From cc5049b43666a6d379e28d70e715eb75802fb546 Mon Sep 17 00:00:00 2001 From: Farid Seifi Date: Thu, 23 Jan 2025 12:54:53 -0500 Subject: [PATCH 1/4] updated the ontology and graph --- koio.graph | 41 ++++++++++-------------- koio.owl | 94 ++++++++++-------------------------------------------- 2 files changed, 34 insertions(+), 101 deletions(-) diff --git a/koio.graph b/koio.graph index 1c77003..43fcda0 100644 --- a/koio.graph +++ b/koio.graph @@ -1,25 +1,18 @@ Optional.of(https://kgrid.org/koio) -https://kgrid.org/koio#Knowledge,1203.1980730125786,-7.650361312359724 -http://www.ebi.ac.uk/swo/SWO_9000050,1029.3810604747566,-90.54328072958918 -https://kgrid.org/koio#Implementation,1415.9124103682955,160.49287831530137 -https://kgrid.org/koio#DeploymentInstruction,1257.3877157360564,84.05262877856467 -https://kgrid.org/koio#Collection,953.279211271965,217.2561381370103 -https://kgrid.org/koio#ProvenanceBundle,936.902804749395,343.12996472914506 -https://kgrid.org/koio#Artifact,840.5302699768746,203.569733392409 -https://kgrid.org/koio#ComputableKnowledgeResource,1240.7894131760838,187.3369068263514 -http://www.ebi.ac.uk/swo/SWO_0000001,965.0536533631409,-5.6471954509344116 -http://purl.obolibrary.org/obo/BFO_0000004,666.6910076313001,55.30209079821628 -https://kgrid.org/koio#Documentation,1416.189281531748,-189.6720112399996 -https://kgrid.org/koio#Bundle,964.5896927634674,275.85946786346096 -http://purl.obolibrary.org/obo/BFO_0000002,650.8910010395479,0.8340121547405852 -http://purl.obolibrary.org/obo/BFO_0000001,532.4726942992013,0.7174923436800127 -https://kgrid.org/koio#Payload,1321.0858543029635,278.86992631207374 -https://kgrid.org/koio#InformationArtifact,1056.9906530271955,144.05162454421486 -https://kgrid.org/koio#Service,1212.4805777197487,-85.18858383374393 -http://purl.obolibrary.org/obo/BFO_0000040,744.7114678936337,127.84050225114133 -http://purl.obolibrary.org/obo/IAO_0000064,967.2755725833505,65.54070309478392 -https://kgrid.org/koio#KnowledgeObject,1411.6668784806593,-85.38758925921736 -https://kgrid.org/koio#ServiceSpecification,1418.7753210835424,402.0356049556368 -http://purl.obolibrary.org/obo/IAO_0000030,855.9734138397787,-91.99642759614589 -https://kgrid.org/koio#Test,879.2218938660237,-183.0009641246091 -http://purl.obolibrary.org/obo/BFO_0000031,662.7221348625433,-90.62570054195788 +https://kgrid.org/koio#Knowledge,1402.2156475443996,-3.987461167602308 +http://www.ebi.ac.uk/swo/SWO_9000050,1609.3402500613392,-135.71904918159714 +https://kgrid.org/koio#Implementation,1387.8301759251583,155.60901145562465 +https://kgrid.org/koio#Collection,1143.7500187993487,234.3496721458783 +https://kgrid.org/koio#Artifact,985.8253090522505,153.5100980807242 +http://purl.obolibrary.org/obo/BFO_0000004,884.0230828869059,-10.63011180741709 +https://kgrid.org/koio#Documentation,1390.5489805184475,-277.5816147141779 +http://purl.obolibrary.org/obo/BFO_0000002,818.1634409834685,-91.9594581791139 +http://purl.obolibrary.org/obo/BFO_0000001,674.1048332298195,-83.52921098574048 +https://kgrid.org/koio#InformationArtifact,1130.2486559223419,146.49355797405315 +https://kgrid.org/koio#Service,1612.9576602132227,-76.6418168293101 +http://purl.obolibrary.org/obo/BFO_0000040,936.4032421359365,80.22280036929494 +https://kgrid.org/koio#KnowledgeObject,1123.5187337597426,-87.82952268905595 +https://kgrid.org/koio#ServiceSpecification,1387.0301864956461,288.4857004681565 +http://purl.obolibrary.org/obo/IAO_0000030,1036.6764876478105,-254.3850006803916 +https://kgrid.org/koio#Test,1586.1616218042054,-245.27026658548513 +http://purl.obolibrary.org/obo/BFO_0000031,865.4026095391185,-187.08207102056994 diff --git a/koio.owl b/koio.owl index 31dffcb..9944aa0 100644 --- a/koio.owl +++ b/koio.owl @@ -104,13 +104,24 @@ It has yet to be determined whether development of KOIO subontologies and/or ext + - + + implemented by, def., is the relationship between a service and a piece of software which includes an implementation of that service for use when the software is executed. + + + + + + + + + @@ -118,7 +129,6 @@ It has yet to be determined whether development of KOIO subontologies and/or ext - hasDeploymentInstruction hasDeploymentInstruction, def., a relation that holds between a whole KnowledgeObject and its DeploymentInstruction parts @@ -149,8 +159,6 @@ http://spdx.org/rdf/terms#documentation - - hasImplementation hasImplementation, def., a relation that holds between a whole KnowledgeObject and its Implementation part(s) @@ -191,7 +199,6 @@ BFO - hasPayload hasPayload, def., a relation that holds between a whole KnowledgeObject and its Payload part(s) @@ -246,7 +253,6 @@ https://spdx.github.io/spdx-spec/v3.0.1/model/Core/Vocabularies/RelationshipType - isDeploymentInstructionPartOf @@ -260,8 +266,6 @@ https://spdx.github.io/spdx-spec/v3.0.1/model/Core/Vocabularies/RelationshipType - - isImplementationPartOf isImplementation, def., a core relation that holds between an Implementation that is part of a Knowledge Object and its whole @@ -287,7 +291,6 @@ BFO - isPayloadPartOf @@ -336,7 +339,6 @@ BFO - adapterType @@ -407,7 +409,6 @@ BFO - From Dublin Core Metadata Element Set Version 1.1 language @@ -477,17 +478,6 @@ Smith & Ceusters, Aboutness: Towards Foundations for the Information Artifac - - - - - - Bundle - Bundle = def., A collection of two or more descriptive statements (sometimes referred to as statements of metadata) about one or more Information Artifacts - - - - @@ -499,29 +489,6 @@ Smith & Ceusters, Aboutness: Towards Foundations for the Information Artifac - - - - - - ComputableKnowledgeResource - ComputableKnowledgeResource = def. An InformationArtifact about some computable knowledge - - - - - - - - - - - DeploymentInstruction - DeploymentInstructions = def. , an InformationArtifact that describes how to deploy a KnowledgeObject in the Knowledge Grid platform - - - - @@ -542,7 +509,7 @@ from SPDX find term hasDocumentation: https://spdx.github.io/spdx-spec/v3.0.1/mo Implementation - Implementation = def., an InformationArtifact that functions as part of a KnowledgeObject AND is comprised of a Payload with a payloadVersionIdentifier + Implementation = def., an InformationArtifact that functions as part of a KnowledgeObject @@ -562,7 +529,7 @@ from SPDX find term hasDocumentation: https://spdx.github.io/spdx-spec/v3.0.1/mo - + Knowledge, def., information or understanding about a subject, obtained through experience or study. knowledge @@ -573,7 +540,6 @@ from SPDX find term hasDocumentation: https://spdx.github.io/spdx-spec/v3.0.1/mo - KnowledgeObject @@ -593,32 +559,10 @@ from SPDX find term hasDocumentation: https://spdx.github.io/spdx-spec/v3.0.1/mo - - - - - - Payload - Payload = def. , an ComputableKnowledgeResource represented in manner that is machine-interpretable - - - - - - - - - - ProvenanceBundle - Provenance Bundle = def, A Bundle of two or more descriptive statements (sometimes referred to as metadata statements) about the ORIGIN(S) of one or more Information Artifacts - - - - - + Service, def., a Service is a defined function or capability provided by a software system. Each Service provides a way to use or interact with a KnowledgeObject, facilitating access and utilization of the Knowledge encapsulated within the KnowledgeObject. service @@ -699,9 +643,7 @@ Souza ÉF, Falbo RD, Vijaykumar NL. ROoST: Reference ontology on software testin - - - + @@ -727,9 +669,7 @@ Souza ÉF, Falbo RD, Vijaykumar NL. ROoST: Reference ontology on software testin - - - + From eb1568cab3d240335b87e4d3f857d80579710161 Mon Sep 17 00:00:00 2001 From: Farid Seifi Date: Thu, 30 Jan 2025 14:25:20 -0500 Subject: [PATCH 2/4] updates to the ontology --- .gitignore | 2 ++ koio.graph | 2 +- koio.owl | 68 +++++++++++++++++++++++++++++++----------- tests/test_ontology.py | 10 ++++++- 4 files changed, 63 insertions(+), 19 deletions(-) diff --git a/.gitignore b/.gitignore index e596cbb..300d9e5 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,5 @@ tests/__pycache__/test_ontology.cpython-311-pytest-8.2.2.pyc catalog-v001.xml koio.properties +tests/__pycache__/test_ontology.cpython-311-pytest-8.3.3.pyc +.python-version diff --git a/koio.graph b/koio.graph index 43fcda0..be4a845 100644 --- a/koio.graph +++ b/koio.graph @@ -1,11 +1,11 @@ Optional.of(https://kgrid.org/koio) +https://kgrid.org/koio#KnowledgeRepresentation,1862.0,80.0 https://kgrid.org/koio#Knowledge,1402.2156475443996,-3.987461167602308 http://www.ebi.ac.uk/swo/SWO_9000050,1609.3402500613392,-135.71904918159714 https://kgrid.org/koio#Implementation,1387.8301759251583,155.60901145562465 https://kgrid.org/koio#Collection,1143.7500187993487,234.3496721458783 https://kgrid.org/koio#Artifact,985.8253090522505,153.5100980807242 http://purl.obolibrary.org/obo/BFO_0000004,884.0230828869059,-10.63011180741709 -https://kgrid.org/koio#Documentation,1390.5489805184475,-277.5816147141779 http://purl.obolibrary.org/obo/BFO_0000002,818.1634409834685,-91.9594581791139 http://purl.obolibrary.org/obo/BFO_0000001,674.1048332298195,-83.52921098574048 https://kgrid.org/koio#InformationArtifact,1130.2486559223419,146.49355797405315 diff --git a/koio.owl b/koio.owl index 9944aa0..ca68e3d 100644 --- a/koio.owl +++ b/koio.owl @@ -104,7 +104,6 @@ It has yet to be determined whether development of KOIO subontologies and/or ext - @@ -140,10 +139,12 @@ It has yet to be determined whether development of KOIO subontologies and/or ext + - + + hasDocumentation, def., a property that indicates an association between a knowledge object, knowledge, or service and documentation that describes, relates to, or provides information about each of these things. has documentation from SPDX find term hasDocumentation: https://spdx.github.io/spdx-spec/v3.0.1/model/Core/Vocabularies/RelationshipType/ @@ -313,6 +314,16 @@ BFO + + + + + + + + + + + + + + + + + @@ -489,19 +508,6 @@ Smith & Ceusters, Aboutness: Towards Foundations for the Information Artifac - - - - - Documentation, def., an information content entity that conveys information, usually in a structured or semi-structured format, about some other thing. - documentation - from SPDX find term Documentation: -http://spdx.org/rdf/terms#documentation -from SPDX find term hasDocumentation: https://spdx.github.io/spdx-spec/v3.0.1/model/Core/Vocabularies/RelationshipType/ - - - - @@ -509,7 +515,7 @@ from SPDX find term hasDocumentation: https://spdx.github.io/spdx-spec/v3.0.1/mo Implementation - Implementation = def., an InformationArtifact that functions as part of a KnowledgeObject + def., a computer or machine processable file that is or informs a series of instructions that can be directly interpreted or executed. @@ -559,11 +565,23 @@ from SPDX find term hasDocumentation: https://spdx.github.io/spdx-spec/v3.0.1/mo + + + + + def., an implementation of knowledge. + knowledge representation + + + + - Service, def., a Service is a defined function or capability provided by a software system. Each Service provides a way to use or interact with a KnowledgeObject, facilitating access and utilization of the Knowledge encapsulated within the KnowledgeObject. + Service, def., a Service is a defined function or capability provided by a software system. Each Service provides a way to use or interact with a KnowledgeObject, facilitating access and utilization of the Knowledge encapsulated within the KnowledgeObject. + +A Service is a specification of what a self-contained piece of software does. service @@ -681,13 +699,21 @@ Souza ÉF, Falbo RD, Vijaykumar NL. ROoST: Reference ontology on software testin + + + + + + + + @@ -701,6 +727,14 @@ Souza ÉF, Falbo RD, Vijaykumar NL. ROoST: Reference ontology on software testin + + + + + + + + diff --git a/tests/test_ontology.py b/tests/test_ontology.py index e48c9bd..ba96775 100644 --- a/tests/test_ontology.py +++ b/tests/test_ontology.py @@ -40,5 +40,13 @@ def test_which_KO_is_implemented_by_a_specific_piece_of_software(graph): KO = next(graph.subjects( KOIO.hasService / SWO.SWO_0000085 , URIRef("https://raw.githubusercontent.com/kgrid-lab/MCBK_2024_demo/main/tobacco/cli_service/cli.ts")),None) assert KOIO.tobaccoKO == KO - +def test_which_KO_bmiTest_belong_to(graph): + KO = next(graph.subjects( KOIO.hasTest , KOIO.bmiTest),None) + assert KOIO.bmiKO == KO + +def test_bmiKO_hasTest(graph): + tests = next(graph.objects( KOIO.bmiKO , KOIO.hasTest),None) + assert tests + + \ No newline at end of file From 40728a32154df01d81949ad826ccfc38bc8dde1c Mon Sep 17 00:00:00 2001 From: Farid Seifi Date: Wed, 12 Feb 2025 11:42:04 -0500 Subject: [PATCH 3/4] KOIO 2.1 restructuring changes + documentation, context, examples, test updates. --- 2.1/context | 136 +++++ 2.1/koio.owl | 499 ++++++++++++++++ context | 152 ++--- .../IAO_0000115___964462205.html | 18 +- .../comment___1501100887.html | 17 +- ...4134.html => contributor___285822827.html} | 30 +- .../definition___344110101.html | 73 --- docs/annotationproperties/index-koio.html | 8 +- docs/annotationproperties/index.html | 8 +- .../isDefinedBy___449337134.html | 97 +--- .../label___653429740.html | 47 +- .../publisher___-666464116.html | 39 ++ .../seeAlso___-1773693006.html | 7 +- ...45035421.html => title___-2003496728.html} | 4 +- .../versionInfo___407301298.html | 2 +- docs/classes/Artifact___194373812.html | 6 +- docs/classes/Bundle___-935486620.html | 53 -- docs/classes/Collection___1610680704.html | 8 +- ...putableKnowledgeResource___1421463014.html | 53 -- .../DeploymentInstruction___1497279275.html | 80 --- docs/classes/Documentation___-550071972.html | 61 -- docs/classes/Implementation___2039871124.html | 36 +- .../InformationArtifact___-669107776.html | 28 +- ...KnowledgeObjectCollection___486619773.html | 8 +- docs/classes/KnowledgeObject___49698815.html | 60 +- docs/classes/Knowledge___617416480.html | 10 +- docs/classes/Payload___-2058487760.html | 80 --- .../ProvenanceBundle___2090337509.html | 53 -- docs/classes/SWO_0000001___59336697.html | 20 +- docs/classes/SWO_0000108___59337665.html | 6 +- docs/classes/SWO_9000050___-543064612.html | 10 + docs/classes/SWO_9000053___-1725111051.html | 4 +- docs/classes/SWO_9000054___-1725111050.html | 2 +- .../ServiceSpecification___614837040.html | 80 --- docs/classes/Service___712367447.html | 17 +- docs/classes/Test___1361131380.html | 17 +- docs/classes/index-koio.html | 24 +- docs/classes/index.html | 24 +- docs/contents.html | 10 +- .../KOIOVersion___550632112.html | 61 ++ docs/dataproperties/access___-64932826.html | 63 --- .../adapterType___1943922155.html | 63 --- .../contributors___-1560462918.html | 63 --- .../description___-366017858.html | 63 --- .../endpoints___-501869504.html | 63 --- .../identifer___1444867900.html | 72 --- docs/dataproperties/index-koio.html | 17 +- docs/dataproperties/index.html | 17 +- .../dataproperties/keywords___1881677420.html | 63 --- .../dataproperties/language___-255061478.html | 53 -- docs/dataproperties/owners___354673378.html | 63 --- docs/dataproperties/title___1468899610.html | 73 --- .../topDataProperty___215468192.html} | 16 +- .../versionIdentifer___-1567431356.html | 81 --- docs/datatypes/Literal___-1897151097.html | 49 -- .../datatypes/PlainLiteral___-1770072891.html | 88 +-- docs/datatypes/decimal___-1060762728.html | 10 + docs/datatypes/index-koio.html | 4 +- docs/datatypes/index.html | 4 +- docs/datatypes/string___799955032.html | 47 ++ docs/index-all.html | 84 +-- .../individuals/CLIService1___1815410686.html | 101 ---- docs/individuals/UUIDDI01___-543222205.html | 139 ----- docs/individuals/UUIDIMP01___-1756391788.html | 169 ------ docs/individuals/UUIDKO1___1989924980.html | 139 ----- .../UUIDPAYLOAD01___150037846.html | 209 ------- docs/individuals/UUIDSS01___-542765730.html | 139 ----- docs/individuals/bmi.js___-1631313774.html | 370 ------------ docs/individuals/bmi.js___-26942853.html | 49 ++ ...8.html => bmiAPIService___-867349989.html} | 36 +- ...7.html => bmiCLIService___1674473557.html} | 36 +- ...rNotebookTutorial.ipynb___-1135923982.html | 139 +++++ ...bmiKOAPIDocumentation.md___-726842491.html | 211 +++++++ .../bmiKODocumentation.md___244515727.html | 221 ++++++++ docs/individuals/bmiKO___1452383780.html | 77 ++- ...nowledgeDocumentation.md___-908001075.html | 261 +++++++++ .../bmiKnowledge___-1370630302.html | 139 ++--- .../bmiTestAPIService___263920973.html | 271 +++++++++ .../individuals/bmiTestKO.ts___174701787.html | 281 +++++++++ .../bmiTestKnowledge.ts___1253403649.html | 171 ++++++ docs/individuals/bmi_cli.ts___-501769552.html | 301 ++++++++++ docs/individuals/cli.ts___-688288001.html | 360 ------------ docs/individuals/cli.ts___2080437965.html | 330 ----------- docs/individuals/index-koio.html | 32 +- docs/individuals/index.html | 32 +- docs/individuals/index70.js___-109516072.html | 350 ------------ docs/individuals/index70.js___2066653614.html | 311 ++++++++++ ...9450.html => tobacco.js___-906850620.html} | 125 ++-- .../tobaccoCLIService___-654503956.html | 353 ++++++++++++ docs/individuals/tobaccoKO___1978188987.html | 99 ++-- .../tobaccoKnowledge___-1584305941.html | 195 +++++-- .../tobacco_cli.ts___-1695286663.html | 411 ++++++++++++++ .../RO_0002502___-47773661.html | 6 +- .../SWO_0000085___59336949.html | 22 +- .../SWO_0004001___59455861.html | 49 ++ ...hasDeploymentInstruction___1153342673.html | 105 ---- .../hasDocumentation___87918850.html | 22 +- .../hasImplementation___342750126.html | 105 ---- .../hasKnowledge___1822278086.html | 9 +- .../hasPart___2055343215.html | 77 --- .../hasPayload___-1690753962.html | 105 ---- .../hasServiceSpecification___-366089014.html | 94 --- .../hasService___1080101245.html | 8 +- .../hasTest___2055466254.html | 10 +- docs/objectproperties/index-koio.html | 15 +- docs/objectproperties/index.html | 15 +- ...loymentInstructionPartOf___1138174539.html | 104 ---- .../isImplementationPartOf___1654476424.html | 104 ---- .../isPartOf___1037151670.html | 77 --- .../isPayloadPartOf___1659698704.html | 104 ---- ...erviceSpecificationPartOf___335074980.html | 104 ---- docs/ontologies/index.html | 4 +- docs/ontologies/koio___-1832827647.html | 45 +- .../bmi_calculator_v_1/bmiKODocumentation.md | 3 + .../bmi_calculator_v_2/bmiKODocumentation.md | 3 + examples/bmi_calculator_v_2/metadata.json | 2 +- .../APIService/bmiKOAPIDocumentation.md | 2 + .../APIService/deployment.yaml | 6 + .../bmi_calculator_v_3/APIService/index70.js | 79 +++ .../APIService/service.yaml | 58 ++ .../bmi_calculator_v_3/CLIService/bmi_cli.ts | 43 ++ examples/bmi_calculator_v_3/Knowledge/bmi.js | 3 + .../Knowledge/bmiKnowledgeDocumentation.md | 1 + .../bmiJupiterNotebookTutorial.ipynb | 104 ++++ .../bmi_calculator_v_3/bmiKODocumentation.md | 3 + examples/bmi_calculator_v_3/license.md | 9 + examples/bmi_calculator_v_3/metadata.json | 129 +++++ .../bmi_calculator_v_3/tests/bmiKOTest.ts | 1 + .../tests/bmiKnowledgeTest.ts | 1 + examples/readme.md | 4 + .../cli_service/batchinput.csv | 0 .../cli_service/cli.ts | 0 .../knowledge/tobacco.js | 0 .../{tobacco => tobacco_v_1}/metadata.json | 2 +- .../tobacco_v_2/cli_service/batchinput.csv | 6 + .../tobacco_v_2/cli_service/tobacco_cli.ts | 72 +++ examples/tobacco_v_2/knowledge/tobacco.js | 12 + examples/tobacco_v_2/license.md | 9 + examples/tobacco_v_2/metadata.json | 55 ++ koio.graph | 4 +- koio.owl | 534 ++++-------------- readme.md | 2 + tests/test_ontology.py | 23 +- 143 files changed, 5377 insertions(+), 6038 deletions(-) create mode 100644 2.1/context create mode 100644 2.1/koio.owl rename docs/annotationproperties/{contributor___1944284134.html => contributor___285822827.html} (61%) delete mode 100644 docs/annotationproperties/definition___344110101.html create mode 100644 docs/annotationproperties/publisher___-666464116.html rename docs/annotationproperties/{title___-345035421.html => title___-2003496728.html} (84%) delete mode 100644 docs/classes/Bundle___-935486620.html delete mode 100644 docs/classes/ComputableKnowledgeResource___1421463014.html delete mode 100644 docs/classes/DeploymentInstruction___1497279275.html delete mode 100644 docs/classes/Documentation___-550071972.html delete mode 100644 docs/classes/Payload___-2058487760.html delete mode 100644 docs/classes/ProvenanceBundle___2090337509.html delete mode 100644 docs/classes/ServiceSpecification___614837040.html create mode 100644 docs/dataproperties/KOIOVersion___550632112.html delete mode 100644 docs/dataproperties/access___-64932826.html delete mode 100644 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docs/individuals/bmiTestAPIService___263920973.html create mode 100644 docs/individuals/bmiTestKO.ts___174701787.html create mode 100644 docs/individuals/bmiTestKnowledge.ts___1253403649.html create mode 100644 docs/individuals/bmi_cli.ts___-501769552.html delete mode 100644 docs/individuals/cli.ts___-688288001.html delete mode 100644 docs/individuals/cli.ts___2080437965.html delete mode 100644 docs/individuals/index70.js___-109516072.html create mode 100644 docs/individuals/index70.js___2066653614.html rename docs/individuals/{tobacco.js___1108439450.html => tobacco.js___-906850620.html} (69%) create mode 100644 docs/individuals/tobaccoCLIService___-654503956.html create mode 100644 docs/individuals/tobacco_cli.ts___-1695286663.html create mode 100644 docs/objectproperties/SWO_0004001___59455861.html delete mode 100644 docs/objectproperties/hasDeploymentInstruction___1153342673.html delete mode 100644 docs/objectproperties/hasImplementation___342750126.html delete mode 100644 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100644 examples/tobacco_v_2/cli_service/batchinput.csv create mode 100644 examples/tobacco_v_2/cli_service/tobacco_cli.ts create mode 100644 examples/tobacco_v_2/knowledge/tobacco.js create mode 100644 examples/tobacco_v_2/license.md create mode 100644 examples/tobacco_v_2/metadata.json diff --git a/2.1/context b/2.1/context new file mode 100644 index 0000000..5968677 --- /dev/null +++ b/2.1/context @@ -0,0 +1,136 @@ +{ + "@id": "https://kgrid.org/koio/2.1/context", + "@context" : { + "koio": "http://kgrid.org/koio#", + "dc": "http://purl.org/dc/elements/1.1/", + "dcterms": "http://purl.org/dc/terms/", + "schema":"http://schema.org/", + + "KnowledgeObject" : { + "@id" : "https://kgrid.org/koio#KnowledgeObject" + }, + "versionInfo" : { + "@id" : "http://www.w3.org/2002/07/owl#versionInfo" + }, + "hasTest" : { + "@id" : "https://kgrid.org/koio#hasTest", + "@type" : "@id" + }, + "topDataProperty" : { + "@id" : "http://www.w3.org/2002/07/owl#topDataProperty" + }, + "Test" : { + "@id" : "https://kgrid.org/koio#Test" + }, + "label" : { + "@id" : "http://www.w3.org/2000/01/rdf-schema#label" + }, + "API" : { + "@id" : "http://www.ebi.ac.uk/swo/interface/SWO_9000054" + }, + "KOIOVersion" : { + "@id" : "https://kgrid.org/koio#KOIOVersion" + }, + "Knowledge" : { + "@id" : "https://kgrid.org/koio#Knowledge" + }, + "Artifact" : { + "@id" : "https://kgrid.org/koio#Artifact" + }, + "MaterialEntity" : { + "@id" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, + "hasPart" : { + "@id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "@type" : "@id" + }, + "CLI" : { + "@id" : "http://www.ebi.ac.uk/swo/interface/SWO_9000053" + }, + "hasService" : { + "@id" : "https://kgrid.org/koio#hasService", + "@type" : "@id" + }, + "isDefinedBy" : { + "@id" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy" + }, + "JavaScript" : { + "@id" : "http://www.ebi.ac.uk/swo/SWO_0000108" + }, + "hasServiceSpecification" : { + "@id" : "https://kgrid.org/koio#hasServiceSpecification", + "@type" : "@id" + }, + "title" : { + "@id" : "http://purl.org/dc/terms/title" + }, + "Implementation" : { + "@id" : "https://kgrid.org/koio#Implementation" + }, + "type" : { + "@id" : "http://www.w3.org/2000/01/rdf-schema#type" + }, + "publisher" : { + "@id" : "http://purl.org/dc/terms/publisher" + }, + "InformationContentEntity" : { + "@id" : "http://purl.obolibrary.org/obo/IAO_0000030" + }, + "hasInterface" : { + "@id" : "http://www.ebi.ac.uk/swo/SWO_0004001", + "@type" : "@id" + }, + "seeAlso" : { + "@id" : "http://www.w3.org/2000/01/rdf-schema#seeAlso" + }, + "Software" : { + "@id" : "http://www.ebi.ac.uk/swo/SWO_0000001" + }, + "comment" : { + "@id" : "http://www.w3.org/2000/01/rdf-schema#comment" + }, + "Service" : { + "@id" : "https://kgrid.org/koio#Service" + }, + "hasDocumentation" : { + "@id" : "https://kgrid.org/koio#hasDocumentation", + "@type" : "@id" + }, + "contributor" : { + "@id" : "http://purl.org/dc/terms/contributor" + }, + "SWO_9000050" : { + "@id" : "http://www.ebi.ac.uk/swo/SWO_9000050" + }, + "InformationArtifact" : { + "@id" : "https://kgrid.org/koio#InformationArtifact" + }, + "KnowledgeObjectCollection" : { + "@id" : "https://kgrid.org/koio#KnowledgeObjectCollection" + }, + "dependsOn" : { + "@id" : "http://purl.obolibrary.org/obo/RO_0002502", + "@type" : "@id" + }, + "implementedBy" : { + "@id" : "http://www.ebi.ac.uk/swo/SWO_0000085", + "@type" : "@id" + }, + "Collection" : { + "@id" : "https://kgrid.org/koio#Collection" + }, + "hasKnowledge" : { + "@id" : "https://kgrid.org/koio#hasKnowledge", + "@type" : "@id" + }, + "definition" : { + "@id" : "http://purl.obolibrary.org/obo/IAO_0000115" + }, + "Python": { + "@id" : "http://www.ebi.ac.uk/swo/SWO_0000118" + }, + "Function":{ + "@id" : "https://w3id.org/function/ontology#Function" + } + } +} diff --git a/2.1/koio.owl b/2.1/koio.owl new file mode 100644 index 0000000..4eb3627 --- /dev/null +++ b/2.1/koio.owl @@ -0,0 +1,499 @@ + + + + + + + Knowledge Systems Lab. Department of Learning Health Sciences. University of Michigan Medical School. +https://knowledge-systems.lab.medicine.umich.edu/ + Allen Flynn + Charles P. Friedman + Farid Seifi + Marisa Conte + Peter Boisvert + Knowledge Object Implementation Ontology (KOIO) + KOIO is an ontology describing Knowledge Objects and their parts as they are implemented in the Knoweldge Grid (KGrid) reference platform. As such, KOIO is subject to evolve as KGrid reference platform development evolves. + +The primary overriding objective of developing and implementing KOIO is to describe Knowledge Objects and their parts in enough detail to achieve a degree interoperability that is sufficient to enable Knowledge Objects to be incorporated into multiple platforms, including but not limited to, the KGrid reference platform + +With the exception of several upper level classes from BFO and IAO, KOIO versions 1.X.X are limited in scope to classes of material entities spanning Knowledge Objects, parts of Knowledge Objects, and Collections of Knowledge Objects. + +It has yet to be determined whether development of KOIO subontologies and/or extensions of KOIO are the preferred method for modeling (a) other KGrid components besides Knowledge Objects and the subcompnent parts of other KGrid components, (b) actions and operations involving Knowledge Objects and KGrid components, and (c) relationships between actions and operations, components, and parts. + 2.1 + + + + + + + + + + + + + + + + + + + + + + + + + depends on, def., indicates that a service uses a specific knowledge + + + + + + + + + + + + Note: KSL added this definition to contextualize the definition below from SWO. +implemented by, def., is the relationship between an abstract KO component and a piece of software (or computer processable content) which includes an implementation of that abstract KO component for use when processed by a computer. + + + + + + + + + + + + + + + + + + + + + + + + hasDocumentation, def., a property that indicates an association between a knowledge object, knowledge, or service and documentation that describes, relates to, or provides information about each of these things. + has documentation + from SPDX find term hasDocumentation: https://spdx.github.io/spdx-spec/v3.0.1/model/Core/Vocabularies/RelationshipType/ +from SPDX find term Documentation: +http://spdx.org/rdf/terms#documentation + + + + + + + + + + + hasKnowledge, def., indicates that a Knowledge Object contains or is associated with specific Knowledge. + has knowledge + + + + + + + + + + + hasService , def., a relation that holds between a whole KnowledgeObject and its Service part(s). Denotes that a KnowledgeObject includes or provides a specific Service. + has service + + + + + + + + + + + + + hasTest, def., a property that links a knowledge object, service, or knowledge to a specific test designed to evaluate its functionality, performance, or reliability. This property signifies that the component has an associated test to verify or validate its behavior. + has test + from SPDX find term hasTest: +https://spdx.github.io/spdx-spec/v3.0.1/model/Core/Vocabularies/RelationshipType/ + + + + + + + + + + + + + + The version of KOIO from which metadata is derived + KOIO version + + + + + + + + + + + + + + Artifact =def. a MaterialEntity created or modified or selected by some agent to realize a certain FUNCTION or ROLE (Examples: a key, a lock, a digital file stored on a particular computing machine, a screwdriver) + + +Smith & Ceusters, Aboutness: Towards Foundations for the Information Artifact Ontology + + artifact + + + + + + + + + Collection = def. an InformationArtifact comprised of two or more InformationArtifacts and at least one collectionIdentifier + + collection + + + + + + + + + + def., a computer or machine processable file that is or informs a series of instructions that can be directly interpreted or executed. + + implementation + + + + + + + + + An InformationArtifact = def., an Artifact that is the IndependentContinuant bearer created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO + Per KOIO, Knowledge Objects are InformationArtifacts by definition. + + information artifact + + + + + + + + + Knowledge, def., information or understanding about a subject, obtained through experience or study. + knowledge + + + + + + + + + + + + + + + KnowledgeObject = def., an Information Artifact capable of serving a role as the atomic unit of computable knowledge and therefore comprised of at least one KnowledgeObjectImplementation + + knowledge object + + + + + + + + + Knowledge Object Collection = def., two or more Knowledge Objects with a collectionIdentifer + + knowledge object collection + + + + + + + + + Service, def., a Service is a defined function or capability provided by a software system. Each Service provides a way to use or interact with a KnowledgeObject, facilitating access and utilization of the Knowledge encapsulated within the KnowledgeObject. + +A Service is a specification of what a self-contained piece of software does. + service + + + + + + + + + Test, def., an information content entity conveying a systematic procedure to assess specific aspects of software performance, functionality, or security. Tests are created to ensure that the software meets specified requirements or to identify any defects. + test + Test Case, Test, Test Code, Code To Be Tested +https://dev.nemo.inf.ufes.br/seon/ROoST.html + +Souza ÉF, Falbo RD, Vijaykumar NL. ROoST: Reference ontology on software testing. Applied Ontology. 2017 Jan 1;12(1):59-90. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2.1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/context b/context index f176139..8037778 100644 --- a/context +++ b/context @@ -3,115 +3,66 @@ "@context" : { "koio": "http://kgrid.org/koio#", "dc": "http://purl.org/dc/elements/1.1/", - + "dcterms": "http://purl.org/dc/terms/", + "schema":"http://schema.org/", + "KnowledgeObject" : { "@id" : "https://kgrid.org/koio#KnowledgeObject" }, - "hasDeploymentInstruction" : { - "@id" : "https://kgrid.org/koio#hasDeploymentInstruction", - "@type" : "@id" - }, - "hasImplementation" : { - "@id" : "https://kgrid.org/koio#hasImplementation", - "@type" : "@id" - }, - "algorithm" : { - "@id" : "http://purl.obolibrary.org/obo/IAO_0000064" - }, - "isImplementationPartOf" : { - "@id" : "https://kgrid.org/koio#isImplementationPartOf", - "@type" : "@id" - }, - "ComputableKnowledgeResource" : { - "@id" : "https://kgrid.org/koio#ComputableKnowledgeResource" + "versionInfo" : { + "@id" : "http://www.w3.org/2002/07/owl#versionInfo" }, - "hasPayload" : { - "@id" : "https://kgrid.org/koio#hasPayload", + "hasTest" : { + "@id" : "https://kgrid.org/koio#hasTest", "@type" : "@id" }, - "endpoints" : { - "@id" : "https://kgrid.org/koio#endpoints", - "@type" : "http://www.w3.org/2000/01/rdf-schema#Literal" + "topDataProperty" : { + "@id" : "http://www.w3.org/2002/07/owl#topDataProperty" }, - "access" : { - "@id" : "https://kgrid.org/koio#access", - "@type" : "http://www.w3.org/2000/01/rdf-schema#Literal" + "Test" : { + "@id" : "https://kgrid.org/koio#Test" }, "label" : { "@id" : "http://www.w3.org/2000/01/rdf-schema#label" }, - "isPayloadPartOf" : { - "@id" : "https://kgrid.org/koio#isPayloadPartOf", - "@type" : "@id" - }, - "isPartOf" : { - "@id" : "https://kgrid.org/koio#isPartOf", - "@type" : "@id" - }, - "isServiceSpecificationPartOf" : { - "@id" : "https://kgrid.org/koio#isServiceSpecificationPartOf", - "@type" : "@id" - }, - "Bundle" : { - "@id" : "https://kgrid.org/koio#Bundle" - }, - "owners" : { - "@id" : "https://kgrid.org/koio#owners", - "@type" : "http://www.w3.org/2000/01/rdf-schema#Literal" + "API" : { + "@id" : "http://www.ebi.ac.uk/swo/interface/SWO_9000054" }, - "Payload" : { - "@id" : "https://kgrid.org/koio#Payload" + "KOIOVersion" : { + "@id" : "https://kgrid.org/koio#KOIOVersion" }, "Knowledge" : { "@id" : "https://kgrid.org/koio#Knowledge" }, - "Test" : { - "@id" : "https://kgrid.org/koio#Test" - }, - "Documentation" : { - "@id" : "https://kgrid.org/koio#Documentation" - }, "Artifact" : { "@id" : "https://kgrid.org/koio#Artifact" }, - "materialEntity" : { + "MaterialEntity" : { "@id" : "http://purl.obolibrary.org/obo/BFO_0000040" }, "hasPart" : { "@id" : "http://purl.obolibrary.org/obo/BFO_0000051", "@type" : "@id" }, + "CLI" : { + "@id" : "http://www.ebi.ac.uk/swo/interface/SWO_9000053" + }, "hasService" : { "@id" : "https://kgrid.org/koio#hasService", "@type" : "@id" }, - "ProvenanceBundle" : { - "@id" : "https://kgrid.org/koio#ProvenanceBundle" - }, - "DeploymentInstruction" : { - "@id" : "https://kgrid.org/koio#DeploymentInstruction" - }, - "versionIdentifer" : { - "@id" : "https://kgrid.org/koio#versionIdentifer", - "@type" : "http://www.w3.org/2000/01/rdf-schema#Literal" - }, - "ServiceSpecification" : { - "@id" : "https://kgrid.org/koio#ServiceSpecification" - }, "isDefinedBy" : { "@id" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy" }, - "keywords" : { - "@id" : "https://kgrid.org/koio#keywords", - "@type" : "http://www.w3.org/2000/01/rdf-schema#Literal" + "JavaScript" : { + "@id" : "http://www.ebi.ac.uk/swo/SWO_0000108" }, "hasServiceSpecification" : { "@id" : "https://kgrid.org/koio#hasServiceSpecification", "@type" : "@id" }, "title" : { - "@id" : "https://kgrid.org/koio#title", - "@type" : "http://www.w3.org/2000/01/rdf-schema#Literal" + "@id" : "http://purl.org/dc/terms/title" }, "Implementation" : { "@id" : "https://kgrid.org/koio#Implementation" @@ -119,11 +70,20 @@ "type" : { "@id" : "http://www.w3.org/2000/01/rdf-schema#type" }, - "identifer" : { - "@id" : "https://kgrid.org/koio#identifer", - "@type" : "http://www.w3.org/2000/01/rdf-schema#Literal" + "publisher" : { + "@id" : "http://purl.org/dc/terms/publisher" }, - "software" : { + "InformationContentEntity" : { + "@id" : "http://purl.obolibrary.org/obo/IAO_0000030" + }, + "hasInterface" : { + "@id" : "http://www.ebi.ac.uk/swo/SWO_0004001", + "@type" : "@id" + }, + "seeAlso" : { + "@id" : "http://www.w3.org/2000/01/rdf-schema#seeAlso" + }, + "Software" : { "@id" : "http://www.ebi.ac.uk/swo/SWO_0000001" }, "comment" : { @@ -132,13 +92,14 @@ "Service" : { "@id" : "https://kgrid.org/koio#Service" }, - "language" : { - "@id" : "https://kgrid.org/koio#language" + "hasDocumentation" : { + "@id" : "https://kgrid.org/koio#hasDocumentation", + "@type" : "@id" }, "contributor" : { - "@id" : "http://purl.org/dc/elements/1.1/contributor" + "@id" : "http://purl.org/dc/terms/contributor" }, - "softwareInterface" : { + "SWO_9000050" : { "@id" : "http://www.ebi.ac.uk/swo/SWO_9000050" }, "InformationArtifact" : { @@ -147,10 +108,6 @@ "KnowledgeObjectCollection" : { "@id" : "https://kgrid.org/koio#KnowledgeObjectCollection" }, - "contributors" : { - "@id" : "https://kgrid.org/koio#contributors", - "@type" : "http://www.w3.org/2000/01/rdf-schema#Literal" - }, "dependsOn" : { "@id" : "http://purl.obolibrary.org/obo/RO_0002502", "@type" : "@id" @@ -159,45 +116,16 @@ "@id" : "http://www.ebi.ac.uk/swo/SWO_0000085", "@type" : "@id" }, - "description" : { - "@id" : "https://kgrid.org/koio#description", - "@type" : "http://www.w3.org/2000/01/rdf-schema#Literal" - }, "Collection" : { "@id" : "https://kgrid.org/koio#Collection" }, - "isDeploymentInstructionPartOf" : { - "@id" : "https://kgrid.org/koio#isDeploymentInstructionPartOf", - "@type" : "@id" - }, "hasKnowledge" : { "@id" : "https://kgrid.org/koio#hasKnowledge", "@type" : "@id" }, - "hasTest" : { - "@id" : "https://kgrid.org/koio#hasTest", - "@type" : "@id" - }, - "hasDocumentation" : { - "@id" : "https://kgrid.org/koio#hasDocumentation", - "@type" : "@id" - }, - "adapterType" : { - "@id" : "https://kgrid.org/koio#adapterType", - "@type" : "http://www.w3.org/2000/01/rdf-schema#Literal" - }, "definition" : { "@id" : "http://purl.obolibrary.org/obo/IAO_0000115" }, - "CLI": { - "@id" : "http://www.ebi.ac.uk/swo/interface/SWO_9000053" - }, - "API": { - "@id" : "http://www.ebi.ac.uk/swo/interface/SWO_9000054" - }, - "JavaScript": { - "@id" : "http://www.ebi.ac.uk/swo/SWO_0000108" - }, "Python": { "@id" : "http://www.ebi.ac.uk/swo/SWO_0000118" }, diff --git a/docs/annotationproperties/IAO_0000115___964462205.html b/docs/annotationproperties/IAO_0000115___964462205.html index 5db7445..0a6280f 100644 --- a/docs/annotationproperties/IAO_0000115___964462205.html +++ b/docs/annotationproperties/IAO_0000115___964462205.html @@ -22,15 +22,21 @@

