├── .github ├── ISSUE_TEMPLATE │ └── new_tutorial.md └── workflows │ └── docs.yml ├── .gitignore ├── CITATION.cff ├── LICENSE ├── Makefile ├── README.md ├── archive_original_cpath_course ├── 00-overview │ └── README.md ├── 01-ScientificComputing │ ├── README.md │ ├── automation.md │ ├── dockersetup.md │ └── scientific-computing.md ├── 01a-Github │ ├── README.md │ ├── github-issues.md │ └── intro-to-github.md ├── 02-LinkedData │ ├── README.md │ ├── cpath.md │ ├── linked-data-landscape.md │ └── linked-data.md ├── 03-RDF │ ├── README.md │ ├── data.csv │ ├── linking-data.md │ └── tables-and-triples.md ├── 04-OntologyTheory │ ├── README.md │ ├── SearchingMondo.md │ ├── add-new-terms.md │ ├── appendix.md │ ├── class-description-view.md │ ├── clone-mond-repo.md │ ├── editing-mondo.md │ ├── github-workflow.md │ ├── images │ │ ├── Screen Shot 2021-04-22 at 10.04.26 PM.png │ │ ├── image1.png │ │ ├── image2.png │ │ └── image3.png │ ├── pull-request.md │ ├── reasoning.md │ └── tradeoff.png ├── 05-OntologyPractise │ ├── README.md │ └── example.owl ├── 06-OntologyDesign │ ├── README.md │ ├── ROBOT_tutorial.md │ ├── animals.tsv │ └── animals2.tsv ├── 07-Review │ ├── README.md │ ├── add-logical-axiom.md │ └── add-logical-axiom_part2.md ├── 08-OntologyDevelopment │ ├── README.md │ ├── ROBOT_tutorial_2.md │ └── practice │ │ ├── Makefile │ │ ├── complete.make │ │ └── templates │ │ ├── assay.tsv │ │ └── disease.tsv ├── 09-DiseasesAndPhenotypes │ ├── README.md │ ├── diseaseontologies.md │ ├── example.md │ └── ontologylandscape.md ├── 10-OntologyMappings │ ├── README.md │ ├── cancermapping.md │ ├── mappings.md │ ├── new-term-request-mondo.md │ ├── new-term-request-obi.md │ └── semantic_etl.md ├── 11-KnowledgeGraphs │ ├── README.md │ ├── Untitled.owl │ ├── exercise.md │ ├── img │ │ ├── neo_properties.png │ │ └── uberon_contraints.png │ ├── insight.md │ ├── kgs.md │ └── person.owl ├── 12-Review │ ├── README.md │ └── modules.md └── README.md ├── docs ├── 404.html ├── config │ └── template.md ├── contributing.md ├── courses │ ├── icbo2021.md │ ├── icbo2022.md │ ├── icbo2023.md │ ├── icbo2024.md │ ├── monarch-obo-training.md │ └── ontology-summit-2023.md ├── explanation │ ├── annotation-properties.md │ ├── existential-restrictions.md │ ├── intro-to-ontologies.md │ ├── logical-axiomatization.md │ ├── ontology-matching.md │ ├── owl-building-blocks.md │ ├── owl-format-variants.md │ ├── subClassOf-vs-equivalentTo.md │ ├── taxon-constraints-explainer.md │ ├── term-comments.md │ ├── which-ontology-to-use.md │ └── writing-good-issues.md ├── getting-started-obook.md ├── getting-started.md ├── howto │ ├── add-coc.md │ ├── add-new-slim.md │ ├── add-taxon-restrictions.md │ ├── are-two-entities-the-same.md │ ├── change-files-pull-request.md │ ├── clone-mondo-repo.md │ ├── create-new-term.md │ ├── create-ontology-from-scratch.md │ ├── create-permid-with-w3id.md │ ├── daily-curator-workflow.md │ ├── deal-with-large-ontologies.md │ ├── deploy-custom-obo-dashboard.md │ ├── edit-in-protege.md │ ├── embed-video.md │ ├── filter-text-file.md │ ├── fixing-conflicts.md │ ├── github-actions.md │ ├── github-create-fork.md │ ├── github-create-pull-request.md │ ├── idrange.md │ ├── install-protege.md │ ├── installing-elk-in-protege.md │ ├── merge-terms.md │ ├── obsolete-term.md │ ├── odk-add-orcidio-module.md │ ├── odk-create-repo.md │ ├── odk-migrate-to-odk.md │ ├── odk-setup.md │ ├── odk-update.md │ ├── ontology-overview.md │ ├── open-science-engineer.md │ ├── prettify.md │ ├── protege-browse-search.md │ ├── respectful-collaboration.md │ ├── revert-commit.md │ ├── review-disease-mappings.md │ ├── review-pull-request.md │ ├── run-odk-with-podman.md │ ├── screenshot.md │ ├── set-up-protege.md │ ├── setup-docker.md │ ├── setup-ontology-development-odk.md │ ├── switching-ontologies.md │ ├── term-request.md │ └── update-import.md ├── images │ ├── FHKB figures │ │ ├── Capture.PNG │ │ ├── class_hierachy_final_1.PNG │ │ ├── class_prop_hierachy_final.png │ │ ├── cousin.png │ │ ├── dragon.png │ │ ├── grandparent.png │ │ ├── images │ │ │ ├── NoteIcon.pdf │ │ │ ├── NoteIconSmall.png │ │ │ ├── TipIcon.pdf │ │ │ ├── VocabIcon.pdf │ │ │ ├── WarningIcon.pdf │ │ │ ├── WarningIcon.png │ │ │ ├── black_camera.png │ │ │ └── code.PNG │ │ ├── licence_logo.png │ │ ├── mother_in_law.png │ │ ├── new │ │ │ ├── childof_property.PNG │ │ │ ├── descendent_ancestor_defined_classes.PNG │ │ │ ├── event_name_hierarchy.PNG │ │ │ ├── prop_uncle.PNG │ │ │ ├── prophierarchyinlaw.PNG │ │ │ └── prophierparentage.PNG │ │ ├── old │ │ │ ├── childof_property.PNG │ │ │ ├── class_hierarchy.PNG │ │ │ ├── descendent_ancestor_defined_classes.PNG │ │ │ ├── event_name_hierarchy.PNG │ │ │ ├── halfsiblings.PNG │ │ │ ├── prop_uncle.PNG │ │ │ ├── property_hierarchy.PNG │ │ │ ├── prophierarchyinlaw.PNG │ │ │ ├── prophierarchyinlawInf.PNG │ │ │ └── prophierparentage.PNG │ │ ├── prop_hierarchy2.png │ │ ├── sex.png │ │ ├── sibling_path.png │ │ ├── siblings.png │ │ ├── sister_in_law.png │ │ ├── spouse.png │ │ └── uncle.png │ ├── Screen Shot 2021-04-22 at 10.04.26 PM.png │ ├── bash_start.png │ ├── changing_pr.png │ ├── changing_pr_commit.png │ ├── chatgpt_more_hallucination_aware.png │ ├── comment.png │ ├── custom_qc_example.png │ ├── custom_qc_example_solved.png │ ├── delphi_racoon_example.jpg │ ├── discussions │ │ ├── intro-to-ontologies │ │ │ ├── cardiac-glial-cell.png │ │ │ ├── definition-example.png │ │ │ ├── hindwing-subclass.png │ │ │ ├── insect-classification.png │ │ │ ├── leg-wing.png │ │ │ ├── neuron-multiple-inheritance.png │ │ │ ├── nose-classification.png │ │ │ ├── paramere.png │ │ │ ├── query-glial-genes.png │ │ │ └── tarsal-segments.png │ │ ├── logical-axiomatization │ │ │ ├── betz-pyramidal.png │ │ │ ├── dl-oxtrneuron.png │ │ │ └── oxtrsst-heirachy.png │ │ └── writing-tickets │ │ │ ├── bad-ticket.png │ │ │ └── good-ticket.png │ ├── disease-model.png │ ├── docker_memory.png │ ├── dosdp_spotted_coat.png │ ├── entity-mappings.png │ ├── entity_mapping.png │ ├── exomiser_tutorial_images │ │ ├── 10_windows.jpg │ │ ├── 11_windows.jpg │ │ ├── 1_mac.jpg │ │ ├── 1_windows.jpg │ │ ├── 2_mac.jpg │ │ ├── 2_windows.jpg │ │ ├── 3_mac.jpg │ │ ├── 3_windows.jpg │ │ ├── 4_windows.jpg │ │ ├── 5_windows.jpg │ │ ├── 6_mac.jpg │ │ ├── 6_windows.jpg │ │ ├── 7_mac.jpg │ │ ├── 7_windows.jpg │ │ ├── 8_mac.jpg │ │ ├── 8_windows.jpg │ │ ├── 9_windows.jpg │ │ ├── HTML_annotated_part2.jpg │ │ ├── HTML_annotated_part3.jpg │ │ └── HTML_annotation_part1.png │ ├── finding-vs-disorder.png │ ├── github organizations teams repos.png │ ├── github-organizations-teams-repos.png │ ├── github_qc_starting.png │ ├── howtoguides │ │ ├── TaxonRestriction │ │ │ ├── intaxon.png │ │ │ └── neverintaxon.png │ │ ├── createnewterm │ │ │ ├── annotations.png │ │ │ ├── logicalaxiom.png │ │ │ ├── newterm.png │ │ │ ├── ref.png │ │ │ └── subclassasserted.png │ │ ├── deploy-custom-dashboard-workflow.png │ │ └── obsolete │ │ │ ├── fig1.png │ │ │ ├── fig2.png │ │ │ ├── fig3.png │ │ │ ├── fig4.png │ │ │ ├── fig5.png │ │ │ └── fig6.png │ ├── image1.png │ ├── image2.png │ ├── image3.png │ ├── index.md │ ├── interdependent_projects.png │ ├── kg-synonyms.png │ ├── lexmatch │ │ └── foodon.png │ ├── linkml1.png │ ├── linkml2.png │ ├── linkml3.png │ ├── linkml4.png │ ├── linkml5.png │ ├── linkml6.png │ ├── llm_basic.png │ ├── llm_learn.png │ ├── mapping-predicates-cheatsheet.png │ ├── mapping-usecase-counting.png │ ├── mapping-usecase-kg.png │ ├── mapping_workflow.png │ ├── odk_docs_cato.png │ ├── odk_docs_pages_settings.png │ ├── odk_workflow_import.png │ ├── odk_workflow_release.png │ ├── odk_workflow_testing.png │ ├── ohmyzsh_start.png │ ├── open_science_contribution1.png │ ├── open_science_contribution2.png │ ├── other-images │ │ └── owl.jpg │ ├── project_ontologies.png │ ├── prompt-icon.jpg.sb-12c70a1b-fkHh2I │ ├── prompt-icon.png │ ├── reference │ │ ├── managing-issues │ │ │ ├── milestone.png │ │ │ ├── project-board.png │ │ │ └── superissue.png │ │ └── protege │ │ │ ├── protege-active-ontology-tab.png │ │ │ ├── protege-buttons.png │ │ │ ├── protege-entities-tab.png │ │ │ └── protege-new-entities-metadata.png │ ├── repo-landing-page.png │ ├── robot_report.png │ ├── robot_report2.png │ ├── screenshot-of-images-in-issues.png │ ├── semantic_spaces.png │ ├── tradeoff.png │ ├── tutorials │ │ ├── disjointness │ │ │ ├── Figure42.png │ │ │ ├── Figure43.png │ │ │ ├── Figure44.png │ │ │ ├── Figure45.png │ │ │ ├── Figure46.png │ │ │ └── Figure47.png │ │ ├── dl-query │ │ │ ├── Figure57.png │ │ │ ├── Figure58.png │ │ │ ├── Figure59.png │ │ │ ├── Figure60.png │ │ │ ├── Figure61.png │ │ │ ├── Figure62.png │ │ │ ├── Figure63.png │ │ │ ├── Figure64.png │ │ │ └── Figure65.png │ │ ├── existential-restrictions │ │ │ ├── ExistentialRestrictionsWithSubclassVSEquivalentTo.png │ │ │ ├── QualifiedExistentialRestriction.png │ │ │ └── QualifiedRestrictionExamples.png │ │ ├── sparql-llm │ │ │ └── basic_sparql_query-no-title.png │ │ ├── subClassOf-vs-equivalentTo │ │ │ ├── CsubClassOfD.png │ │ │ ├── CsubClassOfDExample.png │ │ │ ├── EquivalentTo.png │ │ │ ├── EquivalentToExample.png │ │ │ ├── IndividualOfCnotInD.png │ │ │ ├── IndividualOfDnotInC.png │ │ │ └── SubClassOfWhenNotToUse.png │ │ └── synonyms │ │ │ ├── Picture1.png │ │ │ ├── abbreviation.png │ │ │ ├── annotation.png │ │ │ ├── cancerterm.png │ │ │ ├── synonym-annotation-1.png │ │ │ ├── synonym-annotation-2.png │ │ │ ├── synonym-annotation-3.png │ │ │ ├── synonymannotation.png │ │ │ ├── synonyms.png │ │ │ ├── synonymscope.png │ │ │ ├── synonymtypeproperty.png │ │ │ ├── synonymtypepropertymondo.png │ │ │ ├── tongue.png │ │ │ └── winchester.png │ ├── under-construction.png │ └── upheno_model.png ├── index.md ├── lesson │ ├── analysing-linked-data.md │ ├── automating-ontology-workflows.md │ ├── chatgpt-ontology-curation.md │ ├── contributing-to-obo-ontologies.md │ ├── developing-an-obo-ontology.md │ ├── developing-application-ontologies.md │ ├── entity-matching.md │ ├── getting-hands-on.md │ ├── hackathon.md │ ├── licensing-data-and-software.md │ ├── linkml-helps-with-ontology-use.md │ ├── modelling-with-object-properties.md │ ├── ontology-design.md │ ├── ontology-development.md │ ├── ontology-fundamentals.md │ ├── ontology-pipelines.md │ ├── ontology-term-use.md │ ├── phenotype-data.md │ ├── rdf.md │ ├── semantic-database-fundamentals.md │ ├── synonyms.md │ ├── templates-for-obo.md │ ├── using-disease-and-phenotype-ontologies.md │ └── vocabularies-for-bioinformatics.md ├── overview.md ├── pathways │ ├── ai-powered-semantic-engineer.md │ ├── early-career-data-scientist.md │ ├── ontology-contributor.md │ ├── ontology-curator-go-style.md │ ├── ontology-curator-obi-style.md │ ├── ontology-curator.md │ ├── ontology-engineer.md │ └── pathways.md ├── reference │ ├── base-specification.md │ ├── catalog-xml.md │ ├── chatgpt-prompts-for-ontology-development.md │ ├── formatting-license.md │ ├── frequently-used-odk-commands.md │ ├── gh-actions-errors.md │ ├── git-faq.md │ ├── github-desktop.md │ ├── github-intro.md │ ├── glossary-of-terms.md │ ├── glossary.md │ ├── go-style-annotation-property-practice.md │ ├── llms.md │ ├── managing-issues.md │ ├── medical-ontology-landscape.md │ ├── mungall-blog-radar.md │ ├── obook-maturity-indicator.md │ ├── odk.md │ ├── ontology-curator.md │ ├── ontology-user.md │ ├── other-resources.md │ ├── outreach.md │ ├── protege-faq.md │ ├── protege-interface.md │ ├── reasoning.md │ ├── release-artefacts.md │ ├── semantic-engineering-toolbox.md │ ├── semantic-etl.md │ ├── sparql-basics.md │ ├── sparql-reference.md │ ├── synonym-validation.md │ ├── synonyms-properties.md │ ├── synonyms-types.md │ ├── tables-and-triples.md │ ├── troublehooting-robot.md │ └── wikidata.md ├── resources │ ├── fhkb │ │ ├── fhkb_chapter_10.owl │ │ ├── fhkb_chapter_2.owl │ │ ├── fhkb_chapter_3.owl │ │ ├── fhkb_chapter_4.owl │ │ ├── fhkb_chapter_5.owl │ │ ├── fhkb_chapter_6.owl │ │ ├── fhkb_chapter_7.owl │ │ ├── fhkb_chapter_8.owl │ │ └── fhkb_chapter_9.owl │ ├── obook-badge-development.json │ ├── obook-badge-draft.json │ ├── obook-badge-stable.json │ ├── odk.bat │ └── odk.sh ├── teaching │ └── case-studies.md └── tutorial │ ├── Delphi-method-ontology.md │ ├── basic-dl-query.md │ ├── biomappings.md │ ├── claude-code-getting-started.md │ ├── claude-code-linkml.md │ ├── claude-code-mcps.md │ ├── claude-code-slash-commands.md │ ├── curies.md │ ├── custom-qc.md │ ├── disjointness.md │ ├── dosdp-odk.md │ ├── dosdp-overview.md │ ├── dosdp-template.md │ ├── exomiser-tutorial.md │ ├── fhkb.md │ ├── github-fundamentals.md │ ├── github-issues.md │ ├── intro-cli-1.md │ ├── intro-cli-2.md │ ├── lexmatch-tutorial.md │ ├── linking-data.md │ ├── linking_data │ └── data.csv │ ├── managing-dynamic-imports-odk.md │ ├── managing-ontology-project.md │ ├── managing-ontology-releases-odk.md │ ├── migrating-ontology-to-odk.md │ ├── monarch-kg-neo4j-basics.md │ ├── named-entity-normalization.md │ ├── named-entity-recognition.md │ ├── named-entity-standardization.md │ ├── odk-toolbox.md │ ├── odk-tutorial-2.md │ ├── odk_tutorial_2 │ └── cato-odk.yaml │ ├── ontogpt-workshop.md │ ├── ontogpt.md │ ├── project-ontology-development.md │ ├── pull-requests.md │ ├── resources │ ├── BDK14-exercises │ │ ├── basic-classification │ │ │ └── ubiq-ligase-complex.owl │ │ ├── basic-disjoint │ │ │ └── bad-chromosome.owl │ │ ├── basic-dl-query │ │ │ └── cc.owl │ │ ├── basic-restriction │ │ │ ├── chromosome-parts-interim.owl │ │ │ ├── chromosomePartsInterimAS.owl │ │ │ └── er-sec-complex.owl │ │ ├── basic-subclass │ │ │ ├── chromosome-parts-interim.owl │ │ │ └── chromosome-parts.owl │ │ └── taxon-union │ │ │ └── taxslim-with-union.owl │ ├── biomappings │ │ ├── 1-front.png │ │ ├── 2-summarize.png │ │ ├── 3-search.png │ │ └── 4-commit.png │ ├── gilda │ │ ├── 1-web.png │ │ ├── 2-web-results.png │ │ ├── 3-web-context.png │ │ └── 4-web-context-results.png │ └── ner │ │ ├── 1-web.png │ │ └── 2-web-results.png │ ├── robot-tutorial-1.md │ ├── robot-tutorial-2.md │ ├── robot-tutorial-qc.md │ ├── robot_report │ ├── Makefile │ ├── complete.make │ └── templates │ │ ├── assay.tsv │ │ └── disease.tsv │ ├── robot_tutorial_1 │ ├── animals.tsv │ └── animals2.tsv │ ├── robot_tutorial_qc │ └── example.owl │ ├── setting-up-project-odk.md │ ├── sparql-llm.md │ ├── sparql-report-odk.md │ ├── sparql-report-robot.md │ ├── sparql.md │ ├── sssom-toolkit.md │ ├── sssom-tutorial.md │ └── units.md ├── mkdocs.yml └── odk.sh /.github/ISSUE_TEMPLATE/new_tutorial.