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assess nmdc-schema's interoperability with other environmental science semantic/linked-data resoruces #2335

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turbomam opened this issue Feb 3, 2025 · 8 comments
Open

assess nmdc-schema's interoperability with other environmental science semantic/linked-data resoruces #2335

turbomam opened this issue Feb 3, 2025 · 8 comments
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turbomam commented Feb 3, 2025 •
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For NMDC goal 2.9

Start by doing a lexmatch with envthes and saving the results as something like https://github.com/microbiomedata/nmdc-schema/blob/main/sssom/nmdc-to-envthes.sssom.tsv

roughly

runoak -i sqlite:obo:mixs -a sqlite:obo:envthes lexmatch i^envthes: @ i^mixs:
@turbomam turbomam self-assigned this Feb 3, 2025
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turbomam commented Feb 3, 2025 •
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egrep -v '^#' envthes-to-mixs.sssom.tsv | wc -l

57

that was run in the external-metadata-awareness repo

running the previous lexmatch in nmdc-schema, with our without an initial poetry run gives

Traceback (most recent call last):
  File "/home/mark/.local/bin/runoak", line 5, in <module>
    from oaklib.cli import main
  File "/home/mark/.local/share/pipx/venvs/oaklib/lib/python3.12/site-packages/oaklib/__init__.py", line 11, in <module>
    from oaklib.selector import get_adapter, get_implementation_from_shorthand  # noqa:F401
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mark/.local/share/pipx/venvs/oaklib/lib/python3.12/site-packages/oaklib/selector.py", line 16, in <module>
    from oaklib.implementations import GildaImplementation
  File "/home/mark/.local/share/pipx/venvs/oaklib/lib/python3.12/site-packages/oaklib/implementations/__init__.py", line 20, in <module>
    from oaklib.implementations.ncbi.ncbi_gene_implementation import NCBIGeneImplementation
  File "/home/mark/.local/share/pipx/venvs/oaklib/lib/python3.12/site-packages/oaklib/implementations/ncbi/ncbi_gene_implementation.py", line 14, in <module>
    from oaklib.implementations.ncbi.eutils_implementation import EUtilsImplementation
  File "/home/mark/.local/share/pipx/venvs/oaklib/lib/python3.12/site-packages/oaklib/implementations/ncbi/eutils_implementation.py", line 9, in <module>
    from eutils import Client
  File "/home/mark/.local/share/pipx/venvs/oaklib/lib/python3.12/site-packages/eutils/__init__.py", line 4, in <module>
    import pkg_resources
  File "/home/mark/.local/share/pipx/shared/lib/python3.10/site-packages/pkg_resources/__init__.py", line 2191, in <module>
    register_finder(pkgutil.ImpImporter, find_on_path)
                    ^^^^^^^^^^^^^^^^^^^
AttributeError: module 'pkgutil' has no attribute 'ImpImporter'. Did you mean: 'zipimporter'?
mark@mark-NUC10i7FNH:~/gitrepos/nmdc-schema$ poetry run runoak -i sqlite:obo:mixs -a sqlite:obo:envthes lexmatch i^envthes: @ i^mixs:
Traceback (most recent call last):
  File "/home/mark/.local/bin/runoak", line 5, in <module>
    from oaklib.cli import main
  File "/home/mark/.local/share/pipx/venvs/oaklib/lib/python3.12/site-packages/oaklib/__init__.py", line 11, in <module>
    from oaklib.selector import get_adapter, get_implementation_from_shorthand  # noqa:F401
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mark/.local/share/pipx/venvs/oaklib/lib/python3.12/site-packages/oaklib/selector.py", line 16, in <module>
    from oaklib.implementations import GildaImplementation
  File "/home/mark/.local/share/pipx/venvs/oaklib/lib/python3.12/site-packages/oaklib/implementations/__init__.py", line 20, in <module>
    from oaklib.implementations.ncbi.ncbi_gene_implementation import NCBIGeneImplementation
  File "/home/mark/.local/share/pipx/venvs/oaklib/lib/python3.12/site-packages/oaklib/implementations/ncbi/ncbi_gene_implementation.py", line 14, in <module>
    from oaklib.implementations.ncbi.eutils_implementation import EUtilsImplementation
  File "/home/mark/.local/share/pipx/venvs/oaklib/lib/python3.12/site-packages/oaklib/implementations/ncbi/eutils_implementation.py", line 9, in <module>
    from eutils import Client
  File "/home/mark/.local/share/pipx/venvs/oaklib/lib/python3.12/site-packages/eutils/__init__.py", line 4, in <module>
    import pkg_resources
  File "/home/mark/.local/share/pipx/shared/lib/python3.10/site-packages/pkg_resources/__init__.py", line 2191, in <module>
    register_finder(pkgutil.ImpImporter, find_on_path)
                    ^^^^^^^^^^^^^^^^^^^
AttributeError: module 'pkgutil' has no attribute 'ImpImporter'. Did you mean: 'zipimporter'?