Annotation Property: IAO_0000115

-
-

Usage (10)

+
+

Usage (16)

  • RO_0002502 IAO_0000115 "depends on, def., indicates that a service uses a specific knowledge" 
    • -
  • SWO_0000085 IAO_0000115 "implemented by, def., is the relationship between a service and a piece of software which includes an implementation of that service for use when the software is executed." 
    • -
  • documentation IAO_0000115 "Documentation, def., an information content entity that conveys information, usually in a structured or semi-structured format, about some other thing." 
    • +
  • SWO_0000085 IAO_0000115 "Note: KSL added this definition to contextualize the definition below from SWO.
    implemented by, def., is the relationship between an abstract KO component and a piece of software (or computer processable content) which includes an implementation of that abstract KO component for use when processed by a computer."     
    • +
  • artifact IAO_0000115 "Artifact =def. a MaterialEntity created or modified or selected by some agent to realize a certain FUNCTION or ROLE (Examples: a key, a lock, a digital file stored on a particular computing machine, a screwdriver)


    Smith & Ceusters, Aboutness: Towards Foundations for the Information Artifact Ontology"    (xsd:string) 
    • +
  • collection IAO_0000115 "Collection = def. an InformationArtifact comprised of two or more InformationArtifacts and at least one collectionIdentifier"(xsd:string) 
    • +
  • implementation IAO_0000115 "def., a computer or machine processable file that is or informs a series of instructions that can be directly interpreted or executed."(xsd:string) 
    • +
  • 'information artifact' IAO_0000115 "An InformationArtifact = def., an Artifact that is the IndependentContinuant bearer created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO"(xsd:string) 
    • +
  • 'KOIO version' IAO_0000115 "The version of KOIO from which metadata is derived"(xsd:string) 
  • knowledge IAO_0000115 "Knowledge, def., information or understanding about a subject, obtained through experience or study." 
    • -
  • service IAO_0000115 "Service, def., a Service is a defined function or capability provided by a software system. Each Service provides a way to use or interact with a KnowledgeObject, facilitating access and utilization of the Knowledge encapsulated within the KnowledgeObject." 
    • +
  • 'knowledge object' IAO_0000115 "KnowledgeObject = def., an Information Artifact capable of serving a role as the atomic unit of computable knowledge and therefore comprised of at least one KnowledgeObjectImplementation"(xsd:string) 
    • +
  • 'knowledge object collection' IAO_0000115 "Knowledge Object Collection = def., two or more Knowledge Objects with a collectionIdentifer"(xsd:string) 
    • +
  • service IAO_0000115 "Service, def., a Service is a defined function or capability provided by a software system. Each Service provides a way to use or interact with a KnowledgeObject, facilitating access and utilization of the Knowledge encapsulated within the KnowledgeObject.

    A Service is a specification of what a self-contained piece of software does."     
  • test IAO_0000115 "Test, def., an information content entity conveying a systematic procedure to assess specific aspects of software performance, functionality, or security. Tests are created to ensure that the software meets specified requirements or to identify any defects." 
  • 'has documentation' IAO_0000115 "hasDocumentation, def., a property that indicates an association between a knowledge object, knowledge, or service and documentation that describes, relates to, or provides information about each of these things." 
  • 'has knowledge' IAO_0000115 "hasKnowledge, def., indicates that a Knowledge Object contains or is associated with specific Knowledge." 
    • @@ -38,7 +44,7 @@

    Usage (10)

  • 'has test' IAO_0000115 "hasTest, def., a property that links a knowledge object, service, or knowledge to a specific test designed to evaluate its functionality, performance, or reliability. This property signifies that the component has an associated test to verify or validate its behavior." 
-
+

diff --git a/docs/annotationproperties/comment___1501100887.html b/docs/annotationproperties/comment___1501100887.html index f2b2f86..a987bf7 100644 --- a/docs/annotationproperties/comment___1501100887.html +++ b/docs/annotationproperties/comment___1501100887.html @@ -22,24 +22,15 @@

Annotation Property: rdfs:comment

-
-

Usage (11)

+
+

Usage (2)

    -
  • InformationArtifact rdfs:comment "Per KOIO, Knowledge Objects are InformationArtifacts by definition." 
    • -
  • access rdfs:comment "The expected strings are "public" or "private"" 
    • -
  • contributors rdfs:comment "From Dublin Core Metadata Element Set Version 1.1" 
    • -
  • description rdfs:comment "From Dublin Core Metadata Element Set Version 1.1" 
    • -
  • identifer rdfs:comment "From Dublin Core Metadata Element Set Version 1.1" 
    • -
  • keywords rdfs:comment "From Dublin Core Metadata Element Set Version 1.1" 
    • -
  • language rdfs:comment "From Dublin Core Metadata Element Set Version 1.1" 
    • -
  • owners rdfs:comment "From Dublin Core Metadata Element Set Version 1.1" 
    • -
  • title rdfs:comment "From Dublin Core Metadata Element Set Version 1.1" 
    • -
  • versionIdentifier rdfs:comment "From Dublin Core Metadata Element Set Version 1.1" 
    • +
  • 'information artifact' rdfs:comment "Per KOIO, Knowledge Objects are InformationArtifacts by definition." 
  • rdfs:comment "KOIO is an ontology describing Knowledge Objects and their parts as they are implemented in the Knoweldge Grid (KGrid) reference platform. As such, KOIO is subject to evolve as KGrid reference platform development evolves.

    The primary overriding objective of developing and implementing KOIO is to describe Knowledge Objects and their parts in enough detail to achieve a degree interoperability that is sufficient to enable Knowledge Objects to be incorporated into multiple platforms, including but not limited to, the KGrid reference platform

    With the exception of several upper level classes from BFO and IAO, KOIO versions 1.X.X are limited in scope to classes of material entities spanning Knowledge Objects, parts of Knowledge Objects, and Collections of Knowledge Objects.