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/.github/ISSUE_TEMPLATE/new_tutorial.md -------------------------------------------------------------------------------- /.github/workflows/docs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/.github/workflows/docs.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/.gitignore -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/CITATION.cff -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/LICENSE -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/README.md -------------------------------------------------------------------------------- /archive_original_cpath_course/00-overview/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/00-overview/README.md -------------------------------------------------------------------------------- /archive_original_cpath_course/01-ScientificComputing/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/01-ScientificComputing/README.md -------------------------------------------------------------------------------- /archive_original_cpath_course/01-ScientificComputing/automation.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/01-ScientificComputing/automation.md -------------------------------------------------------------------------------- /archive_original_cpath_course/01-ScientificComputing/dockersetup.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/01-ScientificComputing/dockersetup.md -------------------------------------------------------------------------------- /archive_original_cpath_course/01-ScientificComputing/scientific-computing.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/01-ScientificComputing/scientific-computing.md -------------------------------------------------------------------------------- /archive_original_cpath_course/01a-Github/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/01a-Github/README.md -------------------------------------------------------------------------------- /archive_original_cpath_course/01a-Github/github-issues.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/01a-Github/github-issues.md -------------------------------------------------------------------------------- /archive_original_cpath_course/01a-Github/intro-to-github.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/01a-Github/intro-to-github.md -------------------------------------------------------------------------------- /archive_original_cpath_course/02-LinkedData/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/02-LinkedData/README.md -------------------------------------------------------------------------------- /archive_original_cpath_course/02-LinkedData/cpath.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/02-LinkedData/cpath.md -------------------------------------------------------------------------------- /archive_original_cpath_course/02-LinkedData/linked-data-landscape.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/02-LinkedData/linked-data-landscape.md -------------------------------------------------------------------------------- /archive_original_cpath_course/02-LinkedData/linked-data.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/02-LinkedData/linked-data.md -------------------------------------------------------------------------------- /archive_original_cpath_course/03-RDF/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/03-RDF/README.md -------------------------------------------------------------------------------- /archive_original_cpath_course/03-RDF/data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/03-RDF/data.csv -------------------------------------------------------------------------------- /archive_original_cpath_course/03-RDF/linking-data.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/03-RDF/linking-data.md -------------------------------------------------------------------------------- /archive_original_cpath_course/03-RDF/tables-and-triples.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/03-RDF/tables-and-triples.md -------------------------------------------------------------------------------- /archive_original_cpath_course/04-OntologyTheory/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/04-OntologyTheory/README.md -------------------------------------------------------------------------------- /archive_original_cpath_course/04-OntologyTheory/SearchingMondo.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/04-OntologyTheory/SearchingMondo.md -------------------------------------------------------------------------------- /archive_original_cpath_course/04-OntologyTheory/add-new-terms.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/04-OntologyTheory/add-new-terms.md -------------------------------------------------------------------------------- /archive_original_cpath_course/04-OntologyTheory/appendix.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/04-OntologyTheory/appendix.md -------------------------------------------------------------------------------- /archive_original_cpath_course/04-OntologyTheory/class-description-view.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/04-OntologyTheory/class-description-view.md -------------------------------------------------------------------------------- /archive_original_cpath_course/04-OntologyTheory/clone-mond-repo.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/04-OntologyTheory/clone-mond-repo.md -------------------------------------------------------------------------------- /archive_original_cpath_course/04-OntologyTheory/editing-mondo.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/04-OntologyTheory/editing-mondo.md -------------------------------------------------------------------------------- /archive_original_cpath_course/04-OntologyTheory/github-workflow.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/04-OntologyTheory/github-workflow.md -------------------------------------------------------------------------------- /archive_original_cpath_course/04-OntologyTheory/images/Screen Shot 2021-04-22 at 10.04.26 PM.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/04-OntologyTheory/images/Screen Shot 2021-04-22 at 10.04.26 PM.png -------------------------------------------------------------------------------- /archive_original_cpath_course/04-OntologyTheory/images/image1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/04-OntologyTheory/images/image1.png -------------------------------------------------------------------------------- /archive_original_cpath_course/04-OntologyTheory/images/image2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/04-OntologyTheory/images/image2.png -------------------------------------------------------------------------------- /archive_original_cpath_course/04-OntologyTheory/images/image3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/04-OntologyTheory/images/image3.png -------------------------------------------------------------------------------- /archive_original_cpath_course/04-OntologyTheory/pull-request.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/04-OntologyTheory/pull-request.md -------------------------------------------------------------------------------- /archive_original_cpath_course/04-OntologyTheory/reasoning.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/04-OntologyTheory/reasoning.md -------------------------------------------------------------------------------- /archive_original_cpath_course/04-OntologyTheory/tradeoff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/04-OntologyTheory/tradeoff.png -------------------------------------------------------------------------------- /archive_original_cpath_course/05-OntologyPractise/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/05-OntologyPractise/README.md -------------------------------------------------------------------------------- /archive_original_cpath_course/05-OntologyPractise/example.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/05-OntologyPractise/example.owl -------------------------------------------------------------------------------- /archive_original_cpath_course/06-OntologyDesign/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/06-OntologyDesign/README.md -------------------------------------------------------------------------------- /archive_original_cpath_course/06-OntologyDesign/ROBOT_tutorial.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/06-OntologyDesign/ROBOT_tutorial.md -------------------------------------------------------------------------------- /archive_original_cpath_course/06-OntologyDesign/animals.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/06-OntologyDesign/animals.tsv -------------------------------------------------------------------------------- /archive_original_cpath_course/06-OntologyDesign/animals2.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/06-OntologyDesign/animals2.tsv -------------------------------------------------------------------------------- /archive_original_cpath_course/07-Review/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/07-Review/README.md -------------------------------------------------------------------------------- /archive_original_cpath_course/07-Review/add-logical-axiom.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/07-Review/add-logical-axiom.md -------------------------------------------------------------------------------- /archive_original_cpath_course/07-Review/add-logical-axiom_part2.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/07-Review/add-logical-axiom_part2.md -------------------------------------------------------------------------------- /archive_original_cpath_course/08-OntologyDevelopment/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/08-OntologyDevelopment/README.md -------------------------------------------------------------------------------- /archive_original_cpath_course/08-OntologyDevelopment/ROBOT_tutorial_2.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/08-OntologyDevelopment/ROBOT_tutorial_2.md -------------------------------------------------------------------------------- /archive_original_cpath_course/08-OntologyDevelopment/practice/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/08-OntologyDevelopment/practice/Makefile -------------------------------------------------------------------------------- /archive_original_cpath_course/08-OntologyDevelopment/practice/complete.make: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/08-OntologyDevelopment/practice/complete.make -------------------------------------------------------------------------------- /archive_original_cpath_course/08-OntologyDevelopment/practice/templates/assay.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/08-OntologyDevelopment/practice/templates/assay.tsv -------------------------------------------------------------------------------- /archive_original_cpath_course/08-OntologyDevelopment/practice/templates/disease.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/08-OntologyDevelopment/practice/templates/disease.tsv -------------------------------------------------------------------------------- /archive_original_cpath_course/09-DiseasesAndPhenotypes/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/09-DiseasesAndPhenotypes/README.md -------------------------------------------------------------------------------- /archive_original_cpath_course/09-DiseasesAndPhenotypes/diseaseontologies.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/09-DiseasesAndPhenotypes/diseaseontologies.md -------------------------------------------------------------------------------- /archive_original_cpath_course/09-DiseasesAndPhenotypes/example.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/09-DiseasesAndPhenotypes/example.md -------------------------------------------------------------------------------- /archive_original_cpath_course/09-DiseasesAndPhenotypes/ontologylandscape.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/09-DiseasesAndPhenotypes/ontologylandscape.md -------------------------------------------------------------------------------- /archive_original_cpath_course/10-OntologyMappings/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/10-OntologyMappings/README.md -------------------------------------------------------------------------------- /archive_original_cpath_course/10-OntologyMappings/cancermapping.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/10-OntologyMappings/cancermapping.md -------------------------------------------------------------------------------- /archive_original_cpath_course/10-OntologyMappings/mappings.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/10-OntologyMappings/mappings.md -------------------------------------------------------------------------------- /archive_original_cpath_course/10-OntologyMappings/new-term-request-mondo.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/10-OntologyMappings/new-term-request-mondo.md -------------------------------------------------------------------------------- /archive_original_cpath_course/10-OntologyMappings/new-term-request-obi.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/10-OntologyMappings/new-term-request-obi.md -------------------------------------------------------------------------------- /archive_original_cpath_course/10-OntologyMappings/semantic_etl.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/10-OntologyMappings/semantic_etl.md -------------------------------------------------------------------------------- /archive_original_cpath_course/11-KnowledgeGraphs/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/11-KnowledgeGraphs/README.md -------------------------------------------------------------------------------- /archive_original_cpath_course/11-KnowledgeGraphs/Untitled.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/11-KnowledgeGraphs/Untitled.owl -------------------------------------------------------------------------------- /archive_original_cpath_course/11-KnowledgeGraphs/exercise.