@turbomam turbomam mentioned this issue Feb 7, 2025
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robot convert --input project/owl/nmdc.owl.ttl --output nmdc.owl

2025-02-20 15:23:53,536 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error1 for type Datatype

etc.

more errors 2025-02-20 15:23:53,540 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error2 for type Datatype 2025-02-20 15:23:53,541 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error3 for type Datatype 2025-02-20 15:23:53,544 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error4 for type Datatype 2025-02-20 15:23:53,545 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error5 for type Datatype 2025-02-20 15:23:53,545 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error6 for type Datatype 2025-02-20 15:23:53,545 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error7 for type Datatype 2025-02-20 15:23:53,548 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error8 for type Datatype 2025-02-20 15:23:53,549 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error9 for type Datatype 2025-02-20 15:23:53,550 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error10 for type Datatype 2025-02-20 15:23:53,550 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error11 for type Datatype 2025-02-20 15:23:53,553 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error12 for type Datatype 2025-02-20 15:23:53,554 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error13 for type Datatype 2025-02-20 15:23:53,555 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error14 for type Datatype 2025-02-20 15:23:53,555 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error15 for type Datatype 2025-02-20 15:23:53,556 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error16 for type Datatype 2025-02-20 15:23:53,556 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error17 for type Datatype 2025-02-20 15:23:53,559 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error18 for type Datatype 2025-02-20 15:23:53,560 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error19 for type Datatype 2025-02-20 15:23:53,561 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error20 for type Datatype 2025-02-20 15:23:53,562 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error21 for type Datatype 2025-02-20 15:23:53,563 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error22 for type Datatype 2025-02-20 15:23:53,563 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error23 for type Datatype 2025-02-20 15:23:53,564 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error24 for type Datatype 2025-02-20 15:23:53,564 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error25 for type Datatype 2025-02-20 15:23:53,565 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error26 for type Datatype 2025-02-20 15:23:53,565 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error27 for type Datatype 2025-02-20 15:23:53,566 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error28 for type Datatype 2025-02-20 15:23:53,566 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error29 for type Datatype 2025-02-20 15:23:53,566 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error30 for type Datatype 2025-02-20 15:23:53,568 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error31 for type Datatype 2025-02-20 15:23:53,644 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error32 for type Class 2025-02-20 15:23:53,648 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error33 for type Class 2025-02-20 15:23:53,649 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error34 for type Datatype 2025-02-20 15:23:53,651 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error35 for type Datatype 2025-02-20 15:23:53,651 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error36 for type Datatype 2025-02-20 15:23:53,652 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error37 for type Datatype 2025-02-20 15:23:53,652 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error38 for type Datatype 2025-02-20 15:23:53,652 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error39 for type Datatype 2025-02-20 15:23:53,653 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error40 for type Datatype 2025-02-20 15:23:53,653 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error41 for type Datatype 2025-02-20 15:23:53,653 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error42 for type Datatype 2025-02-20 15:23:53,656 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error43 for type Class 2025-02-20 15:23:53,656 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error44 for type Class 2025-02-20 15:23:53,658 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error45 for type Datatype 2025-02-20 15:23:53,659 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error46 for type Datatype 2025-02-20 15:23:53,659 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error47 for type Class 2025-02-20 15:23:53,659 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error48 for type Class 2025-02-20 15:23:53,664 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error49 for type Class 2025-02-20 15:23:53,665 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error50 for type Class 2025-02-20 15:23:53,671 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error51 for type Datatype 2025-02-20 15:23:53,676 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error52 for type Datatype 2025-02-20 15:23:53,677 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error53 for type Datatype 2025-02-20 15:23:53,680 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error54 for type Datatype 2025-02-20 15:23:53,683 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error55 for type Datatype 2025-02-20 15:23:53,685 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error56 for type Datatype 2025-02-20 15:23:53,687 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error57 for type Datatype 2025-02-20 15:23:53,689 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error58 for type Datatype 2025-02-20 15:23:53,702 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error59 for type Class 2025-02-20 15:23:53,702 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error60 for type Class 2025-02-20 15:23:53,702 