    It has yet to be determined whether development of KOIO subontologies and/or extensions of KOIO are the preferred method for modeling (a) other KGrid components besides Knowledge Objects and the subcompnent parts of other KGrid components, (b) actions and operations involving Knowledge Objects and KGrid components, and (c) relationships between actions and operations, components, and parts."
-
+

diff --git a/docs/annotationproperties/contributor___1944284134.html b/docs/annotationproperties/contributor___285822827.html similarity index 61% rename from docs/annotationproperties/contributor___1944284134.html rename to docs/annotationproperties/contributor___285822827.html index 1ff4a7b..c054af4 100644 --- a/docs/annotationproperties/contributor___1944284134.html +++ b/docs/annotationproperties/contributor___285822827.html @@ -4,10 +4,10 @@ Ontology Browser - + - +

- + + -

Annotation Property: dc:contributor

+

Annotation Property: dcterms:contributor

-
-

Usage (7)

+
+

Usage (5)

    -
  • dc:contributor "Allen Flynn"
    • -
  • dc:contributor "Carl Lagoze"
    • -
  • dc:contributor "Charles P. Friedman"
    • -
  • dc:contributor "George Meng"
    • -
  • dc:contributor "Greg Farris"
    • -
  • dc:contributor "Nate Gittlen"
    • -
  • dc:contributor "Peter Boisvert"
    • +
  • dcterms:contributor "Allen Flynn"
    • +
  • dcterms:contributor "Charles P. Friedman"
    • +
  • dcterms:contributor "Farid Seifi"
    • +
  • dcterms:contributor "Marisa Conte"
    • +
  • dcterms:contributor "Peter Boisvert"
-
+
-
+

OWL HTML inside

diff --git a/docs/annotationproperties/definition___344110101.html b/docs/annotationproperties/definition___344110101.html deleted file mode 100644 index 031430e..0000000 --- a/docs/annotationproperties/definition___344110101.html +++ /dev/null @@ -1,73 +0,0 @@ - - - -Ontology Browser - - - - - - - - - -

Annotation Property: definition

- -
-

Annotations (2)

-
-
    -
  • rdfs:label "definition" @en
    • -
  • definition "definition, def., an Information Artifact about a Thing that annotates the Thing with an Aristotelian description of the Thing"
    • -
-
-
- - -
-

Usage (24)

-
-
    -
  • Artifact definition "Artifact =def. a MaterialEntity created or modified or selected by some agent to realize a certain FUNCTION or ROLE (Examples: a key, a lock, a digital file stored on a particular computing machine, a screwdriver)


    Smith & Ceusters, Aboutness: Towards Foundations for the Information Artifact Ontology"     
    • -
  • Bundle definition "Bundle = def., A collection of two or more descriptive statements (sometimes referred to as statements of metadata) about one or more Information Artifacts" 
    • -
  • Collection definition "Collection = def. an InformationArtifact comprised of two or more InformationArtifacts and at least one collectionIdentifier" 
    • -
  • ComputableKnowledgeResource definition "ComputableKnowledgeResource = def. An InformationArtifact about some computable knowledge" 
    • -
  • DeploymentInstruction definition "DeploymentInstructions = def. , an InformationArtifact that describes how to deploy a KnowledgeObject in the Knowledge Grid platform" 
    • -
  • Implementation definition "Implementation = def., an InformationArtifact that functions as part of a KnowledgeObject AND is comprised of a Payload with a payloadVersionIdentifier" 
    • -
  • InformationArtifact definition "An InformationArtifact = def., an Artifact that is the IndependentContinuant bearer created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO" 
    • -
  • KnowledgeObject definition "KnowledgeObject = def., an Information Artifact capable of serving a role as the atomic unit of computable knowledge and therefore comprised of at least one KnowledgeObjectImplementation" 
    • -
  • KnowledgeObjectCollection definition "Knowledge Object Collection = def., two or more Knowledge Objects with a collectionIdentifer" 
    • -
  • Payload definition "Payload = def. , an ComputableKnowledgeResource represented in manner that is machine-interpretable" 
    • -
  • ProvenanceBundle definition "Provenance Bundle = def, A Bundle of two or more descriptive statements (sometimes referred to as metadata statements) about the ORIGIN(S) of one or more Information Artifacts" 
    • -
  • ServiceSpecification definition "ServiceSpecification = def. , an InformationArtifact that describes a computational service that is somehow enabled by a KnowledgeObject" 
    • -
  • adapterType definition "adapterType = def., a label describing a Knowledge Grid adapter" 
    • -
  • endpoints definition "endpoints = def., is a virtual address for a service that accepts communications back and forth across the network" 
    • -
  • hasDeploymentInstruction definition "hasDeploymentInstruction, def., a relation that holds between a whole KnowledgeObject and its DeploymentInstruction parts" 
    • -
  • hasImplementation definition "hasImplementation, def., a relation that holds between a whole KnowledgeObject and its Implementation part(s)" 
    • -
  • hasPart definition "def = a core relation that holds between a whole and its part

    BFO"     
    • -
  • hasPayload definition "hasPayload, def., a relation that holds between a whole KnowledgeObject and its Payload part(s)" 
    • -
  • hasServiceSpecification definition "hasServiceSpecification, def., a relation that holds between a whole KnowledgeObject and its ServiceSpecification part" 
    • -
  • isDeploymentInstructionPartOf definition "isDeploymentInstruction, def., a core relation that holds between an DeploymentInstruction that is part of a Knowledge Object and its whole" 
    • -
  • isImplementationPartOf definition "isImplementation, def., a core relation that holds between an Implementation that is part of a Knowledge Object and its whole" 
    • -
  • isPartOf definition "isPartOf, def., a core relation that holds between a part and its whole

    BFO"     
    • -
  • isPayloadPartOf definition "isPayload, def., a core relation that holds between an Payload that is part of a Knowledge Object and its whole" 
    • -
  • isServiceSpecificationPartOf definition "isServiceSpecification, def., a core relation that holds between a ServiceSpecification that is part of a Knowledge Object and its whole" 
    • -
-
-
- -
-

-OWL HTML inside -

- - diff --git a/docs/annotationproperties/index-koio.html b/docs/annotationproperties/index-koio.html index 4b380c3..04ece85 100644 --- a/docs/annotationproperties/index-koio.html +++ b/docs/annotationproperties/index-koio.html @@ -23,11 +23,11 @@

koio: annotationproperties (10)

-
+
    -
  • dc:contributor
    • -
  • dc:title
    • -
  • definition
    • +
  • dcterms:contributor
    • +
  • dcterms:publisher
    • +
  • dcterms:title
  • IAO_0000115
  • owl:versionInfo
  • rdfs:comment
    • diff --git a/docs/annotationproperties/index.html b/docs/annotationproperties/index.html index e5611b4..6360e61 100644 --- a/docs/annotationproperties/index.html +++ b/docs/annotationproperties/index.html @@ -1,11 +1,11 @@

    All Annotationproperties (10)

    -
    +
      -
    • dc:contributor
      • -
    • dc:title
      • -
    • definition
      • +
    • dcterms:contributor
      • +
    • dcterms:publisher
      • +
    • dcterms:title
    • IAO_0000115
    • owl:versionInfo
    • rdfs:comment
      • diff --git a/docs/annotationproperties/isDefinedBy___449337134.html b/docs/annotationproperties/isDefinedBy___449337134.html index 46bcdb6..951861b 100644 --- a/docs/annotationproperties/isDefinedBy___449337134.html +++ b/docs/annotationproperties/isDefinedBy___449337134.html @@ -22,108 +22,29 @@

      Annotation Property: rdfs:isDefinedBy

      -
      -

      Usage (33)

      +
      +

      Usage (6)

      -
      +

      diff --git a/docs/annotationproperties/label___653429740.html b/docs/annotationproperties/label___653429740.html index ce84602..7c72639 100644 --- a/docs/annotationproperties/label___653429740.html +++ b/docs/annotationproperties/label___653429740.html @@ -22,54 +22,27 @@

      Annotation Property: rdfs:label

      -
      -

      Usage (41)

      +
      +

      Usage (14)

      -
      +

      diff --git a/docs/annotationproperties/publisher___-666464116.html b/docs/annotationproperties/publisher___-666464116.html new file mode 100644 index 0000000..a84e32b --- /dev/null +++ b/docs/annotationproperties/publisher___-666464116.html @@ -0,0 +1,39 @@ + + + +Ontology Browser + + + + + + +

      + + +

      Annotation Property: dcterms:publisher

      + +
      +

      Usage (1)

      +
      +
        +
      • dcterms:publisher "Knowledge Systems Lab. Department of Learning Health Sciences. University of Michigan Medical School.
        https://knowledge-systems.lab.medicine.umich.edu/"
        • +
      +
      +
      + +
      +

      +OWL HTML inside +

      + + diff --git a/docs/annotationproperties/seeAlso___-1773693006.html b/docs/annotationproperties/seeAlso___-1773693006.html index bee8f78..61b6700 100644 --- a/docs/annotationproperties/seeAlso___-1773693006.html +++ b/docs/annotationproperties/seeAlso___-1773693006.html @@ -22,17 +22,16 @@

      Annotation Property: rdfs:seeAlso

      -
      -

      Usage (4)

      +
      +

      Usage (3)

        -
      • documentation rdfs:seeAlso "from SPDX find term Documentation:
        http://spdx.org/rdf/terms#documentation
        from SPDX find term hasDocumentation: https://spdx.github.io/spdx-spec/v3.0.1/model/Core/Vocabularies/RelationshipType/"         
      • test rdfs:seeAlso "Test Case, Test, Test Code, Code To Be Tested
        https://dev.nemo.inf.ufes.br/seon/ROoST.html

        Souza ÉF, Falbo RD, Vijaykumar NL. ROoST: Reference ontology on software testing. Applied Ontology. 2017 Jan 1;12(1):59-90."         
      • 'has documentation' rdfs:seeAlso "from SPDX find term hasDocumentation: https://spdx.github.io/spdx-spec/v3.0.1/model/Core/Vocabularies/RelationshipType/
        from SPDX find term Documentation:
        http://spdx.org/rdf/terms#documentation"         
      • 'has test' rdfs:seeAlso "from SPDX find term hasTest:
        https://spdx.github.io/spdx-spec/v3.0.1/model/Core/Vocabularies/RelationshipType/"         
      -
      +

      diff --git a/docs/annotationproperties/title___-345035421.html b/docs/annotationproperties/title___-2003496728.html similarity index 84% rename from docs/annotationproperties/title___-345035421.html rename to docs/annotationproperties/title___-2003496728.html index 72b6916..c45e4a1 100644 --- a/docs/annotationproperties/title___-345035421.html +++ b/docs/annotationproperties/title___-2003496728.html @@ -20,13 +20,13 @@

    -

    Annotation Property: dc:title

    +

    Annotation Property: dcterms:title

    Usage (1)

      -
    • dc:title "Knowledge Object Implementation Ontology (KOIO)"
      • +
    • dcterms:title "Knowledge Object Implementation Ontology (KOIO)"
    diff --git a/docs/annotationproperties/versionInfo___407301298.html b/docs/annotationproperties/versionInfo___407301298.html index f0b9e8f..ed8dfce 100644 --- a/docs/annotationproperties/versionInfo___407301298.html +++ b/docs/annotationproperties/versionInfo___407301298.html @@ -26,7 +26,7 @@

    Usage (1)

    diff --git a/docs/classes/Artifact___194373812.html b/docs/classes/Artifact___194373812.html index d18ad83..752d7d6 100644 --- a/docs/classes/Artifact___194373812.html +++ b/docs/classes/Artifact___194373812.html @@ -20,16 +20,16 @@
    -

    Class: Artifact

    +

    Class: artifact

    Annotations (3)

      +
    • IAO_0000115 "Artifact =def. a MaterialEntity created or modified or selected by some agent to realize a certain FUNCTION or ROLE (Examples: a key, a lock, a digital file stored on a particular computing machine, a screwdriver)


      Smith & Ceusters, Aboutness: Towards Foundations for the Information Artifact Ontology"      (xsd:string)
    • rdfs:isDefinedBy http://purl.obolibrary.org/obo/iao.owl
      • -
    • rdfs:label "Artifact" @en
      • -
    • definition "Artifact =def. a MaterialEntity created or modified or selected by some agent to realize a certain FUNCTION or ROLE (Examples: a key, a lock, a digital file stored on a particular computing machine, a screwdriver)


      Smith & Ceusters, Aboutness: Towards Foundations for the Information Artifact Ontology"
      • +
    • rdfs:label "artifact" @en
    diff --git a/docs/classes/Bundle___-935486620.html b/docs/classes/Bundle___-935486620.html deleted file mode 100644 index 3897c13..0000000 --- a/docs/classes/Bundle___-935486620.html +++ /dev/null @@ -1,53 +0,0 @@ - - - -Ontology Browser - - - - - - - - - -

    Class: Bundle

    - -
    -

    Annotations (3)

    -
    -
      -
    • rdfs:isDefinedBy http://kgrid.org/koio/1.0.0/ - -
      • -
    • rdfs:label "Bundle" @en
      • -
    • definition "Bundle = def., A collection of two or more descriptive statements (sometimes referred to as statements of metadata) about one or more Information Artifacts"
      • -
    -
    -
    - - -
    -

    Superclasses (1)

    -
    - -
    -
    - -
    -

    -OWL HTML inside -

    - - diff --git a/docs/classes/Collection___1610680704.html b/docs/classes/Collection___1610680704.html index 85428fe..8cf7a2b 100644 --- a/docs/classes/Collection___1610680704.html +++ b/docs/classes/Collection___1610680704.html @@ -20,17 +20,17 @@
    -

    Class: Collection

    +

    Class: collection

    Annotations (3)

      +
    • IAO_0000115 "Collection = def. an InformationArtifact comprised of two or more InformationArtifacts and at least one collectionIdentifier"(xsd:string)
    • rdfs:isDefinedBy http://kgrid.org/koio/1.0.0/
      • -
    • rdfs:label "Collection" @en
      • -
    • definition "Collection = def. an InformationArtifact comprised of two or more InformationArtifacts and at least one collectionIdentifier"
      • +
    • rdfs:label "collection" @en
    @@ -40,7 +40,7 @@

    Annotations (3)

    Superclasses (1)

    diff --git a/docs/classes/ComputableKnowledgeResource___1421463014.html b/docs/classes/ComputableKnowledgeResource___1421463014.html deleted file mode 100644 index 3ed0fa3..0000000 --- a/docs/classes/ComputableKnowledgeResource___1421463014.html +++ /dev/null @@ -1,53 +0,0 @@ - - - -Ontology Browser - - - - - - - - - -

    Class: ComputableKnowledgeResource

    - -
    -

    Annotations (3)

    -
    -
      -
    • rdfs:isDefinedBy http://kgrid.org/koio/1.0.0/ - -
      • -
    • rdfs:label "ComputableKnowledgeResource" @en
      • -
    • definition "ComputableKnowledgeResource = def. An InformationArtifact about some computable knowledge"
      • -
    -
    -
    - - -
    -

    Superclasses (1)

    -
    - -
    -
    - -
    -

    -OWL HTML inside -

    - - diff --git a/docs/classes/DeploymentInstruction___1497279275.html b/docs/classes/DeploymentInstruction___1497279275.html deleted file mode 100644 index 3c9de6b..0000000 --- a/docs/classes/DeploymentInstruction___1497279275.html +++ /dev/null @@ -1,80 +0,0 @@ - - - -Ontology Browser - - - - - - - - - -

    Class: DeploymentInstruction

    - -
    -

    Annotations (3)

    -
    -
      -
    • rdfs:isDefinedBy http://kgrid.org/koio/1.0.0/ - -
      • -
    • rdfs:label "DeploymentInstruction" @en
      • -
    • definition "DeploymentInstructions = def. , an InformationArtifact that describes how to deploy a KnowledgeObject in the Knowledge Grid platform"
      • -
    -
    -
    - - -
    -

    Superclasses (1)

    -
    - -
    -
    - - -
    -

    Disjoints (2)

    -
    -DeploymentInstruction, -KnowledgeObject
    -
    - - -
    -

    Members (1)

    -
    -UUIDDI01
    -
    - - -
    -

    Usage (3)

    -
    - -
    -
    - -
    -

    -OWL HTML inside -

    - - diff --git a/docs/classes/Documentation___-550071972.html b/docs/classes/Documentation___-550071972.html deleted file mode 100644 index 49dc766..0000000 --- a/docs/classes/Documentation___-550071972.html +++ /dev/null @@ -1,61 +0,0 @@ - - - -Ontology Browser - - - - - - - - - -

    Class: documentation

    - -
    -

    Annotations (3)

    -
    -
      -
    • IAO_0000115 "Documentation, def., an information content entity that conveys information, usually in a structured or semi-structured format, about some other thing."
      • -
    • rdfs:label "documentation"
      • -
    • rdfs:seeAlso "from SPDX find term Documentation:
      http://spdx.org/rdf/terms#documentation
      from SPDX find term hasDocumentation: https://spdx.github.io/spdx-spec/v3.0.1/model/Core/Vocabularies/RelationshipType/"
      • -
    -
    -
    - - -
    -

    Superclasses (1)

    -
    - -
    -
    - - -
    -

    Usage (1)

    -
    - -
    -
    - -
    -

    -OWL HTML inside -

    - - diff --git a/docs/classes/Implementation___2039871124.html b/docs/classes/Implementation___2039871124.html index 9c81808..501e348 100644 --- a/docs/classes/Implementation___2039871124.html +++ b/docs/classes/Implementation___2039871124.html @@ -20,17 +20,17 @@
    -

    Class: Implementation

    +

    Class: implementation

    Annotations (3)

