Request for new terms

[jagadishcs]

@turbomam @cmungall @TBKReddy

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

[cmungall]

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

[jagadishcs]

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]

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

[turbomam]

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

[turbomam]

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

[turbomam]

@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]

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]

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]

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

[turbomam]

Still todo (mostly by me)

• [x] Add term IDs and definitions sources to the Google Sheet as necessary. See #1193 for highest used IDs? Start at 3600090.
• [x] define 'artificial satellite'
• [ ] Add axioms (parthood, composed of etc.) in Protege after template has been executed by robot.
• [ ] resolve uncertainty about intrinsic/extrinsic nature of pathogen suppressive soil
  • see Google Sheet comments
• [x] Use IRI or CURIE forms of ORCIDs, not bare strings

---

• [ ] Add some or all of the below to some or all of the contributor annotations for the templated terms added to EnvO on @jagadishcs' (0000-0002-6670-9157) behalf since I joined BBOP in March.

• @turbomam https://orcid.org/0000-0001-9076-6066

• @kaiiam https://orcid.org/0000-0002-3410-4655

• @pbuttigieg https://orcid.org/0000-0002-4366-3088

• @wdduncan https://orcid.org/0000-0001-9625-1899

• @cmungall https://orcid.org/0000-0002-6601-2165

---

• [ ] Double check terms added since I joined BBOP with regards to #1202

[kaiiam]

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]

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]

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]

@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]

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]

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

[kaiiam]

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]

NMDC-03_EnvO_template_robot_sheet