├── .github └── workflows │ └── build.yml ├── .gitignore ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── build.sh ├── img ├── dark_openMINDS-logo.png ├── dark_openMINDS-logo.svg ├── light_openMINDS-logo.png └── light_openMINDS-logo.svg └── vocab ├── properties.json └── types.json /.github/workflows/build.yml: -------------------------------------------------------------------------------- 1 | # Adapted from https://github.com/HumanBrainProject/openMINDS/blob/871e382/.github/workflows/validate-schemas.yml 2 | # MIT licensed 3 | 4 | # This workflow will install Python dependencies, run tests and lint with a single version of Python 5 | # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions 6 | 7 | name: openMINDS_central_build 8 | 9 | on: 10 | workflow_dispatch: 11 | push: 12 | branches: 13 | - main 14 | 15 | jobs: 16 | build: 17 | runs-on: ubuntu-latest 18 | steps: 19 | 20 | - name: Check out repository code 21 | uses: actions/checkout@v2 22 | with: 23 | # No matter which branch has received the push, we're going to operate on the main branch (since we build everything) 24 | repository: HumanBrainProject/openMINDS 25 | ref: main 26 | path: . 27 | 28 | - name: Set up Python 3.8 29 | uses: actions/setup-python@v2 30 | with: 31 | python-version: 3.8 32 | 33 | - name: Checkout openMINDS 34 | uses: actions/checkout@v2 35 | with: 36 | repository: HumanBrainProject/openMINDS 37 | ref: main 38 | path: openMINDS 39 | 40 | - name: Checkout documentation branch 41 | uses: actions/checkout@v2 42 | with: 43 | repository: HumanBrainProject/openMINDS 44 | ref: documentation 45 | path: openMINDS_documentation 46 | 47 | - name: Run build 48 | run: | 49 | set -e 50 | chmod +x build.sh 51 | ./build.sh 52 | 53 | - name: Push documentation and package 54 | run: | 55 | cd openMINDS_documentation 56 | git config user.name openMINDS 57 | git config user.email openMINDS@ebrains.eu 58 | if [[ $(git add . --dry-run | wc -l) -gt 0 ]]; then 59 | git add . 60 | git commit -m "Update of documentation" 61 | git push 62 | else 63 | echo "Nothing to commit" 64 | fi 65 | cd .. 66 | rm -rf openMINDS_documentation 67 | 68 | 69 | - name: Push vocabulary extraction 70 | run: | 71 | git config user.name openMINDS 72 | git config user.email openMINDS@ebrains.eu 73 | if [[ $(git add vocab --dry-run | wc -l) -gt 0 ]]; then 74 | git add vocab 75 | git commit -m "Automated vocabulary extraction" 76 | git push 77 | else 78 | echo "Nothing to commit" 79 | fi -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | 6 | # C extensions 7 | *.so 8 | 9 | # Distribution / packaging 10 | .Python 11 | build/ 12 | develop-eggs/ 13 | dist/ 14 | downloads/ 15 | expanded/ 16 | documentation/ 17 | generator/ 18 | eggs/ 19 | .eggs/ 20 | lib/ 21 | lib64/ 22 | parts/ 23 | sdist/ 24 | var/ 25 | wheels/ 26 | pip-wheel-metadata/ 27 | share/python-wheels/ 28 | *.egg-info/ 29 | .installed.cfg 30 | *.egg 31 | MANIFEST 32 | 33 | # PyInstaller 34 | # Usually these files are written by a python script from a template 35 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 36 | *.manifest 37 | *.spec 38 | 39 | # Installer logs 40 | pip-log.txt 41 | pip-delete-this-directory.txt 42 | 43 | # Unit test / coverage reports 44 | htmlcov/ 45 | .tox/ 46 | .nox/ 47 | .coverage 48 | .coverage.* 49 | .cache 50 | nosetests.xml 51 | coverage.xml 52 | *.cover 53 | *.py,cover 54 | .hypothesis/ 55 | .pytest_cache/ 56 | 57 | # Translations 58 | *.mo 59 | *.pot 60 | 61 | # Django stuff: 62 | *.log 63 | local_settings.py 64 | db.sqlite3 65 | db.sqlite3-journal 66 | 67 | # Flask stuff: 68 | instance/ 69 | .webassets-cache 70 | 71 | # Scrapy stuff: 72 | .scrapy 73 | 74 | # Sphinx documentation 75 | docs/_build/ 76 | 77 | # PyBuilder 78 | target/ 79 | 80 | # Jupyter Notebook 81 | .ipynb_checkpoints 82 | 83 | # IPython 84 | profile_default/ 85 | ipython_config.py 86 | 87 | # pyenv 88 | .python-version 89 | 90 | # pipenv 91 | # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. 