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error61 for type Datatype 2025-02-20 15:23:53,703 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error62 for type Datatype 2025-02-20 15:23:53,703 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error63 for type Class 2025-02-20 15:23:53,704 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error64 for type Class 2025-02-20 15:23:53,705 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error65 for type Class 2025-02-20 15:23:53,705 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error66 for type Class 2025-02-20 15:23:53,706 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error67 for type Datatype 2025-02-20 15:23:53,707 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error68 for type Class 2025-02-20 15:23:53,707 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error69 for type Class 2025-02-20 15:23:53,707 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error70 for type Class 2025-02-20 15:23:53,710 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error71 for type Class 2025-02-20 15:23:53,710 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error72 for type Class 2025-02-20 15:23:53,715 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error73 for type Class 2025-02-20 15:23:53,715 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error74 for type Class 2025-02-20 15:23:53,716 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error75 for type Class 2025-02-20 15:23:53,716 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error76 for type Class 2025-02-20 15:23:53,716 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error77 for type Datatype 2025-02-20 15:23:53,717 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error78 for type Datatype 2025-02-20 15:23:53,717 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error79 for type Datatype 2025-02-20 15:23:53,718 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error80 for type Datatype 2025-02-20 15:23:53,719 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error81 for type Class 2025-02-20 15:23:53,720 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error82 for type Class 2025-02-20 15:23:53,725 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error83 for type Datatype 2025-02-20 15:23:53,725 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error84 for type Datatype 2025-02-20 15:23:53,726 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error85 for type Datatype 2025-02-20 15:23:53,726 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error86 for type Datatype 2025-02-20 15:23:53,726 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error87 for type Class 2025-02-20 15:23:53,726 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error88 for type Datatype 2025-02-20 15:23:53,727 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error89 for type Class 2025-02-20 15:23:53,727 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error90 for type Datatype 2025-02-20 15:23:53,727 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error91 for type Class 2025-02-20 15:23:53,728 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error92 for type Class 2025-02-20 15:23:53,729 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error93 for type Datatype 2025-02-20 15:23:53,729 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error94 for type Class 2025-02-20 15:23:53,730 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error95 for type Class 2025-02-20 15:23:53,731 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error96 for type Class 2025-02-20 15:23:53,731 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error97 for type Class 2025-02-20 15:23:53,732 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error98 for type Class 2025-02-20 15:23:53,732 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error99 for type Class 2025-02-20 15:23:53,734 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error100 for type Class 2025-02-20 15:23:53,734 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error101 for type Class 2025-02-20 15:23:53,735 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error102 for type Class 2025-02-20 15:23:53,735 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error103 for type Class 2025-02-20 15:23:53,735 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error104 for type Class 2025-02-20 15:23:53,735 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error105 for type Class 2025-02-20 15:23:53,735 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error106 for type Class 2025-02-20 15:23:53,735 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error107 for type Class 2025-02-20 15:23:53,737 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error108 for type Datatype 2025-02-20 15:23:53,738 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error109 for type Class 2025-02-20 15:23:53,738 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error110 for type Class 2025-02-20 15:23:53,739 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error111 for type Class 2025-02-20 15:23:53,739 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error112 for type Class 2025-02-20 15:23:53,740 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error113 for type Class 2025-02-20 15:23:53,740 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error114 for type Class 2025-02-20 15:23:53,741 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error115 for type Class 2025-02-20 15:23:53,741 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error116 for type Class 2025-02-20 15:23:53,742 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error117 for type Class 2025-02-20 15:23:53,742 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error118 for type Class 2025-02-20 15:23:53,743 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error119 for type Datatype 2025-02-20 15:23:53,744 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error120 for type Class 2025-02-20 15:23:53,744 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error121 for type Class 2025-02-20 15:23:53,745 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? http://org.semanticweb.owlapi/error#Error122 for type Datatype (nmdc-schema-py3.11) mark@mark-NUC10i7FNH:~/gitrepos/nmdc-schema$