      +
    • IAO_0000115 "def., a computer or machine processable file that is or informs a series of instructions that can be directly interpreted or executed."(xsd:string)
    • rdfs:isDefinedBy http://kgrid.org/koio/1.0.0/
      • -
    • rdfs:label "Implementation"
      • -
    • definition "Implementation = def., an InformationArtifact that functions as part of a KnowledgeObject AND is comprised of a Payload with a payloadVersionIdentifier"
      • +
    • rdfs:label "implementation"(xsd:string)
    @@ -40,7 +40,7 @@

    Annotations (3)

    Superclasses (1)

    @@ -49,34 +49,20 @@

    Superclasses (1)

    Disjoints (2)

    -Implementation, -KnowledgeObject
    +'knowledge object', +implementation
    -
    -

    Members (1)

    -
    -UUIDIMP01
    -
    - - -
    -

    Usage (9)

    +
    +

    Usage (2)

    -
    +

    diff --git a/docs/classes/InformationArtifact___-669107776.html b/docs/classes/InformationArtifact___-669107776.html index 2d22580..835dd23 100644 --- a/docs/classes/InformationArtifact___-669107776.html +++ b/docs/classes/InformationArtifact___-669107776.html @@ -20,17 +20,17 @@

    -

    Class: InformationArtifact

    +

    Class: 'information artifact'

    Annotations (4)

      +
    • IAO_0000115 "An InformationArtifact = def., an Artifact that is the IndependentContinuant bearer created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO"(xsd:string)
    • rdfs:comment "Per KOIO, Knowledge Objects are InformationArtifacts by definition."
    • rdfs:isDefinedBy http://purl.obolibrary.org/obo/iao.owl
      • -
    • rdfs:label "InformationArtifact" @en
      • -
    • definition "An InformationArtifact = def., an Artifact that is the IndependentContinuant bearer created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO"
      • +
    • rdfs:label "information artifact" @en
    @@ -40,11 +40,31 @@

    Annotations (4)

    Superclasses (1)

    + + + + +
    +

    Usage (1)

    +
    + +
    +
    +

    OWL HTML inside diff --git a/docs/classes/KnowledgeObjectCollection___486619773.html b/docs/classes/KnowledgeObjectCollection___486619773.html index ceb25aa..a4f2d15 100644 --- a/docs/classes/KnowledgeObjectCollection___486619773.html +++ b/docs/classes/KnowledgeObjectCollection___486619773.html @@ -20,17 +20,17 @@

    -

    Class: KnowledgeObjectCollection

    +

    Class: 'knowledge object collection'

    Annotations (3)

      +
    • IAO_0000115 "Knowledge Object Collection = def., two or more Knowledge Objects with a collectionIdentifer"(xsd:string)
    • rdfs:isDefinedBy http://kgrid.org/koio/1.0.0/
      • -
    • rdfs:label "KnowledgeObjectCollection" @en
      • -
    • definition "Knowledge Object Collection = def., two or more Knowledge Objects with a collectionIdentifer"
      • +
    • rdfs:label "knowledge object collection" @en
    @@ -40,7 +40,7 @@

    Annotations (3)

    Superclasses (1)

    diff --git a/docs/classes/KnowledgeObject___49698815.html b/docs/classes/KnowledgeObject___49698815.html index 5051a7a..4a265f1 100644 --- a/docs/classes/KnowledgeObject___49698815.html +++ b/docs/classes/KnowledgeObject___49698815.html @@ -20,72 +20,60 @@
    -

    Class: KnowledgeObject

    +

    Class: 'knowledge object'

    Annotations (3)

      +
    • IAO_0000115 "KnowledgeObject = def., an Information Artifact capable of serving a role as the atomic unit of computable knowledge and therefore comprised of at least one KnowledgeObjectImplementation"(xsd:string)
    • rdfs:isDefinedBy http://kgrid.org/koio/1.0.0/
      • -
    • rdfs:label "KnowledgeObject" @en
      • -
    • definition "KnowledgeObject = def., an Information Artifact capable of serving a role as the atomic unit of computable knowledge and therefore comprised of at least one KnowledgeObjectImplementation"
      • +
    • rdfs:label "knowledge object" @en
    -
    -

    Superclasses (1)

    + +
    -
    -

    Disjoints (5)

    +
    +

    Disjoints (2)

    -DeploymentInstruction, -Implementation, -KnowledgeObject, -Payload, -ServiceSpecification
    -
    +'knowledge object', +implementation
    +
    -
    -

    Members (3)

    +
    +

    Members (2)

    bmiKO, -tobaccoKO, -UUIDKO1
    -
    +tobaccoKO
    +
    -
    -

    Usage (13)

    +
    +

    Usage (4)

    -
    +

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+
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SWO_0000085

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Usage (1)

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SWO_0000085

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'KOIO version'

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Usage (1)

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Usage (1)

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SWO_0000085

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Usage (1)

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Usage (1)

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Usage (1)

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+OWL HTML inside +

+ + diff --git a/docs/individuals/tobaccoKO___1978188987.html b/docs/individuals/tobaccoKO___1978188987.html index ac244df..1316436 100644 --- a/docs/individuals/tobaccoKO___1978188987.html +++ b/docs/individuals/tobaccoKO___1978188987.html @@ -26,37 +26,37 @@

Types (1)

- - @@ -66,7 +66,7 @@

SWO_0000085

@@ -86,78 +86,99 @@

SWO_0000085

- - - -
-

title

+ +
- - + + +
+

SWO_0000085

+
+ +
+
+ + + @@ -177,7 +198,7 @@

'has service'

diff --git a/docs/individuals/tobaccoKnowledge___-1584305941.html b/docs/individuals/tobaccoKnowledge___-1584305941.html index 5b6deee..1872092 100644 --- a/docs/individuals/tobaccoKnowledge___-1584305941.html +++ b/docs/individuals/tobaccoKnowledge___-1584305941.html @@ -32,6 +32,37 @@

Types (1)

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Usage (2)

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RO_0002502

@@ -46,7 +77,7 @@

SWO_0000085

@@ -56,7 +87,7 @@

@@ -67,7 +98,7 @@

Usage (2)

RO_0002502

@@ -77,7 +108,7 @@

SWO_0000085

@@ -87,38 +118,81 @@

- - + + + + + +
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'KOIO version'

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Usage (2)

@@ -129,69 +203,71 @@

Usage (2)

Usage (2)

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hasDeploymentInstruction

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Usage (2)

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Usage (2)

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SWO_0000085

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hasImplementation

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title

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Usage (2)

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Usage (2)

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Usage (2)

Usage (2)

@@ -213,50 +289,61 @@

Usage (2)

Usage (2)

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'has knowledge'

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Usage (2)

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'has service'

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Usage (2)

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Usage (2)

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RO_0002502

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  • tobaccoKnowledge
    • +
+
+
+ + @@ -266,7 +353,7 @@

@@ -287,7 +374,7 @@

'has service'

@@ -297,7 +384,7 @@

@@ -308,7 +395,7 @@

Usage (2)

SWO_0000085

@@ -318,7 +405,7 @@

diff --git a/docs/individuals/tobacco_cli.ts___-1695286663.html b/docs/individuals/tobacco_cli.ts___-1695286663.html new file mode 100644 index 0000000..e79694e --- /dev/null +++ b/docs/individuals/tobacco_cli.ts___-1695286663.html @@ -0,0 +1,411 @@ + + + +Ontology Browser + + + + + + + + + +

Individual: tobacco_cli.ts

+ +
+

Types (1)

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Usage (1)

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SWO_0000085

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SWO_0000085

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'KOIO version'

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Usage (1)

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Usage (1)

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SWO_0000085

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Usage (1)

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Usage (1)

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SWO_0000085

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+
    +
  • tobacco_cli.ts
    • +
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Usage (1)

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SWO_0000085

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Usage (1)

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Usage (1)

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+OWL HTML inside +

+ + diff --git a/docs/objectproperties/RO_0002502___-47773661.html b/docs/objectproperties/RO_0002502___-47773661.html index 53da38e..828d4e2 100644 --- a/docs/objectproperties/RO_0002502___-47773661.html +++ b/docs/objectproperties/RO_0002502___-47773661.html @@ -56,9 +56,9 @@

Ranges (1)

Usage (3)

diff --git a/docs/objectproperties/SWO_0000085___59336949.html b/docs/objectproperties/SWO_0000085___59336949.html index c47016e..32e0181 100644 --- a/docs/objectproperties/SWO_0000085___59336949.html +++ b/docs/objectproperties/SWO_0000085___59336949.html @@ -26,27 +26,29 @@

Annotations (1)

    -
  • IAO_0000115 "implemented by, def., is the relationship between a service and a piece of software which includes an implementation of that service for use when the software is executed."
    • +
  • IAO_0000115 "Note: KSL added this definition to contextualize the definition below from SWO.
    implemented by, def., is the relationship between an abstract KO component and a piece of software (or computer processable content) which includes an implementation of that abstract KO component for use when processed by a computer."
-
-

Domains (1)

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+

Domains (3)

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@@ -56,11 +58,11 @@

Ranges (1)

Usage (5)

diff --git a/docs/objectproperties/SWO_0004001___59455861.html b/docs/objectproperties/SWO_0004001___59455861.html new file mode 100644 index 0000000..e111014 --- /dev/null +++ b/docs/objectproperties/SWO_0004001___59455861.html @@ -0,0 +1,49 @@ + + + +Ontology Browser + + + + + + + + + +

Object Property: SWO_0004001

+ +
+

Domains (1)

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Ranges (1)

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+OWL HTML inside +

+ + diff --git a/docs/objectproperties/hasDeploymentInstruction___1153342673.html b/docs/objectproperties/hasDeploymentInstruction___1153342673.html deleted file mode 100644 index 3ff0891..0000000 --- a/docs/objectproperties/hasDeploymentInstruction___1153342673.html +++ /dev/null @@ -1,105 +0,0 @@ - - - -Ontology Browser - - - - - - - - - -

Object Property: hasDeploymentInstruction

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Annotations (3)

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  • rdfs:isDefinedBy http://kgrid.org/koio/1.0.0/ - -
    • -
  • rdfs:label "hasDeploymentInstruction"
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  • definition "hasDeploymentInstruction, def., a relation that holds between a whole KnowledgeObject and its DeploymentInstruction parts"
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- - diff --git a/docs/objectproperties/hasDocumentation___87918850.html b/docs/objectproperties/hasDocumentation___87918850.html index a75a6e9..70301b2 100644 --- a/docs/objectproperties/hasDocumentation___87918850.html +++ b/docs/objectproperties/hasDocumentation___87918850.html @@ -34,23 +34,25 @@

Annotations (3)

- @@ -66,14 +68,18 @@

Superproperties (1)

-
-

Usage (1)

+
+

Usage (5)

-
+

diff --git a/docs/objectproperties/hasImplementation___342750126.html b/docs/objectproperties/hasImplementation___342750126.html deleted file mode 100644 index ebcb3bb..0000000 --- a/docs/objectproperties/hasImplementation___342750126.html +++ /dev/null @@ -1,105 +0,0 @@ - - - -Ontology Browser - - - - - - -

- - -

Object Property: hasImplementation

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-

Annotations (3)

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-
    -
  • rdfs:isDefinedBy http://kgrid.org/koio/1.0.0/ - -
    • -
  • rdfs:label "hasImplementation"
    • -
  • definition "hasImplementation, def., a relation that holds between a whole KnowledgeObject and its Implementation part(s)"
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Property Characteristics (1)

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- - diff --git a/docs/objectproperties/hasKnowledge___1822278086.html b/docs/objectproperties/hasKnowledge___1822278086.html index 2cb7a9b..c8e5a52 100644 --- a/docs/objectproperties/hasKnowledge___1822278086.html +++ b/docs/objectproperties/hasKnowledge___1822278086.html @@ -37,7 +37,7 @@

Annotations (2)

Domains (1)

@@ -63,16 +63,17 @@

Superproperties (1)

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Usage (3)

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Usage (4)

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diff --git a/docs/objectproperties/hasPart___2055343215.html b/docs/objectproperties/hasPart___2055343215.html deleted file mode 100644 index 50f73d8..0000000 --- a/docs/objectproperties/hasPart___2055343215.html +++ /dev/null @@ -1,77 +0,0 @@ - - - -Ontology Browser - - - - - - -

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Object Property: hasPart

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Annotations (3)

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Property Characteristics (1)

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- - diff --git a/docs/objectproperties/hasPayload___-1690753962.html b/docs/objectproperties/hasPayload___-1690753962.html deleted file mode 100644 index 2fe1013..0000000 --- a/docs/objectproperties/hasPayload___-1690753962.html +++ /dev/null @@ -1,105 +0,0 @@ - - - -Ontology Browser - - - - - - - - - -

Object Property: hasPayload

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Annotations (3)

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    -
  • rdfs:isDefinedBy http://kgrid.org/koio/1.0.0/ - -
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  • definition "hasPayload, def., a relation that holds between a whole KnowledgeObject and its Payload part(s)"
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- - diff --git a/docs/objectproperties/hasServiceSpecification___-366089014.html b/docs/objectproperties/hasServiceSpecification___-366089014.html deleted file mode 100644 index e1606b7..0000000 --- a/docs/objectproperties/hasServiceSpecification___-366089014.html +++ /dev/null @@ -1,94 +0,0 @@ - - - -Ontology Browser - - - - - - - - - -

Object Property: hasServiceSpecification

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Annotations (3)

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  • rdfs:isDefinedBy http://kgrid.org/koio/1.0.0/ - -
    • -
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  • definition "hasServiceSpecification, def., a relation that holds between a whole KnowledgeObject and its ServiceSpecification part"
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- - diff --git a/docs/objectproperties/hasService___1080101245.html b/docs/objectproperties/hasService___1080101245.html index 2891644..274f725 100644 --- a/docs/objectproperties/hasService___1080101245.html +++ b/docs/objectproperties/hasService___1080101245.html @@ -37,7 +37,7 @@

Annotations (2)

Domains (1)

@@ -67,9 +67,9 @@

Superproperties (1)

Usage (4)

diff --git a/docs/objectproperties/hasTest___2055466254.html b/docs/objectproperties/hasTest___2055466254.html index 7c7d013..910a3b3 100644 --- a/docs/objectproperties/hasTest___2055466254.html +++ b/docs/objectproperties/hasTest___2055466254.html @@ -38,8 +38,8 @@

Annotations (3)

Domains (3)

@@ -66,14 +66,16 @@

Superproperties (1)

-
-

Usage (1)

+
+

Usage (3)

-
+

diff --git a/docs/objectproperties/index-koio.html b/docs/objectproperties/index-koio.html index 46b843f..b327011 100644 --- a/docs/objectproperties/index-koio.html +++ b/docs/objectproperties/index-koio.html @@ -21,27 +21,18 @@

-

koio: objectproperties (17)

+

koio: objectproperties (8)

-
+ diff --git a/docs/objectproperties/index.html b/docs/objectproperties/index.html index 9c2bc40..b2b96e6 100644 --- a/docs/objectproperties/index.html +++ b/docs/objectproperties/index.html @@ -1,25 +1,16 @@
-

All Objectproperties (17)

+

All Objectproperties (8)

-
+ diff --git a/docs/objectproperties/isDeploymentInstructionPartOf___1138174539.html b/docs/objectproperties/isDeploymentInstructionPartOf___1138174539.html deleted file mode 100644 index 9c450f2..0000000 --- a/docs/objectproperties/isDeploymentInstructionPartOf___1138174539.html +++ /dev/null @@ -1,104 +0,0 @@ - - - -Ontology Browser - - - - - - - - - -

Object Property: isDeploymentInstructionPartOf

- -
-

Annotations (3)

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    -
  • rdfs:isDefinedBy http://kgrid.org/koio/1.0.0/ - -
    • -
  • rdfs:label "isDeploymentInstructionPartOf"
    • -
  • definition "isDeploymentInstruction, def., a core relation that holds between an DeploymentInstruction that is part of a Knowledge Object and its whole"
    • -
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Property Characteristics (1)

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Usage (2)

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-OWL HTML inside -

- - diff --git a/docs/objectproperties/isImplementationPartOf___1654476424.html b/docs/objectproperties/isImplementationPartOf___1654476424.html deleted file mode 100644 index a473bef..0000000 --- a/docs/objectproperties/isImplementationPartOf___1654476424.html +++ /dev/null @@ -1,104 +0,0 @@ - - - -Ontology Browser - - - - - - - - - -

Object Property: isImplementationPartOf

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Annotations (3)

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-
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  • rdfs:isDefinedBy http://kgrid.org/koio/1.0.0/ - -
    • -
  • rdfs:label "isImplementationPartOf"
    • -
  • definition "isImplementation, def., a core relation that holds between an Implementation that is part of a Knowledge Object and its whole"
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Property Characteristics (1)