92 | # However, in case of collaboration, if having platform-specific dependencies or dependencies 93 | # having no cross-platform support, pipenv may install dependencies that don't work, or not 94 | # install all needed dependencies. 95 | #Pipfile.lock 96 | 97 | # PEP 582; used by e.g. github.com/David-OConnor/pyflow 98 | __pypackages__/ 99 | 100 | # Celery stuff 101 | celerybeat-schedule 102 | celerybeat.pid 103 | 104 | # SageMath parsed files 105 | *.sage.py 106 | 107 | # Environments 108 | .env 109 | .venv 110 | env/ 111 | venv/ 112 | ENV/ 113 | env.bak/ 114 | venv.bak/ 115 | 116 | # Spyder project settings 117 | .spyderproject 118 | .spyproject 119 | 120 | # Rope project settings 121 | .ropeproject 122 | 123 | # mkdocs documentation 124 | /site 125 | 126 | # mypy 127 | .mypy_cache/ 128 | .dmypy.json 129 | dmypy.json 130 | 131 | # Pyre type checker 132 | .pyre/ -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- 1 | # How to contribute 2 | 3 | openMINDS is by design an open-source, community-driven project incorporating input and feedback from all community members independent of their scientific background. 4 | 5 | **Do not be shy!** We, the openMINDS development team, rely on you, as a community member, to get in touch if you have general feedback or a request for a new feature, want to report a bug or have a question. Depending on the type of message for us, you can either contact us via our support-email or via an issue on our GitHub repositories. You are also welcome to contribute to discussion in the issue tracker. 6 | 7 | For more details please go to: [Report & ask questions](#report-questions) 8 | 9 | **Help us directly!** Contributions from outside the openMINDS development team are always very welcome. If you spot a bug and know how to fix it, if you want to extend existing schemas and/or metadata models, or develop new schemas and/or metadata models, feel free to fork this repository and open a pull request with your changes. For larger changes, please raise an issue beforehand to get feedback from the openMINDS development team and the community. 10 | 11 | For more details please go to: [Direct contributions](#direct-contributions) 12 | 13 | **Be nice!** Contributing to openMINDS should be a harassment-free experience for everyone, regardless of age, body size disability, ethnicity, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation. 14 | 15 | For more details please go to: [Code of conduct](#code-of-conduct) 16 | 17 | --- 18 | 19 | ## Report & ask questions 20 | 21 | In particular, general feedback and questions are welcome through our support-email: **`openminds@ebrains.eu`** 22 | 23 | It is also possible to request new features or report bugs this way, but in these cases we prefer if you could raise an issue on the respective GitHub repository (see below). 24 | 25 | If you write us an email, please make sure that you provide a meaningful subject that describes your concern. If your concern is not of general nature, please name the affected GitHub repository and file in your email. In particular for bug reports, provide us with a screen shot or copy of your error message (where applicable). 26 | 27 | You can also report and ask questions through the issue tracker of this GitHub repository. However, if your concern is not of general nature or affecting the central openMINDS repository, please consider raising an issue on the affected openMINDS repository instead. 28 | 29 | If you raise an issue, please make sure that you provide a short meaningful title and a more detailed description that declares your concern. In particular for bug reports, provide us with a screen shot or copy of your error message (where applicable). 30 | 31 | Please also checkout the [openMINDS Community Forum](https://neurostars.org/t/openminds-community-forum-virtual/20156) on INCF NeuroStars. You can just follow discussions of the openMINDS community there or actively participate and inform us about your view of an open topic. 