@turbomam
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turbomam commented Feb 20, 2025 •
edited
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copy nmdc.owl into the semantic-sql project home

poetry run semsql make nmdc.db
Emits some informative error messages about the owl-worthiness of the nmdc schema.

2025.02.20 15:35:04:498 zio-default-blocking-2 WARN uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/doi_value in punning not allowed [Declaration(DataProperty(<https://w3id.org/nmdc/doi_value>)), Declaration(ObjectProperty(<https://w3id.org/nmdc/

  • doi_value>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/doi_value>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/id in punning not allowed [Declaration(NamedIndividual(<https://w3id.org/nmdc/id>)), Declaration(ObjectProperty(<https://w3id.org/nmdc/id>)), Decl

  • aration(DataProperty(<https://w3id.org/nmdc/id>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/input_contig_num in punning not allowed [Declaration(DataProperty(<https://w3id.org/nmdc/input_contig_num>)), Declaration(ObjectProperty(<https://

  • w3id.org/nmdc/input_contig_num>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/input_contig_num>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/mixs/fire in punning not allowed [Declaration(NamedIndividual(<https://w3id.org/mixs/fire>)), Declaration(ObjectProperty(<https://w3id.org/mixs/fire>))

  • ]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/rna_cont_well in punning not allowed [Declaration(NamedIndividual(<https://w3id.org/nmdc/rna_cont_well>)), Declaration(ObjectProperty(<https://w3i

  • d.org/nmdc/rna_cont_well>)), Declaration(DataProperty(<https://w3id.org/nmdc/rna_cont_well>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/contamination in punning not allowed [Declaration(DataProperty(<https://w3id.org/nmdc/contamination>)), Declaration(ObjectProperty(<https://w3id.o

  • rg/nmdc/contamination>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/contamination>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/mixs/pres_animal_insect in punning not allowed [Declaration(DataProperty(<https://w3id.org/mixs/pres_animal_insect>)), Declaration(ObjectProperty(<http

  • s://w3id.org/mixs/pres_animal_insect>)), Declaration(NamedIndividual(<https://w3id.org/mixs/pres_animal_insect>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/ended_at_time in punning not allowed [Declaration(DataProperty(<https://w3id.org/nmdc/ended_at_time>)), Declaration(ObjectProperty(<https://w3id.o

  • rg/nmdc/ended_at_time>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/ended_at_time>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/too_short_contig_num in punning not allowed [Declaration(NamedIndividual(<https://w3id.org/nmdc/too_short_contig_num>)), Declaration(ObjectPropert

  • y(<https://w3id.org/nmdc/too_short_contig_num>)), Declaration(DataProperty(<https://w3id.org/nmdc/too_short_contig_num>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/decimal_degree in punning not allowed [Declaration(NamedIndividual(<https://w3id.org/nmdc/decimal_degree>)), Declaration(Class(<https://w3id.org/n

  • mdc/decimal_degree>)), Declaration(Datatype(<https://w3id.org/nmdc/decimal_degree>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/language_code in punning not allowed [Declaration(Datatype(<https://w3id.org/nmdc/language_code>)), Declaration(Class(<https://w3id.org/nmdc/langu

  • age_code>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/language_code>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/phase in punning not allowed [Declaration(DataProperty(<https://w3id.org/nmdc/phase>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/phase>)

  • ), Declaration(ObjectProperty(<https://w3id.org/nmdc/phase>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/insdc_secondary_sample_identifiers in punning not allowed [Declaration(NamedIndividual(<https://w3id.org/nmdc/insdc_secondary_sample_identifiers>)

