Remove Ontobio from the Build System

[ecwood]

As discussed with Steve in 6/27/24 meeting, we would like to remove our dependency on ontobio in the build system. Per #379, we need to upgrade our Python version, but are having troubles doing this because of dependencies. This is the perfect opportunity to remove ontobio from the build system, thus removing many dependencies as well. It would also potentially help issues such as #367 (though this will require work of its own to do the current categorizing system for those nodes).

[ecwood]

These are the different sections in the owl files we currently use:

{
    "bfo.owl": [
        "Annotation properties",
        "Classes"
    ],
    "bspo.owl": [
        "Annotation properties",
        "Object Properties",
        "Classes",
        "Individuals",
        "General axioms",
        "Rules"
    ],
    "chebi.owl": [
        "Annotation properties",
        "Object Properties",
        "Classes"
    ],
    "cl.owl": [
        "Annotation properties",
        "Object Properties",
        "Classes",
        "Individuals",
        "General axioms"
    ],
    "ddanat.owl": [
        "Annotation properties",
        "Object Properties",
        "Classes"
    ],
    "doid.owl": [
        "Annotation properties",
        "Object Properties",
        "Classes",
        "Annotations",
        "General axioms"
    ],
    "efo.owl": [
        "Annotation properties",
        "Datatypes",
        "Object Properties",
        "Data properties",
        "Classes",
        "Annotations",
        "General axioms"
    ],
    "ehdaa2.owl": [
        "Annotation properties",
        "Object Properties",
        "Classes"
    ],
    "fma.owl": [
        "Annotation properties",
        "Object Properties",
        "Classes"
    ],
    "foodon.owl": [
        "Annotation properties",
        "Datatypes",
        "Object Properties",
        "Data properties",
        "Classes",
        "Individuals",
        "Annotations",
        "General axioms"
    ],
    "genepio.owl": [
        "Annotation properties",
        "Datatypes",
        "Object Properties",
        "Data properties",
        "Classes",
        "Individuals",
        "Annotations",
        "General axioms"
    ],
    "go-plus.owl": [
        "Annotation properties",
        "Object Properties",
        "Classes",
        "Individuals",
        "Annotations",
        "General axioms",
        "Rules"
    ],
    "hp.owl": [
        "Annotation properties",
        "Object Properties",
        "Classes",
        "General axioms",
        "Rules"
    ],
    "ino.owl": [
        "Annotation properties",
        "Object Properties",
        "Data properties",
        "Classes"
    ],
    "mi.owl": [
        "Annotation properties",
        "Classes"
    ],
    "mondo.owl": [
        "Annotation properties",
        "Object Properties",
        "Classes",
        "Individuals",
        "General axioms"
    ],
    "nbo.owl": [
        "Annotation properties",
        "Object Properties",
        "Data properties",
        "Classes",
        "General axioms",
        "Rules"
    ],
    "ordo.owl": [
        "Annotation properties",
        "Object Properties",
        "Data properties",
        "Classes",
        "Annotations"
    ],
    "pato.owl": [
        "Annotation properties",
        "Object Properties",
        "Classes",
        "General axioms",
        "Rules"
    ],
    "pr.owl": [
        "Annotation properties",
        "Object Properties",
        "Classes"
    ],
    "ro.owl": [
        "Annotation properties",
        "Object Properties",
        "Data properties",
        "Classes",
        "Individuals",
        "Annotations",
        "General axioms",
        "Rules"
    ],
    "taxslim.owl": [
        "Annotation properties",
        "Classes"
    ],
    "uberon-ext.owl": [
        "Annotation properties",
        "Object Properties",
        "Classes",
        "Individuals",
        "General axioms",
        "Rules"
    ]
}

[ecwood]

Here is that map pivoted to show which sources include each section:

{
    "Annotation properties": [
        "bfo.owl",
        "bspo.owl",
        "chebi.owl",
        "cl.owl",
        "ddanat.owl",
        "doid.owl",
        "efo.owl",
        "ehdaa2.owl",
        "fma.owl",
        "foodon.owl",
        "genepio.owl",
        "go-plus.owl",
        "hp.owl",
        "ino.owl",
        "mi.owl",
        "mondo.owl",
        "nbo.owl",
        "ordo.owl",
        "pato.owl",
        "pr.owl",
        "ro.owl",
        "taxslim.owl",
        "uberon-ext.owl"
    ],
    "Classes": [
        "bfo.owl",
        "bspo.owl",
        "chebi.owl",
        "cl.owl",
        "ddanat.owl",
        "doid.owl",
        "efo.owl",
        "ehdaa2.owl",
        "fma.owl",
        "foodon.owl",
        "genepio.owl",
        "go-plus.owl",
        "hp.owl",
        "ino.owl",
        "mi.owl",
        "mondo.owl",
        "nbo.owl",
        "ordo.owl",
        "pato.owl",
        "pr.owl",
        "ro.owl",
        "taxslim.owl",
        "uberon-ext.owl"
    ],
    "Object Properties": [
        "bspo.owl",
        "chebi.owl",
        "cl.owl",
        "ddanat.owl",
        "doid.owl",
        "efo.owl",
        "ehdaa2.owl",
        "fma.owl",
        "foodon.owl",
        "genepio.owl",
        "go-plus.owl",
        "hp.owl",
        "ino.owl",
        "mondo.owl",
        "nbo.owl",
        "ordo.owl",
        "pato.owl",
        "pr.owl",
        "ro.owl",
        "uberon-ext.owl"
    ],
    "Individuals": [
        "bspo.owl",
        "cl.owl",
        "foodon.owl",
        "genepio.owl",
        "go-plus.owl",
        "mondo.owl",
        "ro.owl",
        "uberon-ext.owl"
    ],
    "General axioms": [
        "bspo.owl",
        "cl.owl",
        "doid.owl",
        "efo.owl",
        "foodon.owl",
        "genepio.owl",
        "go-plus.owl",
        "hp.owl",
        "mondo.owl",
        "nbo.owl",
        "pato.owl",
        "ro.owl",
        "uberon-ext.owl"
    ],
    "Rules": [
        "bspo.owl",
        "go-plus.owl",
        "hp.owl",
        "nbo.owl",
        "pato.owl",
        "ro.owl",
        "uberon-ext.owl"
    ],
    "Annotations": [
        "doid.owl",
        "efo.owl",
        "foodon.owl",
        "genepio.owl",
        "go-plus.owl",
        "ordo.owl",
        "ro.owl"
    ],
    "Datatypes": [
        "efo.owl",
        "foodon.owl",
        "genepio.owl"
    ],
    "Data properties": [
        "efo.owl",
        "foodon.owl",
        "genepio.owl",
        "ino.owl",
        "nbo.owl",
        "ordo.owl",
        "ro.owl"
    ]
}

[ecwood]

These are the keys in the owl:Class terms:

Key	Percentage of owl:Class Terms with Key
rdf:about	0.9973332283
rdfs:label	0.9730753518
rdfs:subClassOf	0.9541165642
oboInOwl:id	0.828054753
oboInOwl:hasOBONamespace	0.7700541919
obo:IAO_0000115	0.6048541348
oboInOwl:hasExactSynonym	0.5293103703
oboInOwl:hasDbXref	0.4787549159
rdfs:comment	0.38822545
oboInOwl:inSubset	0.2699001314
oboInOwl:hasRelatedSynonym	0.2414102684
owl:equivalentClass	0.205951754
chebi:formula	0.1877056805
chebi:charge	0.1875718005
chebi:mass	0.1867517855
chebi:monoisotopicmass	0.1866996116
chebi:smiles	0.1854070789
chebi:inchi	0.1758454867
chebi:inchikey	0.1758454867
owl:deprecated	0.0515054118
oboInOwl:hasNarrowSynonym	0.04076941629
obo:IAO_0100001	0.03761339194
oboInOwl:creation_date	0.03494465144
ncbitaxon:has_rank	0.02839043742
oboInOwl:created_by	0.02699847908
obo:IAO_0000412	0.02638322168
obo:IAO_0000231	0.02491054157
obo:IAO_0000114	0.02431989447
go:hasDbXref	0.02200455783
oboInOwl:hasAlternativeId	0.02166887339
terms:conformsTo	0.01940078851
skos:exactMatch	0.01905722878
obo:IAO_0000117	0.01861621228
obo:IAO_0000233	0.0185601008
mondo-base:exactMatch	0.01369415309
oboInOwl:hasBroadSynonym	0.01249120182
dcterms:creator	0.01075371492
efo1:gwas_trait	0.009597031014
terms:contributor	0.009029025383
dcterms:contributor	0.007981611187
go:hasExactSynonym	0.006950931992
dc:date	0.00632878371
rdfs:seeAlso	0.005819842789
go:hasSynonym	0.005678087485
efo1:reason_for_obsolescence	0.005497940118
efo1:obsoleted_in_version	0.00547726747
dcterms:date	0.005451672762
obo:RO_0002175	0.004723208001
oboInOwl:consider	0.003149133471
obo:IAO_0000119	0.003005409343
go:hasNarrowSynonym	0.002591956371
obo:UBPROP_0000004	0.002566361663
efo1:definition_citation	0.002438388124
owl:disjointWith	0.002343884588
go:hasBroadSynonym	0.002315336644
foaf:depiction	0.002203113695
obo:IAO_0000116	0.00214700222
rdf:nodeID	0.002123376336
owl:complementOf	0.001948151028
obo:IAO_0000118	0.00193830691
mondo-base:excluded_subClassOf	0.001769972486
obo:RO_0002161	0.00151008776
terms:creator	0.001491383935
efo1:organizational_class	0.001394911575
mondo:excluded_subClassOf	0.001394911575
skos:closeMatch	0.001370301279
obo:UBPROP_0000001	0.001346675395
mondo:excluded_from_qc_check	0.001233468034
mondo-base:closeMatch	0.001184247442
go:id	0.001118291849
dc:creator	0.0009027056559
obo:UBPROP_0000008	0.0007540594683
obo:UBPROP_0000003	0.0007048388764
owl:intersectionOf	0.0007048388764
obo:IAO_0000589	0.0006733376976
obo:UBPROP_0000012	0.0006595559318
vocab:crossSpeciesExactMatch	0.0005266603336
mondo:should_conform_to	0.0005010656258
terms:date	0.0004941747429
obo:UBPROP_0000007	0.0004823618009
obo:RO_0002604	0.0004646423878
go:hasAlternativeId	0.0004124685603
obo:IAO_0000232	0.000347497379
go:hasRelatedSynonym	0.0003445441435
foaf:depicted_by	0.0003317467896
obo:IAO_0000112	0.0002657911964
obo:RO_0002171	0.0002549626662
schema:image	0.000225430311
go:hasOBONamespace	0.0002086953098
go:inSubset	0.0001978667795
obo:UBPROP_0000011	0.0001939291322
obo:UBPROP_0000009	0.000152583835
dc:contributor	0.0001486461876
oboInOwl:xref	0.0001407708929
obo:UBPROP_0000006	0.0001200982443
efo1:EFO_URI	0.0001181294206
go:creation_date	0.0001181294206
obo:IAO_0000111	0.0001171450088
obo:UBPROP_0000010	0.0001171450088
obo:IAO_0000600	0.0001122229496
obo:UBPROP_0000002	0.0001073008904
obo:INO_0000006	9.06E-05
mondo-base:relatedMatch	8.86E-05
skos:broadMatch	8.76E-05
obo:GENEPIO_0000005	8.56E-05
go:created_by	8.17E-05
skos:relatedMatch	7.78E-05
obo:GENEPIO_0000001	7.58E-05
obo:UBPROP_0000013	7.58E-05
obo:GENEPIO_0000006	7.38E-05
obo:IAO_0006012	7.19E-05
obo:BFO_0000179	6.69E-05
obo:BFO_0000180	6.69E-05
rdfs:isDefinedBy	6.69E-05
obo:UBPROP_0000202	6.50E-05
obo:IAO_0000602	5.81E-05
obo:GENEPIO_0000004	5.71E-05
obo:GENEPIO_0001763	5.22E-05
obo:IAO_0000028	5.12E-05
obo:RO_0002174	5.02E-05
efo1:ArrayExpress_label	4.43E-05
obo:UBPROP_0000108	3.74E-05
obo:IAO_0000601	2.76E-05
efo1:SRA_label	2.56E-05
obo:UBPROP_0000104	2.36E-05
skos:narrowMatch	2.26E-05
obo:UBPROP_0000005	1.97E-05
obo:INO_0000036	1.87E-05
obo:UBPROP_0000103	1.77E-05
obo:UBPROP_0000112	1.38E-05
owl:unionOf	1.38E-05
obo:UBPROP_0000107	1.28E-05
obo:UBPROP_0000106	1.18E-05
efo1:source_definition	9.84E-06
obo:UBPROP_0000201	9.84E-06
efo1:branch_class	8.86E-06
obo:UBPROP_0000015	8.86E-06
obo:UBPROP_0000111	7.88E-06
mondo-base:broadMatch	6.89E-06
obo:namespace	6.89E-06
oboInOwl:note	6.89E-06
patterns:createdBy	6.89E-06
mondo-base:excluded_synonym	5.91E-06
mondo:excluded_synonym	5.91E-06
obo:OBI_0001847	5.91E-06
oboInOwl:source	5.91E-06
mondo-base:narrowMatch	4.92E-06
obo:INO_0000087	4.92E-06
obo:OBI_9991118	4.92E-06
pato:seeAlso	4.92E-06
mi:isDefinedBy	3.94E-06
obo:OBI_0001886	2.95E-06
dc:source	1.97E-06
efo1:primary_source	1.97E-06
obo:COB_based_on	1.97E-06
obo:GENEPIO_0000162	1.97E-06
obo:RO_0002475	1.97E-06
obo:UBPROP_0000014	1.97E-06
skos:prefLabel	1.97E-06
obo:IAO_0000598	9.84E-07
obo:RO_0001900	9.84E-07
obo:RO_0002581	9.84E-07
obo:RO_0004050	9.84E-07
obo:UBPROP_0000105	9.84E-07
owl:incompatibleWith	9.84E-07

[ecwood]

KG.10.1pre successfully built without ontobio, so I am closing this issue.