary.org/obo/ #edit    water - intake

# http://purl.obolibrary.org/obo/ENVO_01000703 # precipitation
http://purl.obolibrary.org/obo/ENVO_01000753 # air temperature

#    http://purl.obolibrary.org/obo/ edit #    animal - feed (blood meal)
#    http://purl.obolibrary.org/obo/ edit #    animal - feed (fish meal)
#    http://purl.obolibrary.org/obo/ edit #    animal - feed (other)
#    http://purl.obolibrary.org/obo/ edit (not really ingredient) #    animal - feed (pet food)
#    http://purl.obolibrary.org/obo/     #    animal - fluid, carcass
http://purl.obolibrary.org/obo/ENVO_00003031 #    animal manure
#    http://purl.obolibrary.org/obo/ edit #    animal manure - bovine (dairy liquid)
#    http://purl.obolibrary.org/obo/ edit #    animal manure - composted
http://purl.obolibrary.org/obo/ENVO_00003884 #    animal manure - farmyard
http://purl.obolibrary.org/obo/ENVO_00003859 #    animal manure - horse
#    http://purl.obolibrary.org/obo/    edit #    animal manure - poultry
#    http://purl.obolibrary.org/obo/    edit #    animal manure - poultry (heat treated)
http://purl.obolibrary.org/obo/ENVO_00003927 #    animal manure - stable
#    http://purl.obolibrary.org/obo/    edit #    animal manure product (commercial/retail, heat treated) 

[pbuttigieg]

Below is a list of terms we're currently using, along with commented out items which we'd created placeholders for and which we thought you'd like moved over to ENVO to get ENVO id's ?

Sure, but note that an Agronomy Ontology has spun off from ENVO currently run by @celineaubert. Many of these terms could go there. @celineaubert, below I've listed the terms that I think could fit in AgrO - if any of these are out of scope, let me know and I'll add them to ENVO. I'm placing all animal-related terms in ENVO to prevent mission creep for AgrO. When a broader Agricultural Ontology emerges, we can transfer them.

I presume we need to provide a definition for each of these? How should we do the submissions?

Yes, you could either create new issues for each term or link to a Google Spreadsheet with your proposed definitions. Be careful though, some of the labels you use suggest categorisations not supported by ENVO. For example, ENVO's drainage canal is not limited to agricultural systems. The same is true for drainage ditch Also, it's generally considered problematic to have labels like "animal - housing - built - closed", as these are trying to do the job of the hierarchy and other axioms.

Potential AgrO terms

@Public-Health-Bioinformatics please provide definitions for these too

# http://purl.obolibrary.org/obo/ #    agricultural - crop
subclass of http://purl.obolibrary.org/obo/ENVO_00000042 #    agricultural - drainage canal
subclass of http://purl.obolibrary.org/obo/ENVO_00000140 #    agricultural - drainage ditch
# http://purl.obolibrary.org/obo/ # edit    agricultural - storage - feed
# http://purl.obolibrary.org/obo/ # edit    agricultural - storage - manure

These below could also go in ENVO, but I believe they're relevant to agronomic fertilisers. Note the discussion on manure: https://github.com/EnvironmentOntology/envo/issues/348

#    http://purl.obolibrary.org/obo/ edit #    animal - feed (blood meal)
#    http://purl.obolibrary.org/obo/ edit #    animal - feed (fish meal)
#    http://purl.obolibrary.org/obo/ edit #    animal - feed (other)
#    http://purl.obolibrary.org/obo/ edit #    animal manure - bovine (dairy liquid)
#    http://purl.obolibrary.org/obo/ edit #    animal manure - composted
#    http://purl.obolibrary.org/obo/    edit #    animal manure - poultry
#    http://purl.obolibrary.org/obo/    edit #    animal manure - poultry (heat treated)
#    http://purl.obolibrary.org/obo/    edit #    animal manure product (commercial/retail, heat treated) 

