Final paper edits

docs/publications/BioHackrXiv/paper.bib

@@ -26,7 +26,7 @@ @article{rost2016openms
   publisher={Nature Publishing Group}
 }
 
-@article{doi:10.1128/AEM.01541-09,
+@article{10.1128/AEM.01541-09,
 author = {Patrick D. Schloss and Sarah L. Westcott and Thomas Ryabin and Justine R. Hall and Martin Hartmann and Emily B. Hollister and Ryan A. Lesniewski and Brian B. Oakley and Donovan H. Parks and Courtney J. Robinson and Jason W. Sahl and Blaz Stres and Gerhard G. Thallinger and David J. Van Horn and Carolyn F. Weber},
 title = {Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities},
 journal = {Applied and Environmental Microbiology},
@@ -176,7 +176,7 @@ @article{blankenberg2014dissemination
   publisher={Springer}
 }
 
-@misc{dev-community-tool-table,
+@misc{dev_community_tool_table,
         author = {Bérénice Batut},
 	title = {Creation of an interactive Galaxy tools table for your community (Galaxy Training Materials)},
 	year = {2024},
@@ -199,10 +199,25 @@ @article{Hiltemann_2023
 	journal = {PLoS Computational Biology}
 }
 
-@misc{dev-tool-annotation,
+@misc{dev_tool_annotation,
        author = {Bérénice Batut and Johan Gustafsson and Paul Zierep},
 	title = {Adding and updating best practice metadata for Galaxy tools using the bio.tools registry (Galaxy Training Materials)},
 	year = {2024},
 	url = {https://training.galaxyproject.org/training-material/topics/dev/tutorials/tool-annotation/tutorial.html},
 	note = {Online; accessed Thu Mar 14 2024}
 }
+
+@article{Bolyen2019,
+  title = {Reproducible,  interactive,  scalable and extensible microbiome data science using QIIME 2},
+  volume = {37},
+  ISSN = {1546-1696},
+  url = {http://dx.doi.org/10.1038/s41587-019-0209-9},
+  DOI = {10.1038/s41587-019-0209-9},
+  number = {8},
+  journal = {Nature Biotechnology},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Bolyen,  Evan and Rideout,  Jai Ram and Dillon,  Matthew R. and Bokulich,  Nicholas A. and Abnet,  Christian C. and Al-Ghalith,  Gabriel A. and Alexander,  Harriet and Alm,  Eric J. and Arumugam,  Manimozhiyan and Asnicar,  Francesco and Bai,  Yang and Bisanz,  Jordan E. and Bittinger,  Kyle and Brejnrod,  Asker and Brislawn,  Colin J. and Brown,  C. Titus and Callahan,  Benjamin J. and Caraballo-Rodríguez,  Andrés Mauricio and Chase,  John and Cope,  Emily K. and Da Silva,  Ricardo and Diener,  Christian and Dorrestein,  Pieter C. and Douglas,  Gavin M. and Durall,  Daniel M. and Duvallet,  Claire and Edwardson,  Christian F. and Ernst,  Madeleine and Estaki,  Mehrbod and Fouquier,  Jennifer and Gauglitz,  Julia M. and Gibbons,  Sean M. and Gibson,  Deanna L. and Gonzalez,  Antonio and Gorlick,  Kestrel and Guo,  Jiarong and Hillmann,  Benjamin and Holmes,  Susan and Holste,  Hannes and Huttenhower,  Curtis and Huttley,  Gavin A. and Janssen,  Stefan and Jarmusch,  Alan K. and Jiang,  Lingjing and Kaehler,  Benjamin D. and Kang,  Kyo Bin and Keefe,  Christopher R. and Keim,  Paul and Kelley,  Scott T. and Knights,  Dan and Koester,  Irina and Kosciolek,  Tomasz and Kreps,  Jorden and Langille,  Morgan G. I. and Lee,  Joslynn and Ley,  Ruth and Liu,  Yong-Xin and Loftfield,  Erikka and Lozupone,  Catherine and Maher,  Massoud and Marotz,  Clarisse and Martin,  Bryan D. and McDonald,  Daniel and McIver,  Lauren J. and Melnik,  Alexey V. and Metcalf,  Jessica L. and Morgan,  Sydney C. and Morton,  Jamie T. and Naimey,  Ahmad Turan and Navas-Molina,  Jose A. and Nothias,  Louis Felix and Orchanian,  Stephanie B. and Pearson,  Talima and Peoples,  Samuel L. and Petras,  Daniel and Preuss,  Mary Lai and Pruesse,  Elmar and Rasmussen,  Lasse Buur and Rivers,  Adam and Robeson,  Michael S. and Rosenthal,  Patrick and Segata,  Nicola and Shaffer,  Michael and Shiffer,  Arron and Sinha,  Rashmi and Song,  Se Jin and Spear,  John R. and Swafford,  Austin D. and Thompson,  Luke R. and Torres,  Pedro J. and Trinh,  Pauline and Tripathi,  Anupriya and Turnbaugh,  Peter J. and Ul-Hasan,  Sabah and van der Hooft,  Justin J. J. and Vargas,  Fernando and Vázquez-Baeza,  Yoshiki and Vogtmann,  Emily and von Hippel,  Max and Walters,  William and Wan,  Yunhu and Wang,  Mingxun and Warren,  Jonathan and Weber,  Kyle C. and Williamson,  Charles H. D. and Willis,  Amy D. and Xu,  Zhenjiang Zech and Zaneveld,  Jesse R. and Zhang,  Yilong and Zhu,  Qiyun and Knight,  Rob and Caporaso,  J. Gregory},
+  year = {2019},
+  month = jul,
+  pages = {852–857}
+}