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/11-KnowledgeGraphs/exercise.md -------------------------------------------------------------------------------- /archive_original_cpath_course/11-KnowledgeGraphs/img/neo_properties.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/11-KnowledgeGraphs/img/neo_properties.png -------------------------------------------------------------------------------- /archive_original_cpath_course/11-KnowledgeGraphs/img/uberon_contraints.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/11-KnowledgeGraphs/img/uberon_contraints.png -------------------------------------------------------------------------------- /archive_original_cpath_course/11-KnowledgeGraphs/insight.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/11-KnowledgeGraphs/insight.md -------------------------------------------------------------------------------- /archive_original_cpath_course/11-KnowledgeGraphs/kgs.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/11-KnowledgeGraphs/kgs.md -------------------------------------------------------------------------------- /archive_original_cpath_course/11-KnowledgeGraphs/person.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/11-KnowledgeGraphs/person.owl -------------------------------------------------------------------------------- /archive_original_cpath_course/12-Review/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/12-Review/README.md -------------------------------------------------------------------------------- /archive_original_cpath_course/12-Review/modules.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/12-Review/modules.md -------------------------------------------------------------------------------- /archive_original_cpath_course/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/archive_original_cpath_course/README.md -------------------------------------------------------------------------------- /docs/404.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/404.html -------------------------------------------------------------------------------- /docs/config/template.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/config/template.md -------------------------------------------------------------------------------- /docs/contributing.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/contributing.md -------------------------------------------------------------------------------- /docs/courses/icbo2021.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/courses/icbo2021.md -------------------------------------------------------------------------------- /docs/courses/icbo2022.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/courses/icbo2022.md -------------------------------------------------------------------------------- /docs/courses/icbo2023.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/courses/icbo2023.md -------------------------------------------------------------------------------- /docs/courses/icbo2024.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/courses/icbo2024.md -------------------------------------------------------------------------------- /docs/courses/monarch-obo-training.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/courses/monarch-obo-training.md -------------------------------------------------------------------------------- /docs/courses/ontology-summit-2023.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/courses/ontology-summit-2023.md -------------------------------------------------------------------------------- /docs/explanation/annotation-properties.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/explanation/annotation-properties.md -------------------------------------------------------------------------------- /docs/explanation/existential-restrictions.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/explanation/existential-restrictions.md -------------------------------------------------------------------------------- /docs/explanation/intro-to-ontologies.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/explanation/intro-to-ontologies.md -------------------------------------------------------------------------------- /docs/explanation/logical-axiomatization.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/explanation/logical-axiomatization.md -------------------------------------------------------------------------------- /docs/explanation/ontology-matching.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/explanation/ontology-matching.md -------------------------------------------------------------------------------- /docs/explanation/owl-building-blocks.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/explanation/owl-building-blocks.md -------------------------------------------------------------------------------- /docs/explanation/owl-format-variants.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/explanation/owl-format-variants.md -------------------------------------------------------------------------------- /docs/explanation/subClassOf-vs-equivalentTo.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/explanation/subClassOf-vs-equivalentTo.md -------------------------------------------------------------------------------- /docs/explanation/taxon-constraints-explainer.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/explanation/taxon-constraints-explainer.md -------------------------------------------------------------------------------- /docs/explanation/term-comments.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/explanation/term-comments.md -------------------------------------------------------------------------------- /docs/explanation/which-ontology-to-use.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/explanation/which-ontology-to-use.md -------------------------------------------------------------------------------- /docs/explanation/writing-good-issues.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/explanation/writing-good-issues.md -------------------------------------------------------------------------------- /docs/getting-started-obook.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/getting-started-obook.md -------------------------------------------------------------------------------- /docs/getting-started.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/getting-started.md -------------------------------------------------------------------------------- /docs/howto/add-coc.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/add-coc.md -------------------------------------------------------------------------------- /docs/howto/add-new-slim.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/add-new-slim.md -------------------------------------------------------------------------------- /docs/howto/add-taxon-restrictions.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/add-taxon-restrictions.md -------------------------------------------------------------------------------- /docs/howto/are-two-entities-the-same.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/are-two-entities-the-same.md -------------------------------------------------------------------------------- /docs/howto/change-files-pull-request.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/change-files-pull-request.md -------------------------------------------------------------------------------- /docs/howto/clone-mondo-repo.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/clone-mondo-repo.md -------------------------------------------------------------------------------- /docs/howto/create-new-term.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/create-new-term.md -------------------------------------------------------------------------------- /docs/howto/create-ontology-from-scratch.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/create-ontology-from-scratch.md -------------------------------------------------------------------------------- /docs/howto/create-permid-with-w3id.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/create-permid-with-w3id.md -------------------------------------------------------------------------------- /docs/howto/daily-curator-workflow.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/daily-curator-workflow.md -------------------------------------------------------------------------------- /docs/howto/deal-with-large-ontologies.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/deal-with-large-ontologies.md -------------------------------------------------------------------------------- /docs/howto/deploy-custom-obo-dashboard.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/deploy-custom-obo-dashboard.md -------------------------------------------------------------------------------- /docs/howto/edit-in-protege.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/edit-in-protege.md -------------------------------------------------------------------------------- /docs/howto/embed-video.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/embed-video.md -------------------------------------------------------------------------------- /docs/howto/filter-text-file.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/filter-text-file.md -------------------------------------------------------------------------------- /docs/howto/fixing-conflicts.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/fixing-conflicts.md -------------------------------------------------------------------------------- /docs/howto/github-actions.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/github-actions.md -------------------------------------------------------------------------------- /docs/howto/github-create-fork.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/github-create-fork.md -------------------------------------------------------------------------------- /docs/howto/github-create-pull-request.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/github-create-pull-request.md -------------------------------------------------------------------------------- /docs/howto/idrange.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/idrange.md -------------------------------------------------------------------------------- /docs/howto/install-protege.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/install-protege.md -------------------------------------------------------------------------------- /docs/howto/installing-elk-in-protege.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/installing-elk-in-protege.md -------------------------------------------------------------------------------- /docs/howto/merge-terms.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/merge-terms.md -------------------------------------------------------------------------------- /docs/howto/obsolete-term.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/obsolete-term.md -------------------------------------------------------------------------------- /docs/howto/odk-add-orcidio-module.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/odk-add-orcidio-module.md -------------------------------------------------------------------------------- /docs/howto/odk-create-repo.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/odk-create-repo.md -------------------------------------------------------------------------------- /docs/howto/odk-migrate-to-odk.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/odk-migrate-to-odk.md -------------------------------------------------------------------------------- /docs/howto/odk-setup.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/odk-setup.md -------------------------------------------------------------------------------- /docs/howto/odk-update.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/odk-update.md -------------------------------------------------------------------------------- /docs/howto/ontology-overview.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/ontology-overview.md -------------------------------------------------------------------------------- /docs/howto/open-science-engineer.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/open-science-engineer.md -------------------------------------------------------------------------------- /docs/howto/prettify.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/prettify.md -------------------------------------------------------------------------------- /docs/howto/protege-browse-search.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/protege-browse-search.md -------------------------------------------------------------------------------- /docs/howto/respectful-collaboration.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/respectful-collaboration.md -------------------------------------------------------------------------------- /docs/howto/revert-commit.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/revert-commit.md -------------------------------------------------------------------------------- /docs/howto/review-disease-mappings.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/review-disease-mappings.md -------------------------------------------------------------------------------- /docs/howto/review-pull-request.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/review-pull-request.md -------------------------------------------------------------------------------- /docs/howto/run-odk-with-podman.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/run-odk-with-podman.md -------------------------------------------------------------------------------- /docs/howto/screenshot.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/screenshot.md -------------------------------------------------------------------------------- /docs/howto/set-up-protege.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/set-up-protege.md -------------------------------------------------------------------------------- /docs/howto/setup-docker.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/setup-docker.md -------------------------------------------------------------------------------- /docs/howto/setup-ontology-development-odk.