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resource-table-all: " " - -exclude: - - README.md - - .gitignore - - var/ - - vendor - - Gemfile* - - LICENSE diff --git a/_data/CONTRIBUTORS.yml b/_data/CONTRIBUTORS.yml index 6532fa0..7a46c16 100644 --- a/_data/CONTRIBUTORS.yml +++ b/_data/CONTRIBUTORS.yml @@ -42,3 +42,7 @@ Veit Schwämmle: email: veits@bmb.sdu.dk orcid: 0000-0002-9708-6722 affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark +Mihail Anton: + git: mihai-sysbio + orcid: 0000-0002-7753-9042 + affiliation: ELIXIR \ No newline at end of file diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml index 0da6eff..5eb1c62 100644 --- a/_data/tool_and_resource_list.yml +++ b/_data/tool_and_resource_list.yml @@ -21,7 +21,7 @@ and BioContainers. related_pages: - applications -- id: galaxy_codex +- id: galaxy name: Galaxy Codex url: https://github.com/galaxyproject/galaxy_codex description: @@ -31,7 +31,7 @@ - sources - id: bioconda name: Bioconda - url: https://bioconda.github.io/ + url: https://bioconda.github.io description: Bioconda is a bioinformatics channel for the Conda package manager registry: @@ -60,7 +60,7 @@ biotools: openebench related_pages: - sources -- id: debianmed +- id: debian-med name: Debian Med url: https://www.debian.org/devel/debian-med/index.en.html description: diff --git a/_data/topnav.yml b/_data/topnav.yml index e528ae6..f8b3034 100644 --- a/_data/topnav.yml +++ b/_data/topnav.yml @@ -7,17 +7,15 @@ subitems: url: /sources - title: Applications url: /applications +- title: Documentation + url: /docs +- title: Get support + url: /contacts - title: About subitems: - title: Licence url: /licence - title: Contributors url: /contributors - - title: Contacts - url: /contacts - - title: Publications and presentations + - title: Publications url: /publications - - title: Credits - url: /credits - - title: Documentation - url: /docs diff --git a/_posts/2024-04-29-welcome-to-jekyll.markdown b/_posts/2024-04-29-welcome-to-jekyll.markdown deleted file mode 100644 index bc30d3c..0000000 --- a/_posts/2024-04-29-welcome-to-jekyll.markdown +++ /dev/null @@ -1,28 +0,0 @@ ---- -title: "Welcome to Jekyll!" -date: 2024-04-29 22:09:46 +0200 -categories: jekyll update ---- -You’ll find this post in your `_posts` directory. Go ahead and edit it and re-build the site to see your changes. You can rebuild the site in many different ways, but the most common way is to run `jekyll serve`, which launches a web server and auto-regenerates your site when a file is updated. - -Jekyll requires blog post files to be named according to the following format: - -`YEAR-MONTH-DAY-title.MARKUP` - -Where `YEAR` is a four-digit number, `MONTH` and `DAY` are both two-digit numbers, and `MARKUP` is the file extension representing the format used in the file. After that, include the necessary front matter. Take a look at the source for this post to get an idea about how it works. - -Jekyll also offers powerful support for code snippets: - -{% highlight ruby %} -def print_hi(name) - puts "Hi, #{name}" -end -print_hi('Tom') -#=> prints 'Hi, Tom' to STDOUT. -{% endhighlight %} - -Check out the [Jekyll docs][jekyll-docs] for more info on how to get the most out of Jekyll. File all bugs/feature requests at [Jekyll’s GitHub repo][jekyll-gh]. If you have questions, you can ask them on [Jekyll Talk][jekyll-talk]. - -[jekyll-docs]: https://jekyllrb.com/docs/home -[jekyll-gh]: https://github.com/jekyll/jekyll -[jekyll-talk]: https://talk.jekyllrb.com/ diff --git a/applications.md b/applications.md index c1b186a..ce03fd4 100644 --- a/applications.md +++ b/applications.md @@ -5,4 +5,8 @@ title: Applications page_id: applications --- +RSEc metadata supports a variety of downstream applications, from workflow catalogues to benchmarking dashboards. Browse the examples below to see how the ecosystem is reused and get inspiration for your own integrations. + diff --git a/assets/img/logo-rsec.bmp b/assets/img/logo-rsec.bmp deleted file mode 100644 index 2be6a1b..0000000 Binary files a/assets/img/logo-rsec.bmp and /dev/null differ diff --git a/contacts.md b/contacts.md index 6ccebd1..021762e 100644 --- a/contacts.md +++ b/contacts.md @@ -4,3 +4,29 @@ title: Contacts --- +We are here to help you use, contribute to, and integrate the RSEc metadata. + +
+
+
+
+
Community support
+

