updating my version

.github/workflows/openMINDS_upstream.yml

@@ -0,0 +1,14 @@
+name: openMINDS_upstream
+
+on: 
+  - push
+  - workflow_dispatch
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Trigger central repository
+      run: |
+        curl -XPOST -u "${{secrets.PAT_USERNAME}}:${{secrets.PAT_TOKEN}}" -H "Accept: application/vnd.github.everest-preview+json" -H "Content-Type: application/json" https://api.github.com/repos/openMetadataInitiative/openMINDS/actions/workflows/build.yml/dispatches --data '{"ref": "pipeline", "inputs": {"branch": "${{github.ref_name}}", "repository": "${{ github.repository }}"}'
+        curl -XPOST -u "${{secrets.PAT_USERNAME}}:${{secrets.PAT_TOKEN}}" -H "Accept: application/vnd.github.everest-preview+json" -H "Content-Type: application/json" https://api.github.com/repos/openMetadataInitiative/openMINDS/actions/workflows/build-dev.yml/dispatches --data '{"ref": "pipeline", "inputs": {"branch": "${{github.ref_name}}", "repository": "${{ github.repository }}"}'

CONTRIBUTING.md

@@ -1,92 +1,6 @@
-# How to contribute <a name="top"/>
+# How to contribute
 
-openMINDS is by design an open-source, community-driven project incorporating input and feedback from all community members independent of their scientific background.
+The openMINDS metadata framework is an open-source project and community contributions are highly appreciated. If you want to contribute please follow our :arrow_right: [**contribution guidelines**][contribution-url].
 
-**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.
-
-For more details please go to: [Report & ask questions](#report-questions)
-
-**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.
-
-For more details please go to: [Direct contributions](#direct-contributions)
-
-**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.
-
-For more details please go to: [Code of conduct](#code-of-conduct)
-
----
-
-## Report & ask questions <a name="report-questions"/>
-
-In particular, general feedback and questions are welcome through our support-email: **`[email protected]`** (not active yet)
-
-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).
-
-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). 
-
-You can also report and ask questions through the issue tracker of this GitHub repository. However, if your concern is of general nature or affecting the central openMINDS repository, please consider raising an issue on the central openMINDS repository instead.
-
-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). 
-
-[BACK TO TOP](#top)
-
-## Direct contributions <a name="direct-contributions"/>
-
-If you want to contribute to the openMINDS_computation 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 other openMINDS metadata models, the openMINDS generator or openMINDS (central) should be made on the respective GitHub repository.
-
-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. 
-
-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.
-
-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. 
-
-[BACK TO TOP](#top)
-
-## Code of conduct <a name="code-of-conduct"/>
-
-**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.
-
-#### Our pledge
-
-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.
-
-#### 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:  
-**-** use of sexualized language or imagery  
-**-** unwelcome sexual attention or advances  
-**-** trolling, insulting/derogatory comments, and personal or political attacks  
-**-** public or private harassment  
-**-** publishing others' private information (e.g., email address) without explicit permission  
-**-** other conduct which could reasonably be considered inappropriate in a professional setting  
-
-#### Our responsibility
-
-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 via **`[email protected]`**
-
-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 is adapted from the [Contributor Covenant](http://contributor-covenant.org), [version 1.4](http://contributor-covenant.org/version/1/4).
-
-[BACK TO TOP](#top)
+<!-- MARKDOWN LINKS & IMAGES -->
+[contribution-url]: https://openminds-documentation.readthedocs.io/en/latest/shared/contribution_guidelines.html

LICENSE.txt → LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021 CNRS
+Copyright (c) 2022 CNRS, Forschungszentrum Jülich GmbH, Universitetet i Oslo
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in

README.md

@@ -1,29 +1,74 @@
-<a href="https://github.com/HumanBrainProject/openMINDS_chemicals/blob/v1/img/openMINDS_chem_logo.png">
-    <img src="https://github.com/HumanBrainProject/openMINDS_chemicals/blob/v1/img/light_openMINDS-chem-logo.png" alt="openMINDS chemicals logo" title="openMINDS chemicals" align="right" height="70" />
+<a href="/img/openMINDS_chemicals_logo_light.png">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="/img/openMINDS_chemicals_logo_dark.png">
+    <source media="(prefers-color-scheme: light)" srcset="/img/openMINDS_chemicals_logo_light.png">
+    <img alt="openMINDS_chemicals metadata model" src="/img/openMINDS_chemicals_logo_light.png" title="Logo created by U. Schlegel, L. Zehl, C. Hagen Blixhavn" align="right" height="70">
+  </picture>
 </a>
 
 # openMINDS_chemicals
-A metadata model for chemical substances used in neuroscience; an openMINDS extension.
 
-The **openMINDS_chemicals** repository is part of the **open** **M**etadata **I**nitiative for **N**euroscience **D**ata Structures (**openMINDS**). It extends openMINDS core, by providing schema-templates for adding metadata for simulation and data analysis.
+[![GitHub][license-shield]][license-url]
+[![GitHub contributors][contributors-shield]][contributors-url]
 
-The major versions are developed and maintained in different version-branches. The default branch is always the latest version-branch.
-**Each version can be accessed by checking out the corresponding version-branch.** No major version branch has yet been released. This README describes the development branch ("main").
+The **openMINDS_chemicals** repository hosts one of the metadata models of the **openMINDS metadata framework**. It defines modular metadata schemas for describing chemical substances and mixtures.
 