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- - diff --git a/docs/objectproperties/isPartOf___1037151670.html b/docs/objectproperties/isPartOf___1037151670.html deleted file mode 100644 index cd5d17d..0000000 --- a/docs/objectproperties/isPartOf___1037151670.html +++ /dev/null @@ -1,77 +0,0 @@ - - - -Ontology Browser - - - - - - - - - -

Object Property: isPartOf

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Annotations (3)

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Property Characteristics (1)

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Usage (5)

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- - diff --git a/docs/objectproperties/isPayloadPartOf___1659698704.html b/docs/objectproperties/isPayloadPartOf___1659698704.html deleted file mode 100644 index dadffd2..0000000 --- a/docs/objectproperties/isPayloadPartOf___1659698704.html +++ /dev/null @@ -1,104 +0,0 @@ - - - -Ontology Browser - - - - - - - - - -

Object Property: isPayloadPartOf

- -
-

Annotations (3)

-
-
    -
  • rdfs:isDefinedBy http://kgrid.org/koio/1.0.0/ - -
    • -
  • rdfs:label "isPayloadPartOf"
    • -
  • definition "isPayload, def., a core relation that holds between an Payload that is part of a Knowledge Object and its whole"
    • -
-
-
- - -
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Property Characteristics (1)

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-
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  • Transitive (isPayloadPartOf)
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Domains (1)

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Ranges (1)

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Inverses (1)

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Superproperties (1)

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Usage (2)

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-OWL HTML inside -

- - diff --git a/docs/objectproperties/isServiceSpecificationPartOf___335074980.html b/docs/objectproperties/isServiceSpecificationPartOf___335074980.html deleted file mode 100644 index ca53900..0000000 --- a/docs/objectproperties/isServiceSpecificationPartOf___335074980.html +++ /dev/null @@ -1,104 +0,0 @@ - - - -Ontology Browser - - - - - - - - - -

Object Property: isServiceSpecificationPartOf

- -
-

Annotations (3)

-
-
    -
  • rdfs:isDefinedBy http://kgrid.org/koio/1.0.0/ - -
    • -
  • rdfs:label "isServiceSpecificationPartOf"
    • -
  • definition "isServiceSpecification, def., a core relation that holds between a ServiceSpecification that is part of a Knowledge Object and its whole"
    • -
-
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Property Characteristics (1)

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Domains (1)

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Ranges (1)

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Inverses (1)

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Superproperties (1)

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Usage (2)

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-OWL HTML inside -

- - diff --git a/docs/ontologies/index.html b/docs/ontologies/index.html index 8c7812b..ba849e0 100644 --- a/docs/ontologies/index.html +++ b/docs/ontologies/index.html @@ -1,9 +1,9 @@

All Ontologies (1)

-
+ diff --git a/docs/ontologies/koio___-1832827647.html b/docs/ontologies/koio___-1832827647.html index aeda4de..433ddd9 100644 --- a/docs/ontologies/koio___-1832827647.html +++ b/docs/ontologies/koio___-1832827647.html @@ -4,10 +4,10 @@ Ontology Browser - + - + - +
+

koio

-

https://kgrid.org/koio
http://www.kgrid.org/koio/2.0/koio.owl

+

https://kgrid.org/koio
http://www.kgrid.org/koio/2.1/koio.owl

Loaded from file:////wsl.localhost/Ubuntu/home/faridsei/dev/code/koio/koio.owl

-
-

Annotations (10)

+
+

Annotations (9)

    -
  • dc:contributor "Allen Flynn"
    • -
  • dc:contributor "Carl Lagoze"
    • -
  • dc:contributor "Charles P. Friedman"
    • -
  • dc:contributor "George Meng"
    • -
  • dc:contributor "Greg Farris"
    • -
  • dc:contributor "Nate Gittlen"
    • -
  • dc:contributor "Peter Boisvert"
    • -
  • dc:title "Knowledge Object Implementation Ontology (KOIO)"
    • +
  • dcterms:contributor "Allen Flynn"
    • +
  • dcterms:contributor "Charles P. Friedman"
    • +
  • dcterms:contributor "Farid Seifi"
    • +
  • dcterms:contributor "Marisa Conte"
    • +
  • dcterms:contributor "Peter Boisvert"
    • +
  • dcterms:publisher "Knowledge Systems Lab. Department of Learning Health Sciences. University of Michigan Medical School.
    https://knowledge-systems.lab.medicine.umich.edu/"
    • +
  • dcterms:title "Knowledge Object Implementation Ontology (KOIO)"
  • rdfs:comment "KOIO is an ontology describing Knowledge Objects and their parts as they are implemented in the Knoweldge Grid (KGrid) reference platform. As such, KOIO is subject to evolve as KGrid reference platform development evolves.

    The primary overriding objective of developing and implementing KOIO is to describe Knowledge Objects and their parts in enough detail to achieve a degree interoperability that is sufficient to enable Knowledge Objects to be incorporated into multiple platforms, including but not limited to, the KGrid reference platform

    With the exception of several upper level classes from BFO and IAO, KOIO versions 1.X.X are limited in scope to classes of material entities spanning Knowledge Objects, parts of Knowledge Objects, and Collections of Knowledge Objects.

    It has yet to be determined whether development of KOIO subontologies and/or extensions of KOIO are the preferred method for modeling (a) other KGrid components besides Knowledge Objects and the subcompnent parts of other KGrid components, (b) actions and operations involving Knowledge Objects and KGrid components, and (c) relationships between actions and operations, components, and parts."
    • -
  • owl:versionInfo "2.0"(xsd:decimal)
    • +
  • owl:versionInfo "2.1"(xsd:decimal)
-
+
@@ -48,22 +47,22 @@

References

@@ -83,7 +82,7 @@

Imports (2)