Chat with the team and community, ask questions, and share feedback.

+ Join the Gitter channel +
+
+
+
+
+
+
Report metadata issues
+

Spotted an inconsistency or missing link? Let us know.

+ Open a GitHub issue +
+
+
+
+ + diff --git a/contributors.md b/contributors.md index 2dbe2d9..6360fe4 100644 --- a/contributors.md +++ b/contributors.md @@ -4,7 +4,24 @@ title: Contributors --- - +The Research Software Ecosystem is built by a community across ELIXIR and collaborating organisations. The list below is generated from `_data/CONTRIBUTORS.yml`. {% include contributor-tiles-all.html %} +## Funding + +The ELIXIR Research Software Ecosystem is supported and coordinated by [ELIXIR Europe](https://elixir-europe.org/). + +## Credits + +### Framework + +This website uses the [Jekyll framework](https://jekyllrb.com). + +### Theme + +This website uses the [![theme badge](https://img.shields.io/badge/ELIXIR%20toolkit%20theme-jekyll-blue?color=0d6efd)](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme). + +### Icons + +Network icons created by Freepik - Flaticon diff --git a/credits.md b/credits.md index 311fe3e..a603215 100644 --- a/credits.md +++ b/credits.md @@ -1,21 +1,7 @@ --- -# Feel free to add content and custom Front Matter to this file. -# To modify the layout, see https://jekyllrb.com/docs/themes/#overriding-theme-defaults - -title: Funding +--- +title: Credits (moved) +redirect_to: /contributors --- -The ELIXIR Research Software Ecosystem is supported and coordinated by [ELIXIR Europe](https://elixir-europe.org/). - -## Credits - -### Framework - -This website uses the [Jekyll framework](https://jekyllrb.com) - -### Theme - -This website uses the [![theme badge](https://img.shields.io/badge/ELIXIR%20toolkit%20theme-jekyll-blue?color=0d6efd)](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme) - -### Icons -Network icons created by Freepik - Flaticon +This page has been merged into the Contributors page. You are being redirected. diff --git a/docs.md b/docs.md index 266e6ea..d18c676 100644 --- a/docs.md +++ b/docs.md @@ -5,7 +5,79 @@ title: Documentation --- ## Introduction -The RSEc version-controlled repository federates metadata for research software, predominantly within the life sciences domain. These metadata cover a wide spectrum of use cases, spanning software discovery, evaluation, deployment, and execution. Centralised in an open and version-controlled repository, these metadata can be used to cross-link multiple services, to facilitate curation, and to provide insights on bioinformatics software through their aggregation and analysis. This page contains the information and links to access and understand the software metadata provided by the Research Software Ecosystem, as well as contribution guidelines and support channels. +The RSEc version-controlled repository federates metadata for research software, predominantly within the life sciences domain. These metadata cover a wide spectrum of use cases, spanning software discovery, evaluation, deployment, and execution. + +Centralised in an open and version-controlled repository, the metadata enable cross-linking between services, facilitate curation, and provide insights through aggregation and analysis. This page collects key links to access and understand the software metadata provided by the Research Software Ecosystem, plus contribution guidelines and support channels. + +## Quick start + +
+
+
+
+
1) Browse
+

Open the content repository and explore `data/` (by tool) or `imports/` (by source).

+
+
+
+
+
+
+
2) Check freshness
+

See when imports run in the GitHub Actions workflow.

+
+
+
+
+
+
+
3) Cross-link
+

Use identifiers in the cross-link table below (e.g. bio.tools IDs, Bioconda packages, Galaxy tool IDs).