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/setup-ontology-development-odk.md -------------------------------------------------------------------------------- /docs/howto/switching-ontologies.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/switching-ontologies.md -------------------------------------------------------------------------------- /docs/howto/term-request.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/term-request.md -------------------------------------------------------------------------------- /docs/howto/update-import.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/howto/update-import.md -------------------------------------------------------------------------------- /docs/images/FHKB figures/Capture.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/Capture.PNG -------------------------------------------------------------------------------- /docs/images/FHKB figures/class_hierachy_final_1.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/class_hierachy_final_1.PNG -------------------------------------------------------------------------------- /docs/images/FHKB figures/class_prop_hierachy_final.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/class_prop_hierachy_final.png -------------------------------------------------------------------------------- /docs/images/FHKB figures/cousin.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/cousin.png -------------------------------------------------------------------------------- /docs/images/FHKB figures/dragon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/dragon.png -------------------------------------------------------------------------------- /docs/images/FHKB figures/grandparent.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/grandparent.png -------------------------------------------------------------------------------- /docs/images/FHKB figures/images/NoteIcon.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/images/NoteIcon.pdf -------------------------------------------------------------------------------- /docs/images/FHKB figures/images/NoteIconSmall.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/images/NoteIconSmall.png -------------------------------------------------------------------------------- /docs/images/FHKB figures/images/TipIcon.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/images/TipIcon.pdf -------------------------------------------------------------------------------- /docs/images/FHKB figures/images/VocabIcon.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/images/VocabIcon.pdf -------------------------------------------------------------------------------- /docs/images/FHKB figures/images/WarningIcon.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/images/WarningIcon.pdf -------------------------------------------------------------------------------- /docs/images/FHKB figures/images/WarningIcon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/images/WarningIcon.png -------------------------------------------------------------------------------- /docs/images/FHKB figures/images/black_camera.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/images/black_camera.png -------------------------------------------------------------------------------- /docs/images/FHKB figures/images/code.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/images/code.PNG -------------------------------------------------------------------------------- /docs/images/FHKB figures/licence_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/licence_logo.png -------------------------------------------------------------------------------- /docs/images/FHKB figures/mother_in_law.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/mother_in_law.png -------------------------------------------------------------------------------- /docs/images/FHKB figures/new/childof_property.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/new/childof_property.PNG -------------------------------------------------------------------------------- /docs/images/FHKB figures/new/descendent_ancestor_defined_classes.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/new/descendent_ancestor_defined_classes.PNG -------------------------------------------------------------------------------- /docs/images/FHKB figures/new/event_name_hierarchy.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/new/event_name_hierarchy.PNG -------------------------------------------------------------------------------- /docs/images/FHKB figures/new/prop_uncle.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/new/prop_uncle.PNG -------------------------------------------------------------------------------- /docs/images/FHKB figures/new/prophierarchyinlaw.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/new/prophierarchyinlaw.PNG -------------------------------------------------------------------------------- /docs/images/FHKB figures/new/prophierparentage.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/new/prophierparentage.PNG -------------------------------------------------------------------------------- /docs/images/FHKB figures/old/childof_property.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/old/childof_property.PNG -------------------------------------------------------------------------------- /docs/images/FHKB figures/old/class_hierarchy.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/old/class_hierarchy.PNG -------------------------------------------------------------------------------- /docs/images/FHKB figures/old/descendent_ancestor_defined_classes.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/old/descendent_ancestor_defined_classes.PNG -------------------------------------------------------------------------------- /docs/images/FHKB figures/old/event_name_hierarchy.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/old/event_name_hierarchy.PNG -------------------------------------------------------------------------------- /docs/images/FHKB figures/old/halfsiblings.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/old/halfsiblings.PNG -------------------------------------------------------------------------------- /docs/images/FHKB figures/old/prop_uncle.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/old/prop_uncle.PNG -------------------------------------------------------------------------------- /docs/images/FHKB figures/old/property_hierarchy.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/old/property_hierarchy.PNG -------------------------------------------------------------------------------- /docs/images/FHKB figures/old/prophierarchyinlaw.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/old/prophierarchyinlaw.PNG -------------------------------------------------------------------------------- /docs/images/FHKB figures/old/prophierarchyinlawInf.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/old/prophierarchyinlawInf.PNG -------------------------------------------------------------------------------- /docs/images/FHKB figures/old/prophierparentage.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/old/prophierparentage.PNG -------------------------------------------------------------------------------- /docs/images/FHKB figures/prop_hierarchy2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/prop_hierarchy2.png -------------------------------------------------------------------------------- /docs/images/FHKB figures/sex.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/sex.png -------------------------------------------------------------------------------- /docs/images/FHKB figures/sibling_path.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/sibling_path.png -------------------------------------------------------------------------------- /docs/images/FHKB figures/siblings.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/siblings.png -------------------------------------------------------------------------------- /docs/images/FHKB figures/sister_in_law.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/sister_in_law.png -------------------------------------------------------------------------------- /docs/images/FHKB figures/spouse.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/spouse.png -------------------------------------------------------------------------------- /docs/images/FHKB figures/uncle.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/FHKB figures/uncle.png -------------------------------------------------------------------------------- /docs/images/Screen Shot 2021-04-22 at 10.04.26 PM.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/Screen Shot 2021-04-22 at 10.04.26 PM.png -------------------------------------------------------------------------------- /docs/images/bash_start.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/bash_start.png -------------------------------------------------------------------------------- /docs/images/changing_pr.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/changing_pr.png -------------------------------------------------------------------------------- /docs/images/changing_pr_commit.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/changing_pr_commit.png -------------------------------------------------------------------------------- /docs/images/chatgpt_more_hallucination_aware.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/chatgpt_more_hallucination_aware.png -------------------------------------------------------------------------------- /docs/images/comment.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/comment.png -------------------------------------------------------------------------------- /docs/images/custom_qc_example.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/custom_qc_example.png -------------------------------------------------------------------------------- /docs/images/custom_qc_example_solved.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/custom_qc_example_solved.png -------------------------------------------------------------------------------- /docs/images/delphi_racoon_example.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/delphi_racoon_example.jpg -------------------------------------------------------------------------------- /docs/images/discussions/intro-to-ontologies/cardiac-glial-cell.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/discussions/intro-to-ontologies/cardiac-glial-cell.png -------------------------------------------------------------------------------- /docs/images/discussions/intro-to-ontologies/definition-example.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/discussions/intro-to-ontologies/definition-example.png -------------------------------------------------------------------------------- /docs/images/discussions/intro-to-ontologies/hindwing-subclass.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/discussions/intro-to-ontologies/hindwing-subclass.png -------------------------------------------------------------------------------- /docs/images/discussions/intro-to-ontologies/insect-classification.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/discussions/intro-to-ontologies/insect-classification.png -------------------------------------------------------------------------------- /docs/images/discussions/intro-to-ontologies/leg-wing.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/discussions/intro-to-ontologies/leg-wing.png -------------------------------------------------------------------------------- /docs/images/discussions/intro-to-ontologies/neuron-multiple-inheritance.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/discussions/intro-to-ontologies/neuron-multiple-inheritance.png -------------------------------------------------------------------------------- /docs/images/discussions/intro-to-ontologies/nose-classification.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/discussions/intro-to-ontologies/nose-classification.png -------------------------------------------------------------------------------- /docs/images/discussions/intro-to-ontologies/paramere.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/discussions/intro-to-ontologies/paramere.png -------------------------------------------------------------------------------- /docs/images/discussions/intro-to-ontologies/query-glial-genes.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/discussions/intro-to-ontologies/query-glial-genes.png -------------------------------------------------------------------------------- /docs/images/discussions/intro-to-ontologies/tarsal-segments.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/discussions/intro-to-ontologies/tarsal-segments.png -------------------------------------------------------------------------------- /docs/images/discussions/logical-axiomatization/betz-pyramidal.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/discussions/logical-axiomatization/betz-pyramidal.png -------------------------------------------------------------------------------- /docs/images/discussions/logical-axiomatization/dl-oxtrneuron.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/discussions/logical-axiomatization/dl-oxtrneuron.png -------------------------------------------------------------------------------- /docs/images/discussions/logical-axiomatization/oxtrsst-heirachy.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/discussions/logical-axiomatization/oxtrsst-heirachy.png -------------------------------------------------------------------------------- /docs/images/discussions/writing-tickets/bad-ticket.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/discussions/writing-tickets/bad-ticket.png -------------------------------------------------------------------------------- /docs/images/discussions/writing-tickets/good-ticket.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/discussions/writing-tickets/good-ticket.png -------------------------------------------------------------------------------- /docs/images/disease-model.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/disease-model.png -------------------------------------------------------------------------------- /docs/images/docker_memory.