  • ), Declaration(ObjectProperty(<https://w3id.org/nmdc/insdc_secondary_sample_identifiers>)), Declaration(DataProperty(<https://w3id.org/nmdc/insdc_secondary_sample_identifiers>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/gold_biosample_identifiers in punning not allowed [Declaration(NamedIndividual(<https://w3id.org/nmdc/gold_biosample_identifiers>)), Declaration(O

  • bjectProperty(<https://w3id.org/nmdc/gold_biosample_identifiers>)), Declaration(DataProperty(<https://w3id.org/nmdc/gold_biosample_identifiers>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/ncbi_lineage_tax_ids in punning not allowed [Declaration(ObjectProperty(<https://w3id.org/nmdc/ncbi_lineage_tax_ids>)), Declaration(DataProperty(<

  • https://w3id.org/nmdc/ncbi_lineage_tax_ids>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/ncbi_lineage_tax_ids>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/mgnify_project_identifiers in punning not allowed [Declaration(NamedIndividual(<https://w3id.org/nmdc/mgnify_project_identifiers>)), Declaration(O

  • bjectProperty(<https://w3id.org/nmdc/mgnify_project_identifiers>)), Declaration(DataProperty(<https://w3id.org/nmdc/mgnify_project_identifiers>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/gene_count in punning not allowed [Declaration(ObjectProperty(<https://w3id.org/nmdc/gene_count>)), Declaration(DataProperty(<https://w3id.org/nmd

  • c/gene_count>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/gene_count>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/jgi_portal_study_identifiers in punning not allowed [Declaration(NamedIndividual(<https://w3id.org/nmdc/jgi_portal_study_identifiers>)), Declarati

  • on(DataProperty(<https://w3id.org/nmdc/jgi_portal_study_identifiers>)), Declaration(ObjectProperty(<https://w3id.org/nmdc/jgi_portal_study_identifiers>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/gold_analysis_project_identifiers in punning not allowed [Declaration(NamedIndividual(<https://w3id.org/nmdc/gold_analysis_project_identifiers>)),

  •  Declaration(DataProperty(<https://w3id.org/nmdc/gold_analysis_project_identifiers>)), Declaration(ObjectProperty(<https://w3id.org/nmdc/gold_analysis_project_identifiers>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/dna_cont_well in punning not allowed [Declaration(NamedIndividual(<https://w3id.org/nmdc/dna_cont_well>)), Declaration(ObjectProperty(<https://w3i

  • d.org/nmdc/dna_cont_well>)), Declaration(DataProperty(<https://w3id.org/nmdc/dna_cont_well>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/unbinned_contig_num in punning not allowed [Declaration(DataProperty(<https://w3id.org/nmdc/unbinned_contig_num>)), Declaration(ObjectProperty(<ht

  • tps://w3id.org/nmdc/unbinned_contig_num>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/unbinned_contig_num>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/binned_contig_num in punning not allowed [Declaration(NamedIndividual(<https://w3id.org/nmdc/binned_contig_num>)), Declaration(DataProperty(<https

  • ://w3id.org/nmdc/binned_contig_num>)), Declaration(ObjectProperty(<https://w3id.org/nmdc/binned_contig_num>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/num_16s in punning not allowed [Declaration(NamedIndividual(<https://w3id.org/nmdc/num_16s>)), Declaration(ObjectProperty(<https://w3id.org/nmdc/n

  • um_16s>)), Declaration(DataProperty(<https://w3id.org/nmdc/num_16s>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/insdc_biosample_identifiers in punning not allowed [Declaration(NamedIndividual(<https://w3id.org/nmdc/insdc_biosample_identifiers>)), Declaration

  • (ObjectProperty(<https://w3id.org/nmdc/insdc_biosample_identifiers>)), Declaration(DataProperty(<https://w3id.org/nmdc/insdc_biosample_identifiers>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/websites in punning not allowed [Declaration(ObjectProperty(<https://w3id.org/nmdc/websites>)), Declaration(NamedIndividual(<https://w3id.org/nmdc

  • /websites>)), Declaration(DataProperty(<https://w3id.org/nmdc/websites>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/started_at_time in punning not allowed [Declaration(ObjectProperty(<https://w3id.org/nmdc/started_at_time>)), Declaration(NamedIndividual(<https:/