-
+

OWL HTML inside

diff --git a/examples/bmi_calculator_v_1/bmiKODocumentation.md b/examples/bmi_calculator_v_1/bmiKODocumentation.md new file mode 100644 index 0000000..c69cc05 --- /dev/null +++ b/examples/bmi_calculator_v_1/bmiKODocumentation.md @@ -0,0 +1,3 @@ +The documentation for bmi knowledge object goes here + +The metadata in this example is created usiing KOIO 1.0 \ No newline at end of file diff --git a/examples/bmi_calculator_v_2/bmiKODocumentation.md b/examples/bmi_calculator_v_2/bmiKODocumentation.md new file mode 100644 index 0000000..5cfcbf9 --- /dev/null +++ b/examples/bmi_calculator_v_2/bmiKODocumentation.md @@ -0,0 +1,3 @@ +The documentation for bmi knowledge object goes here + +The metadata in this example is created usiing KOIO 2.0 \ No newline at end of file diff --git a/examples/bmi_calculator_v_2/metadata.json b/examples/bmi_calculator_v_2/metadata.json index 882f4dc..ef70960 100644 --- a/examples/bmi_calculator_v_2/metadata.json +++ b/examples/bmi_calculator_v_2/metadata.json @@ -3,7 +3,7 @@ "koio:kgrid":"2", "@type" : "koio:KnowledgeObject", "dc:identifier" : "ark:calculate_bmi", - "version" : "1.0.0", + "version" : "2.0.0", "dc:title" : "BMI Calculator", "koio:contributors" : "AIIT Team", "dc:description" : "Calculates BMI", diff --git a/examples/bmi_calculator_v_3/APIService/bmiKOAPIDocumentation.md b/examples/bmi_calculator_v_3/APIService/bmiKOAPIDocumentation.md new file mode 100644 index 0000000..fbe8553 --- /dev/null +++ b/examples/bmi_calculator_v_3/APIService/bmiKOAPIDocumentation.md @@ -0,0 +1,2 @@ +The documentation for bmi knowledge object's API service goes here + diff --git a/examples/bmi_calculator_v_3/APIService/deployment.yaml b/examples/bmi_calculator_v_3/APIService/deployment.yaml new file mode 100644 index 0000000..a2374c5 --- /dev/null +++ b/examples/bmi_calculator_v_3/APIService/deployment.yaml @@ -0,0 +1,6 @@ +/calculate70: + post: + engine: + name: org.kgrid.javascript-activator + artifact: index70.js + function: calculate70 \ No newline at end of file diff --git a/examples/bmi_calculator_v_3/APIService/index70.js b/examples/bmi_calculator_v_3/APIService/index70.js new file mode 100644 index 0000000..03f1688 --- /dev/null +++ b/examples/bmi_calculator_v_3/APIService/index70.js @@ -0,0 +1,79 @@ +import { bmi } from "../Knowledge/bmi.js"; +var config; +export function calculate70(inputs){ + var result = { + value : null + } + check(inputs, result); + if(result.resultCode == 1){ + return result; + } + var value = bmi(inputs[config.child_list[71].field],inputs[config.child_list[72].field]); + result = getResult(value); + result.resultCode = 0; + result.resultMsg = "success"; + return result; +} + + +function getResult(value){ + if(typeof(config.result) != "undefined"){ + if(typeof(config.result[value])!= "undefined"){ + return config.result[value]; + } + if(typeof(config.result["-1"])!= "undefined"){ + config.result["-1"].valueDetail.key = value; + config.result["-1"].valueDetail.result[0].desc = config.result["-1"].valueDetail.result[0].desc.format(value); + return config.result["-1"]; + } + } + var temp = {"valueDetail": {"key": value}} + return temp; +} + +String.prototype.format = function() { + if (arguments.length == 0) return this; + var param = arguments[0]; + var s = this; + if (typeof(param) == 'object') { + for (var key in param) s = s.replace(new RegExp("\\{" + key + "\\}", "g"), param[key]); + return s; + } else { + for (var i = 0; i < arguments.length; i++) s = s.replace(new RegExp("\\{" + i + "\\}", "g"), arguments[i]); + return s; + } +} + +function getConfig() { + //var executor = context.getExecutor("aiit-get_config/1.0.0/calculate340") ; + var obj = { + "zhyl96": 70 + }; + return {"id": 70, "title": "BMI 计算", "child_list": {"71": {"id": 71, "title": "weight(kg)", "field": "zhyl24", "data_type": 3, "parent_id": 70}, "72": {"id": 72, "title": "height(cm)", "field": "zhyl55", "data_type": 3, "parent_id": 70}}, "result": {}}; + //return executor.execute(obj); +} + +function check(inputs, result) { + config = getConfig(); + + if (typeof(config.child_list) == "undefined") { + result.resultMsg = "config error"; + result.resultCode = 1; + return; + } + for(var child in config.child_list){ + var field = config.child_list[child].field; + if (typeof(inputs[field]) == "undefined" || inputs[field] == null) { + result.resultMsg = "Wrong input, " + field + " must not be null"; + result.resultCode = 1; + break; + } + + var check = config.child_list[child].check; + if (typeof(check) != "undefined" && check.indexOf(inputs[field]) == -1) { + result.resultMsg = "Wrong input, " + field + " must be one of " + check; + result.resultCode = 1; + break; + } + } +} \ No newline at end of file diff --git a/examples/bmi_calculator_v_3/APIService/service.yaml b/examples/bmi_calculator_v_3/APIService/service.yaml new file mode 100644 index 0000000..76c3c88 --- /dev/null +++ b/examples/bmi_calculator_v_3/APIService/service.yaml @@ -0,0 +1,58 @@ +openapi: 3.0.2 +info: + version: '0.2' + title: BMI Calculator + description: Calculates BMI +servers: +- url: /endpoints/calculate_bmi + description: Calculates BMI +paths: + /calculate70: + post: + description: Calculates BMI + operationId: calculate70 + requestBody: + description: inputs + required: true + content: + application/json: + schema: + $ref: '#/components/schemas/input70' + responses: + '200': + description: response + content: + application/json: + schema: + $ref: '#/components/schemas/output70' + encoding: + recommendation: + contentType: charset=utf-8 +components: + schemas: + input70: + required: + - zhyl24 + - zhyl55 + properties: + zhyl24: + type: number + description: weight (kg) + zhyl55: + type: number + description: height (cm) + output70: + required: + - value + - resultCode + - resultMsg + properties: + value: + type: number + description: risk value + resultCode: + type: number + description: resultCode + resultMsg: + type: string + description: detail result message diff --git a/examples/bmi_calculator_v_3/CLIService/bmi_cli.ts b/examples/bmi_calculator_v_3/CLIService/bmi_cli.ts new file mode 100644 index 0000000..6e639ac --- /dev/null +++ b/examples/bmi_calculator_v_3/CLIService/bmi_cli.ts @@ -0,0 +1,43 @@ +import { Command } from "https://deno.land/x/cliffy@v1.0.0-rc.3/command/mod.ts"; +import { parse } from "https://deno.land/std@0.177.0/encoding/csv.ts"; +import { writeCSV } from "https://deno.land/x/csv/mod.ts"; +import { bmi } from "../Knowledge/bmi.js"; + +await new Command() + .command("batchProcess", "Use knowledge To Calculate Diabetes Diagnosis, in Batch ") + .option("--input_path ", "path to CSV input file",{required: true}) + .action(async (options) => { + + const csvFile = await Deno.readTextFile(options.input_path); + const array = parse(csvFile); + let output=[]; + for (let i = 1; i < array.length; i++) { + const row = array[i]; + const rowData : Record= {}; + + // Iterate over each column and create key-value pairs + for (let j = 0; j < array[0].length; j++) { + const label = array[0][j]; + const value = row[j]; + if (j>0) + rowData[label] = Number(value); + else + rowData[label] = value; + + } + output.push([row[0],bmi(rowData.height,rowData.weight)]) + } + + const f = await Deno.open("outfileBMI.csv", { + write: true, + create: true, + truncate: true, + }); + + await writeCSV(f, output); + + f.close(); + + } + ) + .parse(Deno.args); diff --git a/examples/bmi_calculator_v_3/Knowledge/bmi.js b/examples/bmi_calculator_v_3/Knowledge/bmi.js new file mode 100644 index 0000000..1e689ab --- /dev/null +++ b/examples/bmi_calculator_v_3/Knowledge/bmi.js @@ -0,0 +1,3 @@ +export function bmi(height,weight){ + return Math.floor(height/Math.pow(weight/100,2) * 100)/100; +} \ No newline at end of file diff --git a/examples/bmi_calculator_v_3/Knowledge/bmiKnowledgeDocumentation.md b/examples/bmi_calculator_v_3/Knowledge/bmiKnowledgeDocumentation.md new file mode 100644 index 0000000..7b684b3 --- /dev/null +++ b/examples/bmi_calculator_v_3/Knowledge/bmiKnowledgeDocumentation.md @@ -0,0 +1 @@ +The documentation for bmi knowledge goes here \ No newline at end of file diff --git a/examples/bmi_calculator_v_3/bmiJupiterNotebookTutorial.ipynb b/examples/bmi_calculator_v_3/bmiJupiterNotebookTutorial.ipynb new file mode 100644 index 0000000..a46a006 --- /dev/null +++ b/examples/bmi_calculator_v_3/bmiJupiterNotebookTutorial.ipynb @@ -0,0 +1,104 @@ +{ + "nbformat": 4, + "nbformat_minor": 0, + "metadata": { + "colab": { + "provenance": [] + }, + "kernelspec": { + "name": "python3", + "display_name": "Python 3" + }, + "language_info": { + "name": "python" + } + }, + "cells": [ + { + "cell_type": "markdown", + "source": [ + "# BMI Calculation\n", + "##What is BMI?\n", + "Body Mass Index (BMI) is a simple calculation used to assess whether a person has a healthy body weight for their height. It is commonly used in medical and fitness assessments.\n", + "\n", + "###BMI Formula:\n", + "$$\n", + "BMI = \\frac{\\text{weight (kg)}}{\\text{height (m)}^2}\n", + "$$\n", + "\n", + "Where:\n", + "\n", + "- **Weight** is measured in **kilograms (kg)**\n", + "- **Height** is measured in **meters (m)**\n", + "\n", + "## **BMI Categories**\n", + "\n", + "| **BMI Value** | **Category** |\n", + "|---------------|-----------------|\n", + "| **< 18.5** | Underweight |\n", + "| **18.5 - 24.9** | Normal Weight |\n", + "| **25 - 29.9** | Overweight |\n", + "| **≥ 30** | Obese |\n", + "\n", + "#Example Implementation" + ], + "metadata": { + "id": "cQNRq1LuLV-r" + } + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "RemW1sTbLT-3", + "outputId": "21c05622-c0e5-4e32-989a-2e0066893fa1" + }, + "outputs": [ + { + "output_type": "stream", + "name": "stdout", + "text": [ + "Enter your weight in kg: 65\n", + "Enter your height in meters: 1.82\n", + "Your BMI is: 19.62\n", + "Category: Normal weight\n" + ] + } + ], + "source": [ + "def calculate_bmi():\n", + " try:\n", + " weight = float(input(\"Enter your weight in kg: \"))\n", + " height = float(input(\"Enter your height in meters: \"))\n", + "\n", + " if weight <= 0 or height <= 0:\n", + " print(\"Weight and height must be positive numbers.\")\n", + " return\n", + "\n", + " bmi = weight / (height ** 2)\n", + "\n", + " # Determine BMI category\n", + " if bmi < 18.5:\n", + " category = \"Underweight\"\n", + " elif bmi < 24.9:\n", + " category = \"Normal weight\"\n", + " elif bmi < 29.9:\n", + " category = \"Overweight\"\n", + " else:\n", + " category = \"Obese\"\n", + "\n", + " print(f\"Your BMI is: {bmi:.2f}\")\n", + " print(f\"Category: {category}\")\n", + "\n", + " except ValueError:\n", + " print(\"Please enter valid numeric values.\")\n", + "\n", + "# Run the function\n", + "calculate_bmi()\n" + ] + } + ] +} \ No newline at end of file diff --git a/examples/bmi_calculator_v_3/bmiKODocumentation.md b/examples/bmi_calculator_v_3/bmiKODocumentation.md new file mode 100644 index 0000000..e041046 --- /dev/null +++ b/examples/bmi_calculator_v_3/bmiKODocumentation.md @@ -0,0 +1,3 @@ +The documentation for bmi knowledge object goes here + +The metadata in this example is created usiing KOIO 2.1 \ No newline at end of file diff --git a/examples/bmi_calculator_v_3/license.md b/examples/bmi_calculator_v_3/license.md new file mode 100644 index 0000000..e4c9741 --- /dev/null +++ b/examples/bmi_calculator_v_3/license.md @@ -0,0 +1,9 @@ +MIT license + +Copyright (c) 2024 Regents of the University of Michigan + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. \ No newline at end of file diff --git a/examples/bmi_calculator_v_3/metadata.json b/examples/bmi_calculator_v_3/metadata.json new file mode 100644 index 0000000..24394c1 --- /dev/null +++ b/examples/bmi_calculator_v_3/metadata.json @@ -0,0 +1,129 @@ +{ + "@context": "https://kgrid.org/koio/2.1/context", + "@id": "bmiKO", + "koio:KOIOVersion": "2.1", + "@type": "koio:KnowledgeObject", + "dc:identifier": "ark:calculate_bmi", + "dc:version": "3.0.0", + "dc:title": "BMI Calculator", + "dc:contributors": "AIIT Team", + "dc:description": "Calculates BMI", + "dc:date": "2025-02-06", + "schema:creator": { + "@id": "https://kgrid.org", + "@type": "team", + "schema:ame": "Knowledge Systems Lab", + "schema:affiliation": "Knowledge Systems Lab, University of Michigan Medical School", + "schema:email": "kgrid-developers@umich.edu" + }, + "dc:publisher": "Knowledge Systems Lab", + "dc:bibliographicCitation": "https://pubmed.ncbi.nlm.nih.gov/t34-349/", + "dc:license": "license.md", + "koio:hasService": [ + { + "@id": "_:APIService", + "@type": [ + "koio:Service", + "API" + ], + "dc:description": "This service is used through JavaScript Activator", + "hasServiceSpecification": "APIService/service.yaml", + "dependsOn": "_:bmiKnowledge", + "implementedBy": [ + { + "@id": "APIService", + "@type": [ + "koio:Implementation", + "https://kgrid.org/specs/activationSpec.html#object", + "javascript" + ] + } + ], + "koio:hasDocumentation": [ + { + "@id": "bmiKOAPIDocumentation.md", + "@type": "koio:InformationArtifact", + "dc:title": "Knowledge object's API service documentation", + "dc:description": "Instruction on how to use an activator to use API service" + } + ], + "koio:hasTest": [ + { + "@id": "tests/bmiTestAPIService.ts", + "dc:title": "API service test", + "@type": "koio:Test", + "dc:description": "These tests are written to test the implementation of API service and its usage." + } + ] + }, + { + "@id": "_:CLIService", + "@type": [ + "koio:Service" + ], + "dependsOn": "_:bmiKnowledge", + "implementedBy": [ + { + "@id": "CLIService/bmi_cli.ts", + "@type": [ + "koio:Implementation", + "cli" + ] + } + ] + } + ], + "koio:hasKnowledge": { + "@id": "-:bmiKnowledge", + "@type": "koio:Knowledge", + "implementedBy": { + "@id": "Knowledge/bmi.js", + "@type": [ + "JavaScript", + "function" + ] + }, + "schema:creator": { + "@type": "team", + "schema:name": "DISPLAY Lab" + }, + "koio:hasDocumentation": [ + { + "@id": "bmiKnowledgeDocumentation.md", + "@type": "koio:InformationArtifact", + "dc:title": "BMI Knowledge documentation", + "dc:description": "Documentation for bmi formula and how it is implemented as a function." + } + ], + "koio:hasTest": [ + { + "@id": "tests/bmiKnowledgeTest.ts", + "dc:title": "knowledge test", + "@type": "koio:Test", + "dc:description": "These tests are written to test the implementation of bmi formula." + } + ] + }, + "koio:hasDocumentation": [ + { + "@id": "bmiKODocumentation.md", + "@type": "koio:InformationArtifact", + "dc:title": "Knowledge object documentation", + "dc:description": "Knowledge object read me file." + }, + { + "@id": "bmiJupiterNotebookTutorial.ipynb", + "@type": "koio:InformationArtifact", + "dc:title": "BMI Calculation", + "dc:description": "An interactive jupiter notebook tutorial for BMI calculation." + } + ], + "koio:hasTest": [ + { + "@id": "tests/bmiKOTest.ts", + "dc:title": "KO test", + "@type": "koio:Test", + "dc:description": "These tests are written to test the usage of the knowledge object and provide examples on how to use it." + } + ] +} \ No newline at end of file diff --git a/examples/bmi_calculator_v_3/tests/bmiKOTest.ts b/examples/bmi_calculator_v_3/tests/bmiKOTest.ts new file mode 100644 index 0000000..aae4004 --- /dev/null +++ b/examples/bmi_calculator_v_3/tests/bmiKOTest.ts @@ -0,0 +1 @@ +//Knowledge object general tests go here \ No newline at end of file diff --git a/examples/bmi_calculator_v_3/tests/bmiKnowledgeTest.ts b/examples/bmi_calculator_v_3/tests/bmiKnowledgeTest.ts new file mode 100644 index 0000000..1089045 --- /dev/null +++ b/examples/bmi_calculator_v_3/tests/bmiKnowledgeTest.ts @@ -0,0 +1 @@ +//bmi Knowledge tests go here \ No newline at end of file diff --git a/examples/readme.md b/examples/readme.md new file mode 100644 index 0000000..b0aaad2 --- /dev/null +++ b/examples/readme.md @@ -0,0 +1,4 @@ +Note: +Different examples in this folder use different versions of KOIO. Look at the context link or koio:KOIOVersion in the metadata file for each example to find out which version of KOIO is used to creat each of these examples. + +The examples that are created using the current version of the KOIO are used to create individuals in the OWL file and also to create tests. \ No newline at end of file diff --git a/examples/tobacco/cli_service/batchinput.csv b/examples/tobacco_v_1/cli_service/batchinput.csv similarity index 100% rename from examples/tobacco/cli_service/batchinput.csv rename to examples/tobacco_v_1/cli_service/batchinput.csv diff --git a/examples/tobacco/cli_service/cli.ts b/examples/tobacco_v_1/cli_service/cli.ts similarity index 100% rename from examples/tobacco/cli_service/cli.ts rename to examples/tobacco_v_1/cli_service/cli.ts diff --git a/examples/tobacco/knowledge/tobacco.js b/examples/tobacco_v_1/knowledge/tobacco.js similarity index 100% rename from examples/tobacco/knowledge/tobacco.js rename to examples/tobacco_v_1/knowledge/tobacco.js diff --git a/examples/tobacco/metadata.json b/examples/tobacco_v_1/metadata.json similarity index 97% rename from examples/tobacco/metadata.json rename to examples/tobacco_v_1/metadata.json index 35f7760..9fdae3d 100644 --- a/examples/tobacco/metadata.json +++ b/examples/tobacco_v_1/metadata.json @@ -4,7 +4,7 @@ "@type" : "koio:KnowledgeObject", "dc:title" : "QALY Gain By Stop Using Tobacco", "dc:identifier" : "ark:tobacco", - "version" : "1.3", + "version" : "1.0", "dc:description" : "Quality-Adjusted Life Year Gain By Stop Using Tobacco", "koio:contributors" : "Dr. John Doe", "koio:keywords" : [ "QALY", "Tobacco" ], diff --git a/examples/tobacco_v_2/cli_service/batchinput.csv b/examples/tobacco_v_2/cli_service/batchinput.csv new file mode 100644 index 0000000..b468624 --- /dev/null +++ b/examples/tobacco_v_2/cli_service/batchinput.csv @@ -0,0 +1,6 @@ +id,age,gender,race,racelc,racebc,edu,emp,famlc,smokeyear,quityear,cigpday,bmi,hypertension,cad,famaaa,diabetes,pad,carotid,cerebrovascular,hxbngnbiopsy,biopsyathyperplasia,fambc,sexpartner,fulltmpregnancy,ageat1stbirth,oralcontraceptivecurrent,HPVpositive,colitis,fap,hiv,famcrc,totalcholesterol,hdl,ldl,hicholesterol,sbp,htmedication,a1c,clinical_risk,hiv_risk,cg_risk,syphilis_risk,flu_risk,pneumonia_risk,alcohol_abuse,sexual_risk +TR01-patient-S01,65,1,0,0,1,2,1,2,30,0,20,25,1,1,1,1,1,0,1,1,1,2,1,1,2,1,0,0,1,1,0,200,30,80,1,110,0,0.057,0,0,0,0,0,0,1,1 +TR01-patient-S02,65,0,0,0,1,2,1,2,30,0,20,25,1,1,1,1,1,0,1,1,1,2,1,1,2,1,0,0,1,1,0,200,30,80,1,110,0,0.057,0,0,0,0,0,0,1,1 +TR01-patient-S03,70,1,0,0,1,2,1,2,30,0,20,22,1,1,1,1,1,0,1,1,1,2,0,0,2,1,0,0,1,1,0,200,30,80,1,110,0,0.057,0,0,0,0,0,0,1,1 +TR01-patient-S04,50,0,0,0,0,5,0,0,0,0,0,23.96023669,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,175,55,80,0,120,0,0,0,0,0,0,0,0,1,0 +TR01-patient-S05,-10,0,0,0,0,5,0,0,0,0,0,23.96023669,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,175,55,80,0,120,0,0,0,0,0,0,0,0,1,0 diff --git a/examples/tobacco_v_2/cli_service/tobacco_cli.ts b/examples/tobacco_v_2/cli_service/tobacco_cli.ts new file mode 100644 index 0000000..d0a4e9f --- /dev/null +++ b/examples/tobacco_v_2/cli_service/tobacco_cli.ts @@ -0,0 +1,72 @@ +import { Command } from "https://deno.land/x/cliffy@v1.0.0-rc.3/command/mod.ts"; +import {tobaccoQALY } from "../knowledge/tobacco.js"; +import { parse } from "https://deno.land/std@0.177.0/encoding/csv.ts"; +import { writeCSV } from "https://deno.land/x/csv/mod.ts"; + + +await new Command() + .name("Knowledge object - QALY Gain By Stop Using Tobacco") + .version("1.0.0") + .description("Quality-Adjusted Life Year Gain By Stop Using Tobacco") + + .command("qalyValue", "Use Knowledge To Calculate Quality-Adjusted Life Year Gain By Stop Using Tobacco") + .option("--json_input ", "JSON input string",{required: true}) + .example( + "Execute qalyValue command from source file, with example input", + "deno run --allow-read cli.ts qalyValue --json_input='{ \"features\": { \"age\": 65, \"gender\": 1, \"race\": 0, \"smokeyear\": 30, \"quityear\": 0, \"cigpday\": 20, \"diabetes\": 1, \"totalcholesterol\": 200, \"hdl\": 30, \"sbp\": 110, \"htmedication\": 0, \"alcohol_abuse\": 1 } }'" + ) + .example( + "Execute qalyValue command from installed cli called tobacco, with example input", + "tobacco qalyValue --json_input='{ \"features\": { \"age\": 65, \"gender\": 1, \"race\": 0, \"smokeyear\": 30, \"quityear\": 0, \"cigpday\": 20, \"diabetes\": 1, \"totalcholesterol\": 200, \"hdl\": 30, \"sbp\": 110, \"htmedication\": 0, \"alcohol_abuse\": 1 } }'" + ) + .action((options) => { + const input_data = JSON.parse(options.json_input); + console.log("Quality-Adjusted Life Year Gain By Stop Using Tobacco Is",tobaccoQALY(input_data.features)) + } + ) + + .command("batchProcess", "Use knowledge To Calculate Quality-Adjusted Life Year Gain By Stop Using Tobacco in batch ") + .option("--input_path ", "path to CSV input file",{required: true}) + .example( + "Execute batchProcess command from source file, with example input file", + "deno run --allow-read --allow-write cli.ts batchProcess --input_path='batchinput.csv'" + ) + .example( + "Execute batchProcess command from installed cli called tobacco, with example input file", + "tobacco batchProcess --input_path='batchinput.csv'" + ) + .action(async (options) => { + + const csvFile = await Deno.readTextFile(options.input_path); + const array = parse(csvFile); + let output=[]; + for (let i = 1; i < array.length; i++) { + const row = array[i]; + const rowData : Record= {}; + + // Iterate over each column and create key-value pairs + for (let j = 0; j < array[0].length; j++) { + const label = array[0][j]; + const value = row[j]; + rowData[label] = value; + } + output.push([row[0],tobaccoQALY(rowData)]) + } + + const f = await Deno.open("outfile.csv", { + write: true, + create: true, + truncate: true, + }); + + await writeCSV(f, output); + + f.close(); + + } + ) + .parse(Deno.args); + + + +//deno run --allow-read cli.ts --help \ No newline at end of file diff --git a/examples/tobacco_v_2/knowledge/tobacco.js b/examples/tobacco_v_2/knowledge/tobacco.js new file mode 100644 index 0000000..84f93f6 --- /dev/null +++ b/examples/tobacco_v_2/knowledge/tobacco.js @@ -0,0 +1,12 @@ +export function tobaccoQALY(features) { + if ((features.smokeyear > 0) && (features.quityear == 0) && (features.cigpday > 0)){ + let x = -0.0624067*features.age - 1.314849*(features.gender==0) + 0.0112053*features.age*(features.gender==0) + 5.455188*(features.cigpday < 15) + 8.53844*( (15 <= features.cigpday) && (features.cigpday < 25) ) + 11.44078*(features.cigpday >= 25) - 0.0502293*features.age*(features.cigpday < 15) - 0.0791994*features.age*( (15 <= features.cigpday) && (features.cigpday < 25) ) - 0.1073951*features.age*(features.cigpday >= 25) + 2.765361*(features.gender==0)*(features.cigpday < 15) + 2.598462*(features.gender==0)*( (15 <= features.cigpday) && (features.cigpday < 25) ) + 5.994661*(features.gender==0)*(features.cigpday >= 25) - 0.027659*features.age*(features.gender==0)*(features.cigpday < 15) - 0.0260393*features.age*(features.gender==0)*( (15 <= features.cigpday) && (features.cigpday < 25) ) - 0.061088*features.age*(features.gender==0)*(features.cigpday >= 25) + 6.808624 + if (x > 1){ + return x + } else { + return 1 + } + }else { + return 0 + } +} \ No newline at end of file diff --git a/examples/tobacco_v_2/license.md b/examples/tobacco_v_2/license.md new file mode 100644 index 0000000..e4c9741 --- /dev/null +++ b/examples/tobacco_v_2/license.md @@ -0,0 +1,9 @@ +MIT license + +Copyright (c) 2024 Regents of the University of Michigan + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. \ No newline at end of file diff --git a/examples/tobacco_v_2/metadata.json b/examples/tobacco_v_2/metadata.json new file mode 100644 index 0000000..183095b --- /dev/null +++ b/examples/tobacco_v_2/metadata.json @@ -0,0 +1,55 @@ +{ + "@context": "https://kgrid.org/koio/2.1/context", + "@id": "tobaccoKO", + "koio:KOIOVersion": "2.1", + "@type": "koio:KnowledgeObject", + "dc:identifier": "ark:tobacco", + "version": "2.0.0", + "dc:title": "QALY Gain By Stop Using Tobacco", + "koio:contributors": "Dr. John Doe", + "dc:description": "Quality-Adjusted Life Year Gain By Stop Using Tobacco", + "dc:date": "2025-02-11", + "schema:creator": { + "@id": "https://kgrid.org", + "@type": "team", + "schema:ame": "Knowledge Systems Lab", + "schema:affiliation": "Knowledge Systems Lab, University of Michigan Medical School", + "schema:email": "kgrid-developers@umich.edu" + }, + "dc:publisher": "Knowledge Systems Lab", + "dc:bibliographicCitation": "https://pubmed.ncbi.nlm.nih.gov/a234567/", + "dc:license": "license.md", + "koio:hasService": [ + { + "@id": "_:CLIService", + "@type": [ + "koio:Service" + ], + "dependsOn": "_:tobaccoKnowledge", + "implementedBy": [ + { + "@id": "cli_service/tobacco_cli.ts", + "@type": [ + "koio:Implementation", + "cli" + ] + } + ] + } + ], + "koio:hasKnowledge": { + "@id": "_:tobaccoKnowledge", + "@type": "koio:Knowledge", + "implementedBy": { + "@id": "knowledge/tobacco.js", + "@type": [ + "JavaScript", + "function" + ] + }, + "schema:creator": { + "@type": "team", + "schema:name": "DISPLAY Lab" + } + } +} \ No newline at end of file diff --git a/koio.graph b/koio.graph index be4a845..971b745 100644 --- a/koio.graph +++ b/koio.graph @@ -1,5 +1,4 @@ Optional.of(https://kgrid.org/koio) -https://kgrid.org/koio#KnowledgeRepresentation,1862.0,80.0 https://kgrid.org/koio#Knowledge,1402.2156475443996,-3.987461167602308 http://www.ebi.ac.uk/swo/SWO_9000050,1609.3402500613392,-135.71904918159714 https://kgrid.org/koio#Implementation,1387.8301759251583,155.60901145562465 @@ -11,8 +10,7 @@ http://purl.obolibrary.org/obo/BFO_0000001,674.1048332298195,-83.52921098574048 https://kgrid.org/koio#InformationArtifact,1130.2486559223419,146.49355797405315 https://kgrid.org/koio#Service,1612.9576602132227,-76.6418168293101 http://purl.obolibrary.org/obo/BFO_0000040,936.4032421359365,80.22280036929494 -https://kgrid.org/koio#KnowledgeObject,1123.5187337597426,-87.82952268905595 -https://kgrid.org/koio#ServiceSpecification,1387.0301864956461,288.4857004681565 +https://kgrid.org/koio#KnowledgeObject,1121.9395822717888,30.606838907479275 http://purl.obolibrary.org/obo/IAO_0000030,1036.6764876478105,-254.3850006803916 https://kgrid.org/koio#Test,1586.1616218042054,-245.27026658548513 http://purl.obolibrary.org/obo/BFO_0000031,865.4026095391185,-187.08207102056994 diff --git a/koio.owl b/koio.owl index ca68e3d..4eb3627 100644 --- a/koio.owl +++ b/koio.owl @@ -13,23 +13,23 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" - xmlns:terms="http://purl.org/dc/terms/" + xmlns:dcterms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:edamontology="http://edamontology.org#"> - + - Allen Flynn - Carl Lagoze - Charles P. Friedman - George Meng - Greg Farris - Nate Gittlen - Peter Boisvert - Knowledge Object Implementation Ontology (KOIO) + Knowledge Systems Lab. Department of Learning Health Sciences. University of Michigan Medical School. +https://knowledge-systems.lab.medicine.umich.edu/ + Allen Flynn + Charles P. Friedman + Farid Seifi + Marisa Conte + Peter Boisvert + Knowledge Object Implementation Ontology (KOIO) KOIO is an ontology describing Knowledge Objects and their parts as they are implemented in the Knoweldge Grid (KGrid) reference platform. As such, KOIO is subject to evolve as KGrid reference platform development evolves. The primary overriding objective of developing and implementing KOIO is to describe Knowledge Objects and their parts in enough detail to achieve a degree interoperability that is sufficient to enable Knowledge Objects to be incorporated into multiple platforms, including but not limited to, the KGrid reference platform @@ -37,7 +37,7 @@ The primary overriding objective of developing and implementing KOIO is to descr With the exception of several upper level classes from BFO and IAO, KOIO versions 1.X.X are limited in scope to classes of material entities spanning Knowledge Objects, parts of Knowledge Objects, and Collections of Knowledge Objects. It has yet to be determined whether development of KOIO subontologies and/or extensions of KOIO are the preferred method for modeling (a) other KGrid components besides Knowledge Objects and the subcompnent parts of other KGrid components, (b) actions and operations involving Knowledge Objects and KGrid components, and (c) relationships between actions and operations, components, and parts. - 2.0 + 2.1 @@ -50,36 +50,14 @@ It has yet to be determined whether development of KOIO subontologies and/or ext /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - + - - - - definition - definition, def., an Information Artifact about a Thing that annotates the Thing with an Aristotelian description of the Thing - - - - + - implemented by, def., is the relationship between a service and a piece of software which includes an implementation of that service for use when the software is executed. + Note: KSL added this definition to contextualize the definition below from SWO. +implemented by, def., is the relationship between an abstract KO component and a piece of software (or computer processable content) which includes an implementation of that abstract KO component for use when processed by a computer. @@ -121,20 +101,6 @@ It has yet to be determined whether development of KOIO subontologies and/or ext - - - - - - - - - hasDeploymentInstruction - hasDeploymentInstruction, def., a relation that holds between a whole KnowledgeObject and its DeploymentInstruction parts - - - - @@ -154,19 +120,6 @@ http://spdx.org/rdf/terms#documentation - - - - - - - - hasImplementation - hasImplementation, def., a relation that holds between a whole KnowledgeObject and its Implementation part(s) - - - - @@ -179,34 +132,6 @@ http://spdx.org/rdf/terms#documentation - - - - - - - hasPart - def = a core relation that holds between a whole and its part - -BFO - - - - - - - - - - - - - hasPayload - hasPayload, def., a relation that holds between a whole KnowledgeObject and its Payload part(s) - - - - @@ -219,20 +144,6 @@ BFO - - - - - - - - - hasServiceSpecification - hasServiceSpecification, def., a relation that holds between a whole KnowledgeObject and its ServiceSpecification part - - - - @@ -249,81 +160,6 @@ https://spdx.github.io/spdx-spec/v3.0.1/model/Core/Vocabularies/RelationshipType - - - - - - - - isDeploymentInstructionPartOf - isDeploymentInstruction, def., a core relation that holds between an DeploymentInstruction that is part of a Knowledge Object and its whole - - - - - - - - - - - isImplementationPartOf - isImplementation, def., a core relation that holds between an Implementation that is part of a Knowledge Object and its whole - - - - - - - - - - isPartOf - isPartOf, def., a core relation that holds between a part and its whole - -BFO - - - - - - - - - - - - isPayloadPartOf - isPayload, def., a core relation that holds between an Payload that is part of a Knowledge Object and its whole - - - - - - - - - - - - - isServiceSpecificationPartOf - isServiceSpecification, def., a core relation that holds between a ServiceSpecification that is part of a Knowledge Object and its whole - - - - - - - - - - - - - - - - - - - - - - - - - - - The expected strings are "public" or "private" - - access - - - - - - - - - - adapterType - adapterType = def., a label describing a Knowledge Grid adapter - - - - - - - - - - From Dublin Core Metadata Element Set Version 1.1 - - contributors - - - - - - - - - - From Dublin Core Metadata Element Set Version 1.1 - - description - - - - - - - - - - - endpoints - endpoints = def., is a virtual address for a service that accepts communications back and forth across the network - - - - - + - - - - From Dublin Core Metadata Element Set Version 1.1 - - - - - - - - - - - From Dublin Core Metadata Element Set Version 1.1 - - keywords - - - - - - - - From Dublin Core Metadata Element Set Version 1.1 - - language - - - - - - - - - - From Dublin Core Metadata Element Set Version 1.1 - - owners - - - - - - - - - - From Dublin Core Metadata Element Set Version 1.1 - - title - - - - - - - - - - - From Dublin Core Metadata Element Set Version 1.1 - http://purl.org/dc/elements/1.1/identifier - versionIdentifier + + + The version of KOIO from which metadata is derived + KOIO version @@ -487,12 +196,12 @@ BFO - - Artifact - Artifact =def. a MaterialEntity created or modified or selected by some agent to realize a certain FUNCTION or ROLE (Examples: a key, a lock, a digital file stored on a particular computing machine, a screwdriver) + Artifact =def. a MaterialEntity created or modified or selected by some agent to realize a certain FUNCTION or ROLE (Examples: a key, a lock, a digital file stored on a particular computing machine, a screwdriver) -Smith & Ceusters, Aboutness: Towards Foundations for the Information Artifact Ontology +Smith & Ceusters, Aboutness: Towards Foundations for the Information Artifact Ontology + + artifact @@ -501,9 +210,9 @@ Smith & Ceusters, Aboutness: Towards Foundations for the Information Artifac + Collection = def. an InformationArtifact comprised of two or more InformationArtifacts and at least one collectionIdentifier - Collection - Collection = def. an InformationArtifact comprised of two or more InformationArtifacts and at least one collectionIdentifier + collection @@ -513,9 +222,9 @@ Smith & Ceusters, Aboutness: Towards Foundations for the Information Artifac + def., a computer or machine processable file that is or informs a series of instructions that can be directly interpreted or executed. - Implementation - def., a computer or machine processable file that is or informs a series of instructions that can be directly interpreted or executed. + implementation @@ -524,10 +233,10 @@ Smith & Ceusters, Aboutness: Towards Foundations for the Information Artifac + An InformationArtifact = def., an Artifact that is the IndependentContinuant bearer created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO Per KOIO, Knowledge Objects are InformationArtifacts by definition. - InformationArtifact - An InformationArtifact = def., an Artifact that is the IndependentContinuant bearer created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO + information artifact @@ -546,10 +255,15 @@ Smith & Ceusters, Aboutness: Towards Foundations for the Information Artifac - + + + + + + + KnowledgeObject = def., an Information Artifact capable of serving a role as the atomic unit of computable knowledge and therefore comprised of at least one KnowledgeObjectImplementation - KnowledgeObject - KnowledgeObject = def., an Information Artifact capable of serving a role as the atomic unit of computable knowledge and therefore comprised of at least one KnowledgeObjectImplementation + knowledge object @@ -558,19 +272,9 @@ Smith & Ceusters, Aboutness: Towards Foundations for the Information Artifac + Knowledge Object Collection = def., two or more Knowledge Objects with a collectionIdentifer - KnowledgeObjectCollection - Knowledge Object Collection = def., two or more Knowledge Objects with a collectionIdentifer - - - - - - - - - def., an implementation of knowledge. - knowledge representation + knowledge object collection @@ -587,17 +291,6 @@ A Service is a specification of what a self-contained piece of software does. - - - - - ServiceSpecification - ServiceSpecification = def. , an InformationArtifact that describes a computational service that is somehow enabled by a KnowledgeObject - - - - @@ -623,172 +316,179 @@ Souza ÉF, Falbo RD, Vijaykumar NL. ROoST: Reference ontology on software testin - + - - - - - - + + - + - + - + - - + + + + - + - + - + - + - + + + - + - - - - + + + + + + + + + 2.1 - + - - - - TrialTitle + + - + - + + + - + - - + + + + - + - + + + - + - - - - - - - + + - + - - - + + - + - + - + - - - - + + - + - - - + + - + - + - + - - + + + + + + - + - - + + + + - + - - + + + - + - + diff --git a/readme.md b/readme.md index 530caaf..50fa1b5 100644 --- a/readme.md +++ b/readme.md @@ -59,6 +59,7 @@ Here are the roles of people who will contribute in the development of this onto - Issue templates will be used to help contributors know all the details needed for their proposed changes (i.e. add term, add synonym, revise subclass relationship, new annotation, Obsolete a term, …) when adding a new issue - A branch will be created for the work needed to be done to complete each approved change - Changes are only considered complete and ready for merge to the main when the OWL file, documentation, tests, context files, graph and examples are updated + - Example in a released KOIO owl file will conform to the version of that file and only to the version of that file. - All existing and new tests should pass before commiting any changes to a branch. - Once the changes are finalized they will be merged to the main branch @@ -85,6 +86,7 @@ sudo apt install default-jre java -jar owl2jsonld-0.2.1-standalone.jar file:///path/to/owl/file/koio.owl -o context.json ``` +Note: path to owl file must be an IRI starting with `file://`. ## Tools - Ontology [validation service](http://iot.ee.surrey.ac.uk/SSNValidation/) - [JSON LD Playground](https://json-ld.org/playground/) diff --git a/tests/test_ontology.py b/tests/test_ontology.py index ba96775..d13091b 100644 --- a/tests/test_ontology.py +++ b/tests/test_ontology.py @@ -17,7 +17,7 @@ def graph(): def test_what_KOs_are_implemented_by_KOIO(graph): KO_list = set(graph.subjects( RDF.type,KOIO.KnowledgeObject)) - assert {KOIO.UUIDKO1, KOIO.tobaccoKO, KOIO.bmiKO} == KO_list + assert { KOIO.tobaccoKO, KOIO.bmiKO} == KO_list def test_what_KOs_have_at_least_one_service(graph): @@ -34,19 +34,28 @@ def test_what_KOs_have_at_least_a_service_of_type_API(graph): def test_what_services_are_implemented_for_a_specific_KO(graph): service_list = set(graph.objects( KOIO.tobaccoKO , KOIO.hasService)) - assert {KOIO.CLIService1} == service_list + assert {KOIO.tobaccoCLIService} == service_list def test_which_KO_is_implemented_by_a_specific_piece_of_software(graph): - KO = next(graph.subjects( KOIO.hasService / SWO.SWO_0000085 , URIRef("https://raw.githubusercontent.com/kgrid-lab/MCBK_2024_demo/main/tobacco/cli_service/cli.ts")),None) + KO = next(graph.subjects( KOIO.hasService / SWO.SWO_0000085 , URIRef("https://kgrid.org/koio#tobacco_cli.ts")),None) assert KOIO.tobaccoKO == KO def test_which_KO_bmiTest_belong_to(graph): - KO = next(graph.subjects( KOIO.hasTest , KOIO.bmiTest),None) + KO = next(graph.subjects( KOIO.hasTest , URIRef("https://kgrid.org/koio#bmiTestKO.ts")),None) assert KOIO.bmiKO == KO -def test_bmiKO_hasTest(graph): +def test_if_bmiKO_hasTest(graph): tests = next(graph.objects( KOIO.bmiKO , KOIO.hasTest),None) assert tests - - \ No newline at end of file +def test_which_KO_bmiDocumentation_belong_to(graph): + KO = next(graph.subjects( KOIO.hasDocumentation , URIRef("https://kgrid.org/koio#bmiKODocumentation.md")),None) + assert KOIO.bmiKO == KO + +def test_if_bmiKO_hasDocumentation(graph): + documents = next(graph.objects( KOIO.bmiKO , KOIO.hasDocumentation),None) + assert documents + +def test_that_toboccoKO_has_no_Documentation(graph): + documents = next(graph.objects( KOIO.tobaccoKO , KOIO.hasDocumentation),None) + assert not documents \ No newline at end of file From 445d0cf826d508dd28c565c0dba6c1a6efd35ef9 Mon Sep 17 00:00:00 2001 From: faridseifi <44787630+faridseifi@users.noreply.github.com> Date: Wed, 12 Feb 2025 11:45:57 -0500 Subject: [PATCH 4/4] Update readme.md --- readme.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/readme.md b/readme.md index 50fa1b5..48ce8c1 100644 --- a/readme.md +++ b/readme.md @@ -7,7 +7,7 @@ permalink: /index.html # KOIO - The Knowledge Object Implementation Ontology The [KOIO repository](https://github.com/kgrid/koio) is used for evolving, sharing, and managing KOIO. KOIO formally defines the structure of Knowledge Objects using linked data representations made available in canonical OWL files. -![test](https://github.com/user-attachments/assets/1d656312-ab07-48d9-98f3-2abd1e3aa523) +![image](https://github.com/user-attachments/assets/cd93852c-ad4c-4916-9df0-d1846e51b2b7) A Knowledge Object is a formally-stuctured information content resource that, when concretized, becomes a compound digital object. By intention, KOIO specifies a lightweight or minimalist user-oriented, computation-focused digital object container specifically for packaging and organizing machine-processable knowledge assets that include "code that runs."