ENVO terms

We have dairy, litter, vehicle,

Additionally, would human house do the job for residential building? Or is this a union of things like apartment buildings etc?

http://purl.obolibrary.org/obo/ENVO_00003040 #    animal - housing - built
# http://purl.obolibrary.org/obo/ # edit    animal - housing - built - closed
# http://purl.obolibrary.org/obo/ # edit    animal - housing - built - open
# http://purl.obolibrary.org/obo/ # edit    animal - litter / cage / bedding
# http://purl.obolibrary.org/obo/ # edit    animal - petting zoo
# http://purl.obolibrary.org/obo/    edit #    drain
# http://purl.obolibrary.org/obo/ # edit    building - abattoir or meat processing
# http://purl.obolibrary.org/obo/ # edit    building - agricultural fair
# http://purl.obolibrary.org/obo/edit #    building - daycare
# http://purl.obolibrary.org/obo/edit #    building - fish processing
# http://purl.obolibrary.org/obo/ # edit    building - long term care facility
# http://purl.obolibrary.org/obo/  #edit    building - residential
# http://purl.obolibrary.org/obo/  #edit    building - restaurant
# http://purl.obolibrary.org/obo/  #edit    campground
# http://purl.obolibrary.org/obo/  #edit    social gathering 
# http://purl.obolibrary.org/obo/ # edit    water - waste water - industrial
# http://purl.obolibrary.org/obo/    edit #    sewage - raw sewage
# http://purl.obolibrary.org/obo/ # edit (not necessarily Private)    water - pool
# http://purl.obolibrary.org/obo/  #    water - canal
# http://purl.obolibrary.org/obo/  #edit    water - hot-tub / jacuzzi spa
# http://purl.obolibrary.org/obo/ #edit    water - intake
#    http://purl.obolibrary.org/obo/ edit (not really ingredient) #    animal - feed (pet food)

Other terms

I'm not sure what you mean with http://purl.obolibrary.org/obo/ # animal - fluid, carcass we have bodily fluid, based on UBERON and carcass.

[cmungall]

The question of how to divide terms between AgrO and ENVO is difficult. We want to avoid complex mutual imports. But I think all the decisions above make sense. One possibility is that AgrO tends towards agronomic processes, instruments, variables and qualities.

[Public-Health-Bioinformatics]

Ok, thanks for grilling these terms. I'll prepare a spreadsheet and elucidate on some of them. You are right, there are a few conjunctive terms, like "animal - fluid, carcass" which we should keep as separate descriptors. We have a few veterinary epidemiologist/genomics experts working with us now on the sampling metadata, helping define precise environmental descriptors for sample/swab work.

[Public-Health-Bioinformatics]

I just realized the animal food items best fit in FoodOn (doh!).

[celineaubert]

Some classes are already in AgrO: crop: http://purl.obolibrary.org/obo/AGRO_00000325 fish meal: http://purl.obolibrary.org/obo/AGRO_00000083 blood meal: http://purl.obolibrary.org/obo/AGRO_00000086 liquid manure: http://purl.obolibrary.org/obo/AGRO_00000078 poultry litter: http://purl.obolibrary.org/obo/AGRO_00000080 There are also other animal manures in AgrO. A release will be done soon, so you will be able to navigate through the differentes classes. However, there is nothing concerning storage buildings. If you provide defintions, @marieALaporte and I will look where those classes might fit best.

[Public-Health-Bioinformatics]

Ok, thanks, and glad to see crop etc. there. So Agro is now the home for manures and composts?! Makes sense. The google docs sheet I'm doing with Gregory Harhay of entries we need for agriculture sector buildings has a focus on identifying places that samples are taken from. I'll send it to you and Pier once its finished.

Thanks!

[Public-Health-Bioinformatics]

About FoodOn, I realize now agricultural animal feed items should originate from AGRO?! I just checked what FoodOn has for "animal feed" ...