  • /w3id.org/nmdc/started_at_time>)), Declaration(DataProperty(<https://w3id.org/nmdc/started_at_time>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/gold_sequencing_project_identifiers in punning not allowed [Declaration(ObjectProperty(<https://w3id.org/nmdc/gold_sequencing_project_identifiers>

  • )), Declaration(DataProperty(<https://w3id.org/nmdc/gold_sequencing_project_identifiers>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/gold_sequencing_project_identifiers>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/num_t_rna in punning not allowed [Declaration(ObjectProperty(<https://w3id.org/nmdc/num_t_rna>)), Declaration(DataProperty(<https://w3id.org/nmdc/

  • num_t_rna>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/num_t_rna>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/num_5s in punning not allowed [Declaration(DataProperty(<https://w3id.org/nmdc/num_5s>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/num_5

  • s>)), Declaration(ObjectProperty(<https://w3id.org/nmdc/num_5s>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/insdc_analysis_identifiers in punning not allowed [Declaration(ObjectProperty(<https://w3id.org/nmdc/insdc_analysis_identifiers>)), Declaration(Na

  • medIndividual(<https://w3id.org/nmdc/insdc_analysis_identifiers>)), Declaration(DataProperty(<https://w3id.org/nmdc/insdc_analysis_identifiers>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/has_function in punning not allowed [Declaration(ObjectProperty(<https://w3id.org/nmdc/has_function>)), Declaration(DataProperty(<https://w3id.org

  • /nmdc/has_function>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/has_function>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/gff_coordinate in punning not allowed [Declaration(DataProperty(<https://w3id.org/nmdc/gff_coordinate>)), Declaration(ObjectProperty(<https://w3id

  • .org/nmdc/gff_coordinate>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/gff_coordinate>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/gnps_task_identifiers in punning not allowed [Declaration(NamedIndividual(<https://w3id.org/nmdc/gnps_task_identifiers>)), Declaration(ObjectPrope

  • rty(<https://w3id.org/nmdc/gnps_task_identifiers>)), Declaration(DataProperty(<https://w3id.org/nmdc/gnps_task_identifiers>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/insdc_bioproject_identifiers in punning not allowed [Declaration(DataProperty(<https://w3id.org/nmdc/insdc_bioproject_identifiers>)), Declaration(

  • NamedIndividual(<https://w3id.org/nmdc/insdc_bioproject_identifiers>)), Declaration(ObjectProperty(<https://w3id.org/nmdc/insdc_bioproject_identifiers>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/unit in punning not allowed [Declaration(Class(<https://w3id.org/nmdc/unit>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/unit>)), Declara

  • tion(Datatype(<https://w3id.org/nmdc/unit>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/num_23s in punning not allowed [Declaration(DataProperty(<https://w3id.org/nmdc/num_23s>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/num

  • _23s>)), Declaration(ObjectProperty(<https://w3id.org/nmdc/num_23s>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/rna_volume in punning not allowed [Declaration(DataProperty(<https://w3id.org/nmdc/rna_volume>)), Declaration(ObjectProperty(<https://w3id.org/nmd

  • c/rna_volume>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/rna_volume>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/dna_concentration in punning not allowed [Declaration(DataProperty(<https://w3id.org/nmdc/dna_concentration>)), Declaration(ObjectProperty(<https:

  • //w3id.org/nmdc/dna_concentration>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/dna_concentration>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/img_identifiers in punning not allowed [Declaration(NamedIndividual(<https://w3id.org/nmdc/img_identifiers>)), Declaration(DataProperty(<https://w

  • 3id.org/nmdc/img_identifiers>)), Declaration(ObjectProperty(<https://w3id.org/nmdc/img_identifiers>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/dna_volume in punning not allowed [Declaration(DataProperty(<https://w3id.org/nmdc/dna_volume>)), Declaration(NamedIndividual(<https://w3id.org/nm

  • dc/dna_volume>)), Declaration(ObjectProperty(<https://w3id.org/nmdc/dna_volume>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/low_depth_contig_num in punning not allowed [Declaration(NamedIndividual(<https://w3id.org/nmdc/low_depth_contig_num>)), Declaration(ObjectPropert

