[CC, EAL] Pattern-based classes add (desc for issues) #1228

KrishnaTO · 2021-10-29T01:13:27Z

Creates classes from patterns per issues from Agronomy project
MAJOR REVISION (nov 15,2021): gathering all pattern-based class additions into this PR. Reverted previous terms in CC to EAL to place classes appropriately.

Chemical Concentration [CC]
closes #394
closes #401
closes #402
closes #403
closes #404
closes #405
closes #406
closes #407
closes #408
closes #409
closes #410
closes #411
closes #412
closes #414

Entity Attribute Location [EAL]
closes #369
closes #370
closes #371
closes #372
closes #373
closes #374
closes #396
closes #413
closes #429

Entity Attribute [EA]
closes #368
closes #360
closes #361 (associated term in PR #1244)
closes #366 (formerly PR #1235)

Addresses issues EnvironmentOntology#369 EnvironmentOntology#370 EnvironmentOntology#371 EnvironmentOntology#372 EnvironmentOntology#373 EnvironmentOntology#374 EnvironmentOntology#401 EnvironmentOntology#402 EnvironmentOntology#403 EnvironmentOntology#404 EnvironmentOntology#405 EnvironmentOntology#406 EnvironmentOntology#407 EnvironmentOntology#408 EnvironmentOntology#409 EnvironmentOntology#410 EnvironmentOntology#411 EnvironmentOntology#412 EnvironmentOntology#414

KrishnaTO · 2021-10-29T01:21:52Z

Note on Chemical_concentration.owl file deletions: the output was made using the classes to be added only (the old classes [ENVO:3100001: ENVO:3200059] were re-added for record keeping to chemical_concentration.csv).

Possible explanation for danger of using existing classes in csv: was re-introducing old terms, which may have had manually updated annotations and causing mismatch?

Ran dosdp run per previous commit with current class substitution.

cmungall · 2021-11-01T03:05:18Z

This looks good to me. I don't fully understand the deletion issue. It is important to have well-defined SOPs for DPs, see https://docs.google.com/document/d/1KXv-Tm3HvypjucFZeLLPjCdgkof5f0Re5_5GbFfQLWU/edit#heading=h.i814vcicxu55

This reverts commit e74d8aa.

This reverts commit 0064be2.

KrishnaTO · 2021-11-02T01:29:46Z

@cmungall Resolved! I was attempting to go by the backroads on that one, without noting the highway (make recipe).

Need to add make instruction somewhere (wiki, README in folders /modules or /pattern, README-editors.md, or SOP):
run in /src/envo/: make modules/$.owl

This reverts commit d8e1124.

Corrected previous commit's EAL pattern ids Imported pato term: duration Added class 'hours of sunshine' using EA pattern and revised label to correct string

src/envo/modules/chemical_concentration.csv

Depends on PR EnvironmentOntology#1228 for parent class

closes EnvironmentOntology#361

… [EA] Added 'evaporation', 'evapotranspiration', 'rain' volumes

Added classes: - water infiltration - soil water infiltration

Added classes: - exchangeable potassium - exchangeable ion

relation to 'CEC'

… Added CC patterns Added patterns for classes: - exchangeable potassium content in soil - residual water content in soil - exchangeable calcium content in soil

EnvironmentOntology#432 Added classes in EA pattern Added classes: - soil water infiltration speed - topsoil thickness - soil drainage speed - air temperature amplitude

Imported PATO term corrected EA IRI

KrishnaTO · 2021-12-26T23:53:38Z

Added additional terms per patterns templates:

Chemical Concentration [CC]
exchangeable potassium content in soil | #415
residual water content in soil | #417
exchangeable calcium content in soil | #418

Entity Attribute [EA]
soil water infiltration speed | #395
topsoil thickness | #398
soil drainage speed | #420
air temperature amplitude | #432

KrishnaTO · 2021-12-26T23:54:35Z

As of now, all pattern based terms are added from the Agronomy project of ENVO and this PR can be committed.

pbuttigieg · 2022-08-10T10:51:40Z

Conflicting IDs in the entity_attribute.txt file below, changing to ENVO:09200032 and ENVO:09200033

ENVO:09200022,,PATO:0001309,duration,ENVO:01001211,stellar radiation
ENVO:09200023,,PATO:0001025,pressure,ENVO:01000268,atmospheric water vapour

entity_attribute.owl needs regeneration.