Would AGRO want all of the animal feed related items other than "food for non-food animals" and food for laboratory animals"?

[pbuttigieg]

Would AGRO want all of the animal feed related items other than "food for non-food animals" and food for laboratory animals"?

Wouldn't all food stay in FOODON? It's tricky, but I think FOODON's focus on food composition and nutrition is more valuable here. AGRO can import them.

[marieALaporte]

Céline left one month ago and I am just taking over Agro now, trying to catch up on things. Can we discuss that on Skype so I can understand what we should be doing on our end. I am planning for a release this week, but I can wait until we discuss.

[pbuttigieg]

@marieALaporte I'll be back from conferencing tomorrow. We could Skype anytime that day. Call if you see me online.

[Public-Health-Bioinformatics]

Ok. If you all have agreement on that. Happy to incorporate all animal foods.

In other news a FoodOn/GenEpiO contributor Gregory Harhay is working on: https://docs.google.com/spreadsheets/d/13d-FcjcvsY-vsJI9A7ueAB29L5EKTv4Kzhu3ULMDR3g/edit#gid=0 to provide adequate definitions. This is our preliminary guess about which of these terms should end up in AGRO vs ENVO. We'll let you know when it is finished.

[pbuttigieg]

In editor's version

http://purl.obolibrary.org/obo/ENVO_00003040 #   animal - housing - built
http://purl.obolibrary.org/obo/ENVO_01000921 #   animal - housing - built - closed
http://purl.obolibrary.org/obo/ENVO_01000918 #  animal - housing - built - open
http://purl.obolibrary.org/obo/ENVO_00002191 #   animal - litter
http://purl.obolibrary.org/obo/ENVO_01000922 #   animal cage
http://purl.obolibrary.org/obo/ENVO_01000923 #   animal - petting zoo
http://purl.obolibrary.org/obo/ENVO_01000924 #   drain
http://purl.obolibrary.org/obo/ENVO_01000925 #   building - abattoir or meat processing
http://purl.obolibrary.org/obo/ENVO_01000927 #   building - daycare
http://purl.obolibrary.org/obo/ENVO_01000928 #   building - fish processing
http://purl.obolibrary.org/obo/ENVO_00000014 #   water - canal
http://purl.obolibrary.org/obo/ENVO_00002018 #   sewage - raw sewage

Double check these

http://purl.obolibrary.org/obo/ENVO_00002001 # edit    water - waste water - industrial 

ENVO's waste water class isn't strictly industrial - do you need it to be?

Clarification needed

http://purl.obolibrary.org/obo/ # edit    animal bedding

Is this not the same as animal litter?

http://purl.obolibrary.org/obo/ # edit    building - agricultural fair

This isn't really a building, more of a gathering. Would need a def here.

http://purl.obolibrary.org/obo/ # edit (not necessarily Private)    water - pool

Are we talking about a swimming pool?

punt to other ontologies

http://purl.obolibrary.org/obo/  #edit    social gathering 

I suggest you punt this to PCO (@ramonawalls). We can re-import this into ENVO and describe the environment determined by a gathering (of humans?) if needed.

http://purl.obolibrary.org/obo/ edit (not really ingredient) #    animal - feed (pet food)

FOODON should contain this.

TODO:

http://purl.obolibrary.org/obo/ # edit    building - long term care facility
http://purl.obolibrary.org/obo/  #edit    building - residential
http://purl.obolibrary.org/obo/  #edit    building - restaurant
http://purl.obolibrary.org/obo/  #edit    campground
http://purl.obolibrary.org/obo/  #edit    water - hot-tub / jacuzzi spa
http://purl.obolibrary.org/obo/ #edit    water - intake

[ramonawalls]

@Public-Health-Bioinformatics, please file a term request issue for http://purl.obolibrary.org/obo/ #edit social gathering in the PCO tracker (https://github.com/PopulationAndCommunityOntology/pco/issues). There are a several new terms in PCO, so I'd like to add social gathering as well before doing a release.

