seed repo

.github/workflows/docs.yml

@@ -0,0 +1,27 @@
+# Basic ODK workflow
+name: Docs
+
+# Controls when the action will run. 
+on:
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  build:
+    name: Deploy docs
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v3
+
+      - name: Deploy docs
+        uses: mhausenblas/mkdocs-deploy-gh-pages@master
+        # Or use mhausenblas/mkdocs-deploy-gh-pages@nomaterial to build without the mkdocs-material theme
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          CONFIG_FILE: mkdocs.yaml
+

.github/workflows/qc.yml

@@ -0,0 +1,33 @@
+# Basic ODK workflow
+
+name: CI
+
+# Controls when the action will run. 
+on:
+  # Triggers the workflow on push or pull request events but only for the main branch
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "ontology_qc"
+  ontology_qc:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:v1.4.3
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v3
+
+      - name: Run ontology QC checks
+        env:
+          DEFAULT_BRANCH: main
+        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false
+

.gitignore

@@ -0,0 +1,44 @@
+.DS_Store
+semantic.cache
+bin/
+
+*.tmp
+*.tmp.obo
+*.tmp.owl
+*.tmp.json
+
+.github/token.txt
+
+src/ontology/mirror
+src/ontology/mirror/*
+src/ontology/reports/*
+src/ontology/vivo.owl
+src/ontology/vivo.obo
+src/ontology/vivo.json
+src/ontology/vivo-base.*
+src/ontology/vivo-basic.*
+src/ontology/vivo-full.*
+src/ontology/vivo-simple.*
+src/ontology/vivo-simple-non-classified.*
+
+src/ontology/seed.txt
+src/ontology/dosdp-tools.log
+src/ontology/ed_definitions_merged.owl
+src/ontology/ontologyterms.txt
+src/ontology/simple_seed.txt
+src/ontology/patterns
+src/ontology/merged-vivo-edit.owl
+
+src/ontology/target/
+src/ontology/tmp/*
+!src/ontology/tmp/README.md
+
+src/ontology/run.sh.conf
+src/ontology/run.sh.env
+
+src/ontology/imports/*_terms_combined.txt
+
+src/patterns/data/**/*.ofn
+src/patterns/data/**/*.txt
+src/patterns/pattern_owl_seed.txt
+src/patterns/all_pattern_terms.txt

CODE_OF_CONDUCT.md

@@ -0,0 +1,46 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to make participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by [contacting the project team](contact.md). All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This code of conduct has been derived from the excellent code of conduct of the [ATOM project](https://github.com/atom/atom/blob/master/CODE_OF_CONDUCT.md) which in turn is adapted from the [Contributor Covenant][homepage], version 1.4, available at [https://contributor-covenant.org/version/1/4][version]
+
+[homepage]: https://contributor-covenant.org
+[version]: https://contributor-covenant.org/version/1/4/