docs/publications/BioHackrXiv/paper.md

@@ -61,22 +61,22 @@ authors_short: Paul Zierep, Bérénice Batut, \emph{et al.}
 
 # Introduction or Background
 
-Galaxy[@citesAsAuthority:10.1093/nar/gkac247] is a web-based analysis platform offering almost 10,000 different tools, which are developed in various GitHub repositories.  
+Galaxy [@citesAsAuthority:10.1093/nar/gkac247] is a web-based analysis platform offering almost 10,000 different tools, which are developed in various GitHub repositories.  
 Furthermore, the Galaxy community embraces granular implementation of software tools as sub-modules. 
 In practice, this means that tool suites are separated into sets of Galaxy tools, also known as Galaxy wrappers, that contain functionality of a corresponding sub-component.
-Some key examples of tool suites include [Mothur](https://bio.tools/mothur)[@citesAsAuthority:doi:10.1128/AEM.01541-09] and [OpenMS](https://bio.tools/openms)[@citesAsAuthority:rost2016openms], which translate to tens and even hundreds of Galaxy tools. 
+Some key examples of tool suites include [QIIME 2](https://bio.tools/qiime2) [@citesAsAuthority:Bolyen2019] and [OpenMS](https://bio.tools/openms) [@citesAsAuthority:rost2016openms], which translate to tens and even hundreds of Galaxy tools. 
 While granularity supports the composability of tools into diverse purpose-specific workflows, this decentralised development and modular architecture can make it difficult for Galaxy users to find and use tools. 
 It may also result in Galaxy tool-wrapper developers duplicating efforts by simultaneously wrapping the same software. 
-This is further complicated by the scarcity of tool metadata, which prevents filtering of tools as relevant for a specific scientific community or domain, and makes it impossible to employ advanced filtering by ontology terms like the ones from EDAM[@citesAsAuthority:black2021edam]. 
+This is further complicated by the scarcity of tool metadata, which prevents filtering of tools as relevant for a specific scientific community or domain, and makes it impossible to employ advanced filtering by ontology terms like the ones from EDAM [@citesAsAuthority:black2021edam]. 
 The final challenge is also an opportunity: the global and cross-domain nature of Galaxy means that it is a big community. 
 Solving the visibility of tools across this "ecosystem", and the resulting benefits, are far-reaching for the global collaborative development of data-analysis tools and workflows.
 