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/docker_memory.png -------------------------------------------------------------------------------- /docs/images/dosdp_spotted_coat.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/dosdp_spotted_coat.png -------------------------------------------------------------------------------- /docs/images/entity-mappings.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/entity-mappings.png -------------------------------------------------------------------------------- /docs/images/entity_mapping.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/entity_mapping.png -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/10_windows.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/10_windows.jpg -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/11_windows.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/11_windows.jpg -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/1_mac.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/1_mac.jpg -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/1_windows.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/1_windows.jpg -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/2_mac.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/2_mac.jpg -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/2_windows.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/2_windows.jpg -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/3_mac.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/3_mac.jpg -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/3_windows.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/3_windows.jpg -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/4_windows.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/4_windows.jpg -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/5_windows.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/5_windows.jpg -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/6_mac.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/6_mac.jpg -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/6_windows.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/6_windows.jpg -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/7_mac.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/7_mac.jpg -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/7_windows.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/7_windows.jpg -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/8_mac.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/8_mac.jpg -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/8_windows.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/8_windows.jpg -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/9_windows.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/9_windows.jpg -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/HTML_annotated_part2.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/HTML_annotated_part2.jpg -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/HTML_annotated_part3.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/HTML_annotated_part3.jpg -------------------------------------------------------------------------------- /docs/images/exomiser_tutorial_images/HTML_annotation_part1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/exomiser_tutorial_images/HTML_annotation_part1.png -------------------------------------------------------------------------------- /docs/images/finding-vs-disorder.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/finding-vs-disorder.png -------------------------------------------------------------------------------- /docs/images/github organizations teams repos.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/github organizations teams repos.png -------------------------------------------------------------------------------- /docs/images/github-organizations-teams-repos.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/github-organizations-teams-repos.png -------------------------------------------------------------------------------- /docs/images/github_qc_starting.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/github_qc_starting.png -------------------------------------------------------------------------------- /docs/images/howtoguides/TaxonRestriction/intaxon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/howtoguides/TaxonRestriction/intaxon.png -------------------------------------------------------------------------------- /docs/images/howtoguides/TaxonRestriction/neverintaxon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/howtoguides/TaxonRestriction/neverintaxon.png -------------------------------------------------------------------------------- /docs/images/howtoguides/createnewterm/annotations.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/howtoguides/createnewterm/annotations.png -------------------------------------------------------------------------------- /docs/images/howtoguides/createnewterm/logicalaxiom.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/howtoguides/createnewterm/logicalaxiom.png -------------------------------------------------------------------------------- /docs/images/howtoguides/createnewterm/newterm.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/howtoguides/createnewterm/newterm.png -------------------------------------------------------------------------------- /docs/images/howtoguides/createnewterm/ref.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/howtoguides/createnewterm/ref.png -------------------------------------------------------------------------------- /docs/images/howtoguides/createnewterm/subclassasserted.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/howtoguides/createnewterm/subclassasserted.png -------------------------------------------------------------------------------- /docs/images/howtoguides/deploy-custom-dashboard-workflow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/howtoguides/deploy-custom-dashboard-workflow.png -------------------------------------------------------------------------------- /docs/images/howtoguides/obsolete/fig1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/howtoguides/obsolete/fig1.png -------------------------------------------------------------------------------- /docs/images/howtoguides/obsolete/fig2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/howtoguides/obsolete/fig2.png -------------------------------------------------------------------------------- /docs/images/howtoguides/obsolete/fig3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/howtoguides/obsolete/fig3.png -------------------------------------------------------------------------------- /docs/images/howtoguides/obsolete/fig4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/howtoguides/obsolete/fig4.png -------------------------------------------------------------------------------- /docs/images/howtoguides/obsolete/fig5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/howtoguides/obsolete/fig5.png -------------------------------------------------------------------------------- /docs/images/howtoguides/obsolete/fig6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/howtoguides/obsolete/fig6.png -------------------------------------------------------------------------------- /docs/images/image1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/image1.png -------------------------------------------------------------------------------- /docs/images/image2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/image2.png -------------------------------------------------------------------------------- /docs/images/image3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/image3.png -------------------------------------------------------------------------------- /docs/images/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/index.md -------------------------------------------------------------------------------- /docs/images/interdependent_projects.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/interdependent_projects.png -------------------------------------------------------------------------------- /docs/images/kg-synonyms.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/kg-synonyms.png -------------------------------------------------------------------------------- /docs/images/lexmatch/foodon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/lexmatch/foodon.png -------------------------------------------------------------------------------- /docs/images/linkml1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/linkml1.png -------------------------------------------------------------------------------- /docs/images/linkml2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/linkml2.png -------------------------------------------------------------------------------- /docs/images/linkml3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/linkml3.png -------------------------------------------------------------------------------- /docs/images/linkml4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/linkml4.png -------------------------------------------------------------------------------- /docs/images/linkml5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/linkml5.png -------------------------------------------------------------------------------- /docs/images/linkml6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/linkml6.png -------------------------------------------------------------------------------- /docs/images/llm_basic.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/llm_basic.png -------------------------------------------------------------------------------- /docs/images/llm_learn.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/llm_learn.png -------------------------------------------------------------------------------- /docs/images/mapping-predicates-cheatsheet.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/mapping-predicates-cheatsheet.png -------------------------------------------------------------------------------- /docs/images/mapping-usecase-counting.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/mapping-usecase-counting.png -------------------------------------------------------------------------------- /docs/images/mapping-usecase-kg.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/mapping-usecase-kg.png -------------------------------------------------------------------------------- /docs/images/mapping_workflow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/mapping_workflow.png -------------------------------------------------------------------------------- /docs/images/odk_docs_cato.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/odk_docs_cato.png -------------------------------------------------------------------------------- /docs/images/odk_docs_pages_settings.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/odk_docs_pages_settings.png -------------------------------------------------------------------------------- /docs/images/odk_workflow_import.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/odk_workflow_import.png -------------------------------------------------------------------------------- /docs/images/odk_workflow_release.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/odk_workflow_release.png -------------------------------------------------------------------------------- /docs/images/odk_workflow_testing.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/odk_workflow_testing.png -------------------------------------------------------------------------------- /docs/images/ohmyzsh_start.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/ohmyzsh_start.png -------------------------------------------------------------------------------- /docs/images/open_science_contribution1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/open_science_contribution1.png -------------------------------------------------------------------------------- /docs/images/open_science_contribution2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/open_science_contribution2.png -------------------------------------------------------------------------------- /docs/images/other-images/owl.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/other-images/owl.jpg -------------------------------------------------------------------------------- /docs/images/project_ontologies.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/project_ontologies.png -------------------------------------------------------------------------------- /docs/images/prompt-icon.jpg.sb-12c70a1b-fkHh2I: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/prompt-icon.jpg.sb-12c70a1b-fkHh2I -------------------------------------------------------------------------------- /docs/images/prompt-icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/prompt-icon.png -------------------------------------------------------------------------------- /docs/images/reference/managing-issues/milestone.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/reference/managing-issues/milestone.png -------------------------------------------------------------------------------- /docs/images/reference/managing-issues/project-board.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/reference/managing-issues/project-board.png -------------------------------------------------------------------------------- /docs/images/reference/managing-issues/superissue.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/reference/managing-issues/superissue.png -------------------------------------------------------------------------------- /docs/images/reference/protege/protege-active-ontology-tab.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/reference/protege/protege-active-ontology-tab.png -------------------------------------------------------------------------------- /docs/images/reference/protege/protege-buttons.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/reference/protege/protege-buttons.png -------------------------------------------------------------------------------- /docs/images/reference/protege/protege-entities-tab.