  • y(<https://w3id.org/nmdc/low_depth_contig_num>)), Declaration(DataProperty(<https://w3id.org/nmdc/low_depth_contig_num>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/bytes in punning not allowed [Declaration(Datatype(<https://w3id.org/nmdc/bytes>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/bytes>)), D

  • eclaration(Class(<https://w3id.org/nmdc/bytes>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/insdc_experiment_identifiers in punning not allowed [Declaration(ObjectProperty(<https://w3id.org/nmdc/insdc_experiment_identifiers>)), Declaratio

  • n(NamedIndividual(<https://w3id.org/nmdc/insdc_experiment_identifiers>)), Declaration(DataProperty(<https://w3id.org/nmdc/insdc_experiment_identifiers>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/external_database_identifiers in punning not allowed [Declaration(DataProperty(<https://w3id.org/nmdc/external_database_identifiers>)), Declaratio

  • n(ObjectProperty(<https://w3id.org/nmdc/external_database_identifiers>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/external_database_identifiers>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/insdc_assembly_identifiers in punning not allowed [Declaration(DataProperty(<https://w3id.org/nmdc/insdc_assembly_identifiers>)), Declaration(Obje

  • ctProperty(<https://w3id.org/nmdc/insdc_assembly_identifiers>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/insdc_assembly_identifiers>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/number_of_contig in punning not allowed [Declaration(DataProperty(<https://w3id.org/nmdc/number_of_contig>)), Declaration(ObjectProperty(<https://

  • w3id.org/nmdc/number_of_contig>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/number_of_contig>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/rna_sample_name in punning not allowed [Declaration(ObjectProperty(<https://w3id.org/nmdc/rna_sample_name>)), Declaration(NamedIndividual(<https:/

  • /w3id.org/nmdc/rna_sample_name>)), Declaration(DataProperty(<https://w3id.org/nmdc/rna_sample_name>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/infiltrations in punning not allowed [Declaration(DataProperty(<https://w3id.org/nmdc/infiltrations>)), Declaration(NamedIndividual(<https://w3id.

  • org/nmdc/infiltrations>)), Declaration(ObjectProperty(<https://w3id.org/nmdc/infiltrations>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/insdc_sra_ena_study_identifiers in punning not allowed [Declaration(ObjectProperty(<https://w3id.org/nmdc/insdc_sra_ena_study_identifiers>)), Decl

  • aration(NamedIndividual(<https://w3id.org/nmdc/insdc_sra_ena_study_identifiers>)), Declaration(DataProperty(<https://w3id.org/nmdc/insdc_sra_ena_study_identifiers>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/rna_concentration in punning not allowed [Declaration(NamedIndividual(<https://w3id.org/nmdc/rna_concentration>)), Declaration(DataProperty(<https

  • ://w3id.org/nmdc/rna_concentration>)), Declaration(ObjectProperty(<https://w3id.org/nmdc/rna_concentration>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/total_bases in punning not allowed [Declaration(ObjectProperty(<https://w3id.org/nmdc/total_bases>)), Declaration(NamedIndividual(<https://w3id.or

  • g/nmdc/total_bases>)), Declaration(DataProperty(<https://w3id.org/nmdc/total_bases>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/alternative_identifiers in punning not allowed [Declaration(DataProperty(<https://w3id.org/nmdc/alternative_identifiers>)), Declaration(ObjectProp

  • erty(<https://w3id.org/nmdc/alternative_identifiers>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/alternative_identifiers>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/gold_study_identifiers in punning not allowed [Declaration(ObjectProperty(<https://w3id.org/nmdc/gold_study_identifiers>)), Declaration(DataProper

  • ty(<https://w3id.org/nmdc/gold_study_identifiers>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/gold_study_identifiers>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/completeness in punning not allowed [Declaration(DataProperty(<https://w3id.org/nmdc/completeness>)), Declaration(NamedIndividual(<https://w3id.or

  • g/nmdc/completeness>)), Declaration(ObjectProperty(<https://w3id.org/nmdc/completeness>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/jgi_portal_analysis_project_identifiers in punning not allowed [Declaration(ObjectProperty(<https://w3id.org/nmdc/jgi_portal_analysis_project_iden

