Combined feature updates

CITATION.cff

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+cff-version: 1.2.0
+message: "If you use the DOME Registry, please cite the original GigaScience publication as follows."
+authors:
+  - family-names: Attafi
+    given-names: Omar Abdelghani
+    orcid: "https://orcid.org/0009-0002-2327-9430"
+title: "DOME Registry"
+version: 1.0.3
+date-released: 2024-12-11
+preferred-citation:
+  type: article
+  authors:
+    - family-names: Attafi
+      given-names: Omar Abdelghani
+      orcid: "https://orcid.org/0009-0002-2327-9430"
+    - family-names: Clementel
+      given-names: Damiano
+      orcid: "https://orcid.org/0000-0002-7395-2921"
+    - family-names: Kyritsis
+      given-names: Konstantinos
+      orcid: "https://orcid.org/0000-0001-8035-341X"
+    - family-names: Capriotti
+      given-names: Emidio
+      orcid: "https://orcid.org/0000-0002-2323-0963"
+    - family-names: Farrell
+      given-names: Gavin
+      orcid: "https://orcid.org/0000-0001-5166-8551"
+    - family-names: Fragkouli
+      given-names: Styliani-Christina
+      orcid: "https://orcid.org/0000-0003-4067-7123"
+    - family-names: Castro
+      given-names: Leyla Jael
+      orcid: "https://orcid.org/0000-0003-3986-0510"
+    - family-names: Hatos
+      given-names: András
+      orcid: "https://orcid.org/0000-0001-9224-9820"
+    - family-names: Lenaerts
+      given-names: Tom
+      orcid: "https://orcid.org/0000-0003-3645-1455"
+    - family-names: Mazurenko
+      given-names: Stanislav
+      orcid: "https://orcid.org/0000-0003-3659-4819"
+    - family-names: Mozaffari
+      given-names: Soroush
+    - family-names: Pradelli
+      given-names: Franco
+      orcid: "https://orcid.org/0000-0002-7152-5512"
+    - family-names: Ruch
+      given-names: Patrick
+      orcid: "https://orcid.org/0000-0002-3374-2962"
+    - family-names: Savojardo
+      given-names: Castrense
+      orcid: "https://orcid.org/0000-0002-7359-0633"
+    - family-names: Turina
+      given-names: Paola
+      orcid: "https://orcid.org/0000-0001-9174-511X"
+    - family-names: Zambelli
+      given-names: Federico
+      orcid: "https://orcid.org/0000-0003-3487-4331"
+    - family-names: Piovesan
+      given-names: Damiano
+      orcid: "https://orcid.org/0000-0001-8210-2390"
+    - family-names: Monzon
+      given-names: Alexander Miguel
+      orcid: "https://orcid.org/0000-0003-0362-8218"
+    - family-names: Psomopoulos
+      given-names: Fotis
+      orcid: "https://orcid.org/0000-0002-0222-4273"
+    - family-names: Tosatto
+      given-names: Silvio C E
+      orcid: "https://orcid.org/0000-0003-4525-7793"
+  title: "DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology"
+  journal: "GigaScience"
+  volume: 13
+  year: 2024
+  doi: "10.1093/gigascience/giae094"
+  url: "https://doi.org/10.1093/gigascience/giae094"

