Integration/pno #256

jmwhorton · 2022-06-13T20:42:13Z

Additions and updates for the integration of PNO terms into IAO:
(issue: #237 )

Added IAO:0020000 identifier.
Added IAO:0020001 grapheme.
Added IAO:0020010 identifier creating process.
Added IAO:0020015 personal name.
Added IAO:0020016 given name.
Added IAO:0020017 family name.
Added IAO:0020020 code set.
Moved IAO:0000579 (centrally registered identifier registry) under 'code set'.

Edited IAO:0020000 identifier, expanded class specification. Added IAO:0020001 grapheme. Added IAO:0020002 utterance. Added IAO:0020010 dubbing process. Added IAO:0020015 personal name. Added IAO:0020016 given name. Added IAO:0020017 family name. Added IAO:0020020 code set. Moved IAO:0000579 under 'code set'. Added OBI:0100026 organism. Added NCBITaxon:9606 Homo sapiens.

cmungall · 2022-06-13T21:03:54Z

iao.owl

+                <owl:intersectionOf rdf:parseType="Collection">
+                    <owl:Restriction>
+                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
+                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>


This doesn't resolve.

I'm not sure what to use here. I can't find a working resource for BFO 'entity.' The link below also has the same unresolvable url. Can you point me in the right direction?

https://www.ebi.ac.uk/ols/ontologies/bfo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000001&lang=en&viewMode=All&siblings=false

@cmungall I am not quite sure what you mean.
I'd prefer to change the axioms as: equivalent: 'information content entity' and (is_specified_output_of some 'identifier creating process') and subClassOf: denotes some entity

@cmungall The http://purl.obolibrary.org/obo/BFO_0000001 link now resolves correctly. It must have just been down temporarily.

cmungall · 2022-06-13T21:05:19Z

iao.owl

+    <!-- http://purl.obolibrary.org/obo/IAO_0020010 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0020010">
+        <owl:equivalentClass>


I recommend all logical definitions have a genus even if this is redundant with domain/range

Genus added to definition (moved to iao-edit.owl)

cmungall · 2022-06-13T21:08:07Z

iao.owl

+            </owl:Class>
+        </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0020000"/>
+        <obo:IAO_0000115 xml:lang="en">A personal name is a proper name identifying an individual person.</obo:IAO_0000115>


note the genus in the text and the label of the genus don't match

Definition updated (moved to iao-edit.owl)

cmungall · 2022-06-13T21:09:05Z

iao.owl

@@ -7242,6 +7388,18 @@ No imports</obo:IAO_0000115>



+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_9606 -->


consider adding this in the imports

Hi @jmwhorton, if you are not sure how to import OBO terms to IAO in the import-OBO.owl file, I can help with it.

Thank you, @zhengj2007. I believe I have figured it out.

Both 'organism' and 'Homo sapiens' need go to the import-OBO.owl. The IAO using ontoFox to extract the terms from external ontologies. Please add the terms in OntoFox-input.txt and run ontoFox tool to generate the import-OBO.owl.

Thank you, @zhengj2007. You were correct, I was about to do it the wrong way!

Added import to OntoFox-input.txt

cmungall · 2022-06-13T21:09:39Z

iao.owl

+    <!-- http://purl.obolibrary.org/obo/NCBITaxon_9606 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_9606">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>


avoid injection

Added import to OntoFox-input.txt

cmungall

Thanks for your contribution!

Necessary changes:

You should edit https://github.com/information-artifact-ontology/IAO/blob/master/src/ontology/iao-edit.owl not the release file
Fix the BFO ID that doesn't resolve

All other comments are advisory only

Also, remember to link to an issue that provides context for a PR

I think this is the one:

Integrate PNO into IAO #237

Edited IAO:0020000 identifier, expanded class specification. Added IAO:0020001 grapheme. Added IAO:0020002 utterance. Added IAO:0020010 identifier creating process. Added IAO:0020015 personal name. Added IAO:0020016 given name. Added IAO:0020017 family name. Added IAO:0020020 code set. Moved IAO:0000579 under 'code set'. Added OBI:0100026 organism. Added NCBITaxon:9606 Homo sapiens. Per request: added superclass to 'identifier creating process' equivalence class. Per request: corrected definition for 'personal name.'