pbuttigieg · 2022-08-10T10:52:30Z

Most changes to envo-edit.owl all need definitional, placement, content-level, grammatical, and logical review.

pbuttigieg · 2022-08-10T10:55:00Z

The pato_terms.txt conflicts are trivial, but the import is severely compromised. Regeneration needed.

pbuttigieg · 2022-08-10T10:58:09Z

regenerate pato_import.owl
regenerate entity_attribute.owl

pbuttigieg

See #1330

* Added CC pattern classes (desc for issues list) Addresses issues #369 #370 #371 #372 #373 #374 #401 #402 #403 #404 #405 #406 #407 #408 #409 #410 #411 #412 #414 * Added CC pattern class per issue #394 Ran dosdp run per previous commit with current class substitution. * Revert "Added CC pattern class per issue #394" This reverts commit e74d8aa. * Revert "Added CC pattern classes (desc for issues list)" This reverts commit 0064be2. * Rerun pattern add using make recipe * Revert "Rerun pattern add using make recipe" This reverts commit d8e1124. * Added EAL and CC pattern-based classes See issues from list for classes added: Chemical Concentration [CC] closes #369 closes #394 closes #401 closes #402 closes #403 closes #404 closes #405 closes #406 closes #407 closes #408 closes #409 closes #410 closes #411 closes #412 closes #414 Entity Attribute Location [EAL] closes #367 closes #370 closes #371 closes #372 closes #373 closes #374 closes #396 closes #413 closes #429 * #368 [EA] Added class 'color of soil' * #360 Added class 'hours of sunshine' Corrected previous commit's EAL pattern ids Imported pato term: duration Added class 'hours of sunshine' using EA pattern and revised label to correct string * #366 Add class 'pressure of vapour' * #361 [EA] Added class 'runoff volume' closes #361 * #353,#354,#355 [EA] Added 'evaporation', 'evapotranspiration', 'rain' volumes * Added classes for water infiltration Added classes: - water infiltration - soil water infiltration * #415 added classes for exchangeable potassium Added classes: - exchangeable potassium - exchangeable ion * #417 added class 'residual water' * Added class 'exchangeable calcium' * Added class 'cation exchange capacity' * update DL 'exchangeable ion' relation to 'CEC' * #422 added class 'percentage base saturation' * #415 #417 #418 Added CC patterns Added patterns for classes: - exchangeable potassium content in soil - residual water content in soil - exchangeable calcium content in soil * Update 'water infiltration' DL * #395 #398 #420 #432 Added classes in EA pattern Added classes: - soil water infiltration speed - topsoil thickness - soil drainage speed - air temperature amplitude * run robot dosdp patterns for CC & EA Imported PATO term corrected EA IRI * regenerating pato_import.owl * fixing semantics for manually added classes in #1228 * fixing unsatisfiable axiom https://github.com/EnvironmentOntology/envo/runs/7767526832?check_suite_focus=true#step:4:26 * deleting envo-edit-module-merged.owl * fixing erroneous EAL patterns, manual reconfig of generated classes, IDs commented out in EAL txt module file * attempting fix of https://github.com/EnvironmentOntology/envo/runs/7771430536?check_suite_focus=true#step:4:26 * regenerating all modules Co-authored-by: Krishna Udaiwal <krishna.u@hotmail.com> Co-authored-by: pier.buttigieg <pier.buttigieg@gitlab.hzdr.de>

Added CC pattern class per issue EnvironmentOntology#394

e74d8aa

Ran dosdp run per previous commit with current class substitution.

cmungall requested a review from pbuttigieg November 1, 2021 03:01

KrishnaTO added 3 commits November 1, 2021 18:35

Revert "Added CC pattern class per issue EnvironmentOntology#394"

5200c85

This reverts commit e74d8aa.

Revert "Added CC pattern classes (desc for issues list)"

895c962

This reverts commit 0064be2.

Rerun pattern add using make recipe

d8e1124

This was referenced Nov 5, 2021

Import classes from ENVO AgriculturalSemantics/agro#139

Closed

fixes #402 #1221

Closed

Revert "Rerun pattern add using make recipe"

f018778

This reverts commit d8e1124.