32 | 33 | [BACK TO TOP](#top) 34 | 35 | ## Direct contributions 36 | 37 | If you want to contribute to the central openMINDS repository directly, feel free to fork it and open pull requests with your changes. Note, that larger changes and new features should be first raised and discussed as an issue before making a pull request. Minor bug fixes can, of course, still be made directly as a pull request without raising an issue first. Direct contributions to one of the openMINDS metadata models or the openMINDS generator should be made on the respective GitHub repository. 38 | 39 | Please be aware that on any openMINDS version branch which has an official release tag in place, only backwards compatible changes are accepted. This can include corrections of typos in instructions, introduction of additional properties to schemas, loosening constraints on expected value numbers or formats, granting additional relations between schemas, and adding new schemas (if they do not require relational changes in existing schemas). Except for typo corrections, these changes (if accepted) are typically later tagged as sub-releases for the respective major version (e.g., v1.1) by the openMINDS development team. 40 | 41 | Non-backwards compatible changes are only accepted for version branches that do not have an official release tag yet, or lead to the creation of a new version branch (with a respectively increased major version number). This is true for renaming of existing properties, increasing constraints on expected value numbers or formats, removing relations between schemas and adding new schemas, if they cause relational changes in existing schemas. 42 | 43 | For all contributions, make sure that you describe well what you plan to do / have done to speed up the evaluation / review process of your issue / pull request. The assigned member of the openMINDS development team will get back to you as soon as possible to discuss or give the blessing to your contribution. Note that, all contributing community members are welcome to provide comments on active issues and pull requests. 44 | 45 | [BACK TO TOP](#top) 46 | 47 | ## Code of conduct 48 | 49 | **Contributing to openMINDS should be a harassment-free experience for everyone** regardless of age, body size disability, ethnicity, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation. 50 | 51 | #### Our pledge 52 | 53 | In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making 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. 54 | 55 | #### Our standards 56 | 57 | Examples of behavior that contributes to creating a positive environment include: 58 | **+** using welcoming and inclusive language 59 | **+** being respectful of differing viewpoints and experiences 60 | **+** gracefully accepting constructive criticism 61 | **+** focusing on what is best for the community 62 | **+** showing empathy towards other community members 63 | 64 | Examples of unacceptable behavior by participants include: 65 | **-** use of sexualized language or imagery 66 | **-** unwelcome sexual attention or advances 67 | **-** trolling, insulting/derogatory comments, and personal or political attacks 68 | **-** public or private harassment 69 | **-** publishing others' private information (e.g., email address) without explicit permission 70 | **-** other conduct which could reasonably be considered inappropriate in a professional setting 71 | 72 | #### Our responsibility 73 | 74 | 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. 75 | 76 | 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. 77 | 78 | #### Scope 79 | 80 | 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. 81 | 82 | #### Enforcement 83 | 84 | Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team via **`support@ebrains.eu`** 85 | 86 | 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. 87 | 88 | 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. 89 | 90 | #### Attribution 91 | 92 | This code of conduct is adapted from the [Contributor Covenant](http://contributor-covenant.org), [version 1.4](http://contributor-covenant.org/version/1/4). 