Krishna to agro prj patterns for #1228

[pbuttigieg]

Closes #1228
Closes #1323 (en passant)

[matentzn]

I will look into it CDNO reported the same CompositionalDietaryNutritionOntology/cdno#97

[pbuttigieg]

Class curation report for your information @marieALaporte @KrishnaTO

• exchangeable ion - this is not a quality and the definitions don't hold. It and its subclasses have been repositioned and definitions edited. They have been made more generic, and hold in materials other than soil. The equivalence axioms have been removed. See also NTR: Ion exchange #1331
• exchangeable calcium - should be under the Ca2+ class in CHEBI. Need to update the CHEBI import for that. The exact synonyms are incorrect and have been replaced. xref: Import: CHEBI Calcium and Postassium ions #1333
• exchangeable potassium - similar to above.
• cation exchange capacity - the functional relation axiom does not hold and has been removed. The superclass molecular quality is incorrect, as the quality does not inhere in the molecule. Moved to physical quality which inheres in environmental material.
• percentage base saturation - this is an information artifact. It will be refactored into a subclass of CEC as its definition suggests, and defined as a quality. All acronyms are expanded in definitions. The comment is appended with non-essential information in the definition.
• residual water - the definition chosen from the source material was rewritten for clarity (e.g. the liquid water doesn't have a "water phase"). The label is changed to reflect that this is a soil-specific class. Residual water just means left over water.
• water infiltration - this is not a quality, but a process and has been edited to be so under water flow process.
• soil water infiltration - this was a subclass of soil, despite being defined as a process. The correction of water infiltration improves this, which is now its subclass with more correct axioms. The label has been changed to be more precise.

[kaiiam]

I also note that there is an irregular file src/envo/envo-edit-module-merged.owl which should NOT have been merged into this PR that needs to be deleted if this PR is to proceed.

[pbuttigieg]

@matentzn @cmungall

As @kaiiam notes above, the various intermediate files that are created in the make flow should be cleaned up. Is this done in the new ODK releases?

[pbuttigieg]

Stuff left to do:

• regenerate entity_attribute.owl when @matentzn fixes ODK (entity_attribute.csv is updated)
• clean up temporary files generated by ODK as noted above by @kaiiam

[kaiiam]

the various intermediate files that are created in the make flow

I'm guessing the intermediate file here was created using the ENVO-Robot-template-and-merge-workflow? If it says only to commit the changes envo-edit.owl.

[pbuttigieg]

the various intermediate files that are created in the make flow

I'm guessing the intermediate file here was created using the ENVO-Robot-template-and-merge-workflow? If it says only to commit the changes envo-edit.owl.

I guess seed.txt is another residual file to be removed

[pbuttigieg]

'http://purl.obolibrary.org/obo/ENVO_09000029 ' breaks the reasoner (malformed logic) and is imported from the EAL module. I'm deleting the line in the EAL and noting the ID is used for a manually added term. Not great, but we need an SOP on fixing / removing pattern-based terms from the modules.

EDIT:

http://purl.obolibrary.org/obo/ENVO_09000028 was quite weird too. It is the evaporation of liquid water in soil, which shouldn't be an EAL pattern, as it's a process. Fixed manually and the ID makred and commented out in EAL.txt. The reasoner didn't seem to catch this @matentzn. The offending stanza below.

    <!-- http://purl.obolibrary.org/obo/ENVO_09000028 -->

    <owl:Class rdf:about="http://purl.obolibrary.org/obo/ENVO_09000028">
        <owl:equivalentClass>
            <owl:Class>
                <owl:intersectionOf rdf:parseType="Collection">
                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ENVO_02500034"/>
                    <owl:Restriction>
                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
                        <owl:someValuesFrom>
                            <owl:Class>
                                <owl:intersectionOf rdf:parseType="Collection">
                                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/ENVO_00002006"/>
                                    <owl:Restriction>
                                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/ENVO_00001998"/>
                                    </owl:Restriction>
                                </owl:intersectionOf>
                            </owl:Class>
                        </owl:someValuesFrom>
                    </owl:Restriction>
                </owl:intersectionOf>
            </owl:Class>
        </owl:equivalentClass>
        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The evaporation of a liquid water when measured in soil.</obo:IAO_0000115>
        <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">soil liquid water evaporation</oboInOwl:hasExactSynonym>
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">evaporation of liquid water in soil</rdfs:label>
    </owl:Class>

[pbuttigieg]

@KrishnaTO @marieALaporte please be more careful when using patterns

Your ENVO:09000021 and ENVO:09000020 duplicated existing classes and require considerable time to hunt down and fix. Your ENVO:09000029 and ENVO:09000028 (noted above) have now also deregularised our EAL.txt file. Those classes will be created (manually with the same IDs), but may be obsoleted with fresh IDs down the line.

[pbuttigieg]

Stuff left to do:

• regenerate entity_attribute.owl when @matentzn fixes ODK (entity_attribute.csv is updated) See Weird bug I cant figure out: permission denied INCATools/ontology-development-kit#651

[pbuttigieg]

Now, this will be interesting: some of the other PRs from @KrishnaTO have not been merged yet, so classes like "runoff", mentioned in the module CSVs will not be available. I wonder what's going to happen...

[KrishnaTO]

@KrishnaTO @marieALaporte please be more careful when using patterns

Your ENVO:09000021 and ENVO:09000020 duplicated existing classes and require considerable time to hunt down and fix. Your ENVO:09000029 and ENVO:09000028 (noted above) have now also deregularised our EAL.txt file. Those classes will be created (manually with the same IDs), but may be obsoleted with fresh IDs down the line.

@pbuttigieg Just to confirm, ENVO:09000021 and ENVO:09000020 were pre-existing EAL patterns, if you look at the history of the file.

If the duplicate issue you're referring to is the failed check, we didn't work on either of those entities.
I do remember being extremely careful with these pattern files, with what faculties were available to me at that time, such as catching ENVO:09000029 and ENVO:09000028.