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‎.github/ISSUE_TEMPLATE/new-ontology.yml‎

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attributes:
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label: Ontology Download Link
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description: What URL can be used to download your Ontology?
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placeholder: e.g. https://github.com/obophenotype/uberon/raw/master/uberon.owl
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placeholder: e.g. https://github.com/obophenotype/uberon/blob/master/uberon.obo
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validations:
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required: true
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render: yaml
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description: |
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Please provide a list of current uses for your ontology in YAML format as a list of objects with `user`, `description`, and `example` keys like in the following example:
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```yaml
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- user: https://www.rhea-db.org/
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description: Rhea uses CHEBI to annotate reaction participants
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attributes:
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value: |
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# Finishing Up
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This final section asks you to introspect on your ontology request.
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- type: textarea
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id: scenarios
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required: false
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- label: My ontology has a specific release file with a version IRI and a `dc:license` annotation, serialised in RDF/XML.
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required: false
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- label: I understand that term definitions, while not mandatory, are key to understanding the intentions of a term especially when the ontology is used in curation. I made sure that a reasonable majority of terms in my ontology have definitions, using the [IAO:0000115](https://ontobee.org/ontology/IAO?iri=http://purl.obolibrary.org/obo/IAO_0000115) property.
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- label: My identifiers (classes and properties IRIs) are formatted according to the [OBO Foundry Identifier Policy](http://obofoundry.org/id-policy)
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required: false
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- label: My term labels are in English and conform to the OBO Foundry [Naming Conventions](http://obofoundry.org/principles/fp-012-naming-conventions.html)
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required: false
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- label: I understand that term definitions are key to understanding the intentions of a term, especially when the ontology is used in curation. I made sure that a reasonable majority of terms in my ontology--and all top level terms--have definitions, in English, using the [IAO:0000115](https://ontobee.org/ontology/IAO?iri=http://purl.obolibrary.org/obo/IAO_0000115) property.
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required: false
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- label: For every term in my ontology, I checked whether another OBO Foundry ontology has one with the same meaning. If so, I re-used that term directly (not by cross-reference, by directly using the IRI).
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required: false