Added NCBITaxon_9606 'Homo sapiens.' Added OBI_0100026 'organism.'

This reverts commit 7df8e9e.

This reverts commit 24168c6.

zhengj2007 · 2022-06-22T18:01:54Z

All edits look good to me except 'family name' and 'given name'. Both of them are subClass of 'personal name' and also part_of 'personal name'. Does not seem correct.

Edited IAO_0020017 'family name', moved under 'identifier', 'part of' axiom removed, definition updated. Edited IAO_0020016 'given name', 'part of' axiom removed.

jmwhorton · 2022-06-23T14:01:33Z

Per conversation with @zhengj2007 and @mbrochhausen, 'family name' and 'given name' have been updated. Please let me know if the new definition for 'family name' is acceptable (updated to reflect change in hierarchy).

Edited IAO:0000579 CRID registry, updated definition and example of usage. Removed IAO:0020002 utterance. Edited IAO:0020001 grapheme, added comment. Edited IAO:0020015 personal name, updated definition, added comment, removed equivalent class. Edited IAO:0020020 code set, updated definition, added comment and contributor.

This reverts commit ab75d1a.

jmwhorton · 2022-07-20T15:23:17Z

Changes have been made per the 2022-07-18 OBI call.

@alanruttenberg, I do have a question for you. Based on your provided definition of 'code set,' I left it under 'information content entity' because it was worded as such. Please, let me know if the final intention was to move 'code set' under 'data set,' and I can get that change made.

alanruttenberg · 2022-07-20T19:41:05Z

My recollection was that the discussion had it that it would not be under data set.

zhengj2007

Better to associated tracker, #237, using IAO_0000233 'term tracker item', with all the terms added/changed in the pull request.

Update definitions of 'personal name', 'family name' and 'given name' using Aristotle format. For example, personal name: 'An identifier referring to an individual entity that is ascribed personhood by the user of the identifier'.

Did not find term 'IAO:0020002 utterance'

Question: why move the 'family name' as sibling of 'person name' but still keep 'given name' as child of 'person name'?

Add Alan Ruttenberg as term editor of 'code set'. You can also add your name as term editor for the terms you made changes.

IAO_0000233 'term tracker item' added to all new/updated terms. Personal, family, and given name definitions change to Aristotelian format. Term editor added to all new/updated terms.

jmwhorton · 2022-07-28T20:47:23Z

@zhengj2007, the requested changes have been made. Thank you for your time.

IAO_0000233 has been added to all new and updated terms.
Personal, family, and given name definitions have been updated to correct format.
Utterance was removed per the 2022-07-18 OBI call. Integrate PNO into IAO #237 has been updated to reflect decisions.
Family name was moved (per the 2022-07-18 OBI call) because it refers to the name of a family, and does not refer to a person (like a 'personal name'). A 'given name' refers to an individual person, making it still a subclass of 'personal name'. (This is to the best of my recollection. I would welcome a better explanation if I've misrepresented the reason here.)
'Term editor' annotations have been added.

zhengj2007

Remove 'identifier' from ontoFox input file and rerun ontoFox to update import_OBO.owl since the term has added in iao_edit.owl
Also update the definition of 'grapheme' and 'identifier creating process' to start with its parent label.
Thanks!

Edited IAO:0020000 'identifier' definition. Edited IAO:0020001 'grapheme' definition. Edited IAO:0020010 'identifier creating process' definition.

jmwhorton · 2022-07-29T14:33:23Z

@zhengj2007, the requested changes have been made. Thanks!

jmwhorton · 2022-09-08T17:21:40Z

Good afternoon, @cmungall. When you have a moment, we just need one more review on these changes before merging them. Thanks!

mbrochhausen · 2022-10-11T09:07:27Z

I think we agreed to have it be a sibling to data set.