[Public-Health-Bioinformatics]

Ok, I'll have a close look at this tomorrow.

One thing to verify is that our updated wish list is at https://docs.google.com/spreadsheets/d/13d-FcjcvsY-vsJI9A7ueAB29L5EKTv4Kzhu3ULMDR3g/edit#gid=0 , but that Gregory hasn't finished his pass at term definitions yet. But I like the definitions you have cooked up so far too! Thanks.

Also I have to discuss with him how long the definitions need to be (as they appear in the google spreadsheet).

About animal – feed, on that spreadsheet we're actually asking for a new item "silage' under it, not "animal – feed" any more. In case I didn't mention it before, Gregory is an Animal Veterinarian and so is listing off all the sites that samples are extracted from.

About: waste water – industrial. Hmm. The term was obtained from a sample sheet that had no further explanation. It made me think of the distinction between agricultural waste water and manufacturing effluent/tailing pond water. But we could try to do without the distinction and just revisit if someone requests it?

Ciao,

Damion

[pbuttigieg]

About animal – feed, on that spreadsheet we're actually asking for a new item "silage' under it, not "animal – feed" any more. In case I didn't mention it before, Gregory is an Animal Veterinarian and so is listing off all the sites that samples are extracted from.

Makes sense, I suppose this can be imported into FOODON for the food uses of silage. We do have these terms: http://purl.obolibrary.org/obo/ENVO_00003030 http://purl.obolibrary.org/obo/ENVO_00003071 http://purl.obolibrary.org/obo/ENVO_00003900 http://purl.obolibrary.org/obo/ENVO_00003978

I notice quite a few carcass terms. We have some in ENVO, which makes sense, however, the treatment of carcasses for consumption etc should probably be expanded on in FOODON.

In editors' version

http://purl.obolibrary.org/obo/ENVO_01000932  #  building - long term care facility
http://purl.obolibrary.org/obo/ENVO_01000933  #  building - residential
http://purl.obolibrary.org/obo/ENVO_01000934  #  building - restaurant
http://purl.obolibrary.org/obo/ENVO_01000935 #   campground
http://purl.obolibrary.org/obo/ENVO_01000938 #   water - hot-tub / jacuzzi spa

@Public-Health-Bioinformatics thank you for requesting "hot tub". This is a great day. @cmungall - Because of such content, I will now start naming the releases (in the description, the tags will still be dates). Due to hot tubs and time crystals, the next one will be "Hot tub time machine"

Also added:

http://purl.obolibrary.org/obo/ENVO_01000937 # impromptu campground
http://purl.obolibrary.org/obo/ENVO_01000936 # dedicated campground

Needs clarification

http://purl.obolibrary.org/obo/ #edit    water - intake

I assume we're dealing with the constructed kind? I found a pretty good definition from The Great Soviet Encyclopedia:

a hydraulic-engineering installation for obtaining water from a source of supply (river, lake, reservoir, and so on) for purposes of hydroelectric power engineering, water supply, or irrigation. Water intake works are intended to ensure the delivery of water into a conduit (a canal, pipeline, tunnel, and so on) in specified amounts, of the proper quality, and according to a water-consumption chart.

Water Intake Works. (n.d.) The Great Soviet Encyclopedia, 3rd Edition. (1970-1979). Retrieved March 27 2017 from http://encyclopedia2.thefreedictionary.com/Water+Intake+Works

[pbuttigieg]

@Public-Health-Bioinformatics many of the requested terms have been released today.

[pbuttigieg]

@Public-Health-Bioinformatics any input on the clarification request above?

[Public-Health-Bioinformatics]

First, thanks for the Mar 27 terms! About water intake, great definition, yes, that's the one. Trust the soviet socialist republics to get it right!

[Public-Health-Bioinformatics]

I will add all carcass terms to FoodOn now since Gregor seems to have finished supplying definitions there.