-For more information on openMINDS in general and the processing pipelines for the schema-templates please go to the main repository: https://github.com/HumanBrainProject/openMINDS
+To generally learn more about the openMINDS metadata framework please go to :arrow_right: [**ReadTheDocs**][docu-url].  
+There you can also explore directly the :arrow_right: [**openMINDS_chemicals schema specifications**][docu-chemicals-url].
 
-## schemas
-The computation schemas are defined as JSON-schema inspired templates with only a few customized technical properties (prefixed with `"_"`). These simplified schema-templates are easy to read and can be robustly translated to other, well known target formats (e.g., HTML, JSON-schema, etc.).
+## How to cite
 
-## tests
-In **tests** you can find JSON-LD documents designed to test the validation behaviour of each schema.
-Each document follows the naming convention `{schema_name}-{custom_test_name}.jsonld`. For test cases supposed to fail the validation, the suffix **`-nok`** should be attached (`{schema_name}-{custom_test_name}-nok.jsonld`). The tests are validated every time a change is introduced and therefore ensure the correct behavior of the schemas.
+For specifically referencing the openMINDS_chemicals metadata model, please use the following RRID Portal record:  
+```
+openMINDS chemicals metadata model (RRID:SCR_026248)
+```
 
-## examples
-In **examples** you will find several possible serializations of the openMINDS_computation metadata model. The scope of each example is described in its README. The correspondingly generated JSON-LD documents may be further structured (e.g., grouped according to the schema they are validated against).
+Please reference in addition openMINDS in general, using our main RRID Portal record:  
+```
+openMINDS metadata framework (RRID:SCR_023173)
+```
 
 ## How to contribute
-Please check our [contribution document](./CONTRIBUTING.md).
 
-## License
-This work is licensed under the MIT License.
+The openMINDS metadata framework is an open-source project and community contributions are highly appreciated. If you want to contribute please follow our :arrow_right: [**contribution guidelines**][contribution-url].
+
+Schema contributions to openMINDS_chemicals should be raised and discussed on the :arrow_right: [**issue tracker**][issuetracker-chemicals]  
+
+General usage questions should be raised and discussed in our :arrow_right: [**community forum**][community-forum].  
+Alternatively you can email us: `[email protected]`
+
+## Funding and acknowledgements
+
+The openMINDS metadata framework development started in the [Human Brain Project (HBP)][hbp-website], funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreements [SGA-1 (No.720270)][hbp-sga1-doi], [SGA-2 (No.785907)][hbp-sga2-doi], and [SGA-3 (No. 945539)][hbp-sga3-doi]. 
+
+The framework is further developed as part of the EBRAINS 2.0 project, funded from the European Union's Research and Innovation Program Horizon Europe under Grant Agreement [GA (No.101147319)][ebrains2-doi].
+
+The framework also receives support from the [BigBrain Project](https://bigbrainproject.org/), funded by [HIBALL][hiball-url].
+
+## Collaboration partners
+
+The openMINDS metadata framework is closely collaborating with the [InterLex Project][interlex-dashboard] of the [SciCrunch Data and Resource Infrastructure][scicrunch-website] and the [KnowledgeSpace][ks-website] hosted by the [International Neuroinformatics Coordinating Facility (INCF)][incf-website].
+
+
+<!-- MARKDOWN LINKS & IMAGES -->
+[community-forum]: https://neurostars.org/t/about-the-openminds-category/31428
+[contribution-url]: https://openminds-documentation.readthedocs.io/en/latest/shared/contribution_guidelines.html
+[contributors-url]: https://github.com/openMetadataInitiative/openMINDS_chemicals/graphs/contributors
+[contributors-shield]: https://img.shields.io/github/contributors/openMetadataInitiative/openMINDS_chemicals
+[docu-url]: https://openminds-documentation.readthedocs.io
+[docu-chemicals-url]: https://openminds-documentation.readthedocs.io/en/v3.0/schema_specifications/chemicals.html
+[ebrains2-doi]: https://doi.org/10.3030/101147319
+[hiball-url]: https://bigbrainproject.org/hiball.html
+[hbp-sga1-doi]: https://doi.org/10.3030/720270
+[hbp-sga2-doi]: https://doi.org/10.3030/785907
+[hbp-sga3-doi]: https://doi.org/10.3030/945539
+[hbp-website]: https://www.humanbrainproject.eu
+[incf-website]: https://www.incf.org
+[interlex-dashboard]: https://scicrunch.org/scicrunch/interlex/dashboard
+[issuetracker-chemicals]: https://github.com/openMetadataInitiative/openMINDS_chemicals/issues
+[issuetracker-instances]: https://github.com/openMetadataInitiative/openMINDS_instances/issues
+[issuetracker-main]: https://github.com/openMetadataInitiative/openMINDS/issues
+[ks-website]: https://knowledge-space.org
+[license-url]: https://raw.githubusercontent.com/openMetadataInitiative/openMINDS_chemicals/v1/LICENSE
+[license-shield]: https://img.shields.io/github/license/openMetadataInitiative/openMINDS_chemicals
+[scicrunch-website]: https://scicrunch.org