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/reference/protege/protege-entities-tab.png -------------------------------------------------------------------------------- /docs/images/reference/protege/protege-new-entities-metadata.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/reference/protege/protege-new-entities-metadata.png -------------------------------------------------------------------------------- /docs/images/repo-landing-page.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/repo-landing-page.png -------------------------------------------------------------------------------- /docs/images/robot_report.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/robot_report.png -------------------------------------------------------------------------------- /docs/images/robot_report2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/robot_report2.png -------------------------------------------------------------------------------- /docs/images/screenshot-of-images-in-issues.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/screenshot-of-images-in-issues.png -------------------------------------------------------------------------------- /docs/images/semantic_spaces.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/semantic_spaces.png -------------------------------------------------------------------------------- /docs/images/tradeoff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tradeoff.png -------------------------------------------------------------------------------- /docs/images/tutorials/disjointness/Figure42.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/disjointness/Figure42.png -------------------------------------------------------------------------------- /docs/images/tutorials/disjointness/Figure43.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/disjointness/Figure43.png -------------------------------------------------------------------------------- /docs/images/tutorials/disjointness/Figure44.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/disjointness/Figure44.png -------------------------------------------------------------------------------- /docs/images/tutorials/disjointness/Figure45.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/disjointness/Figure45.png -------------------------------------------------------------------------------- /docs/images/tutorials/disjointness/Figure46.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/disjointness/Figure46.png -------------------------------------------------------------------------------- /docs/images/tutorials/disjointness/Figure47.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/disjointness/Figure47.png -------------------------------------------------------------------------------- /docs/images/tutorials/dl-query/Figure57.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/dl-query/Figure57.png -------------------------------------------------------------------------------- /docs/images/tutorials/dl-query/Figure58.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/dl-query/Figure58.png -------------------------------------------------------------------------------- /docs/images/tutorials/dl-query/Figure59.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/dl-query/Figure59.png -------------------------------------------------------------------------------- /docs/images/tutorials/dl-query/Figure60.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/dl-query/Figure60.png -------------------------------------------------------------------------------- /docs/images/tutorials/dl-query/Figure61.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/dl-query/Figure61.png -------------------------------------------------------------------------------- /docs/images/tutorials/dl-query/Figure62.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/dl-query/Figure62.png -------------------------------------------------------------------------------- /docs/images/tutorials/dl-query/Figure63.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/dl-query/Figure63.png -------------------------------------------------------------------------------- /docs/images/tutorials/dl-query/Figure64.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/dl-query/Figure64.png -------------------------------------------------------------------------------- /docs/images/tutorials/dl-query/Figure65.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/dl-query/Figure65.png -------------------------------------------------------------------------------- /docs/images/tutorials/existential-restrictions/ExistentialRestrictionsWithSubclassVSEquivalentTo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/existential-restrictions/ExistentialRestrictionsWithSubclassVSEquivalentTo.png -------------------------------------------------------------------------------- /docs/images/tutorials/existential-restrictions/QualifiedExistentialRestriction.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/existential-restrictions/QualifiedExistentialRestriction.png -------------------------------------------------------------------------------- /docs/images/tutorials/existential-restrictions/QualifiedRestrictionExamples.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/existential-restrictions/QualifiedRestrictionExamples.png -------------------------------------------------------------------------------- /docs/images/tutorials/sparql-llm/basic_sparql_query-no-title.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/sparql-llm/basic_sparql_query-no-title.png -------------------------------------------------------------------------------- /docs/images/tutorials/subClassOf-vs-equivalentTo/CsubClassOfD.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/subClassOf-vs-equivalentTo/CsubClassOfD.png -------------------------------------------------------------------------------- /docs/images/tutorials/subClassOf-vs-equivalentTo/CsubClassOfDExample.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/subClassOf-vs-equivalentTo/CsubClassOfDExample.png -------------------------------------------------------------------------------- /docs/images/tutorials/subClassOf-vs-equivalentTo/EquivalentTo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/subClassOf-vs-equivalentTo/EquivalentTo.png -------------------------------------------------------------------------------- /docs/images/tutorials/subClassOf-vs-equivalentTo/EquivalentToExample.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/subClassOf-vs-equivalentTo/EquivalentToExample.png -------------------------------------------------------------------------------- /docs/images/tutorials/subClassOf-vs-equivalentTo/IndividualOfCnotInD.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/subClassOf-vs-equivalentTo/IndividualOfCnotInD.png -------------------------------------------------------------------------------- /docs/images/tutorials/subClassOf-vs-equivalentTo/IndividualOfDnotInC.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/subClassOf-vs-equivalentTo/IndividualOfDnotInC.png -------------------------------------------------------------------------------- /docs/images/tutorials/subClassOf-vs-equivalentTo/SubClassOfWhenNotToUse.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/subClassOf-vs-equivalentTo/SubClassOfWhenNotToUse.png -------------------------------------------------------------------------------- /docs/images/tutorials/synonyms/Picture1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/synonyms/Picture1.png -------------------------------------------------------------------------------- /docs/images/tutorials/synonyms/abbreviation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/synonyms/abbreviation.png -------------------------------------------------------------------------------- /docs/images/tutorials/synonyms/annotation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/synonyms/annotation.png -------------------------------------------------------------------------------- /docs/images/tutorials/synonyms/cancerterm.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/synonyms/cancerterm.png -------------------------------------------------------------------------------- /docs/images/tutorials/synonyms/synonym-annotation-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/synonyms/synonym-annotation-1.png -------------------------------------------------------------------------------- /docs/images/tutorials/synonyms/synonym-annotation-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/synonyms/synonym-annotation-2.png -------------------------------------------------------------------------------- /docs/images/tutorials/synonyms/synonym-annotation-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/synonyms/synonym-annotation-3.png -------------------------------------------------------------------------------- /docs/images/tutorials/synonyms/synonymannotation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/synonyms/synonymannotation.png -------------------------------------------------------------------------------- /docs/images/tutorials/synonyms/synonyms.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/synonyms/synonyms.png -------------------------------------------------------------------------------- /docs/images/tutorials/synonyms/synonymscope.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/synonyms/synonymscope.png -------------------------------------------------------------------------------- /docs/images/tutorials/synonyms/synonymtypeproperty.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/synonyms/synonymtypeproperty.png -------------------------------------------------------------------------------- /docs/images/tutorials/synonyms/synonymtypepropertymondo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/synonyms/synonymtypepropertymondo.png -------------------------------------------------------------------------------- /docs/images/tutorials/synonyms/tongue.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/synonyms/tongue.png -------------------------------------------------------------------------------- /docs/images/tutorials/synonyms/winchester.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/tutorials/synonyms/winchester.png -------------------------------------------------------------------------------- /docs/images/under-construction.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/under-construction.png -------------------------------------------------------------------------------- /docs/images/upheno_model.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/images/upheno_model.png -------------------------------------------------------------------------------- /docs/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/index.md -------------------------------------------------------------------------------- /docs/lesson/analysing-linked-data.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/analysing-linked-data.md -------------------------------------------------------------------------------- /docs/lesson/automating-ontology-workflows.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/automating-ontology-workflows.md -------------------------------------------------------------------------------- /docs/lesson/chatgpt-ontology-curation.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/chatgpt-ontology-curation.md -------------------------------------------------------------------------------- /docs/lesson/contributing-to-obo-ontologies.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/contributing-to-obo-ontologies.md -------------------------------------------------------------------------------- /docs/lesson/developing-an-obo-ontology.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/developing-an-obo-ontology.md -------------------------------------------------------------------------------- /docs/lesson/developing-application-ontologies.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/developing-application-ontologies.md -------------------------------------------------------------------------------- /docs/lesson/entity-matching.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/entity-matching.md -------------------------------------------------------------------------------- /docs/lesson/getting-hands-on.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/getting-hands-on.md -------------------------------------------------------------------------------- /docs/lesson/hackathon.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/hackathon.md -------------------------------------------------------------------------------- /docs/lesson/licensing-data-and-software.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/licensing-data-and-software.md -------------------------------------------------------------------------------- /docs/lesson/linkml-helps-with-ontology-use.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/linkml-helps-with-ontology-use.md -------------------------------------------------------------------------------- /docs/lesson/modelling-with-object-properties.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/modelling-with-object-properties.md -------------------------------------------------------------------------------- /docs/lesson/ontology-design.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/ontology-design.md -------------------------------------------------------------------------------- /docs/lesson/ontology-development.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/ontology-development.md -------------------------------------------------------------------------------- /docs/lesson/ontology-fundamentals.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/ontology-fundamentals.md -------------------------------------------------------------------------------- /docs/lesson/ontology-pipelines.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/ontology-pipelines.md -------------------------------------------------------------------------------- /docs/lesson/ontology-term-use.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/ontology-term-use.md -------------------------------------------------------------------------------- /docs/lesson/phenotype-data.