‎.github/ISSUE_TEMPLATE/pre-submission.md‎

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name: Pre-submission Inquiry
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description: Make a pre-submission inquiry for an ontology. The purpose of a pre-submission inquiry is to announce an early ontology project that is not yet ready for review. It also serves as a reservation of an ontology namespace for 6 months.
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title: Pre-submission Inquiry for Ontology [NAME]
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labels: [ pre-submission ]
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body:
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- type: markdown
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attributes:
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value: |
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Do _NOT_ use this form to register a new ontology with the OBO Foundry. Please read the instructions provided here: http://obofoundry.org/docs/NewOntologyRegistrationInstructions.html.
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- type: input
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id: title
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attributes:
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label: Title
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description: What is the full title of your ontology? Please do not include redundant acronyms.
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placeholder: ex. Chemical Entities of Biological Interest
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validations:
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required: true
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- type: input
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id: slug
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attributes:
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label: Short Description
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description: Please provide a short description of your ontology in one sentence.
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validations:
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required: true
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- type: input
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id: idspace
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attributes:
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label: Identifier Space
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description: What is the prefix for the identifier space associated with your ontology? This is typically all capital letters with at least 3, ideally 4 or more, characters. This MUST NOT conflict with any entries in the [Bioregistry](https://bioregistry.io/registry) nor [BioPortal](https://bioportal.bioontology.org). See OBO Principle [FP-003 "URI/Identifier Space"](https://obofoundry.org/principles/fp-003-uris.html).
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placeholder: ex. UBERON
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validations:
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required: true
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- type: dropdown
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id: domain
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validations:
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required: true
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attributes:
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label: Domain
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description: Please choose the domain that best describes your ontology
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options:
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- upper
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- anatomy and development
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- health
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- phenotype
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- investigations
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- environment
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- biochemistry
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- microbiology
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- agriculture
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- diet, metabolomics, and nutrition
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- biological systems
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- information technology
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- organisms
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- information
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- simulation
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- type: markdown
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attributes:
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value: |
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# Links
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This section of the ontology request form contains links to various resources associated with your ontology.
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- type: input
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id: repository
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attributes:
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label: Source Code Repository
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description: What is the URL of the repository? Typically, this will be a link to a public GitHub or Gitlab repository.
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placeholder: e.g. https://github.com/obophenotype/uberon/
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validations:
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required: true
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- type: input
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id: tracker
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attributes:
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label: Issue Tracker
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description: What is the URL of the public issue tracker? Typically, this will be the link to the GitHub repository with a trailing `/issues` URL part.
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placeholder: e.g. https://github.com/obophenotype/uberon/issues
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validations:
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required: true
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- type: input
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id: download
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attributes:
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label: Ontology Download Link
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description: What URL can be used to download your ontology?
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placeholder: e.g. https://github.com/obophenotype/uberon/raw/master/uberon.owl
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validations:
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required: true
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- type: markdown
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attributes:
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value: |
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# Contact
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This section of the ontology request form contains information about the contact person for the ontology. See also OBO Principle [FP-011 "Locus of Authority"](https://obofoundry.org/principles/fp-011-locus-of-authority.html)
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- type: input
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id: contact-name
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attributes:
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label: Contact Name
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description: What is the full name of the contact for the ontology?
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placeholder: e.g. Charles Tapley Hoyt
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validations:
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required: true
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- type: input
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id: contact-email
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attributes:
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label: Contact Email
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description: What is the email address of the contact for the ontology?
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placeholder: e.g. cthoyt@gmail.com
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validations:
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required: true
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- type: input
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id: contact-github
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attributes:
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label: Contact GitHub Username
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description: What is the GitHub username of the contact for the ontology? Do not include the @ symbol.
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placeholder: e.g. cthoyt
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validations:
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required: true
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- type: input
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id: contact-orcid
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attributes:
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label: Contact ORCID Identifier
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description: What is the ORCID identifier of the contact for the ontology? ORCID identifiers can be made at https://orcid.org.
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placeholder: e.g. 0000-0003-4423-4370
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validations:
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required: true
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- type: markdown
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attributes:
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value: |
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# Other information
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- type: textarea
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id: scenarios
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attributes:
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label: Intended Use Cases and/or Related Projects
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description: For projects, please include a link to their websites or other location to find more information.
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validations:
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required: false
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- type: textarea
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id: remarks
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attributes:
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label: Additional comments or remarks
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description: Is there any other information that will be helpful for the OBO community and reviewers of your ontology?
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validations:
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required: false
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‎.github/workflows/build.yml‎

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commit-message: Update OBO foundry metadata
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title: 'Update OBO foundry metadata'
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body: |
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Recreates all OBO metadata
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Recreates all OBO metadata.
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assignees: deepakunni3

‎.github/workflows/obo-test.yml‎

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jobs:
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test:
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runs-on: ubuntu-latest
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if: github.triggering_actor != 'github-actions[bot]'
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steps:
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- uses: actions/checkout@v2
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- uses: actions/setup-python@v2

‎.github/workflows/qa.yml‎

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lint:
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name: Lint
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runs-on: ubuntu-latest
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if: github.triggering_actor != 'github-actions[bot]'
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strategy:
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matrix:
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python-version: [ "3.7", "3.10" ]
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python-version: [ "3.8", "3.10" ]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}

‎CONTRIBUTING.md‎

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All Python code in this repository should conform to `black` and `isort`. You
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can automatically apply them with `tox -e lint`.
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<a id="newsletter"></a>
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## Adding Newsletter Entries
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This site uses Jekyll's built-in blog system for newsletters. Take the following steps to get a new post up:
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1. Create a markdown file in the [`_posts`](_posts) directory. This file name should start with the date of writing in
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YYYY-MM-DD format, then the remainder of the file name can be a short description of the contents. Use lowercase
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words and have dashes between them instead of spaces. Example: `2023-06-16-inaugural-newsletter.md`.
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2. At the top of the the markdown file, you need the following "frontmatter" (which is YAML hiding between two `---`)
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```yaml
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---
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layout: post
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categories: newsletter
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title: YOUR TITLE
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author: YOUR NAME
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date: YYYY-MM-DD
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---
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```
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Where you replace the title and author fields with free text and the date field with a day formatted with YYYY-MM-DD
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that matches the file name.
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3. Do not begin the newsletter with a title (that uses a `#` in markdown).
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4. The first paragraph of text in the newsletter will serve as a short description

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