Add mapping relations #14

gouttegd · 2023-01-16T19:47:40Z

This PR implements the proposal in #3.

That is, it adds properties intended to represent mapping relations:

skos:semanticRelation
- skos:mappingRelation
  - skos:closeMatch
    - skos:exactMatch
  - semapv:isomorphicMatch
    - skos:exactMatch
    - semapv:crossSpeciesExactMatch
  - semapv:nonIsomorphicMatch
    - skos:broadMatch
      - semapv:crossSpeciesBroadMatch
    - skos:narrowMatch
      - semapv:crossSpeciesNarrowMatch
    - skos:relatedMatch
      - semapv:crossSpeciesExactMatch

This commit adds a handful of properties intended to represent mapping relations. Some of these properties are directly taken from the SKOS specification, but re-classified in a custom hierarchy. The others are new properties specifically intended to represent cross-species mappings. This is an implementation of the proposal in mapping-commons#3.

matentzn · 2023-01-23T09:56:20Z

semapv-properties.tsv

@@ -0,0 +1,14 @@
+IRI	skos:prefLabel	skos:definition	dc:source	skos:example	rdfs:comment	altLabel	Parent
+ID	A skos:prefLabel	A skos:definition	A dc:source	A skos:example	A rdfs:comment	A skos:altLabel	SC % SPLIT=|
+skos:semanticRelation	semantic relation	A link between two concepts.	https://www.w3.org/TR/skos-reference/				


Contrary what I suggested on the ticket, I dont think we need this, I would prefer to have skos:mappingRelation in the root, and that's it. Let me know if you think differently.

Fine with me.

matentzn · 2023-01-23T10:05:15Z

semapv-properties.tsv

@@ -0,0 +1,14 @@
+IRI	skos:prefLabel	skos:definition	dc:source	skos:example	rdfs:comment	altLabel	Parent


add column rdfs:isDefinedBy

Intended to hold what type of value? An IRI to the defining standard (e.g. SKOS)? In that case should that replace dc:source?

Its the standard property we use to say: this term is defined in FBBT. This term is defined in Mondo. This term is defined in SKOS. Its intended to reference the actual RDF, not a website

gouttegd · 2023-01-23T15:47:30Z

Following discussion with @matentzn, semapv:crossSpeciesCloseMatch to be added (in addition to the changes already requested above) before the PR can be merged.

@matentzn : Not sure where you intended to place this relation? As a direct subclass of skos:closeMatch? Of semapv:nonIsomorphicMatch? Of both?

Remove skos:semanticRelation from the semapv-properties file. Use skos:mappingRelation as root for the mapping properties.

matentzn

Added some change requests, OWL also needs to be regenerated!

Overall, great.

matentzn · 2023-01-26T11:20:11Z

semapv-properties.tsv

@@ -0,0 +1,14 @@
+IRI	skos:prefLabel	skos:definition	dc:source	skos:example	rdfs:comment	altLabel	Parent	rdfs:isDefinedBy
+ID	A skos:prefLabel	A skos:definition	A dc:source	A skos:example	A rdfs:comment	A skos:altLabel	SC % SPLIT=|	A rdfs:isDefinedBy


Suggested change

ID A skos:prefLabel A skos:definition A dc:source A skos:example A rdfs:comment A skos:altLabel SC % SPLIT=| A rdfs:isDefinedBy

ID A skos:prefLabel A skos:definition A dc:source A skos:example A rdfs:comment A skos:altLabel SP % SPLIT=| A rdfs:isDefinedBy

Doh! Of course, sorry about that.

@matentzn One last clarification needed: For the above to work, the template needs a TYPE column, otherwise the terms are still created as owl:Class (and have no parents because no SC).

Which raises the question: should these properties by defined as owl:AnnotationProperty or as owl:ObjectProperty? I think they should be AP, but unless I missed something you never explicitly described them as such in your proposal (#3). The discussion about the rationale for using OP rather than AP does not make things any clearer to me — rather to the contrary…

TYPE must be annotation property - else it does not work with the OWL object model (in which triples of the form are interpreted as annotation assertions most of the time).

