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EnvironmentOntology / envo

A community-driven ontology for the representation of environments
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Request for new terms #1191

Closed jagadishcs closed 1 year ago

jagadishcs commented 3 years ago

@turbomam @cmungall @TBKReddy

Request for creation of new EnvO terms for the list provided here

cmungall commented 3 years ago

I think pathogen-suppressive is a better term that disease-suppressive (but include full synonyms). Do you have a ref for this concept?

jagadishcs commented 3 years ago

References for Disease/pathogen suppressive soils: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953945/ https://www.frontiersin.org/articles/10.3389/fmicb.2017.02529/full https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/suppressive-soils I have moved Disease suppressive soil to the exact synonym field and provided 'pathogen-suppressive soil' in the label field.

turbomam commented 3 years ago

You can see related stuff I'm working on here: https://github.com/turbomam/envo-robot-helpers

turbomam commented 3 years ago

Working in https://github.com/EnvironmentOntology/envo/tree/issue-1191-Jagadish-20210625

turbomam commented 3 years ago

Set sharing level for https://docs.google.com/spreadsheets/d/12GICSjx2s3Ey0Crv9uMdkW8unt3LxPcOS2_u7EMAr38/edit#gid=154764881 to public based on email from @jagadishcs

turbomam commented 3 years ago

@jagadishcs is the table below a good sample for motivating the "back yard" term request? Do you have any other examples from other sources? I got the example row from the Biosample tab in the goldData file at https://gold.jgi.doe.gov/download?mode=site_excel via https://gold.jgi.doe.gov/downloads

I'm especially interested in whether "back yard" could be used in contexts besides US residences. Its meaning seems to have very strong geographical and cultural baggage. As in, a British person would be much more likely to call the same space a "garden" even if it didn't have formal plantings. And there are lots of examples for using "yard" in agricultural or industrial contexts.

At a minimum, I propose labeling this 'residential back yard' and giving it a synonym 'back garden'. Maybe @cmungall @wdduncan @kaiiam or @pbuttigieg will have additional or different perspectives.

BIOSAMPLE GOLD ID BIOSAMPLE NAME BIOSAMPLE NCBI TAX ID BIOSAMPLE NCBI TAX NAME BIOSAMPLE SAMPLE COLLECTION SITE BIOSAMPLE GEOGRAPHIC LOCATION BIOSAMPLE LATITUDE BIOSAMPLE LONGITUDE BIOSAMPLE ECOSYSTEM BIOSAMPLE ECOSYSTEM CATEGORY BIOSAMPLE ECOSYSTEM TYPE BIOSAMPLE ECOSYSTEM SUBTYPE BIOSAMPLE SPECIFIC ECOSYSTEM
Gb0145243 Enriched backyard soil microbial communities from Emeryville, California, USA - eDNA 3rd pass 37_C BE-Lig BY 410658 soil metagenome enriched backyard soil USA: Emeryville, California 37.83 -122.29 Environmental Terrestrial Soil Unclassified Unclassified
turbomam commented 3 years ago

I'd also like to review the meaning of

...at the back of a house

Does at the back of imply further away from the house, relative to some road?

Are houses the only structures that have back yards? How about a school or an apartment block? Your definition for 'yard' is

An area of land immediately adjacent to a building or a group of buildings.

So could we use this definition for 'back yard'?

A yard which is behind a building or group of buildings, relative to some entity like a road?

smrgeoinfo commented 3 years ago

I don't see why 'relative to some entity like a road' is necessary.

backyard--an area of vegetated land adjacent to the back of a building and part of the property that includes the building.

requires that the building have a defined front and back. Otherwise its just a yard. A parking lot at the back of a building is not a yard (or garden) If the back of the building abuts 'vegetated' land (i.e. not paved or built up) that belongs to a different property, it is not a backyard.

turbomam commented 3 years ago

Thanks @smrgeoinfo . We're going to save this term for a future pull request.

turbomam commented 2 years ago

Still todo (mostly by me)

kaiiam commented 2 years ago

Switch to DC annotation predicates instead of oboInOwl predicates?

My understanding was that we were favoring the use of oboInOwl for ENVO, AFAIK this isn't standardized across OBO yet. What I put as the template strings in the ENVO-Robot-template-and-merge-workflow was my understanding the APs we agreed to be using if that's the the case please let me know and I can update that protocol.

turbomam commented 2 years ago

Hi, @kaiiam. On Thursday the 5th, @pbuttigieg suggested using DC predicates for the term creator and the term creation date. I agree that there is a strong precedent for using oboInOwl in EnvO.

I don't have a strong preference, but @pbuttigieg , @wdduncan and I did talk some about recording term contributors in addition to term creators. dc:contributor could be used for that. Is there something in oboInOwl or IAO that you would recommend for that?

kaiiam commented 2 years ago

The above protocol links to this example sheet with what I understood to be our standard APs in ENVO. Unfortunately we have used both DC and oboInOwl. I don't care either way I though @pbuttigieg had decided we should use oboInOwl but if we want to change that's fine we just just pick one and go with it.

creation date created by
oboInOwl:creation_date^^xsd:dateTime oboInOwl:created_by
turbomam commented 2 years ago

@pbuttigieg and @jagadishcs

Cook, R. J. (2014). Plant Health Management: Pathogen Suppressive Soils. Encyclopedia of Agriculture and Food Systems, 441–455. doi:10.1016/b978-0-444-52512-3.00182-0

uses the following citation to define Pathogen-Suppressive Soils

Baker, K.F., Cook, R.J., 1974. Biological Control of Plant Pathogens. San Francisco, CA: W. H. Freeman and Co. Book, reprinted in 1982, St. Paul, MN: American Phytopathological Society. Bangera, M.G., Thomashow, L.S., 1

The 2014 paper describes the mechanism of pathogen suppression solely in terms of the presence of other (non-pathogenic?) microorganisms, not chemical additives. I haven't found a way to read the 1974 book onloine.

@pbuttigieg I think you already anticipated this. Does this information have any effect on how you'd like to model 'pathogen-suppressive soil'?

turbomam commented 2 years ago

Thanks @kaiiam

I was especially interested if you knew of any oboInOwl predicate for non-creator contributors, or if there is any EnvO precedent for making that distinction.

cmungall commented 2 years ago

please make a separate ticket for anything regarding the schema for annotation assertions. For now stick with what we do already in envo

kaiiam commented 2 years ago

any oboInOwl predicate for non-creator contributors, or if there is any EnvO precedent for making that distinction.

Not as far as I'm aware to either. My understanding is we just add oboInOwl#created_by APs linking to ORCIDs (as URLs) for anyone who contributed anything (and who wants attribution).

turbomam commented 2 years ago

NMDC-03_EnvO_template_robot_sheet