Class declarations w/out further assertions not in serialization #90

joeflack4 · 2023-01-15T00:23:45Z

Overview

Context
I opened an issue in robot, and @matentzn thought I should mirror here (CC @julesjacobsen ).

My team is doing some conversions from OWL -> Obographs JSON -> FHIR JSON, and we noticed that some concepts were missing from the output.

I took a look, and these are all root nodes; they are all rdfs:subClassOf owl:Thing.

Edges that reference these nodes exist, but the declaration of the nodes themselves do not. It's not just a FHIR JSON issue. I looked in my Obographs JSON (downloadable here), and the declarations are missing there as well.

I imagine this is an issue for the other ontologies I'm working with, but for this particular ontology, comploinc.owl, these are the declarations of the root nodes that are missing from the Obographs JSON:

    <owl:Class rdf:about="https://loinc.org/LP70625-6A">
        <rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
    </owl:Class>
    <owl:Class rdf:about="https://loinc.org/lc0000001">
        <rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
    </owl:Class>
    <owl:Class rdf:about="https://loinc.org/LP33117-0">
        <rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
    </owl:Class>
    <owl:Class rdf:about="https://loinc.org/LP33103-0">
        <rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
    </owl:Class>

Expected vs Actual

Expected
I would expect to see something like this in my Obographs JSON:

{
  "id": "https://loinc.org/LP33117-0",
  "type": "CLASS"
}

Or maybe something like this, with one or more nulls for missing properties:

{
  "id": "https://loinc.org/LP33117-0",
  "type": "CLASS",
  "lbl": null,
  "meta": {
    "definition": null,
    ...
  }
}

Actual
No declarations appear.

Reproducibility

Download merged_reasoned_loinc.owl
Download robot 1.9.1 if not already present
Run : `java -jar robot convert -i path/to/merged_reasoned_loinc.owl -o path/to/outfile.json --format json'

What I tried

I examined the CLI to see if there was an option dealing with root nodes, but I didn't see anything in java -jar bin/robot.jar convert -h that seems like it could help with this.

Additional information

In this example, only root nodes (subClassOf owl:Thing) were missing, but in some other ontologies I looked at, there may have been other cases missing. Will update if I have more time to get concrete examples.

Related: ontodev/robot#1082

The text was updated successfully, but these errors were encountered:

dosumis · 2023-01-15T10:32:13Z

This is a potentially an issue for my group too. We have been encouraging use of OBOgraphs JSON over OBO as part of external collaborations. We need to be aware of any cases where terms will be lost.

Quick question: Is this affecting only bare declarations? Does adding at least one annotation property axiom fix it?

- Add: Param: --native-uri-stems: A comma-separated list of URI stems that will be used to determine whether a concept is native to the CodeSystem. As of 2023-01-15, there is still a bug in the Obographs spec and/or `robot` where certain nodes are not being converted. This converter adds back the nodes, but to know which ones belong to the CodeSystem itself and are not foreign concepts, this parameter is necessary. OAK also makes use of this parameter. See also: geneontology/obographs#90

- Add: param: --native-uri-stems: A comma-separated list of URI stems that will be used to determine whether a concept is native to the CodeSystem. As of 2023-01-15, there is still a bug in the Obographs spec and/or `robot` where certain nodes are not being converted. This converter adds back the nodes, but to know which ones belong to the CodeSystem itself and are not foreign concepts, this parameter is necessary. OAK also makes use of this parameter. See also: geneontology/obographs#90 - Add: params: --dev-oak-path and --dev-oak-interpreter-path: If you want to use a local development version of OAK, specify these paths.

matentzn · 2023-03-28T16:23:18Z

a second small test ontology

Prefix(:=<http://www.semanticweb.org/matentzn/ontologies/2021/11/untitled-ontology-544#>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://www.semanticweb.org/matentzn/ontologies/2021/11/untitled-ontology-544>

Declaration(Class(<http://purl.obolibrary.org/obo/upheno/workshop2021/TMP_0000060>))
)

Pipeline:

robot convert -i single_declaration.owl -f json -o out.json

Results in:

{
  "graphs" : [ {
    "id" : "http://www.semanticweb.org/matentzn/ontologies/2021/11/untitled-ontology-544"
  } ]
}

@cmungall can you confirm that the output should be:

{
  "graphs" : [ {
    "id" : "http://www.semanticweb.org/matentzn/ontologies/2021/11/untitled-ontology-544",
    "nodes" : [ {
      "id" : "http://purl.obolibrary.org/obo/upheno/workshop2021/TMP_0000060",
      "type" : "CLASS"
    } ]
  } ]
}

matentzn · 2023-03-28T16:31:51Z

I think the issue is roughly around this ballpark:

Here we check something about Declaration axioms:

https://github.com/geneontology/obographs/blob/master/obographs-owlapi/src/main/java/org/geneontology/obographs/owlapi/FromOwl.java#L100

Maybe its sufficient when you encounter declaration axioms to do:

String subj = getIndividualId(e);
nodeIds.add(subj);

?