Longer discussion!

matentzn · 2023-01-26T11:20:50Z

semapv-properties.tsv

+skos:relatedMatch	related match	A match where the subject and the object are inherently related, but where none is in any way more general than the other.	https://www.w3.org/TR/skos-reference/				semapv:nonIsomorphicMatch	http://www.w3.org/2004/02/skos/core#
+semapv:isomorphicMatch	isomorphic match	A match where the subject is isomorphic to the object, i.e. considered of identical or similar form, shape, or structure.	https://github.com/mapping-commons/semantic-mapping-vocabulary/issues/3				skos:mappingRelation	
+semapv:nonIsomorphicMatch	non-isomorphic match	A match where the subject cannot be considered isomorphic to the object, i.e. considered of identical or similar form, shape, or structure. The object corresponds to exactly one subject in the subject_source.	https://github.com/mapping-commons/semantic-mapping-vocabulary/issues/3				skos:mappingRelation	
+semapv:crossSpeciesExactMatch	cross-species exact match	A match where the subject is considered analogous to the object in a different taxonomic grouping.	https://github.com/mapping-commons/semantic-mapping-vocabulary/issues/3	FBbt:00005074 (D. melanogaster “muscle cell”) and CL:0000187 (taxon-neutral “muscle cell”) are a cross-species exact match.			semapv:isomorphicMatch|skos:relatedMatch	


Suggested change

semapv:crossSpeciesExactMatch cross-species exact match A match where the subject is considered analogous to the object in a different taxonomic grouping. https://github.com/mapping-commons/semantic-mapping-vocabulary/issues/3 FBbt:00005074 (D. melanogaster “muscle cell”) and CL:0000187 (taxon-neutral “muscle cell”) are a cross-species exact match. semapv:isomorphicMatch|skos:relatedMatch

semapv:crossSpeciesExactMatch cross-species exact match A match where the subject is considered analogous to the object in a different taxonomic grouping. https://github.com/mapping-commons/semantic-mapping-vocabulary/issues/3 FBbt:00005074 (D. melanogaster "muscle cell") and CL:0000187 (taxon-neutral "muscle cell") are a cross-species exact match. semapv:isomorphicMatch|skos:relatedMatch

Ah, someone doesn’t like typographically correct quote characters! :D Fine, I’ll change them – reluctantly, for the record.

What do you mean typographically correct? Is the one you put the right one? If so you should ignore my comment!

If you care about typography (most people don’t, and it’s probably fine – I am one of the annoying few who do :p ), in English you should never use straight quotes ("). They are a typographical abomination from the era of typewriters, allowed to persist in the computer age by the use of 7-bits character encodings.

Proper quotes should be curved, with the opening quote (“, U+201C) being different from the closing quote (”, U+201D).

Same for the apostrophe. A proper apostrophe is curved (’), not straight (').

That’s just a pet peeve of mine. Poor typography makes me sad. :p

matentzn · 2023-01-26T11:21:43Z

semapv-properties.tsv

+semapv:isomorphicMatch	isomorphic match	A match where the subject is isomorphic to the object, i.e. considered of identical or similar form, shape, or structure.	https://github.com/mapping-commons/semantic-mapping-vocabulary/issues/3				skos:mappingRelation	
+semapv:nonIsomorphicMatch	non-isomorphic match	A match where the subject cannot be considered isomorphic to the object, i.e. considered of identical or similar form, shape, or structure. The object corresponds to exactly one subject in the subject_source.	https://github.com/mapping-commons/semantic-mapping-vocabulary/issues/3				skos:mappingRelation	
+semapv:crossSpeciesExactMatch	cross-species exact match	A match where the subject is considered analogous to the object in a different taxonomic grouping.	https://github.com/mapping-commons/semantic-mapping-vocabulary/issues/3	FBbt:00005074 (D. melanogaster “muscle cell”) and CL:0000187 (taxon-neutral “muscle cell”) are a cross-species exact match.			semapv:isomorphicMatch|skos:relatedMatch	
+semapv:crossSpeciesBroadMatch	cross-species broad match	A match where the subject is considered analogous to the subject in a different taxonomic grouping, but the object refers to a broader concept.	https://github.com/mapping-commons/semantic-mapping-vocabulary/issues/3	FBbt:00007091 (D. melanogaster “subperineurial glial sheath”) and UBERON:0000202 (taxon-neutral “glial blood brain barrier”) are a cross-species broad match.			skos:broadMatch	