93 | 94 | [BACK TO TOP](#top) 95 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2020 Forschungszentrum Jülich GmbH 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # WARNING: DEPRECATED REPOSITORY 2 | 3 | **openMINDS moved now to a new GitHub organization: https://github.com/openMetadataInitiative** 4 | 5 | **This movement led to a couple of changes. SUMMARY OF CHANGES:** 6 | + ▶️ https://github.com/openMetadataInitiative/openMINDS 7 | + branch 'main' contains vocabulary and fully extended openMINDS schemas in openMINDS syntax 8 | + fully extended openMINDS schemas in openMINDS syntax use the extension `*.schema.omi.json` 9 | + schemas are build for openMINDS versions in dedicated folders in branch 'main' 10 | + code for gathering and extending schemas in the main branch is located in branch 'pipeline' 11 | + ▶️ https://github.com/openMetadataInitiative/openMINDS_json-schema 12 | + branch 'main' contains extended openMINDS schemas (per openMINDS version) formatted in JSON-Schema 13 | + code for reformmating schemas is located in branch 'pipeline' 14 | + ▶️ https://github.com/openMetadataInitiative/openMINDS_instances 15 | + branch 'main' contains libraries of controlled metadata instances and graph structures for selected schemas across openMINDS metadata models 16 | + instances and graph strucutres are build for openMINDS versions in dedicated folders in branch 'main' 17 | + ▶️ https://github.com/openMetadataInitiative/openMINDS_Python 18 | + branch 'main' contains extended openMINDS schemas (per openMINDS version) coded as Python classes plus other code for openMINDS Python package 19 | + code for building openMINDS schema classes is located in branch 'pipeline' 20 | + ▶️ https://github.com/openMetadataInitiative/openMINDS_MATLAB 21 | + branch 'main' contains extended openMINDS schemas (per openMINDS version) coded as Python classes plus other code for openMINDS MATLAB package 22 | + code for building openMINDS schema classes is located in branch 'pipeline' 23 | + ▶️ https://github.com/openMetadataInitiative/openMINDS_documentation 24 | + builds the documentation for openMINDS on Read-The-Docs (https://openminds-documentation.readthedocs.io) 25 | 26 | 27 | 28 | 29 | 30 | openMINDS logo 31 | 32 | 33 | 34 | # Welcome to openMINDS! 35 | 36 | The **open** **M**etadata **I**nitiative for **N**euroscience **D**ata **S**tructures, short **openMINDS**, is a metadata framework that develops and maintains a set of metadata models as well as libraries of controlled terminologies, brain atlases, and common coordinate spaces for neuroscience graph databases. 37 | 38 | Note that this GitHub only hosts a summary of the openMINDS documentation. For a full documenation please navigate to the [**openMINDS Collab**](https://wiki.ebrains.eu/bin/view/Collabs/openminds/). For browsing through schemas and lists of all controlled terminologies, brain atlases, and common coordinate spaces please navigate to the [**openMINDS HTML docu**](https://humanbrainproject.github.io/openMINDS/). 39 | 40 | **You need help?** Just get in touch via GitHub issue trackers, or our support email: **`openminds@ebrains.eu`** 41 | 42 | ## Documentation (summary) 43 | 44 | Depending on the version (cf. GitHub branches), openMINDS currently ingests the following metadata models: 45 | 46 | [openMINDS_core](https://github.com/HumanBrainProject/openMINDS_core) - covers general origin, location and content of research products. 47 | [openMINDS_SANDS](https://github.com/HumanBrainProject/openMINDS_SANDS) - covers brain atlases, as well as anatomical locations and relations of non-atlas data. 48 | [openMINDS_controlledTerms](https://github.com/HumanBrainProject/openMINDS_controlledTerms) - covers consistent definitions of neuroscience terms. 49 | [openMINDS_computation](https://github.com/HumanBrainProject/openMINDS_computation) (in dev) - covers provenance of simulations, data analysis and visualizations in neuroscience. 50 | [openMINDS_publications](https://github.com/HumanBrainProject/openMINDS_publications) (in dev) - covers definitions for scholarly publications, including live papers. 