+
+
+
+
+
+
+
4) Report
+

Open an issue in the content repo tracker if you spot a problem.

+
+
+
+
+ +## How to use the metadata + +
+
+
+
+
Discover tools
+

Search `data/tool-id` folders to see aggregated metadata across registries.

+
+
+
+
+
+
+
Validate metadata
+

Compare entries across sources (e.g. bio.tools vs OpenEBench) and file PRs to fix discrepancies.

+
+
+
+
+
+
+
Integrate programmatically
+

Consume raw JSON/YAML from the repository, mirror it, or automate updates with the weekly imports.

+
+
+
+
+ + ## Metadata Repository contents @@ -13,32 +85,28 @@ The RSEc metadata can be accessed on [the GitHub dedicated repository](https://g
Fig. 1: Example organisation of the metadata files imported in the RSEc metadata repository -

-

- {% mermaid %} - graph LR - root[https://github.com/research-software-ecosystem/content]; - root--> /imports[imports]; - /imports--> /imports/biotools[biotools]; - /imports/biotools--> /imports/biotools/software1[software1.biotools.json]; - /imports/biotools--> /imports/biotools/software2[software2.biotools.json]; - /imports/biotools--> /imports/biotools/software3[software3.biotools.json]; - /imports--> /imports/bioconda[bioconda]; - /imports/bioconda--> /imports/bioconda/software1[bioconda_software1.yaml]; - /imports/bioconda--> /imports/bioconda/software2[bioconda_software2.yaml]; - /imports/bioconda--> /imports/bioconda/software4[bioconda_software4.yaml]; - root--> /data[data]; - /data--> /data/software1[software1]; - /data/software1--> /data/software1/software1biotoolsjson[software1.biotools.json]; - /data/software1--> /data/software1/software1biocondayaml[bioconda_software1.yaml]; - /data--> /data/software2[software2]; - /data/software2--> /data/software2/software2biotoolsjson[software2.biotools.json]; - /data/software2--> /data/software2/software2biocondayaml[bioconda_software2.yaml]; - /data--> /data/software3[software3]; - /data/software3--> /data/software3/software3biotoolsjson[software3.biotools.json]; - {% endmermaid %} -
-