Suggested change

semapv:crossSpeciesBroadMatch cross-species broad match A match where the subject is considered analogous to the subject in a different taxonomic grouping, but the object refers to a broader concept. https://github.com/mapping-commons/semantic-mapping-vocabulary/issues/3 FBbt:00007091 (D. melanogaster “subperineurial glial sheath”) and UBERON:0000202 (taxon-neutral “glial blood brain barrier”) are a cross-species broad match. skos:broadMatch

semapv:crossSpeciesBroadMatch cross-species broad match A match where the subject is considered analogous to the subject in a different taxonomic grouping, but the object refers to a broader concept. https://github.com/mapping-commons/semantic-mapping-vocabulary/issues/3 FBbt:00007091 (D. melanogaster "subperineurial glial sheath") and UBERON:0000202 (taxon-neutral "glial blood brain barrier") are a cross-species broad match. skos:broadMatch

matentzn · 2023-01-26T15:59:42Z

Ready to merge?

gouttegd · 2023-01-26T16:26:01Z

If you’re happy with it, yes.

matentzn · 2023-01-26T17:06:57Z

THANK YOU!

gouttegd · 2023-01-26T17:19:54Z

🎉 This is only 253 days after that meeting with Shawn and David when we first talked about the need for specific relations for cross-species mappings, and in which you told me “just open a ticket on OMO to request these relations and I’ll make sure they are created.” :D

matentzn · 2023-01-26T17:21:53Z

Thats nothing :P Fast turnaround!

gouttegd · 2023-01-26T17:22:52Z

I kind of knew you were going to say that! :D

cthoyt · 2023-01-29T18:11:56Z

this is great! Thanks @gouttegd , I will switch biomappings over to use these newly minted relations too :)

gouttegd added 2 commits January 16, 2023 19:36

Add generated files.

8c97a34

matentzn reviewed Jan 23, 2023

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gouttegd mentioned this pull request Jan 23, 2023

Proposal for a new classification of mapping relations #3

Closed

gouttegd added 4 commits January 24, 2023 19:11

Remove skos:semanticRelation.

2aefb0c

Remove skos:semanticRelation from the semapv-properties file. Use skos:mappingRelation as root for the mapping properties.

Add rdfs:isDefinedBy to borrowed terms.

66f11a6

Add semapv:crossSpeciesCloseMatch.

bb0815b

Rebuild generated files.

0c57a20

gouttegd requested a review from matentzn January 25, 2023 11:46

matentzn requested changes Jan 26, 2023

View reviewed changes

gouttegd added 2 commits January 26, 2023 15:40

Define mapping relations as annotation properties.

c9d702b

Rebuild generated files.

15c389d

matentzn approved these changes Jan 26, 2023

View reviewed changes

matentzn merged commit 46b3221 into mapping-commons:main Jan 26, 2023

gouttegd deleted the add-mapping-relations branch January 26, 2023 17:20

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Add mapping relations #14

Add mapping relations #14

gouttegd commented Jan 16, 2023

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cthoyt commented Jan 29, 2023

		@@ -0,0 +1,14 @@
		IRI skos:prefLabel skos:definition dc:source skos:example rdfs:comment altLabel Parent

		@@ -0,0 +1,14 @@
		IRI skos:prefLabel skos:definition dc:source skos:example rdfs:comment altLabel Parent rdfs:isDefinedBy
		ID A skos:prefLabel A skos:definition A dc:source A skos:example A rdfs:comment A skos:altLabel SC % SPLIT=\| A rdfs:isDefinedBy

Add mapping relations #14

Add mapping relations #14

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matentzn commented Jan 26, 2023

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