KrishnaTO marked this pull request as draft November 15, 2021 19:12

KrishnaTO changed the title ~~Added CC pattern classes (desc for issues list)~~ [CC, EAL] Pattern-based classes add (desc for issues) Nov 15, 2021

KrishnaTO added 2 commits November 15, 2021 14:31

EnvironmentOntology#368 [EA] Added class 'color of soil'

6857ffb

KrishnaTO mentioned this pull request Nov 16, 2021

New class: volumetric water content in soil #425

Closed

KrishnaTO added 2 commits November 16, 2021 13:43

EnvironmentOntology#360 Added class 'hours of sunshine'

ce3f1fe

Corrected previous commit's EAL pattern ids Imported pato term: duration Added class 'hours of sunshine' using EA pattern and revised label to correct string

EnvironmentOntology#366 Add class 'pressure of vapour'

70ef56a

cmungall reviewed Nov 17, 2021

View reviewed changes

src/envo/modules/chemical_concentration.csv Show resolved Hide resolved

KrishnaTO added a commit to KrishnaTO/envo that referenced this pull request Nov 17, 2021

EnvironmentOntology#425 Added class volumetric water content in soil

e2b264a

Depends on PR EnvironmentOntology#1228 for parent class

This was referenced Nov 17, 2021

[#425] Added class 'volumetric water content in soil' KrishnaTO/envo#2

Draft

[#361] Added class 'runoff' #1244

Closed

KrishnaTO added 2 commits November 18, 2021 12:37

EnvironmentOntology#361 [EA] Added class 'runoff volume'

8dbadf3

closes EnvironmentOntology#361

EnvironmentOntology#353,EnvironmentOntology#354,EnvironmentOntology#355…

6dada00

… [EA] Added 'evaporation', 'evapotranspiration', 'rain' volumes

KrishnaTO marked this pull request as ready for review December 7, 2021 16:18

KrishnaTO added 4 commits December 9, 2021 09:37

Merge branch 'master' into agro-prj-patterns

a30c1bf

Added classes for water infiltration

48ac44c

Added classes: - water infiltration - soil water infiltration

EnvironmentOntology#415 added classes for exchangeable potassium

5c40b30

Added classes: - exchangeable potassium - exchangeable ion

EnvironmentOntology#417 added class 'residual water'

e9927f7

KrishnaTO added 15 commits December 22, 2021 11:37

Added class 'exchangeable calcium'

da31cc4

Added class 'cation exchange capacity'

30d6557

update DL 'exchangeable ion'

bc5b1f0

relation to 'CEC'

EnvironmentOntology#422 added class 'percentage base saturation'

7780bea

Merge branch 'issue-415' into agro-prj-patterns

2dfac44

Merge branch 'issue-417' into agro-prj-patterns

acbc244

Merge branch 'issue-418' into agro-prj-patterns

bf702bd

EnvironmentOntology#415 EnvironmentOntology#417 EnvironmentOntology#418…

dac398f

… Added CC patterns Added patterns for classes: - exchangeable potassium content in soil - residual water content in soil - exchangeable calcium content in soil

Merge branch 'issue-395' into agro-prj-patterns

f6feb89

Update 'water infiltration' DL

c658664

Merge branch 'issue-395' into agro-prj-patterns

59a0049

EnvironmentOntology#395 EnvironmentOntology#398 EnvironmentOntology#420

3b99e56

EnvironmentOntology#432 Added classes in EA pattern Added classes: - soil water infiltration speed - topsoil thickness - soil drainage speed - air temperature amplitude

EnvironmentOntology#398 added synonym 'topsoil'

1c9e902

Merge branch 'issue-398' into agro-prj-patterns

4eb8738

run robot dosdp patterns for CC & EA

d8a1e03

Imported PATO term corrected EA IRI

KrishnaTO mentioned this pull request Jan 18, 2022

#393 added class 'soil water potential' #1267

Closed

pbuttigieg added a commit that referenced this pull request Aug 10, 2022

fixing merge conflicts on #1228, prep regeneration

0770472

This was referenced Aug 10, 2022

Krishna to agro prj patterns for #1228 #1330

Merged

NTR: Ion exchange #1331

Open

pbuttigieg pushed a commit that referenced this pull request Aug 10, 2022

fixing semantics for manually added classes in #1228

8eff912

pbuttigieg reviewed Aug 10, 2022

View reviewed changes

pbuttigieg closed this in #1330 Aug 10, 2022

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[CC, EAL] Pattern-based classes add (desc for issues) #1228

[CC, EAL] Pattern-based classes add (desc for issues) #1228

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[CC, EAL] Pattern-based classes add (desc for issues) #1228

[CC, EAL] Pattern-based classes add (desc for issues) #1228

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