 To provide the scientific community with a comprehensive list of annotated Galaxy tools, 
-we developed a pipeline at the [ELIXIR BioHackathon Europe 2023](https://2023.biohackathon-europe.org) that collects Galaxy wrappers from a list of GitHub repositories and automatically extracts their metadata (including Conda version [@citesAsAuthority:conda], bio.tools identifier[@citesAsAuthority:biotoolsSchema, @usesDataFrom:Ison2019], BIII identifier[@citesAsAuthority:bioimageWorkflows], and EDAM annotations). 
-The workflow also queries the availability of the tools from the three main Galaxy servers (_usegalaxy.*_) as well as usage statistics from [usegalaxy.eu](https://usegalaxy.eu) (Note: the other main Galaxy servers, [usegalaxy.org](https://usagalaxy.org) and [usegalaxy.org.au](https://usagalaxy.org.au), will be queried for usage statistics in coming updates). 
+we developed a pipeline at the [ELIXIR BioHackathon Europe 2023](https://2023.biohackathon-europe.org) that collects Galaxy wrappers from a list of GitHub repositories and automatically extracts their metadata (including Conda version [@citesAsAuthority:conda], bio.tools identifier [@citesAsAuthority:biotoolsSchema][@usesDataFrom:Ison2019], BIII identifier [@citesAsAuthority:bioimageWorkflows], and EDAM annotations). 
+The workflow also queries the availability of the tools from the three main Galaxy servers (usegalaxy.*) as well as usage statistics from [usegalaxy.eu](https://usegalaxy.eu) (Note: the other main Galaxy servers, [usegalaxy.org](https://usagalaxy.org) and [usegalaxy.org.au](https://usagalaxy.org.au), will be queried for usage statistics in coming updates). 
 
 Crucially, the pipeline can filter its inputs to only include tools that are relevant to a specific research community. 
-Based on the selected filters, a community-specific interactive table is generated that can be embedded, _e.g._ into the respective [Galaxy Hub](https://galaxyproject.org/) webpage or [Galaxy subdomain](https://galaxyproject.org/eu/subdomains/). 
+Based on the selected filters, a community-specific interactive table is generated that can be embedded, e.g. into the respective [Galaxy Hub](https://galaxyproject.org/) webpage or [Galaxy subdomain](https://galaxyproject.org/eu/subdomains/). 
 This table allows further filtering and searching for fine-grained tool selection. 
 The pipeline is fully automated and executes on a weekly basis. 
 Any scientific community can apply the pipeline to create a table specific to their needs.
@@ -97,14 +97,14 @@ Here, we describe the methods and processes that resulted from this project, and
 ## Domain-specific interactive tools table
 
 To create the domain-specific interactive tools table, Galaxy tool-wrapper suites are first parsed from across multiple GitHub repositories. 
-In effect, the repositories monitored by the planemo-monitor[@citesAsAuthority:Bray2022.03.13.483965] are scraped using a custom script. 
+In effect, the repositories monitored by the planemo-monitor [@citesAsAuthority:Bray2022.03.13.483965] are scraped using a custom script. 
 The planemo-monitor is part of the Galaxy tool-update infrastructure, and keeps track of the most up-to-date tool development repositories.
 
 Metadata is extracted from each parsed tool-wrapper suite. 
 This includes: wrapper suite ID, scientific category, Bioconda dependency, and a repository URL from bio.tools. 
 As a tool suite can be composed of multiple individual tools, the tool IDs for each tool are also extracted.
-The bio.tools reference is used to request metadata annotations via the bio.tools API, including bio.tools description and functionality annotation using EDAM ontology concepts[@usesDataFrom:black2021edam]. 
-The latest Conda package version is retrieved via the Bioconda API and compared to the Galaxy tool version to determine the tool’s update state (_i.e._ to update, or no update required). 
+The bio.tools reference is used to request metadata annotations via the bio.tools API, including bio.tools description and functionality annotation using EDAM ontology concepts [@usesDataFrom:black2021edam]. 
+The latest Conda package version is retrieved via the Bioconda API and compared to the Galaxy tool version to determine the tool’s update state (i.e. to update, or no update required). 
 
 The Galaxy API is used to query if each tool is installed on one of the three usegalaxy.* Galaxy servers ([usegalaxy.eu](https://usegalaxy.eu/), [usegalaxy.org](https://usegalaxy.org/), [usegalaxy.org.au](https://usegalaxy.org.au/)). Furthermore, the tool usage statistics can be retrieved from an SQL query that needs to be executed by Galaxy administrators. 
 The query used in the current implementation shows the overall tool usage as well as how many users executed a tool in the last 2 years on the European server ([usegalaxy.eu](https://usegalaxy.eu/)). 
@@ -130,7 +130,7 @@ The workflow is run weekly via GitHub Actions continuous integration, providing
 The usage of an iframe enables updates for the table to propagate automatically to any website where it is deployed. 
 