CODE_OF_CONDUCT.md

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+# Community Code of Conduct for the DOME Registry
+
+The **DOME Registry**, managed by the **UNIPD Biocomputing Lab** and the **ELIXIR Europe Machine Learning Focus Group**, is dedicated to providing a welcoming and supportive environment for all people, regardless of background or identity. We do not tolerate behaviour that is disrespectful to our community members or that excludes, intimidates, or causes discomfort to others. 
+
+We do not tolerate discrimination or harassment based on characteristics including, but not limited to: gender identity and expression, sexual orientation, disability, physical appearance, body size, citizenship, nationality, ethnic or social origin, pregnancy, familial status, veteran status, genetic information, religion or belief (or lack thereof), membership of a national minority, property, age, education, socio-economic status, technical choices, and experience level.
+
+Everyone who participates in the DOME Registry and OSAI ecosystem contributions is required to conform to this Code of Conduct. This applies to all spaces managed by the project including, but not limited to, workshops, and communications online via GitHub or other project channels. By participating, contributors indicate their acceptance of the procedures by which the project team resolves any incidents, which may include the storage and processing of their personal information.
+
+---
+
+## Expected Behaviour
+
+We are confident that our community members will together build a supportive and collaborative atmosphere. The following guidelines set out explicitly what we hope you will consider to be appropriate community conduct:
+
+* **Be respectful of different viewpoints and experiences.** Do not engage in homophobic, racist, transphobic, ageist, ableist, sexist, or otherwise exclusionary behaviour.
+* **Use welcoming and inclusive language.** Exclusionary comments or jokes, threats, or violent language are not acceptable. Do not address others in an angry, intimidating, or demeaning manner. Be patient and respectful of the fact that English is a second (or third!) language for many participants.
+* **Do not harass people.** Harassment includes unwanted physical contact, sexual attention, or repeated social contact. Consent is explicit, conscious, and continuous. If someone tells you to stop, do so immediately.
+* **Respect the privacy and safety of others.** Do not take photographs of others without their permission. Do not share other participants’ personal experiences without express permission. "Doxing" (posting personally identifying information without consent) is a form of harassment.
+* **Be considerate of participation.** Everyone should have an opportunity to be heard. In discussion sessions, please keep comments succinct to allow maximum engagement. Do not interrupt others on the basis of disagreement.
+* **Don’t be a bystander.** If you see something inappropriate happening, speak up. If you do not feel comfortable intervening, please ask a member of the project team for support.
+* **Do not gaslight.** Gaslighting is a tactic in which a person makes a victim question their reality. Look out for the signs in yourself and others ([5 tactics for gaslighting](https://www.psychologytoday.com/gb/blog/how-be-yourself/201801/how-recognize-5-tactics-gaslighting)).
+* **Be intentional in your actions and humble in your mistakes.**
+
+All interactions should be professional regardless of platform. See [this explanation of the four social rules](https://www.recurse.com/manual#sub-sec-social-rules) (no feigning surprise, no well-actuallys, no back-seat driving, no subtle -isms) for further recommendations for inclusive behaviours.
+
+---
+
+## Unacceptable Behaviour
+
+Examples of unacceptable behaviour at any project event or platform include:
+
+* Written or verbal comments which have the effect of excluding people based on membership of any specific group.
+* Causing someone to fear for their safety, such as through stalking, following, or intimidation.
+* Violent threats or language directed against another person.
+* The display of sexual or violent images.
+* Unwelcome sexual attention or non-consensual physical contact.
+* Sustained disruption of talks, events, or communications.
+* Insults, put-downs, or exclusionary jokes.
+* Excessive swearing or incitement to self-harm.
+* Publication of private communication without consent.
+
+---
+
+## Reporting Violations
+
+Instances of abusive, harassing, or otherwise unacceptable behaviour may be reported by contacting the project team at **gavimichael.farrell@studenti.unipd.it**. 
+
+All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. 
+
+---
+
+## Consequences of Unacceptable Behaviour
+
+Participants asked to stop any inappropriate behaviour are expected to comply immediately. If a participant engages in behaviour that violates this Code of Conduct, the project team may warn the offender, ask them to leave the event or platform, or impose any other appropriate sanctions.
+
+---
+
+## Acknowledgements
+
+This Code of Conduct is adapted from the [RSQKit Code of Conduct](https://github.com/EVERSE-ResearchSoftware/RSQKit?tab=coc-ov-file), which was adapted from the [RDMKit Code of conduct](https://github.com/elixir-europe/rdmkit/blob/master/CODE_OF_CONDUCT.md). The RDMKit CoC was derived from the [Turing Way Project Code of Conduct](https://github.com/alan-turing-institute/the-turing-way/blob/master/CODE_OF_CONDUCT.md) which in turn was adapted from [Carpentries Code of Conduct](https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html), and with sections from the [Alan Turing Institute Data Study Group Code of Conduct](https://docs.google.com/document/d/1iv2cizNPUwtEhHqaezAzjIoKkaIX02f7XbYmFMXDTGY/edit). 
+
+The Carpentries Code of Conduct was adapted from guidelines written by the [Django Project](https://www.djangoproject.com/conduct/enforcement-manual/), based on the [Ada Initiative template](http://geekfeminism.wikia.com/wiki/Conference_anti-harassment/Responding_to_reports) and the [PyCon 2013 Procedure for Handling Harassment Incidents](https://us.pycon.org/2013/about/code-of-conduct/harassment-incidents/). 
+
+The Turing Institute Data Study Group Code of Conduct was adapted from the [Citizen Lab Summer Institute 2017 Code of Conduct](https://citizenlab.ca/summerinstitute/codeofconduct.html) (CC BY 2.5 CA). Citizen Lab based their code on the [xvzf Code of Conduct](http://xvzf.io/#coc), the [Contributor Covenant](http://contributor-covenant.org/), and the [Django Code of Conduct and Reporting Guide](https://www.djangoproject.com/conduct/).
+
+This Code of Conduct is licensed under a [Creative Commons Attribution 4.0 International](https://creativecommons.org/licenses/by/4.0/) (CC BY 4.0) license. By contributing to the DOME Registry, you agree to license your contributions under CC BY 4.0 and abide by this Code of Conduct.

