ODK Schema

ODK Project Configuration Schema

• allow_equivalents (string): can be all, none or asserted-only (see ROBOT documentation: http://robot.obolibrary.org/reason). Default: "asserted-only".

• catalog_file (string): Name of the catalog file to be used by the build. Default: "catalog-v001.xml".

• ci (list): continuous integration defaults; currently available: travis, github_actions, gitlab-ci. Default: ["github_actions"].

• Items (string)

• components:

  • base_iris (list) A list of URI prefixes used to identify terms belonging to the component.
  • Items (string)
  • filename (string) The filename of this component.
  • make_base (boolean): if make_base is true, the file is turned into a base (works with source). Default: false.
  • mappings (list) A list of SSSOM template names. If set, these will be used to source this component.
  • Items (string)
  • source (string) The URL source for which the component should be obtained.
  • sssom_tool_options (string): SSSOM toolkit options passed to the sssom command used to generate this product command. Default: "".
  • template_options (string) ROBOT options passed to the template command.
  • templates (list) A list of ROBOT template names. If set, these will be used to source this component.
  • Items (string)
  • use_mappings (boolean): If true, the component will be sourced from one or more SSSOM mapping files. Default: false.
  • use_template (boolean): If true, the component will be sourced by a template. Default: false.
  • directory (string): directory where components are maintained. Default: components.
  • products (list)
    • base_iris (list) A list of URI prefixes used to identify terms belonging to the component.
    • Items (string)
    • filename (string) The filename of this component.
    • make_base (boolean): if make_base is true, the file is turned into a base (works with source). Default: false.
    • mappings (list) A list of SSSOM template names. If set, these will be used to source this component.
    • Items (string)
    • source (string) The URL source for which the component should be obtained.
    • sssom_tool_options (string): SSSOM toolkit options passed to the sssom command used to generate this product command. Default: "".
    • template_options (string) ROBOT options passed to the template command.
    • templates (list) A list of ROBOT template names. If set, these will be used to source this component.
    • Items (string)
    • use_mappings (boolean): If true, the component will be sourced from one or more SSSOM mapping files. Default: false.
    • use_template (boolean): If true, the component will be sourced by a template. Default: false.

• contact (string) Single contact for ontology as required by OBO.

• contributors (list) List of ontology contributors (currently setting this has no effect).

• Items (string)

• create_obo_metadata (boolean): if true OBO Markdown and PURL configs are created. Default: true.

• creators (list) List of ontology creators (currently setting this has no effect).

• Items (string)

• custom_makefile_header (string): A multiline string that is added to the Makefile. Default: "\n# ----------------------------------------\n# More information: https://github.com/INCATools/ontology-development-kit/\n".

• description (string): Provide a short description of the ontology. Default: "None".

• documentation:

  • documentation_system (string): Currently, only mkdocs is supported. Default: "mkdocs".

• dosdp_tools_options (string): default parameters for dosdp-tools. Default: "--obo-prefixes=true".

• edit_format (string): Format in which the edit file is managed, either obo or owl. Default: "owl".

• ensure_valid_rdfxml (boolean): When enabled, ensure that any RDF/XML product file is valid. Default: true.

• exclude_tautologies (string): Remove tautologies such as A SubClassOf: owl:Thing or owl:Nothing SubclassOf: A. For more information see http://robot.obolibrary.org/reason#excluding-tautologies. Default: "structural".

• export_formats (list): A list of export formats you wish your release artefacts to be exported to, such as owl, obo, gz, ttl. Default: ["owl", "obo"].

• Items (string)

• export_project_yaml (boolean): Flag to set if you want a full project.yaml to be exported, including all the default options. Default: false.

• extra_rdfxml_checks (boolean): When enabled, RDF/XML product files are checked against additional parsers. Default: false.

• git_main_branch (string): The main branch for your repo, such as main, or (now discouraged) master. Default: "main".

• git_user (string): GIT user name (necessary for generating releases). Default: "".

• github_org (string): Name of github org or username where repo will live. Examples: obophenotype, cmungall. Default: "".

• gzip_main (boolean): if true add a gzipped version of the main artefact. Default: false.

• id (string): OBO id for this ontology. Must be lowercase Examples: uberon, go, cl, envo, chebi. Default: "".

• import_component_format (string): The default serialisation for all components and imports. Default: "ofn".

• import_group:

  • disabled (boolean): if set then this is not used. Default: false.
  • ids (list) potentially deprecated, specify explicit product list instead.
  • Items (string)
  • rebuild_if_source_changes (boolean): if false then upstream ontology is re-downloaded any time edit file changes. Default: true.
  • annotate_defined_by (boolean): If set to true, the annotation rdfs:definedBy is added for each external class. In the case of use_base_merging is also true, this will be added to the imports/merged_import.owl file. When imports are not merged, the annotation is added during the release process to the full release artefact. Default: False.
  • annotation_properties (list): Define which annotation properties to pull in. Default: ['rdfs:label', 'IAO:0000115'].
  • base_merge_drop_equivalent_class_axioms (boolean): If set to true, equivalent class axioms will be removed before extracting a module with the base-merging process. Default: True.
  • directory (string): directory where imports are extracted into to. Default: imports/.
  • exclude_iri_patterns (list): List of IRI patterns. If set, IRIs matching and IRI pattern will be removed from the import. Default: ``.
  • export_obo (boolean): If set to true, modules will not only be created in OWL, but also OBO format. Default: False.
  • mirror_max_time_download (integer): Corresponds to the cURL --max-time parameter (in seconds), see http://www.ipgp.fr/~arnaudl/NanoCD/software/win32/curl/docs/curl.html. Default: 200.
  • mirror_retry_download (integer): Corresponds to the cURL --retry parameter, see http://www.ipgp.fr/~arnaudl/NanoCD/software/win32/curl/docs/curl.html. Default: 4.
  • module_type (string): Module type. Supported: slme, minimal, custom. Default: slme.
  • module_type_slme (string): SLME module type. Supported: BOT, TOP, STAR. Default: BOT.
  • products (list)
    • description (string) A concise textual description of the product.
    • id (string, required) ontology project identifier / shorthand; e.g. go, obi, envo.
    • maintenance (string): A setting that can be used to change certain assets that are typically managed automatically (by ODK) to manual or other maintenance strategies. Default: "manual".
    • rebuild_if_source_changes (boolean): If false then previously downloaded versions of external ontologies are used. Default: true.
    • robot_settings:
      • memory_gb (integer) Amount of memory in GB to provide for tool such as robot.
    • annotation_properties (list): Define which annotation properties to pull in. Default: ['rdfs:label', 'IAO:0000115'].
    • base_iris (list): if specified this URL is used rather than the default OBO PURL for the main OWL product. Default: ``.
    • is_large (boolean): if large, ODK may take measures to reduce the memory footprint of the import. Default: False.
    • make_base (boolean): if make_base is true, try to extract a base file from the mirror. Default: False.
    • mirror_from (string): if specified this URL is used rather than the default OBO PURL for the main OWL product. Default: ``.
    • mirror_type (string): Define the type of the mirror for your import. Supported: base, custom, no_mirror. Default: ``.
    • module_type (string): Module type. Supported: slme, minimal, custom, mirror. Default: ``.
    • module_type_slme (string): SLME module type. Supported: BOT, TOP, STAR. Default: BOT.
    • slme_individuals (string): See http://robot.obolibrary.org/extract#syntactic-locality-module-extractor-slme. Default: include.
    • use_base (boolean): if use_base is true, try use the base IRI instead of normal one to mirror from. Default: False.
    • use_gzipped (boolean): if use_gzipped is true, try use the base IRI instead of normal one to mirror from. Default: False.
  • release_imports (boolean): If set to True, imports are copied to the release directory. Default: False.
  • slme_individuals (string): See http://robot.obolibrary.org/extract#syntactic-locality-module-extractor-slme. Default: include.
  • use_base_merging (boolean): If set to true, mirrors will be merged before determining a suitable seed. This can be a quite costly process. Default: False.

• import_pattern_ontology (boolean): if true import pattern.owl. Default: false.

• license (string): Which license is ontology supplied under - must be an IRI. Default: "https://creativecommons.org/licenses/unspecified".

• namespaces (list) A list of namespaces that are considered at home in this ontology. Used for certain filter commands.

• Items (string)

• obo_format_options (string): Additional args to pass to robot when saving to obo. TODO consider changing to a boolean for checks. Default: "".

• owltools_memory (string): OWLTools memory, for example 4GB. Default: "".

• pattern_pipelines_group:

  • disabled (boolean): if set then this is not used. Default: false.
  • ids (list) potentially deprecated, specify explicit product list instead.
  • Items (string)
  • rebuild_if_source_changes (boolean): if false then upstream ontology is re-downloaded any time edit file changes. Default: true.
  • directory (string): directory where pattern source lives, also where TSV exported to. Default: ../patterns/.
  • matches (list)
    • description (string) A concise textual description of the product.
    • id (string, required) ontology project identifier / shorthand; e.g. go, obi, envo.
    • maintenance (string): A setting that can be used to change certain assets that are typically managed automatically (by ODK) to manual or other maintenance strategies. Default: "manual".
    • rebuild_if_source_changes (boolean): If false then previously downloaded versions of external ontologies are used. Default: true.
    • robot_settings:
      • memory_gb (integer) Amount of memory in GB to provide for tool such as robot.
    • dosdp_tools_options (string): Default: --obo-prefixes=true.
    • ontology (string): Default: $(SRC).
  • products (list)
  • ...

• primary_release (string): Which release file should be published as the primary release artefact, i.e. foo.owl. Default: "full".

• public_release (string): if true add functions to run automated releases (experimental). Current options are: github_curl, github_python. Default: "none".

• public_release_assets (list) A list of files that gets added to a github/gitlab/etc release (as assets). If this option is not set (None), the standard ODK assets will be deployed.

• Items (string)

• reasoner (string): Name of reasoner to use in ontology pipeline, see robot reason docs for allowed values. Default: "ELK".