cmungall · 2023-03-28T17:46:31Z

Yes, I confirm that a node without lbl should be made. Representation should be isomorphic to standard owl serializations as far as possible, fewest surprises. If groups want to filter danglings post-hoc they can do this

julesjacobsen · 2023-05-02T16:18:24Z

Working on this now. @matentzn's case is sorted, but this leads to lots (all?) of the example cases breaking due to new un-labeled nodes being included, and a more consistently ordered by type, which I suppose is a good thing. For example

BEFORE:

---
graphs:
- id: "http://purl.obolibrary.org/obo/test.owl"
  meta:
    basicPropertyValues:
    - pred: "http://www.w3.org/2000/01/rdf-schema#comment"
      val: "test manus ontology"
  nodes:
  - id: "http://purl.obolibrary.org/obo/BFO_0000050"
    type: "PROPERTY"
    meta:
      xrefs:
      - val: "BFO:0000050"
      basicPropertyValues:
      - pred: "http://www.geneontology.org/formats/oboInOwl#shorthand"
        val: "part_of"
  - id: "http://purl.obolibrary.org/obo/IAO_0000115"
    lbl: "definition"
    type: "PROPERTY"
  - id: "http://purl.obolibrary.org/obo/UBERON_0002101"
    lbl: "limb"
    type: "CLASS"
  - id: "http://purl.obolibrary.org/obo/UBERON_0002102"
    lbl: "forelimb"
    type: "CLASS"
  - id: "http://purl.obolibrary.org/obo/UBERON_0002398"
    lbl: "manus"
    type: "CLASS"
    meta:
      definition:
        val: "."
  - id: "http://purl.obolibrary.org/obo/UBERON_0002470"
    lbl: "autopod region"
    type: "CLASS"
  - id: "http://www.geneontology.org/formats/oboInOwl#hasDbXref"
    lbl: "database_cross_reference"
    type: "PROPERTY"
  - id: "http://www.geneontology.org/formats/oboInOwl#shorthand"
    lbl: "shorthand"
    type: "PROPERTY"
  edges:
  - sub: "http://purl.obolibrary.org/obo/UBERON_0002102"
    pred: "is_a"
    obj: "http://purl.obolibrary.org/obo/UBERON_0002101"
  - sub: "http://purl.obolibrary.org/obo/UBERON_0002398"
    pred: "is_a"
    obj: "http://purl.obolibrary.org/obo/UBERON_0002470"
  - sub: "http://purl.obolibrary.org/obo/UBERON_0002398"
    pred: "http://purl.obolibrary.org/obo/BFO_0000050"
    obj: "http://purl.obolibrary.org/obo/UBERON_0002102"
  - sub: "http://purl.obolibrary.org/obo/UBERON_0002470"
    pred: "http://purl.obolibrary.org/obo/BFO_0000050"
    obj: "http://purl.obolibrary.org/obo/UBERON_0002101"

AFTER:

---
graphs:
- id: "http://purl.obolibrary.org/obo/test.owl"
  meta:
    basicPropertyValues:
    - pred: "http://www.w3.org/2000/01/rdf-schema#comment"
      val: "test manus ontology"
  nodes:
  - id: "http://purl.obolibrary.org/obo/UBERON_0002101"
    lbl: "limb"
    type: "CLASS"
  - id: "http://purl.obolibrary.org/obo/UBERON_0002102"
    lbl: "forelimb"
    type: "CLASS"
  - id: "http://purl.obolibrary.org/obo/UBERON_0002398"
    lbl: "manus"
    type: "CLASS"
    meta:
      definition:
        val: "."
  - id: "http://purl.obolibrary.org/obo/UBERON_0002470"
    lbl: "autopod region"
    type: "CLASS"
  - id: "http://purl.obolibrary.org/obo/BFO_0000050"
    type: "PROPERTY"
    meta:
      xrefs:
      - val: "BFO:0000050"
      basicPropertyValues:
      - pred: "http://www.geneontology.org/formats/oboInOwl#shorthand"
        val: "part_of"
  - id: "http://purl.obolibrary.org/obo/IAO_0000115"
    lbl: "definition"
    type: "PROPERTY"
  - id: "http://www.geneontology.org/formats/oboInOwl#hasDbXref"
    lbl: "database_cross_reference"
    type: "PROPERTY"
  - id: "http://www.geneontology.org/formats/oboInOwl#id"
    type: "PROPERTY"
  - id: "http://www.geneontology.org/formats/oboInOwl#shorthand"
    lbl: "shorthand"
    type: "PROPERTY"
  - id: "http://www.w3.org/2000/01/rdf-schema#label"
    type: "PROPERTY"
  edges:
  - sub: "http://purl.obolibrary.org/obo/UBERON_0002102"
    pred: "is_a"
    obj: "http://purl.obolibrary.org/obo/UBERON_0002101"
  - sub: "http://purl.obolibrary.org/obo/UBERON_0002398"
    pred: "is_a"
    obj: "http://purl.obolibrary.org/obo/UBERON_0002470"
  - sub: "http://purl.obolibrary.org/obo/UBERON_0002398"
    pred: "http://purl.obolibrary.org/obo/BFO_0000050"
    obj: "http://purl.obolibrary.org/obo/UBERON_0002102"
  - sub: "http://purl.obolibrary.org/obo/UBERON_0002470"
    pred: "http://purl.obolibrary.org/obo/BFO_0000050"
    obj: "http://purl.obolibrary.org/obo/UBERON_0002101"

note that all the OwlDeclarationAxioms are grouped and listed by node with type CLASS, PROPERTY, INDIVIDUAL. If you'd prefer a different order, say so now.