51 | [openMINDS_chemicals](https://github.com/HumanBrainProject/openMINDS_chemicals) (in dev) - covers consistent definitions of chemical substances and mixtures. 52 | [openMINDS_ephys](https://github.com/HumanBrainProject/openMINDS_ephys) (in dev) - covers provenance of electrophysiology experiments. 53 | 54 | #### What you can find below: 55 | 1. [How to contribute](#how-to-contribute) 56 | 2. [Technical overview & guidelines](#technical-overview-and-guidelines) 57 | 3. [How to get started](#how-to-get-started) 58 | 4. [License, adoptions & acknowledgements](#license-adoptions-acknowledgements) 59 | 60 | --- 61 | 62 | ## How to contribute 63 | 64 | The openMINDS development team currently unites knowledge from the EBRAINS Curation Service, the EBRAINS Knowledge Graph, the EBRAINS Atlas Service, and the INCF Knowledge Space teams. **Contributions from the whole community are welcome and highly appreciated!** 65 | 66 | In order to facilitate contributions from all community members independent of their scientific background, all openMINDS metadata models are defined using a light-weighted schema template syntax. Although this schema template syntax is inspired by JSON-Schema, it outsources most technicalities, making the openMINDS schemas more human-readable, especially for untrained eyes. 67 | 68 | If you have general feedback or a request for a new feature, want to report a bug or have a question, please get in touch with us via our support-email (**`openminds@ebrains.eu`**) or via the issue tracker on one of our GitHub repositories. You can also follow or actively participate in the discussions on the [openMINDS Community Forum](https://neurostars.org/t/openminds-community-forum-virtual/20156) on INCF NeuroStars. 69 | 70 | If you spot a bug and know how to fix it, if you want to extend existing schemas and/or metadata models, or develop new schemas and/or metadata models, feel always free to contribute directly by raising an issue and making a pull request on the respective GitHub repository. 71 | 72 | For more information on how to contribute, please have a look at our [CONTRIBUTING](./CONTRIBUTING.md) document. 73 | 74 | [BACK TO TOP](#welcome) 75 | 76 | ## Technical overview & guidelines 77 | 78 | In summary, the central openMINDS GitHub repository has a **main** branch (where you are right now), a **documentation** branch, and **version** branches (naming convention: `vX`; e.g., `v1`). Official releases (naming convention: `vX.Y`; e.g., `v1.0`) are tagged and provided as release packages. 79 | 80 | The **main** branch hosts the general [README](./README.md) (this document), the [LICENSE](./LICENSE) document, the [CONTRIBUTING](./CONTRIBUTING.md) document, and the general [openMINDS logo](./img/openMINDS_logo.png). In addition, it maintains the openMINDS vocabulary ([vocab](./vocab)) which provides general definitions and references for schema types and properties used across all openMINDS metadata models and their versions, and the [bash script](./build.sh) that builds the content of the documentation and version branches. 81 | 82 | The **documentation** branch hosts the HTML files that build the [openMINDS GitHub pages](https://humanbrainproject.github.io/openMINDS/), as well as a ZIP file for each version branch and official release containing the respective openMINDS schemas in the currently supported formats, such as the openMINDS syntax (`.schema.tpl.json`), JSON-Schema (`.schema.json`), or HTML (`.html`). 83 | 84 | The **version** branches host the respective openMINDS schemas of a major version by ingesting the corresponding metadata models as git-submodules. We chose this modular design to facilitate extensions and maintenance of existing, as well as development and integration of new openMINDS metadata models and schemas. Note that the version branches can have official release tags. 85 | 86 | If a version branch has an official release tag, only backwards compatible changes can be merged on this branch. This can include corrections of typos in instructions, introduction of additional properties to schemas, loosening constraints on expected value numbers or formats, granting additional relations between schemas, and adding new schemas (if they do not require relational changes in existing schemas). Except for typo corrections, these changes are typically tagged as sub-releases for the respective major version (e.g., v1.1). 