+ {% mermaid %} + graph LR + root[https://github.com/research-software-ecosystem/content]; + root--> /imports[imports]; + /imports--> /imports/biotools[biotools]; + /imports/biotools--> /imports/biotools/software1[software1.biotools.json]; + /imports/biotools--> /imports/biotools/software2[software2.biotools.json]; + /imports/biotools--> /imports/biotools/software3[software3.biotools.json]; + /imports--> /imports/bioconda[bioconda]; + /imports/bioconda--> /imports/bioconda/software1[bioconda_software1.yaml]; + /imports/bioconda--> /imports/bioconda/software2[bioconda_software2.yaml]; + /imports/bioconda--> /imports/bioconda/software4[bioconda_software4.yaml]; + root--> /data[data]; + /data--> /data/software1[software1]; + /data/software1--> /data/software1/software1biotoolsjson[software1.biotools.json]; + /data/software1--> /data/software1/software1biocondayaml[bioconda_software1.yaml]; + /data--> /data/software2[software2]; + /data/software2--> /data/software2/software2biotoolsjson[software2.biotools.json]; + /data/software2--> /data/software2/software2biocondayaml[bioconda_software2.yaml]; + /data--> /data/software3[software3]; + /data/software3--> /data/software3/software3biotoolsjson[software3.biotools.json]; + {% endmermaid %}
## Supported Formats @@ -60,14 +128,14 @@ Most metadata formats for a given source include cross-links to other sources: | Destination / **Source** | bio.tools | OpenEBench | Bioconda | Biocontainers | Galaxy Codex | Debian Med | BIII | Bioconductor | |--------------|-----------|------------|----------|---------------|--------------|------------|-----------|------------| -| **bio.tools** | XXXXXXXXX | | url entries of the `download` key where `url` starts with `"https://anaconda.org/bioconda/"`, the remainer of the url being the Bioconda package name | | | url entries of the `download` key where `url` starts with `"https://tracker.debian.org/pkg/"`, the remainer of the url being the Debian package name | | | -| **OpenEBench** | List elements that have and `@id` key starting with `"https://openebench.bsc.es/monitor/metrics/biotools"` |XXXXXXXXX | List elements that have and `@id` key starting with `"https://openebench.bsc.es/monitor/metrics/bioconda"` | | List elements that have and `@id` key starting with `"https://openebench.bsc.es/monitor/metrics/galaxy"` | | | | -| **Bioconda** | YAML list `extra.identifiers`, CURIEs starting with `"biotools:"` | | XXXXXXXXX| | | For _usegalaxy.eu_, YAML list `extra.identifiers`, CURIEs starting with `"usegalaxy-eu:"` | | | -| **Biocontainers** | | | | XXXXXXXXX | | | | | -| **Galaxy Codex** | 'bio.tool_id' key in the JSON file | | 'Conda_id' key in the JSON file | | XXXXXXXXX | | | | -| **Debian Med** | YAML list registries, CURIES are in `entry` key when `name` is `"bio.tools"` | | YAML list registries, CURIES are in `entry` key when `name` is `"conda:bioconda"` | | | XXXXXXXXX | | | -| **BIII** | | | | | | | XXXXXXXXX | | -| **Bioconductor** | | | | | | | | XXXXXXXXX | +| **bio.tools** | n/a | | url entries of the `download` key where `url` starts with `"https://anaconda.org/bioconda/"`, the remainer of the url being the Bioconda package name | | | url entries of the `download` key where `url` starts with `"https://tracker.debian.org/pkg/"`, the remainer of the url being the Debian package name | | | +| **OpenEBench** | List elements that have and `@id` key starting with `"https://openebench.bsc.es/monitor/metrics/biotools"` |n/a | List elements that have and `@id` key starting with `"https://openebench.bsc.es/monitor/metrics/bioconda"` | | List elements that have and `@id` key starting with `"https://openebench.bsc.es/monitor/metrics/galaxy"` | | | | +| **Bioconda** | YAML list `extra.identifiers`, CURIEs starting with `"biotools:"` | | n/a| | | For _usegalaxy.eu_, YAML list `extra.identifiers`, CURIEs starting with `"usegalaxy-eu:"` | | | +| **Biocontainers** | | | | n/a | | | | | +| **Galaxy Codex** | 'bio.tool_id' key in the JSON file | | 'Conda_id' key in the JSON file | | n/a | | | | +| **Debian Med** | YAML list registries, CURIES are in `entry` key when `name` is `"bio.tools"` | | YAML list registries, CURIES are in `entry` key when `name` is `"conda:bioconda"` | | | n/a | | | +| **BIII** | | | | | | | n/a | | +| **Bioconductor** | | | | | | | | n/a | ## Metadata Import Workflow @@ -78,42 +146,37 @@ The metadata is imported and updated using a [GitHub actions workflow](https://g - commits this version of the metadata. The outline of this workflow is illustrated in Fig. 2. -| Resource Description | CI code location | -|-----------------------|------------------| -| Bio.tools | [https://github.com/research-software-ecosystem/utils/tree/main/biotools-import](https://github.com/research-software-ecosystem/utils/tree/main/biotools-import) | -| OpenEBench | [https://github.com/research-software-ecosystem/utils/tree/main/openebench-import](https://github.com/research-software-ecosystem/utils/tree/main/openebench-import) | -| Bioconda | [https://github.com/research-software-ecosystem/utils/tree/main/bioconda-import](https://github.com/research-software-ecosystem/utils/tree/main/bioconda-import) | -| Biocontainers | [https://github.com/research-software-ecosystem/utils/tree/main/biocontainers-import](https://github.com/research-software-ecosystem/utils/tree/main/biocontainers-import) | -| Galaxy Codex | [https://github.com/research-software-ecosystem/utils/tree/main/galaxytool-import](https://github.com/research-software-ecosystem/utils/tree/main/galaxytool-import) | -| Debian Med | [https://github.com/research-software-ecosystem/utils/tree/main/debian-med-import](https://github.com/research-software-ecosystem/utils/tree/main/debian-med-import) | -| BIII | [https://github.com/research-software-ecosystem/utils/tree/main/biii-import](https://github.com/research-software-ecosystem/utils/tree/main/biii-import) | +
+
+
Weekly cadence
+
All sources refreshed via GitHub Actions
+
+
+
Source-specific jobs
+
Isolated workflows per source for traceability
+
+
+
Version controlled
+
Every import is committed for full history
+
+
CI Import workflows in the repository -

