From 8016925565bdfa96afdd8b386103cfaa996a6295 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Thu, 21 Mar 2024 08:22:47 +0000 Subject: [PATCH] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bérénice Batut --- docs/publications/BioHackrXiv/paper.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/publications/BioHackrXiv/paper.md b/docs/publications/BioHackrXiv/paper.md index c14517ea..9e36e28f 100644 --- a/docs/publications/BioHackrXiv/paper.md +++ b/docs/publications/BioHackrXiv/paper.md @@ -176,7 +176,7 @@ These are described in more detail below. ## Prototype interactive table for Galaxy communities -The described workflow for the Galaxy tool metadata extractor (see Figure \ref{metadata_extractor_pipeline}) was successfully implemented ([GitHub repository](https://github.com/galaxyproject/galaxy_tool_extractor)) and could more than 1,300 Galaxy tool suites (see the [GitHub repository pages](https://galaxyproject.github.io/galaxy_tool_metadata_extractor) for an up-to-date table). +The described workflow for the Galaxy tool metadata extractor (see Figure \ref{metadata_extractor_pipeline}) was successfully implemented ([GitHub repository](https://github.com/galaxyproject/galaxy_tool_extractor)) and could extract more than 1,300 Galaxy tool suites (see the [GitHub repository pages](https://galaxyproject.github.io/galaxy_tool_metadata_extractor) for an up-to-date table). Of those tool suites, only 267 had a bio.tools identifier, which highlights the importance of performing the annotation process in parallel and complementing the tools with additional metadata. An example view of the created interactive table is shown in Figure \ref{web_table}. As mentioned above, the filtered table for the microGalaxy community has already been embedded in the [Hub page for microGalaxy](https://galaxyproject.org/community/sig/microbial#tools), as well as the dedicated [microGalaxy subdomain](https://microgalaxy.usegalaxy.eu/). @@ -210,7 +210,7 @@ The guidelines created were also used to update the [best practices for creating The project was able to successfully meet its aim of creating reusable prototypes and processes that make the richness of the Galaxy tools ecosystem more discoverable and understandable. Central to this work was the Galaxy tool metadata extractor pipeline, which is currently generating comprehensive and interactive tabular summaries of Galaxy tools for the [microbial data](https://galaxyproject.org/community/sig/microbial/) and [image analysis](https://galaxyproject.org/use/imaging/) communities within Galaxy (with EU BioHackathon 2023 [Project 16](https://github.com/elixir-europe/biohackathon-projects-2023/tree/main/16)). The metadata extractor can be reused by any Galaxy group or community. For example, the [biodiversity and ecology](https://galaxyproject.org/use/ecology/) community will employ this pipeline in the near future [@citesAsAuthority:elixirBiodiversity]. The generated tabular tool summary provides valuable information that extends beyond the use case of listing community tools. Therefore, an integration with the [Research Software Ecosystem (RSEc)](https://github.com/research-software-ecosystem/content) [@citesAsAuthority:RSEc] is currently being worked on. -Various updates of the Galaxy tool metadata extractor pipeline are also envisioned, such as the integration of comprehensive usage statistics for all large Galaxy servers, and additional bio.tools metadata, and a user-friendly integration of manual curation steps. +Various updates of the Galaxy tool metadata extractor pipeline are also envisioned, such as the integration of comprehensive usage statistics for all large Galaxy servers, additional bio.tools metadata, and a user-friendly integration of manual curation steps. A set of updates to standards and processes was also created. These will support the ongoing growth of the metadata hosted by the interactive tables: primarily by helping communities to maintain and extend the annotations of Galaxy tool wrappers, and the bio.tools ecosystem on which these wrapper annotations depend.