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/phenotype-data.md -------------------------------------------------------------------------------- /docs/lesson/rdf.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/rdf.md -------------------------------------------------------------------------------- /docs/lesson/semantic-database-fundamentals.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/semantic-database-fundamentals.md -------------------------------------------------------------------------------- /docs/lesson/synonyms.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/synonyms.md -------------------------------------------------------------------------------- /docs/lesson/templates-for-obo.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/templates-for-obo.md -------------------------------------------------------------------------------- /docs/lesson/using-disease-and-phenotype-ontologies.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/using-disease-and-phenotype-ontologies.md -------------------------------------------------------------------------------- /docs/lesson/vocabularies-for-bioinformatics.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/lesson/vocabularies-for-bioinformatics.md -------------------------------------------------------------------------------- /docs/overview.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/overview.md -------------------------------------------------------------------------------- /docs/pathways/ai-powered-semantic-engineer.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/pathways/ai-powered-semantic-engineer.md -------------------------------------------------------------------------------- /docs/pathways/early-career-data-scientist.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/pathways/early-career-data-scientist.md -------------------------------------------------------------------------------- /docs/pathways/ontology-contributor.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/pathways/ontology-contributor.md -------------------------------------------------------------------------------- /docs/pathways/ontology-curator-go-style.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/pathways/ontology-curator-go-style.md -------------------------------------------------------------------------------- /docs/pathways/ontology-curator-obi-style.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/pathways/ontology-curator-obi-style.md -------------------------------------------------------------------------------- /docs/pathways/ontology-curator.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/pathways/ontology-curator.md -------------------------------------------------------------------------------- /docs/pathways/ontology-engineer.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/pathways/ontology-engineer.md -------------------------------------------------------------------------------- /docs/pathways/pathways.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/pathways/pathways.md -------------------------------------------------------------------------------- /docs/reference/base-specification.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/base-specification.md -------------------------------------------------------------------------------- /docs/reference/catalog-xml.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/catalog-xml.md -------------------------------------------------------------------------------- /docs/reference/chatgpt-prompts-for-ontology-development.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/chatgpt-prompts-for-ontology-development.md -------------------------------------------------------------------------------- /docs/reference/formatting-license.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/formatting-license.md -------------------------------------------------------------------------------- /docs/reference/frequently-used-odk-commands.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/frequently-used-odk-commands.md -------------------------------------------------------------------------------- /docs/reference/gh-actions-errors.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/gh-actions-errors.md -------------------------------------------------------------------------------- /docs/reference/git-faq.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/git-faq.md -------------------------------------------------------------------------------- /docs/reference/github-desktop.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/github-desktop.md -------------------------------------------------------------------------------- /docs/reference/github-intro.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/github-intro.md -------------------------------------------------------------------------------- /docs/reference/glossary-of-terms.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/glossary-of-terms.md -------------------------------------------------------------------------------- /docs/reference/glossary.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/glossary.md -------------------------------------------------------------------------------- /docs/reference/go-style-annotation-property-practice.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/go-style-annotation-property-practice.md -------------------------------------------------------------------------------- /docs/reference/llms.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/llms.md -------------------------------------------------------------------------------- /docs/reference/managing-issues.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/managing-issues.md -------------------------------------------------------------------------------- /docs/reference/medical-ontology-landscape.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/medical-ontology-landscape.md -------------------------------------------------------------------------------- /docs/reference/mungall-blog-radar.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/mungall-blog-radar.md -------------------------------------------------------------------------------- /docs/reference/obook-maturity-indicator.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/obook-maturity-indicator.md -------------------------------------------------------------------------------- /docs/reference/odk.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/odk.md -------------------------------------------------------------------------------- /docs/reference/ontology-curator.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/ontology-curator.md -------------------------------------------------------------------------------- /docs/reference/ontology-user.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/ontology-user.md -------------------------------------------------------------------------------- /docs/reference/other-resources.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/other-resources.md -------------------------------------------------------------------------------- /docs/reference/outreach.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/outreach.md -------------------------------------------------------------------------------- /docs/reference/protege-faq.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/protege-faq.md -------------------------------------------------------------------------------- /docs/reference/protege-interface.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/protege-interface.md -------------------------------------------------------------------------------- /docs/reference/reasoning.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/reasoning.md -------------------------------------------------------------------------------- /docs/reference/release-artefacts.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/release-artefacts.md -------------------------------------------------------------------------------- /docs/reference/semantic-engineering-toolbox.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/semantic-engineering-toolbox.md -------------------------------------------------------------------------------- /docs/reference/semantic-etl.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/semantic-etl.md -------------------------------------------------------------------------------- /docs/reference/sparql-basics.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/sparql-basics.md -------------------------------------------------------------------------------- /docs/reference/sparql-reference.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/sparql-reference.md -------------------------------------------------------------------------------- /docs/reference/synonym-validation.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/synonym-validation.md -------------------------------------------------------------------------------- /docs/reference/synonyms-properties.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/synonyms-properties.md -------------------------------------------------------------------------------- /docs/reference/synonyms-types.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/synonyms-types.md -------------------------------------------------------------------------------- /docs/reference/tables-and-triples.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/tables-and-triples.md -------------------------------------------------------------------------------- /docs/reference/troublehooting-robot.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/troublehooting-robot.md -------------------------------------------------------------------------------- /docs/reference/wikidata.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/reference/wikidata.md -------------------------------------------------------------------------------- /docs/resources/fhkb/fhkb_chapter_10.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/resources/fhkb/fhkb_chapter_10.owl -------------------------------------------------------------------------------- /docs/resources/fhkb/fhkb_chapter_2.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/resources/fhkb/fhkb_chapter_2.owl -------------------------------------------------------------------------------- /docs/resources/fhkb/fhkb_chapter_3.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/resources/fhkb/fhkb_chapter_3.owl -------------------------------------------------------------------------------- /docs/resources/fhkb/fhkb_chapter_4.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/resources/fhkb/fhkb_chapter_4.owl -------------------------------------------------------------------------------- /docs/resources/fhkb/fhkb_chapter_5.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/resources/fhkb/fhkb_chapter_5.owl -------------------------------------------------------------------------------- /docs/resources/fhkb/fhkb_chapter_6.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/resources/fhkb/fhkb_chapter_6.owl -------------------------------------------------------------------------------- /docs/resources/fhkb/fhkb_chapter_7.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/resources/fhkb/fhkb_chapter_7.owl -------------------------------------------------------------------------------- /docs/resources/fhkb/fhkb_chapter_8.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/resources/fhkb/fhkb_chapter_8.owl -------------------------------------------------------------------------------- /docs/resources/fhkb/fhkb_chapter_9.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/resources/fhkb/fhkb_chapter_9.owl -------------------------------------------------------------------------------- /docs/resources/obook-badge-development.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/resources/obook-badge-development.json -------------------------------------------------------------------------------- /docs/resources/obook-badge-draft.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/resources/obook-badge-draft.json -------------------------------------------------------------------------------- /docs/resources/obook-badge-stable.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/resources/obook-badge-stable.json -------------------------------------------------------------------------------- /docs/resources/odk.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/resources/odk.bat -------------------------------------------------------------------------------- /docs/resources/odk.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/resources/odk.sh -------------------------------------------------------------------------------- /docs/teaching/case-studies.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/teaching/case-studies.md -------------------------------------------------------------------------------- /docs/tutorial/Delphi-method-ontology.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/Delphi-method-ontology.md -------------------------------------------------------------------------------- /docs/tutorial/basic-dl-query.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/basic-dl-query.md -------------------------------------------------------------------------------- /docs/tutorial/biomappings.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/biomappings.md -------------------------------------------------------------------------------- /docs/tutorial/claude-code-getting-started.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/claude-code-getting-started.md -------------------------------------------------------------------------------- /docs/tutorial/claude-code-linkml.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/claude-code-linkml.md -------------------------------------------------------------------------------- /docs/tutorial/claude-code-mcps.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/claude-code-mcps.md -------------------------------------------------------------------------------- /docs/tutorial/claude-code-slash-commands.