  • tifiers>)), Declaration(DataProperty(<https://w3id.org/nmdc/jgi_portal_analysis_project_identifiers>)), Declaration(NamedIndividual(<https://w3id.org/nmdc/jgi_portal_analysis_project_identifiers>))]    

  • Illegal redeclarations of entities: reuse of entity https://w3id.org/nmdc/emsl_project_identifiers in punning not allowed [Declaration(NamedIndividual(<https://w3id.org/nmdc/emsl_project_identifiers>)), Declaration(DataP

  • roperty(<https://w3id.org/nmdc/emsl_project_identifiers>)), Declaration(ObjectProperty(<https://w3id.org/nmdc/emsl_project_identifiers>))]

2025.02.20 15:35:04:734 zio-default-blocking-2 INFO org.renci.relationgraph.RelationGraph$
Running reasoner
Done running reasoner
2025.02.20 15:35:10:867 ZScheduler-Worker-7 INFO org.renci.relationgraph.Main.program:40
Done computing relations

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copy nmdc.db into external-metadata-awareness, or some other repo that has OAK installed

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turbomam commented Feb 20, 2025 •
edited
Loading 

poetry run runoak \
    -i nmdc.db \
    -a sqlite:obo:envthes lexmatch \
    --output nmdc_mixs_vs_envthes.SSSOM.tsv \
    i^mixs: @ i^envthes:
poetry run runoak \
    -i nmdc.db \
    -a sqlite:obo:envthes lexmatch \
    --output nmdc_nmdc_vs_envthes.SSSOM.tsv \
    i^nmdc: @ i^envthes:

etc

then copy those back to nmdc-schema

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What else to compare it to?

What other catalogs to look in besides https://s3.amazonaws.com/bbop-sqlite ?

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run the lexmatch agaisnt the submission schema too

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turbomam commented Feb 22, 2025 •
edited
Loading 

poetry run linkml generate owl \
    --stacktrace \
    src/nmdc_submission_schema/schema/nmdc_submission_schema.yaml 
Traceback (most recent call last):
  File "/home/mark/gitrepos/submission-schema/.venv/bin/linkml", line 8, in <module>
    sys.exit(linkml())
             ^^^^^^^^
  File "/home/mark/gitrepos/submission-schema/.venv/lib/python3.11/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mark/gitrepos/submission-schema/.venv/lib/python3.11/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/home/mark/gitrepos/submission-schema/.venv/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mark/gitrepos/submission-schema/.venv/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mark/gitrepos/submission-schema/.venv/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mark/gitrepos/submission-schema/.venv/lib/python3.11/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mark/gitrepos/submission-schema/.venv/lib/python3.11/site-packages/linkml/generators/owlgen.py", line 1376, in cli
    print(gen.serialize(**kwargs))
          ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mark/gitrepos/submission-schema/.venv/lib/python3.11/site-packages/linkml/generators/owlgen.py", line 224, in serialize
    self.as_graph()
  File "/home/mark/gitrepos/submission-schema/.venv/lib/python3.11/site-packages/linkml/generators/owlgen.py", line 197, in as_graph
    self.add_class(cls)
  File "/home/mark/gitrepos/submission-schema/.venv/lib/python3.11/site-packages/linkml/generators/owlgen.py", line 406, in add_class
    superclass_expr = self.transform_class_expression(cls)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mark/gitrepos/submission-schema/.venv/lib/python3.11/site-packages/linkml/generators/owlgen.py", line 526, in transform_class_expression
    slot_uri = self._prop_uri(slot)
               ^^^^^^^^^^^^^^^^^^^^
  File "/home/mark/gitrepos/submission-schema/.venv/lib/python3.11/site-packages/linkml/generators/owlgen.py", line 1211, in _prop_uri
    return URIRef(self.schemaview.get_uri(p, expand=True, native=self.use_native_uris))
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mark/gitrepos/submission-schema/.venv/lib/python3.11/site-packages/linkml_runtime/utils/schemaview.py", line 1090, in get_uri
    schema = next(sc for sc in self.schema_map.values() if sc.id == e.from_schema)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
StopIteration

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