…

On Wed, Jul 20, 2022 at 2:41 PM Alan Ruttenberg ***@***.***> wrote: My recollection was that the discussion had it that it would not be under data set. — Reply to this email directly, view it on GitHub <#256 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACF6DLTRYKQ2OWX5Y4YSRG3VVBI53ANCNFSM5YVOK4SQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

zhengj2007 · 2022-10-17T18:48:41Z

Hi @jmwhorton The changes have been reviewed during OBI call. There is no objection on the changes for few months. I think you can merge the changes into IAO.

StroemPhi · 2022-10-24T08:28:47Z

Hi, when can we expect this change to be released?

zhengj2007 · 2022-10-24T13:37:54Z

I am going to make a new release as soon as possible.

StroemPhi · 2022-10-24T13:47:55Z

Thank you @zhengj2007 🚀

jmwhorton added 2 commits May 24, 2022 14:29

Correcting 'identifier creating process' to match PNO

7df8e9e

cmungall reviewed Jun 13, 2022

View reviewed changes

cmungall requested changes Jun 13, 2022

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cmungall mentioned this pull request Jun 13, 2022

Improve the CONTRIBUTING.md.jinja2 template INCATools/ontology-development-kit#380

Closed

jmwhorton added 4 commits June 16, 2022 09:52

Adding 'organism' and 'Homo sapiens.'

ab75d1a

Added NCBITaxon_9606 'Homo sapiens.' Added OBI_0100026 'organism.'

Revert "Correcting 'identifier creating process' to match PNO"

be6d1c8

This reverts commit 7df8e9e.

Revert "Integrating PNO terms to IAO, plus some term reorganization."

951f77f

This reverts commit 24168c6.

jmwhorton added 2 commits June 22, 2022 14:52

Edited IAO:0020000 identifier, equivalent class

7203232

Adjusting family and given name.

713bb19

Edited IAO_0020017 'family name', moved under 'identifier', 'part of' axiom removed, definition updated. Edited IAO_0020016 'given name', 'part of' axiom removed.

jmwhorton added 2 commits July 20, 2022 09:15

Revert "Adding 'organism' and 'Homo sapiens.'"

f3f7605

This reverts commit ab75d1a.

zhengj2007 mentioned this pull request Jul 28, 2022

Integrate PNO into IAO #237

Closed

jmwhorton requested review from cmungall and zhengj2007 July 28, 2022 17:27

zhengj2007 requested changes Jul 28, 2022

View reviewed changes

Improvements from review.

d09bdf6

IAO_0000233 'term tracker item' added to all new/updated terms. Personal, family, and given name definitions change to Aristotelian format. Term editor added to all new/updated terms.

zhengj2007 self-requested a review July 28, 2022 21:10

zhengj2007 requested changes Jul 28, 2022

View reviewed changes

Updating definitions to correct Aristotelian format.

beea25a

Edited IAO:0020000 'identifier' definition. Edited IAO:0020001 'grapheme' definition. Edited IAO:0020010 'identifier creating process' definition.

Removing PNO from imports.

00cbde9

zhengj2007 approved these changes Jul 30, 2022

View reviewed changes

This was referenced Sep 8, 2022

move and improve AEON:0000027 'academic field descriptor' tibonto/aeon#156

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rethink the modeling of 'academic field descriptor' and 'event topic descriptor' classes tibonto/aeon#108

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jmwhorton merged commit af0c901 into master Oct 17, 2022

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Integration/pno #256

Integration/pno #256

jmwhorton commented Jun 13, 2022 •

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StroemPhi commented Oct 24, 2022

		@@ -7242,6 +7388,18 @@ No imports</obo:IAO_0000115>



		<!-- http://purl.obolibrary.org/obo/NCBITaxon_9606 -->

Integration/pno #256

Integration/pno #256

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