- {% mermaid %} - graph TB - A[bio.tools] --> Y(metadata import) - B[OpenEBench] --> Y(metadata import) - C[BioConda] --> Y(metadata import) - D[BIII] --> Y(metadata import) - E[BioContainers] --> Y(metadata import) - F[Galaxy CoDeX] --> Y(metadata import) - G[Debian Med] --> Y(metadata import) - Y(metadata import) --> Z[RSEc] - {% endmermaid %} -

+ {% mermaid %} + graph TB + A[bio.tools] --> Y(metadata import) + B[OpenEBench] --> Y(metadata import) + C[BioConda] --> Y(metadata import) + D[BIII] --> Y(metadata import) + E[BioContainers] --> Y(metadata import) + F[Galaxy CoDeX] --> Y(metadata import) + G[Debian Med] --> Y(metadata import) + Y(metadata import) --> Z[RSEc] + {% endmermaid %}
## Contributing guidelines We welcome any contribution to the project. Please refer to the [governance document](https://github.com/research-software-ecosystem/content/blob/master/GOVERNANCE.md), and get in contact with us (see _Contact Information_). - -## Citation - -Ienasescu H, Capella-Gutiérrez S, Coppens F _et al._ The ELIXIR research software ecosystem [version 1; not peer reviewed]. _F1000Research_ 2023, 12:988 (slides) [https://doi.org/10.7490/f1000research.1119585.1](https://doi.org/10.7490/f1000research.1119585.1) - -## Contact Information - -A public channel is available on gitter to get in contact with the project team: [https://app.gitter.im/#/room/#bio-tools_ecosystem:gitter.im](https://app.gitter.im/#/room/#bio-tools_ecosystem:gitter.im) diff --git a/index.md b/index.md index 535dce7..587b814 100644 --- a/index.md +++ b/index.md @@ -1,21 +1,56 @@ --- -# Feel free to add content and custom Front Matter to this file. -# To modify the layout, see https://jekyllrb.com/docs/themes/#overriding-theme-defaults - +title: The Ecosystem ---
-

- ELIXIR Research Software Ecosystem (RSEc) centralizes and curates high-quality metadata for computational biology software tools, providing a single, trusted resource for researchers. By synchronizing metadata from major software-related services, RSEc enables the discovery, validation and cross-linking of software information. Researchers can use the resource to explore software metadata and improve the consistency and quality of information across the computational biology landscape. -

-

- RSEc is open, version-controlled and hosted on GitHub. This centralized approach facilitates curation, promotes interoperability and supports the development of new services, ultimately enhancing the reliability and utility of research software. -

-

- ELIXIR is a European research infrastructure which manages and safeguards the massive amounts of life science data and tools being generated by publicly-funded research. RSEc has been developed as part of the ELIXIR Tools Platform. +

Reliable metadata for research software

+

+ ELIXIR Research Software Ecosystem (RSEc) curates trusted, cross-linked metadata for computational biology tools so you can discover, validate, and integrate software with confidence.

+
    +
  • Single entry point for metadata from major registries.
    • +
  • Open, version-controlled, and reusable by design.
    • +
  • Purpose-built for researchers, curators, and tool developers.
    • +
+
+ Explore the metadata + How to contribute +
RSEc diagram
+ +
+

How it helps

+
+
+
+
+
Discover
+

Find the right tool faster with unified identifiers and registry cross-links.

+ Browse sources → +
+
+
+
+
+
+
Validate
+

Compare metadata across services to spot gaps or conflicts before publishing.

+ See validation tips → +
+
+
+
+
+
+
Integrate
+

Use the open repository in workflows, dashboards, and registries without lock-in.