87 | 88 | If a version branch does not have an official release tag, yet, also non-backwards compatible changes can be merged on this branch. This can include renaming of existing properties, increasing constraints on expected value numbers or formats, removing relations between schemas and adding new schemas, if they cause relational changes in existing schemas. In case all version branches have official release tags, a new non-backwards compatible change would lead to the creation of a new version branch (with a respectively increased major version number). 89 | 90 | The setup of the central openMINDS GitHub repository is maintained by the openMINDS integration pipeline (cf. [openMINDS_generator](https://github.com/HumanBrainProject/openMINDS_generator) GitHub repository). The pipeline is configured in such a way, that each commit on one of the openMINDS submodules will trigger a new build of the central openMINDS repository ensuring that its content is always up-to-date. This pipeline also interprets and extends the openMINDS schema syntax to other schema representation formats (such as JSON-Schema, see above). 91 | 92 | [BACK TO TOP](#welcome) 93 | 94 | ## How to get started 95 | 96 | You can either download one of the release packages, or use `git clone` to be able to work locally with released versions or the "unstable" version branches: 97 | 98 | git clone https://github.com/HumanBrainProject/openMINDS.git 99 | 100 | Once, you cloned the repository, you can list the availabel version branches: 101 | 102 | git branch -a 103 | 104 | and checkout the one you like to work on, e.g.,: 105 | 106 | git checkout v2 107 | 108 | Note that you might also see some feature branches of current developments that on the long run will be merged into one of version branches. These feature branches do not follow any naming convention. 109 | 110 | If you rather like to work with a stable release, you can also list all available release tags: 111 | 112 | git tag -l 113 | 114 | and checkout the stable version branch you like to work with via the respective release tag, e.g.,: 115 | 116 | git checkout tags/ 117 | 118 | As mentioned above, on each version branch, a version-specific set of distributed GitHub repositories is ingested as git-submodules, each defining a particular metadata model for neuroscience. To be able to use these metadata models, the submodules need to be initialised: 119 | 120 | git submodule init 121 | 122 | and updated: 123 | 124 | git submodule update 125 | 126 | After completion of this step your local repository is on the most recent state of the selected openMINDS version branch. 127 | 128 | [BACK TO TOP](#welcome) 129 | 130 | ## License, adoptions & acknowledgements 131 | 132 | openMINDS is licensed under the MIT License. 133 | 134 | Within EBRAINS, the openMINDS metadata models are adopted by the EBRAINS Knowledge Graph and Interactive Brain Atlas. In addition, openMINDS is currently in the process of being adopted by the Japan Brain/MINDS project. 135 | 136 | **Logo:** The openMINDS logo was created by U. Schlegel, based on an original sketch by C. Hagen Blixhavn and feedback by L. Zehl. 137 | 138 | The openMINDS project is powered by [HBP](https://www.humanbrainproject.eu) (Human Brain Project) and [EBRAINS](https://ebrains.eu/): The metadata model specifications as well as surrounding code and tools were developed developed in part or in whole in the Human Brain Project, funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No. 720270, No. 785907, and No. 945539 (Human Brain Project SGA1, SGA2, and SGA3). 139 | 140 | [BACK TO TOP](#welcome) 141 | -------------------------------------------------------------------------------- /build.