CONTRIBUTING.md

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+# Contributing to the DOME Registry
+
+Thank you for your interest in contributing to the DOME Registry. This project, hosted by the **UNIPD Biocomputing Lab**, aims to provide a curated, FAIR-compliant registry for machine learning methods in the life sciences.
+
+We primarily use a GitHub-based workflow. Contributions are made via Pull Requests (PRs) which are then reviewed and merged by the UNIPD lead developer. For general enquiries or coordination before starting a large contribution, you can reach the team at **contact@dome-ml.org**.
+
+## On this page
+* [How to Contribute](#how-to-contribute)
+    * [Reporting Issues or Suggesting Improvements](#reporting-issues-or-suggesting-improvements)
+    * [Submitting Changes via Pull Requests](#submitting-changes-via-pull-requests)
+* [What to Contribute](#what-to-contribute)
+* [What Not to Contribute](#what-not-to-contribute)
+* [Contribution Licensing](#contribution-licensing)
+* [Review Process](#review-process)
+
+---
+
+## How to Contribute
+
+### Reporting Issues or Suggesting Improvements
+If you find a bug, want to suggest a new feature, or have an idea for improving the registry structure:
+
+1. **Check existing issues:** See if someone has already reported the same item or made a similar suggestion.
+2. **Create a new issue:** If not, please [create a new issue](https://github.com/Biocomputing-UP/dome-registry/issues) (ensure you use the correct repository link).
+    * Provide a clear title and description.
+    * For bug reports, include steps to reproduce the issue.
+    * For complex suggestions, feel free to email **contact@dome-ml.org** to discuss the roadmap.
+
+### Submitting Changes via Pull Requests
+This is the preferred way to modify the registry code, documentation, or static resources.
+
+1. **Fork the Repository:** Create your own copy of the [DOME Registry repository](https://github.com/Biocomputing-UP/dome-registry) on GitHub.
+2. **Create a Local Branch:** In your forked repository, create a new branch for your changes.
+    ```bash
+    git checkout -b feature/add-new-integration
+    ```
+3. **Make Your Changes:**
+    * Add your modifications or corrections to the relevant files.
+    * Ensure each change is clear, concise, and follows the existing style.
+4. **Commit Your Changes:**
+    ```bash
+    git add .
+    git commit -m "feat: add EPMC integration description"
+    ```
+    (Use clear, descriptive commit messages starting with a prefix like `feat:`, `fix:`, or `docs:`).
+5. **Push to Your Fork:**
+    ```bash
+    git push origin feature/add-new-integration
+    ```
+6. **Open a Pull Request:**
+    * Navigate to the original DOME Registry repository on GitHub.
+    * Click the "New Pull Request" button.
+    * Provide a clear title and a brief description of your changes.
+    * Submit the Pull Request for review.
+
+---
+
+## What to Contribute
+We welcome contributions that add or improve:
+
+* **Registry Metadata:** Corrections to existing method descriptions or improvements to metadata schemas.
+* **Documentation:** Improvements to the README, API documentation, or user tutorials.
+* **Bug Fixes:** Resolving issues in the registry front-end or back-end integration scripts.
+* **Integration Standards:** Updates to Bioschemas markup or other FAIR-related annotations.
+
+---
+
+## What Not to Contribute
+* Off-topic content that does not align with the goals of promoting FAIR machine learning methods.
+* Proprietary code or resources that do not permit open-access sharing.
+* Changes to core infrastructure without prior discussion via an Issue or email.
+* Promotional material or advertisements.
+
+---
+
+## Contribution Licensing
+By contributing to this project, you agree that your contributions will be licensed under the project's **CC-BY-4.0** license. All contributed content must respect the copyrights and intellectual property of others.
+
+---
+
+## Review Process
+The **UNIPD lead developer** will review all Pull Requests.
+* We aim to provide feedback on contributions promptly.
+* Requests for changes or clarifications may be made via comments on the Pull Request.
+* Once the PR is approved and passes any automated checks, the UNIPD lead developer will merge it into the `main` branch.
+
+For any questions regarding the review process or if you need to report an urgent issue, please contact **contact@dome-ml.org**.
+
+We appreciate your effort in helping the UNIPD Biocomputing Lab build a robust and FAIR ecosystem for machine learning methods.

LICENSE.md

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+# License
+
+The content of this repository, specifically the curated lists of Open and Sustainable AI (OSAI) ecosystem components, is licensed under the Creative Commons Attribution 4.0 International License (CC BY 4.0).
+
+You are free to share and adapt the material for any purpose, even commercially, as long as you give appropriate credit.
+
+For the full license text, please see: https://creativecommons.org/licenses/by/4.0/legalcode
+
+A human-readable summary is available at: https://creativecommons.org/licenses/by/4.0/