+ View applications → +
+
+
+
+
diff --git a/licence.md b/licence.md index 3f8679a..8aeb690 100644 --- a/licence.md +++ b/licence.md @@ -1,8 +1,7 @@ --- # Feel free to add content and custom Front Matter to this file. # To modify the layout, see https://jekyllrb.com/docs/themes/#overriding-theme-defaults - +title: License --- - [Code for the Research Software Ecosystem](https://github.com/research-software-ecosystem/utils) is available under the terms of the [MIT license](https://github.com/research-software-ecosystem/utils/blob/main/LICENSE). -- [Contents of the Research Software Ecosystem](https://github.com/research-software-ecosystem/content) is available under the terms of the [Creative Commons Attribution 4.0 International license](https://github.com/research-software-ecosystem/content/blob/master/LICENSE), unless stated otherwise for specific contr -ibutions. +- [Contents of the Research Software Ecosystem](https://github.com/research-software-ecosystem/content) is available under the terms of the [Creative Commons Attribution 4.0 International license](https://github.com/research-software-ecosystem/content/blob/master/LICENSE), unless stated otherwise for specific contributions. diff --git a/publications.md b/publications.md index 28db3ce..c6b0eab 100644 --- a/publications.md +++ b/publications.md @@ -4,6 +4,11 @@ title: Publications --- +## Citation + + +## Presentations + * BOSC 2023 Presentation (slides) [Ienasescu H, Capella-Gutiérrez S, Coppens F et al. The ELIXIR research software ecosystem [version 1; not peer reviewed]. F1000Research 2023, 12:988 (slides) (https://doi.org/10.7490/f1000research.1119585.1) ](https://doi.org/10.7490/f1000research.1119585.1) * BOSC 2023 Poster (slides): [Ienasescu H, Capella-Gutiérrez S, Coppens F et al. The ELIXIR research software ecosystem: an open software metadata commons (BOSC track) [version 1; not peer reviewed]. F1000Research 2023, 12:1044 (slides) (https://doi.org/10.7490/f1000research.1119604.1)](https://doi.org/10.7490/f1000research.1119604.1) * ELIXIR All Hands 2023 Poster: [Capella-Guttierez S, Grüning B, Gustafsson J et al. The ELIXIR tools ecosystem [version 1; not peer reviewed]. F1000Research 2023, 12(ELIXIR):608 (poster) (https://doi.org/10.7490/f1000research.1119451.1)](https://doi.org/10.7490/f1000research.1119451.1) diff --git a/sources.md b/sources.md index 09ce142..4ce8966 100644 --- a/sources.md +++ b/sources.md @@ -4,3 +4,70 @@ title: Sources page_id: sources --- + +The RSEc aggregates metadata from the registries and services below. Each source is refreshed regularly through the automated import workflows described in the documentation. Pick a source to see what is covered and where to dive into example records. + +{% assign source_items = site.data.tool_and_resource_list | where_exp:"item","item.related_pages contains 'sources'" | sort:"name" %} + +
+ {% for resource in source_items %} + {% assign import_slug = resource.id %} + {% assign view_url = resource.url %} + {% if import_slug %} + {% assign view_url = "https://github.com/research-software-ecosystem/content/tree/master/imports/" | append: import_slug %} + {% assign workflow_url = "https://github.com/research-software-ecosystem/utils/tree/main/" | append: import_slug | append: "-import" %} + {% endif %} + +
+
+
+
+
+
{{ resource.name }}
+ {% assign display_url = resource.url | remove: "https://" | remove: "http://" | remove: "www." | replace: "/" ,"" %} +
+ {{ display_url }} +
+
+
+ {% if resource.registry.fairsharing %} + + Standards/Databases + + {% endif %} + {% if resource.registry.biotools %} + + Tool info + + {% endif %} + {% if resource.registry.tess %} + + Training + + {% endif %} +
+
+

{{ resource.description | strip_newlines | replace: " ", " " }}

+
+ View metadata + {% if import_slug %} + Import workflow + {% endif %} +
+
+
+
+ {% endfor %} +
+ +