• release_artefacts (list): A list of release artefacts you wish to be exported. Supported: base, full, baselite, simple, non-classified, simple-non-classified, basic. Default: ["full", "base"].

• Items (string)

• release_date (boolean): if true, releases will be tagged with a release date (oboInOwl:date). Default: false.

• release_diff (boolean): When enabled, a diff is generated between the current release and the new one. Default: false.

• release_materialize_object_properties (list) Define which object properties to materialise at release time.

• Items (string)

• release_use_reasoner (boolean): If set to True, the reasoner will be used during the release process. The reasoner is used for three operations: reason (the classification/subclassOf hierarchy computation); materialize (the materialisation of simple existential/ object property restrictions); reduce (the removal of redundant subclassOf axioms). Default: true.

• remove_owl_nothing (boolean): Flag to set if you want odk to remove owl:Nothing from releases. Default: false.

• repo (string): Name of repo (do not include org). E.g. cell-ontology. Default: "".

• robot_java_args (string): Java args to pass to ROBOT at runtime, such as -Xmx6G. Default: "".

• robot_report (object): Block that includes settings for ROBOT report, ROBOT verify and additional reports that are generated. Default: {"custom_profile": false, "custom_sparql_checks": ["owldef-self-reference", "iri-range", "label-with-iri", "multiple-replaced_by", "dc-properties"], "custom_sparql_exports": ["basic-report", "class-count-by-prefix", "edges", "xrefs", "obsoletes", "synonyms"], "ensure_owl2dl_profile": true, "fail_on": null, "release_reports": false, "report_on": ["edit"], "sparql_test_on": ["edit"], "use_base_iris": true, "use_labels": true}.

• robot_settings:

  • memory_gb (integer) Amount of memory in GB to provide for tool such as robot.

• robot_version (string) Only set this if you want to pin to a specific robot version.

• sssom_mappingset_group:

  • directory (string): Default: "../mappings".
  • products (list)
    • description (string) A concise textual description of the product.
    • id (string, required) ontology project identifier / shorthand; e.g. go, obi, envo.
    • maintenance (string): A setting that can be used to change certain assets that are typically managed automatically (by ODK) to manual or other maintenance strategies. Default: "manual".
    • rebuild_if_source_changes (boolean): If false then previously downloaded versions of external ontologies are used. Default: true.
    • robot_settings:
    • memory_gb (integer) Amount of memory in GB to provide for tool such as robot.
  • mirror_from (string): if specified this URL is used to mirror the mapping set. Default: ``.
  • source_file (string): The name of the file from which the mappings should be extracted. Default: ``.
  • sssom_tool_options (string): SSSOM toolkit options passed to the sssom command used to generate this product command. Default: ``.
  • release_mappings (boolean): If set to True, mappings are copied to the release directory. Default: false.

• subset_group:

  • disabled (boolean): if set then this is not used. Default: false.
  • ids (list) potentially deprecated, specify explicit product list instead.
  • Items (string)
  • rebuild_if_source_changes (boolean): if false then upstream ontology is re-downloaded any time edit file changes. Default: true.
  • directory (string): directory where subsets are placed after extraction from ontology. Default: subsets/.
  • products (list)
    • description (string) A concise textual description of the product.
    • id (string, required) ontology project identifier / shorthand; e.g. go, obi, envo.
    • maintenance (string): A setting that can be used to change certain assets that are typically managed automatically (by ODK) to manual or other maintenance strategies. Default: "manual".
    • rebuild_if_source_changes (boolean): If false then previously downloaded versions of external ontologies are used. Default: true.
    • robot_settings:
      • memory_gb (integer) Amount of memory in GB to provide for tool such as robot.
    • creators (list): list of people that are credited as creators/maintainers of the subset. Default: ``.

• title (string): Concise descriptive text about this ontology. Default: "".

• travis_emails (list) Emails to use in travis configurations.

• Items (string)

• uribase (string): Base URI for PURLs. For an example see https://gitlab.c-path.org/c-pathontology/critical-path-ontology. Default: "http://purl.obolibrary.org/obo".

• uribase_suffix (string) Suffix for the uri base. If not set, the suffix will be the ontology id by default.

• use_context (boolean): If True, a context file is created that allows the user to specify prefixes used across the project. Default: false.

• use_custom_import_module (boolean): if true add a custom import module which is managed through a robot template. This can also be used to manage your module seed. Default: false.

• use_dosdps (boolean): if true use dead simple owl design patterns. Default: false.

• use_edit_file_imports (boolean): If True, ODK will release the ontology with imports explicitly specified by owl:imports in the edit file. If False, ODK will build and release the ontology with all imports and all components specified in the ODK config file. Default: true.

• use_env_file_docker (boolean): if true environment variables are collected by the docker wrapper and passed into the container. Default: false.

• use_external_date (boolean): Flag to set if you want odk to use the host date rather than the docker internal date. Default: false.

• use_mappings (boolean): if true use SSSOM mapping files. Default: false.

• use_templates (boolean): if true use ROBOT templates. Default: false.

• workflows (list): Workflows that are synced when updating the repo. Currently available: docs, diff, qc, release-diff. Default: ["docs"].

• Items (string)