AFTER, contains the following additional unlabeled PROPERTY axioms:

  - id: "http://www.geneontology.org/formats/oboInOwl#id"
    type: "PROPERTY"
...
  - id: "http://www.w3.org/2000/01/rdf-schema#label"
    type: "PROPERTY"

julesjacobsen · 2023-05-02T16:42:05Z

@joeflack4 do these files match your expectations?
merged-reasoned-loinc-obographs-0.3.1.zip

joeflack4 · 2023-05-02T18:29:47Z

@julesjacobsen This looks great to me!
@matentzn Whenever this is done, I just need to get this update into robot as well. Let me know if you think I should make an issue there.
@cthoyt And when that happens, if bioontologies can also be updated, I can switch my package(s) to use that instead of robot directly. FYI this is concerning an Obographs fix where some term references would appear as a subject or object in "edges", but the class declaration for the term would not appear in "nodes".

matentzn · 2023-05-03T09:45:58Z

This does look great! I will take a closer look when I see the PR with the example cases fixed..

cthoyt · 2023-05-03T11:31:02Z

@joeflack4 I don't think this will make a difference on the bioontologies implementation. If you upgrade your ROBOT, then it should work!

Change for geneontology#90 - ensure all declared nodes (CLASS, INDIVIDUAL, PROPERTY) are added even if unlabelled. Change for geneontology#93 - log untranslated axioms to WARN Update examples/ with changes Enable obographs-cli to convert ttl to json and yaml

joeflack4 · 2023-05-03T22:00:44Z

@cthoyt Oh of course, I forgot, Charlie, that bioontologies pulls it from the PATH.

Change for #65 - add PropertyType to PROPERTY Nodes Change for #90 - ensure all declared nodes (CLASS, INDIVIDUAL, PROPERTY) are added even if unlabelled. Change for #93 - log untranslated axioms to WARN Update examples/ with changes Update schema/ with changes Enable obographs-cli to convert ttl to json and yaml Update for #103 - remove Guava dependency from core Update Junit to Jupiter 5.0.3 Update version to 0.3.1

julesjacobsen · 2023-11-08T11:20:25Z

@joeflack4 This is part of the new 0.3.1 release

joeflack4 · 2023-11-08T21:19:29Z

Thanks so much!

joeflack4 mentioned this issue Jan 15, 2023

Obographs: Class declarations w/out further assertions not in serialization ontodev/robot#1082

Open

1 task

joeflack4 mentioned this issue Jan 15, 2023

referenced, but not defined codes timsbiomed/owl-on-fhir-content#5

Open

julesjacobsen self-assigned this Apr 27, 2023

joeflack4 mentioned this issue May 2, 2023

Upgrade robot for Obographs bugfix when ready timsbiomed/owl-on-fhir#5

Open

julesjacobsen mentioned this issue May 3, 2023

Datatype Properties not represented as nodes? #71

Open

julesjacobsen mentioned this issue May 3, 2023

Ch.. Ch.. Ch.. Ch.. Changes... #98

Merged

julesjacobsen mentioned this issue Oct 26, 2023

EPIC: Version 0.4.0 #101

Open

6 tasks

julesjacobsen closed this as completed Nov 8, 2023

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Class declarations w/out further assertions not in serialization #90

Class declarations w/out further assertions not in serialization #90

joeflack4 commented Jan 15, 2023 •

edited

dosumis commented Jan 15, 2023

matentzn commented Mar 28, 2023

matentzn commented Mar 28, 2023

cmungall commented Mar 28, 2023

julesjacobsen commented May 2, 2023 •

edited

julesjacobsen commented May 2, 2023

joeflack4 commented May 2, 2023

matentzn commented May 3, 2023

cthoyt commented May 3, 2023

joeflack4 commented May 3, 2023

julesjacobsen commented Nov 8, 2023

joeflack4 commented Nov 8, 2023

Class declarations w/out further assertions not in serialization #90

Class declarations w/out further assertions not in serialization #90

Comments

joeflack4 commented Jan 15, 2023 • edited

Overview

Expected vs Actual

Reproducibility

What I tried

Additional information

dosumis commented Jan 15, 2023

matentzn commented Mar 28, 2023

matentzn commented Mar 28, 2023

cmungall commented Mar 28, 2023

julesjacobsen commented May 2, 2023 • edited

julesjacobsen commented May 2, 2023

joeflack4 commented May 2, 2023

matentzn commented May 3, 2023

cthoyt commented May 3, 2023

joeflack4 commented May 3, 2023

julesjacobsen commented Nov 8, 2023

joeflack4 commented Nov 8, 2023

joeflack4 commented Jan 15, 2023 •

edited

julesjacobsen commented May 2, 2023 •

edited