CONTRIBUTING.md

@@ -0,0 +1,95 @@
+# Contributing to The VIVO Ontology
+
+:+1: First of all: Thank you for taking the time to contribute!
+
+The following is a set of guidelines for contributing to VIVO. 
+These guidelines are not strict rules. Use your best judgment, and feel free to propose 
+changes to this document in a pull request.
+
+## Table Of Contents
+
+- [Code of Conduct](#code-of-conduct)
+- [Guidelines for Contributions and Requests](#contributions)
+    * [Reporting problems with the ontology](#reporting-bugs)
+    * [Requesting new terms](#requesting-terms)
+    * [Adding new terms by yourself](#adding-terms)
+- [Best practices](#best-practices)
+    * [How to write a great issue?](#great-issues)
+    * [How to create a great pull/merge request?](#great-pulls)
+
+<a id="code-of-conduct"></a>
+
+## Code of Conduct
+
+The The VIVO Ontology team strives to create a
+welcoming environment for editors, users and other contributors.
+Please carefully read our [Code of Conduct](CODE_OF_CONDUCT.md).
+
+<a id="contributions"></a>
+
+## Guidelines for Contributions and Requests
+
+<a id="reporting-bugs"></a>
+
+### Reporting problems with the ontology
+
+Please use our [Issue Tracker](https://github.com/StroemPhi/vivo/issues/) for reporting problems with the ontology. 
+To learn how to write a good issue [see here](#great-issues).
+
+<a id="requesting-terms"></a>
+
+### Requesting new terms
+
+Before you write a new request, please consider the following: 
+
+- **Does the term already exist?** Before submitting suggestions for new ontology terms, check whether the term exist, 
+either as a primary term or a synonym term. You can search for your term using [OLS](http://www.ebi.ac.uk/ols/ontologies/vivo).
+- **Can you provide a definition for the term?** It should be very clear what the term means, and you should be
+able to provide a concise definition, ideally with a scientific reference.
+- **Is the ontology in scope for the term?** Sometimes, it is hard to tell whether a term "belongs" in
+and ontology. A rule of thumb is "if a similar term already exists, the new term is probably in scope."
+It can be very helpful to mention a very similar concept as part of the term request!
+
+#### Who can request a term?
+
+Anyone can request new terms. However, there is not guarantee that your term will be added automatically. Since this is a 
+community resource, it is often necessary to do at least some of the work of adding the term yourself, see below.
+
+#### How to write a new term request
+
+Request a new term _via_ the GitHub [Issue Tracker](https://github.com/StroemPhi/vivo/issues/).
+
+It is important to remember that it takes a lot of time for curators to process issues submitted to the tracker.
+To make this work easier, please always use issue templates if they are available (https://github.com/StroemPhi/vivo/issues/new/choose).
+
+For how to write a good term request, please read the [best practices carefully](#great-issues).
+
+<a id="adding-terms"></a>
+
+### How to add a new term
+
+If you have never editted this ontology before, first follow a [general tutorial](https://oboacademy.github.io/obook/lesson/contributing-to-obo-ontologies)
+
+**Process**:
+
+1. Clone the repository (In case you are not an offical team member, create a fork first)
+1. Create new branch in git, for example `git checkout -b issue123`
+1. Open src/ontology/vivo-edit.owl in your favourite editor, i.e. [Protege](https://protege.stanford.edu/). **Careful:** double check you are editing the correct file. There are many ontology files in this repository, but only one _editors file_!
+1. Perform your edit and save your changes
+1. Commit changes to branch
+1. Push changes upstream
+1. Create pull request
+
+## Best Practices
+
+<a id="great-issues"></a>
+
+### How to write great issues?
+
+Please refer to the [OBO Academy best practices](https://oboacademy.github.io/obook/lesson/term-request/).
+
+<a id="great-pulls"></a>
+
+### How to create a great pull/merge request?
+
+Please refer to the [OBO Academy best practices](https://oboacademy.github.io/obook/howto/github-create-pull-request/)

README.md

@@ -0,0 +1,29 @@
+
+![Build Status](https://github.com/StroemPhi/vivo/workflows/CI/badge.svg)
+# The VIVO Ontology
+
+Description: The VIVO Ontology is used to represent scholarship.
+
+More information can be found at http://obofoundry.org/ontology/vivo
+
+## Versions
+
+### Stable release versions
+
+The latest version of the ontology can always be found at:
+
+http://vivoweb.org/ontology/core/vivo.owl
+
+(note this will not show up until the request has been approved by obofoundry.org)
+
+### Editors' version
+
+Editors of this ontology should use the edit version, [src/ontology/vivo-edit.owl](src/ontology/vivo-edit.owl)
+
+## Contact
+
+Please use this GitHub repository's [Issue tracker](https://github.com/StroemPhi/vivo/issues) to request new terms/classes or report errors or specific concerns related to the ontology.
+
+## Acknowledgements
+
+This ontology repository was created using the [Ontology Development Kit (ODK)](https://github.com/INCATools/ontology-development-kit).

docs/cite.md

@@ -0,0 +1 @@
+# How to cite VIVO

docs/contributing.md

@@ -0,0 +1 @@
+# How to contribute to VIVO

docs/index.md

@@ -0,0 +1,7 @@
+# VIVO Ontology Documentation
+
+[//]: # "This file is meant to be edited by the ontology maintainer."
+
+Welcome to the VIVO documentation!
+
+You can find descriptions of the standard ontology engineering workflows [here](odk-workflows/index.md).

docs/odk-workflows/ContinuousIntegration.md

@@ -0,0 +1,25 @@
+# Introduction to Continuous Integration Workflows with ODK
+
+Historically, most repos have been using Travis CI for continuous integration testing and building, but due to
+runtime restrictions, we recently switched a lot of our repos to GitHub actions. You can set up your repo with CI by adding 
+this to your configuration file (src/ontology/vivo-odk.yaml):
+
+```
+ci:
+  - github_actions
+```
+
+When [updateing your repo](RepoManagement.md), you will notice a new file being added: `.github/workflows/qc.yml`.
+
+This file contains your CI logic, so if you need to change, or add anything, this is the place!
+
+Alternatively, if your repo is in GitLab instead of GitHub, you can set up your repo with GitLab CI by adding 
+this to your configuration file (src/ontology/vivo-odk.yaml):
+
+```
+ci:
+  - gitlab-ci
+```
+
+This will add a file called `.gitlab-ci.yml` in the root of your repo.
+