[Public-Health-Bioinformatics]

What do you think about "kiosk" and "food truck". Are these kinds of thing still within ENVO purview?

Also, building parts like sink, shower and bathtub, are they good for ENVO?

[Public-Health-Bioinformatics]

About: animal bedding. Yes you are right, it is "animal litter". Sorry! Done.

building - agricultural fair ... right; that should be "building - agricultural fairground", encompassing all the temporary animal housing and husbandry facilities etc. (Adapted from Wikipedia definition https://en.wikipedia.org/wiki/Agricultural_show ): "An agricultural fairground is the permanent site for agricultural shows in which the equipment, animals, sports and recreation associated with agriculture and animal husbandry are presented."

residential building ... yes, this is a union of things like apartment buildings, private home, hotel etc.

pool ... yes, this should be "swimming pool (public or private)" . Wikipedia: A swimming pool, swimming bath, wading pool, or paddling pool is a structure designed to hold water to enable swimming or other leisure activities

I have stocked the ENVO section of our term sheet with mainly wikipedia definitions: https://docs.google.com/spreadsheets/d/13d-FcjcvsY-vsJI9A7ueAB29L5EKTv4Kzhu3ULMDR3g/edit#gid=0

Thanks for reviewing this.

[pbuttigieg]

First, thanks for the Mar 27 terms! About water intake, great definition, yes, that's the one. Trust the soviet socialist republics to get it right!

Thanks for the requests! I'll move on the USSR term and def.

I will add all carcass terms to FoodOn now since Gregor seems to have finished supplying definitions there.

Great, but please be sure that these are carcasses intended for human consumption. Whalefalls or deer rotting in a forest are more ENVO domain for now I think (even though they are food) as we can axiomatise them for effectively.

What do you think about "kiosk" and "food truck". Are these kinds of thing still within ENVO purview? Also, building parts like sink, shower and bathtub, are they good for ENVO?

For the moment, yes, as we don't have ontologies that deal with such things in the OBO sphere yet. We'll incubate this branch as we did the food branch. Please create a new issue for those requests and add some proposed defs.

building - agricultural fair ... right; that should be "building - agricultural fairground", encompassing all the temporary animal housing and husbandry facilities etc. (Adapted from Wikipedia definition https://en.wikipedia.org/wiki/Agricultural_show ): "An agricultural fairground is the permanent site for agricultural shows in which the equipment, animals, sports and recreation associated with agriculture and animal husbandry are presented."

Hmm, still trick as this is a site which occasionally has the rest of the party around. I'll see what I can do, but you want to capture the active fairground rather than the allocated space, right?

residential building ... yes, this is a union of things like apartment buildings, private home, hotel etc.

We have residential building, but we exclude hotels and other places intended for short term stays. I can create a union class if needed, but note that hotels are not usually considered residences in national statistics.

pool ... yes, this should be "swimming pool (public or private)" . Wikipedia: A swimming pool, swimming bath, wading pool, or paddling pool is a structure designed to hold water to enable swimming or other leisure activities

Looks good, will add.

[Public-Health-Bioinformatics]

About agricultural fairground - our intention is to describe the place where a specimen was extracted. (How recently activity was there would have to be a second dimension of description I think.)

For "residential building", glad to see it there. I think then we'd need another category to cover hotel (& motel, bed&breakfast etc.), for specimen site, and it looks like https://en.wikipedia.org/wiki/Hotel could cover this. I'm recalling Legionnaire's outbreak (https://en.wikipedia.org/wiki/1976_Philadelphia_Legionnaires%27_disease_outbreak)

I will put above distilled, outstanding items into new issues list. Thx.

[pbuttigieg]

This is pretty much done right @Public-Health-Bioinformatics? Xref #505

Sent from my Samsung SM-G950F using FastHub

[Public-Health-Bioinformatics]

seems like it is; I've just left a few comments under AgrO issues board. So this could be closed.