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/claude-code-slash-commands.md -------------------------------------------------------------------------------- /docs/tutorial/curies.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/curies.md -------------------------------------------------------------------------------- /docs/tutorial/custom-qc.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/custom-qc.md -------------------------------------------------------------------------------- /docs/tutorial/disjointness.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/disjointness.md -------------------------------------------------------------------------------- /docs/tutorial/dosdp-odk.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/dosdp-odk.md -------------------------------------------------------------------------------- /docs/tutorial/dosdp-overview.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/dosdp-overview.md -------------------------------------------------------------------------------- /docs/tutorial/dosdp-template.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/dosdp-template.md -------------------------------------------------------------------------------- /docs/tutorial/exomiser-tutorial.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/exomiser-tutorial.md -------------------------------------------------------------------------------- /docs/tutorial/fhkb.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/fhkb.md -------------------------------------------------------------------------------- /docs/tutorial/github-fundamentals.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/github-fundamentals.md -------------------------------------------------------------------------------- /docs/tutorial/github-issues.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/github-issues.md -------------------------------------------------------------------------------- /docs/tutorial/intro-cli-1.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/intro-cli-1.md -------------------------------------------------------------------------------- /docs/tutorial/intro-cli-2.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/intro-cli-2.md -------------------------------------------------------------------------------- /docs/tutorial/lexmatch-tutorial.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/lexmatch-tutorial.md -------------------------------------------------------------------------------- /docs/tutorial/linking-data.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/linking-data.md -------------------------------------------------------------------------------- /docs/tutorial/linking_data/data.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/linking_data/data.csv -------------------------------------------------------------------------------- /docs/tutorial/managing-dynamic-imports-odk.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/managing-dynamic-imports-odk.md -------------------------------------------------------------------------------- /docs/tutorial/managing-ontology-project.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/managing-ontology-project.md -------------------------------------------------------------------------------- /docs/tutorial/managing-ontology-releases-odk.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/managing-ontology-releases-odk.md -------------------------------------------------------------------------------- /docs/tutorial/migrating-ontology-to-odk.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/migrating-ontology-to-odk.md -------------------------------------------------------------------------------- /docs/tutorial/monarch-kg-neo4j-basics.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/monarch-kg-neo4j-basics.md -------------------------------------------------------------------------------- /docs/tutorial/named-entity-normalization.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/named-entity-normalization.md -------------------------------------------------------------------------------- /docs/tutorial/named-entity-recognition.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/named-entity-recognition.md -------------------------------------------------------------------------------- /docs/tutorial/named-entity-standardization.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/named-entity-standardization.md -------------------------------------------------------------------------------- /docs/tutorial/odk-toolbox.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/odk-toolbox.md -------------------------------------------------------------------------------- /docs/tutorial/odk-tutorial-2.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/odk-tutorial-2.md -------------------------------------------------------------------------------- /docs/tutorial/odk_tutorial_2/cato-odk.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/odk_tutorial_2/cato-odk.yaml -------------------------------------------------------------------------------- /docs/tutorial/ontogpt-workshop.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/ontogpt-workshop.md -------------------------------------------------------------------------------- /docs/tutorial/ontogpt.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/ontogpt.md -------------------------------------------------------------------------------- /docs/tutorial/project-ontology-development.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/project-ontology-development.md -------------------------------------------------------------------------------- /docs/tutorial/pull-requests.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/pull-requests.md -------------------------------------------------------------------------------- /docs/tutorial/resources/BDK14-exercises/basic-classification/ubiq-ligase-complex.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/resources/BDK14-exercises/basic-classification/ubiq-ligase-complex.owl -------------------------------------------------------------------------------- /docs/tutorial/resources/BDK14-exercises/basic-disjoint/bad-chromosome.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/resources/BDK14-exercises/basic-disjoint/bad-chromosome.owl -------------------------------------------------------------------------------- /docs/tutorial/resources/BDK14-exercises/basic-dl-query/cc.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/resources/BDK14-exercises/basic-dl-query/cc.owl -------------------------------------------------------------------------------- /docs/tutorial/resources/BDK14-exercises/basic-restriction/chromosome-parts-interim.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/resources/BDK14-exercises/basic-restriction/chromosome-parts-interim.owl -------------------------------------------------------------------------------- /docs/tutorial/resources/BDK14-exercises/basic-restriction/chromosomePartsInterimAS.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/resources/BDK14-exercises/basic-restriction/chromosomePartsInterimAS.owl -------------------------------------------------------------------------------- /docs/tutorial/resources/BDK14-exercises/basic-restriction/er-sec-complex.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/resources/BDK14-exercises/basic-restriction/er-sec-complex.owl -------------------------------------------------------------------------------- /docs/tutorial/resources/BDK14-exercises/basic-subclass/chromosome-parts-interim.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/resources/BDK14-exercises/basic-subclass/chromosome-parts-interim.owl -------------------------------------------------------------------------------- /docs/tutorial/resources/BDK14-exercises/basic-subclass/chromosome-parts.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/resources/BDK14-exercises/basic-subclass/chromosome-parts.owl -------------------------------------------------------------------------------- /docs/tutorial/resources/BDK14-exercises/taxon-union/taxslim-with-union.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/resources/BDK14-exercises/taxon-union/taxslim-with-union.owl -------------------------------------------------------------------------------- /docs/tutorial/resources/biomappings/1-front.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/resources/biomappings/1-front.png -------------------------------------------------------------------------------- /docs/tutorial/resources/biomappings/2-summarize.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/resources/biomappings/2-summarize.png -------------------------------------------------------------------------------- /docs/tutorial/resources/biomappings/3-search.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/resources/biomappings/3-search.png -------------------------------------------------------------------------------- /docs/tutorial/resources/biomappings/4-commit.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/resources/biomappings/4-commit.png -------------------------------------------------------------------------------- /docs/tutorial/resources/gilda/1-web.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/resources/gilda/1-web.png -------------------------------------------------------------------------------- /docs/tutorial/resources/gilda/2-web-results.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/resources/gilda/2-web-results.png -------------------------------------------------------------------------------- /docs/tutorial/resources/gilda/3-web-context.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/resources/gilda/3-web-context.png -------------------------------------------------------------------------------- /docs/tutorial/resources/gilda/4-web-context-results.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/resources/gilda/4-web-context-results.png -------------------------------------------------------------------------------- /docs/tutorial/resources/ner/1-web.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/resources/ner/1-web.png -------------------------------------------------------------------------------- /docs/tutorial/resources/ner/2-web-results.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/resources/ner/2-web-results.png -------------------------------------------------------------------------------- /docs/tutorial/robot-tutorial-1.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/robot-tutorial-1.md -------------------------------------------------------------------------------- /docs/tutorial/robot-tutorial-2.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/robot-tutorial-2.md -------------------------------------------------------------------------------- /docs/tutorial/robot-tutorial-qc.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/robot-tutorial-qc.md -------------------------------------------------------------------------------- /docs/tutorial/robot_report/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/robot_report/Makefile -------------------------------------------------------------------------------- /docs/tutorial/robot_report/complete.make: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/robot_report/complete.make -------------------------------------------------------------------------------- /docs/tutorial/robot_report/templates/assay.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/robot_report/templates/assay.tsv -------------------------------------------------------------------------------- /docs/tutorial/robot_report/templates/disease.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/robot_report/templates/disease.tsv -------------------------------------------------------------------------------- /docs/tutorial/robot_tutorial_1/animals.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/robot_tutorial_1/animals.tsv -------------------------------------------------------------------------------- /docs/tutorial/robot_tutorial_1/animals2.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/robot_tutorial_1/animals2.tsv -------------------------------------------------------------------------------- /docs/tutorial/robot_tutorial_qc/example.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/robot_tutorial_qc/example.owl -------------------------------------------------------------------------------- /docs/tutorial/setting-up-project-odk.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/setting-up-project-odk.md -------------------------------------------------------------------------------- /docs/tutorial/sparql-llm.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/sparql-llm.md -------------------------------------------------------------------------------- /docs/tutorial/sparql-report-odk.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/sparql-report-odk.md -------------------------------------------------------------------------------- /docs/tutorial/sparql-report-robot.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/sparql-report-robot.md -------------------------------------------------------------------------------- /docs/tutorial/sparql.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/sparql.md -------------------------------------------------------------------------------- /docs/tutorial/sssom-toolkit.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/sssom-toolkit.md -------------------------------------------------------------------------------- /docs/tutorial/sssom-tutorial.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/sssom-tutorial.md -------------------------------------------------------------------------------- /docs/tutorial/units.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/docs/tutorial/units.md -------------------------------------------------------------------------------- /mkdocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/mkdocs.yml -------------------------------------------------------------------------------- /odk.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OBOAcademy/obook/HEAD/odk.sh --------------------------------------------------------------------------------