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # The script requires the openMIINDS repository to be cloned in the same root directory into the directory "openMINDS_documentation". 4 | # This needs to be done externally since we need to push back to it and this can only be achieved when the repo is cloned via the workflow action 5 | if [ ! -d "openMINDS_documentation" ]; then 6 | echo "You need to clone openMINDS (SSH) to the directory openMINDS_documentation first, before you can run the build script" 7 | echo "In the console, execute git clone 'git@github.com:HumanBrainProject/openMINDS.git' openMINDS_documentation" 8 | exit 1 9 | fi 10 | 11 | commitAndPush(){ 12 | git config user.name openMINDS 13 | git config user.email openMINDS@ebrains.eu 14 | if [[ $(git add . --dry-run | wc -l) -gt 0 ]]; then 15 | git add . 16 | git commit -m "Update submodule references" 17 | git push 18 | else 19 | echo "Nothing to commit" 20 | fi 21 | } 22 | 23 | 24 | FIRST_BUILD=1 25 | build(){ 26 | echo "" 27 | echo "*************************" 28 | echo "Building $1" 29 | echo "*************************" 30 | echo "" 31 | git checkout $1 32 | # Ensure submodules are properly fetched 33 | if [[ $4 == 'branch' ]] 34 | then 35 | git fetch 36 | # If it's a branch build, we need to make sure we're at the head of the branch 37 | git reset --hard origin/$1 38 | git submodule sync 39 | git submodule update --init --recursive --remote 40 | git clean -dffx 41 | # We push the synchronized state of the repository to follow the head of the submodules 42 | commitAndPush 43 | elif [[ $4 == 'tag' ]] 44 | then 45 | git fetch 46 | git reset --hard $1 47 | git submodule sync 48 | #For tags we explicitly don't set the "--remote" flag (since we want the commit which is recorded as part of the tag 49 | git submodule update --init --recursive 50 | git clean -dffx 51 | # And obviously we don't push back since we don't want to change the tag 52 | fi 53 | 54 | #Use the vocab from the central repository - we remove an existing one (although there should be none) 55 | rm -rf vocab 56 | cp -r ../vocab . 57 | 58 | # Linting... 59 | # stop the build if there are Python syntax errors or undefined names 60 | flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics 61 | # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide 62 | flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics 63 | 64 | # Run the generator logic 65 | if [[ $FIRST_BUILD == 1 ]] 66 | then 67 | echo "First build" 68 | python ../openMINDS_generator/openMINDS.py --path ../openMINDS --reinit --current "$1" --allVersionBranches "$2" --allTags "$3" 69 | else 70 | python ../openMINDS_generator/openMINDS.py --path ../openMINDS --current "$1" --allVersionBranches "$2" --allTags "$3" 71 | fi 72 | FIRST_BUILD=0 73 | # Copy expanded schemas into target 74 | echo "Copy expanded schemas into target" 75 | mkdir target/schema.tpl.json 76 | cp -r expanded/* target/schema.tpl.json 77 | 78 | #Also move the version specific property and types files 79 | mv properties-$1.json target/properties.json 80 | mv types-$1.json target/types.json 81 | 82 | # Copy instances to target 83 | cp -r instances/* target/instances/ 84 | for d in * 85 | do 86 | if [ -d $d ] && [ "$d" != "target" ] && [ -d "$d/instances" ] 87 | then 88 | TARGET="target/instances/$d/$(cat $d/version.txt)/" 89 | mkdir -p $TARGET 90 | echo "Copy instances to target" 91 | cp -r $d/instances/* $TARGET 92 | fi 93 | done 94 | 95 | # Copy documentation 96 | rm -rf ../openMINDS_documentation/$1 97 | mkdir -p ../openMINDS_documentation/$1 98 | 99 | # ZIP data 100 | cd target && zip -r "../../openMINDS_documentation/openMINDS-$1.zip" . && cd .. 101 | 102 | cp -r target/html/* ../openMINDS_documentation/$1 103 | cp -r target/uml/* ../openMINDS_documentation/$1 104 | cp -r target/schema.json/* ../openMINDS_documentation/$1 105 | mv ../openMINDS_documentation/$1/central.html ../openMINDS_documentation/index.html 106 | cp -r vocab .. 107 | rm -rf 108 | 109 | } 110 | 111 | echo "Clearing existing elements..." 