 Any Galaxy community can use the pipeline by adding a folder in the [project GitHub repository](https://github.com/galaxyproject/galaxy_tool_extractor/). 
-To initialise the pipeline for a new community you need to add a new subfolder of `data/communities/` , and inside it add a file called 'categories' with a list of Galaxy ToolShed [@blankenberg2014dissemination] categories. 
+To initialise the pipeline for a new community you need to add a new subfolder of `data/communities/` , and inside it add a file called 'categories' with a list of Galaxy ToolShed [@citesAsAuthority:blankenberg2014dissemination] categories. 
 Additionally, tools that should be excluded or included after filtering, can be added to respective files as well. 
 A working example of the community configuration files can be found in the folder for the microGalaxy community.
 
@@ -150,7 +150,7 @@ The reason for this is that even if a bio.tools identifier exists in a tool wrap
 This is an observation based on real-world annotation errors and serves as a useful supporting step to improve Galaxy wrapper annotations and the completeness of the bio.tools registry. 
 In addition, if a bio.tools identifier is not included in the wrapper, this does not mean that there is not a bio.tools identifier available in the registry.
 
-There are then two curation paths to choose from, depending on whether a bio.tools identifier exists in the XML wrapper. In both cases, if no bio.tools entry exists, a new entry should be created and updated using the bio.tools wizard. The creation and update of an entry includes adding concepts from the EDAM ontology. This annotation process can be simplified through the use of [EDAM Browser](https://edamontology.github.io/edam-browser/)[@citesAsAuthority:edamBrowser, @citesAsAuthority:edamBrowserCode].
+There are then two curation paths to choose from, depending on whether a bio.tools identifier exists in the XML wrapper. In both cases, if no bio.tools entry exists, a new entry should be created and updated using the bio.tools wizard. The creation and update of an entry includes adding concepts from the EDAM ontology. This annotation process can be simplified through the use of [EDAM Browser](https://edamontology.github.io/edam-browser/) [@citesAsAuthority:edamBrowser][@citesAsAuthority:edamBrowserCode].
 
 In the case where no bio.tools identifier exists in the Galaxy XML wrapper, the development repository needs to be forked and a new branch created. 
 A new xref snippet can then be added, and a pull request opened against the original repository.
@@ -162,7 +162,7 @@ Figure \ref{annotation_workflow} shows a step-by-step breakdown of the above pro
 
 # Outcomes and results
 
-There were multiple concrete outcomes from this BioHackathon project, including the ability to create interactive Galaxy tools tables as needed for scientific communities, a process for updating bio.tools, in-development Galaxy Training Network (GTN) tutorials[@citesAsAuthority:batut_community-driven_2018] describing this process, and an update to the [Galaxy IUC](https://galaxyproject.org/iuc/) tool wrapping [standards](https://galaxy-iuc-standards.readthedocs.io/en/latest/index.html). 
+There were multiple concrete outcomes from this BioHackathon project, including the ability to create interactive Galaxy tools tables as needed for scientific communities, a process for updating bio.tools, in-development Galaxy Training Network (GTN) tutorials [@citesAsAuthority:batut_community-driven_2018] describing this process, and an update to the [Galaxy IUC](https://galaxyproject.org/iuc/) tool wrapping [standards](https://galaxy-iuc-standards.readthedocs.io/en/latest/index.html). 
 These are described in more detail below.
 
 
@@ -191,17 +191,17 @@ A rerun of the Galaxy tool metadata extractor pipeline collected the additional
 
 To provide the Galaxy research communities with simple and straightforward guide to annotating their respective tool stacks, the described work has been converted into two GTN tutorials:
 
-- [Adding and updating best practice metadata for Galaxy tools using the bio.tools registry](https://gxy.io/GTN:T00421) [@citeAs:dev-tool-annotation]
-- [Creation of an interactive Galaxy tools table for your community](https://training.galaxyproject.org/training-material/topics/dev/tutorials/community-tool-table/tutorial.html) [@citeAs:dev-community-tool-table]
+- [Adding and updating best practice metadata for Galaxy tools using the bio.tools registry](https://gxy.io/GTN:T00421) [@citesAsAuthority:dev-tool-annotation]
+- [Creation of an interactive Galaxy tools table for your community](https://training.galaxyproject.org/training-material/topics/dev/tutorials/community-tool-table/tutorial.html) [@citesAsAuthority:dev-community-tool-table]
 
 The guidelines created were also used to update the [best practices for creating Galaxy tools of the IUC repository](https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html).
 
 
 # Conclusion and outlook
 
 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)[@citeAsAuthority:RSEc] is currently being worked on.
+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, additional bio.tools metadata, and a user-friendly integration of manual curation steps.
 
 A set of updates to standards and processes was also created.