112 | rm -rf openMINDS_generator 113 | 114 | echo "Cloning openMINDS_generator and installing requirements" 115 | git clone https://github.com/HumanBrainProject/openMINDS_generator.git 116 | cd openMINDS_generator 117 | git pull 118 | git reset --hard origin/main 119 | python -m pip install --upgrade pip 120 | pip install flake8 pytest 121 | if [ -f requirements.txt ]; then pip install -r requirements.txt; fi 122 | cd .. 123 | 124 | echo "Ensure documentation branch in openMINDS_documentation" 125 | cd openMINDS_documentation 126 | git checkout documentation 127 | git pull 128 | git reset --hard origin/documentation 129 | #Remove all content since it should be fully reconstructed 130 | rm -rf * 131 | cd .. 132 | 133 | cd openMINDS 134 | 135 | ALL_VERSION_BRANCHES=$(curl -s https://api.github.com/repos/HumanBrainProject/openMINDS/branches | grep -P -o "(?<=\"name\": \")v[0-9]+.*?(?=\")") 136 | ALL_TAGS=$(curl -s https://api.github.com/repos/HumanBrainProject/openMINDS/tags | grep -P -o "(?<=\"name\": \")v[0-9]+.*?(?=\")") 137 | VERSION_BRANCH_LABELS=$(echo $ALL_VERSION_BRANCHES, | tr ' ' ',' | sed 's/.$//') 138 | TAG_LABELS=$(echo $ALL_TAGS | tr ' ' ',') 139 | 140 | echo "Building all version-branches (head)" 141 | for version in $ALL_VERSION_BRANCHES; 142 | do if [[ $version =~ ^v[0-9]+.*$ ]]; then build $version "$VERSION_BRANCH_LABELS" "$TAG_LABELS" 'branch'; fi; done 143 | 144 | echo "Building all tags" 145 | for version in $ALL_TAGS; 146 | do if [[ $version =~ ^v[0-9]+.*$ ]]; then build $version "$VERSION_BRANCH_LABELS", "$TAG_LABELS" 'tag'; fi; done 147 | 148 | #build v1 "v1,v2,v3" "v1.0.0,v2.0.0" 'branch' 149 | -------------------------------------------------------------------------------- /img/dark_openMINDS-logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanBrainProject/openMINDS/52a3fd7aa578498ab485c80f4e438990abd49ec6/img/dark_openMINDS-logo.png -------------------------------------------------------------------------------- /img/dark_openMINDS-logo.svg: -------------------------------------------------------------------------------- 1 | 2 | 18 | 20 | 30 | 37 | 41 | 45 | 49 | 50 | 61 | 72 | 83 | 94 | 105 | 116 | 127 | 138 | 149 | 150 | 169 | 171 | 172 | 174 | image/svg+xml 175 | 177 | 178 | 179 | 180 | 181 | 187 | 194 | 195 | 199 | 202 | 210 | 218 | 224 | 230 | 236 | 242 | 243 | 249 | 255 | 261 | 262 | 268 | 276 | 284 | 292 | 300 | 308 | 316 | 323 | 330 | 338 | 339 | 340 | 341 | -------------------------------------------------------------------------------- /img/light_openMINDS-logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanBrainProject/openMINDS/52a3fd7aa578498ab485c80f4e438990abd49ec6/img/light_openMINDS-logo.png -------------------------------------------------------------------------------- /img/light_openMINDS-logo.svg: -------------------------------------------------------------------------------- 1 | 2 | 18 | 20 | 30 | 37 | 41 | 45 | 49 | 50 | 61 | 72 | 83 | 94 | 105 | 116 | 127 | 138 | 149 | 160 | 161 | 180 | 182 | 183 | 185 | image/svg+xml 186 | 188 | 189 | 190 | 191 | 192 | 197 | 200 | 208 | 216 | 222 | 228 | 234 | 240 | 241 | 247 | 253 | 259 | 260 | 266 | 274 | 282 | 290 | 298 | 306 | 314 | 322 | 329 | 336 | 344 | 345 | 346 | 347 | -------------------------------------------------------------------------------- /vocab/types.json: -------------------------------------------------------------------------------- 1 | { 2 | "https://openminds.ebrains.eu/chemicals/AmountOfChemical": { 3 | "description": "Structured information about the amount of a given chemical that was used.", 4 | "label": "Amount of chemical", 5 | "schemas": [ 6 | "chemicals/v1/amountOfChemical" 7 | ], 8 | "translatableTo": null 9 | }, 10 | "https://openminds.ebrains.eu/chemicals/ChemicalMixture": { 11 | "description": "Structured information about a mixture of chemical substances.", 12 | "label": "Chemical mixture", 13 | "schemas": [ 14 | "chemicals/v1/chemicalMixture" 15 | ], 16 | "translatableTo": null 17 | }, 18 | "https://openminds.ebrains.eu/chemicals/ChemicalSubstance": 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