RDMKit by RDMkit by ELIXIR-CONVERGE is licensed under a
Are you working in the Life Sciences with data? Do you feel overwhelmed when you think about Research Data Management?
RDMKit by RDMkit by ELIXIR-CONVERGE is licensed under a
Are you working in the Life Sciences with data? Do you feel overwhelmed when you think about Research Data Management?
The ELIXIR Research Data Management Kit (RDMKit) is an online guide containing good data management practices applicable to research projects from the - beginning to the end. Developed and managed by people who work every day with life science data, RDMKit has +
The ELIXIR Research Data Management Kit (RDMkit) is an online guide containing good data management practices applicable to research projects from the + beginning to the end. Developed and managed by people who work every day with life science data, RDMkit has guidelines, information and pointers, organised in many different ways to help you with problems throughout the data’s life cycle.
diff --git a/images/github_way_flow.svg b/images/github_way_flow.svg index ac612584d..206ba6769 100644 --- a/images/github_way_flow.svg +++ b/images/github_way_flow.svg @@ -1,3 +1,3 @@ - \ No newline at end of file + \ No newline at end of file diff --git a/images/googledoc_way_flow.svg b/images/googledoc_way_flow.svg index 4c60593de..fa168aba1 100644 --- a/images/googledoc_way_flow.svg +++ b/images/googledoc_way_flow.svg @@ -1,3 +1,3 @@ - \ No newline at end of file + \ No newline at end of file diff --git a/index.md b/index.md index 2befefef9..780ac1dc1 100644 --- a/index.md +++ b/index.md @@ -6,6 +6,6 @@ search: exclude {% include landingpage.html %} ### Contributors -This project would not be possible without the many amazing community contributors. RDMKit is an open community project, and you are welcome to [join us](how_to_contribute)! +This project would not be possible without the many amazing community contributors. RDMkit is an open community project, and you are welcome to [join us](how_to_contribute)! {% include contributor-carousel.html %} diff --git a/pages/about.md b/pages/about.md index 125b8ffdc..e57b93d7d 100644 --- a/pages/about.md +++ b/pages/about.md @@ -3,27 +3,27 @@ title: About toc: false --- -## Who is the RDMKit for? -The ELIXIR Research Data Management Kit (RDMKit) has been designed to guide life scientists in their efforts to better manage their research data following the FAIR Principles. It is based on the various steps of the data lifecycle, although not all the steps will be relevant to everyone. RDMKit can be navigated via ‘role’, ‘domain’, ‘examples’ and ‘problems’. The contents are generated and maintained by the ELIXIR community coming together as part of the [ELIXIR-CONVERGE](https://elixir-europe.org/about-us/how-funded/eu-projects/converge) project. +## Who is the RDMkit for? +The ELIXIR Research Data Management Kit (RDMkit) has been designed to guide life scientists in their efforts to better manage their research data following the FAIR Principles. It is based on the various steps of the data lifecycle, although not all the steps will be relevant to everyone. RDMkit can be navigated via ‘role’, ‘domain’, ‘examples’ and ‘problems’. The contents are generated and maintained by the ELIXIR community coming together as part of the [ELIXIR-CONVERGE](https://elixir-europe.org/about-us/how-funded/eu-projects/converge) project. ## Why are the FAIR principles needed? At the heart of FAIR Science lies good data management practice. This is increasingly important as life science research becomes data-intensive and traditional ‘wet labs’ make space for ‘dry (computer) labs’. Having that in mind, the [FAIR Principles](https://www.nature.com/articles/sdata201618) were designed to improve the infrastructure supporting the reuse of research data. The intention of these principles is to act as a guide to improve the **F**indability, **A**ccessibility, **I**nteroperability and **R**euse of digital assets. The increasing volume, complexity and speed of data creation made scientists rely on computational support exponentially. Therefore, the FAIR Principles place specific emphasis on enhancing the ability of machines to automatically find and use data, as well as supporting its reuse by other scientists, which facilitates knowledge discovery and improves research transparency. -## What does the RDMKit aim to achieve? +## What does the RDMkit aim to achieve? More than ever, scientists need relevant tools and guidance to better manage their data and hence contribute to making FAIR Science a reality as well as help researchers be more productive for themselves and their collaborators. -- **For researchers** - RDMKit is a one stop shop of information, advice and signposting to research data management know-how, tools, examples and best practice. Struggling with writing your project data management plan? Then RDMKit can help. +- **For researchers** - RDMkit is a one stop shop of information, advice and signposting to research data management know-how, tools, examples and best practice. Struggling with writing your project data management plan? Then RDMkit can help. -- **For data managers in laboratories, facilities or universities** - RDMKit is a resource for your researchers, a complement to your own resources and a guide to the specific challenges of RDM for life science researchers. +- **For data managers in laboratories, facilities or universities** - RDMkit is a resource for your researchers, a complement to your own resources and a guide to the specific challenges of RDM for life science researchers. -- **For funding agencies and policy makers** - RDMKit is the resource researchers can turn to at the proposal stage of the research, throughout their projects and when publishing their results. Remember that the cost of not having FAIR research data has been estimated at €10.2bn annually in Europe. By using RDMKit and better managing data, the outcomes of your investments will be contributing to strengthening regional, national and European economies. +- **For funding agencies and policy makers** - RDMkit is the resource researchers can turn to at the proposal stage of the research, throughout their projects and when publishing their results. Remember that the cost of not having FAIR research data has been estimated at €10.2bn annually in Europe. By using RDMkit and better managing data, the outcomes of your investments will be contributing to strengthening regional, national and European economies. ## Funding acknowledgement -RDMKit was developed with funding from the European Union’s Horizon 2020 Research and Innovation programme under grant agreement No 871075, as part of the ELIXIR-CONVERGE project. We are grateful to all who contributed their time to producing contents for RDMKit. +RDMkit was developed with funding from the European Union’s Horizon 2020 Research and Innovation programme under grant agreement No 871075, as part of the ELIXIR-CONVERGE project. We are grateful to all who contributed their time to producing contents for RDMkit. -## How to cite the RDMKit +## How to cite the RDMkit ELIXIR (2020) Research Data Management Kit. A deliverable from the EU-funded ELIXIR-CONVERGE project (grant agreement 871075). URL: https://rdmkit.elixir-europe.org The ELIXIR Research Data Management Kit makes all of their materials publicly available under [Open Source Initiative](https://opensource.org/licenses) licenses. @@ -32,6 +32,6 @@ Software are made available under an [MIT license](https://opensource.org/licens For full details on licensing, please visit https://github.com/elixir-europe/rdmkit/blob/master/LICENSE -## The editors of RDMKit +## The editors of RDMkit {% include contributor-carousel.html custom="Bert Droesbeke, Carole Goble, Daniel Faria, Flora D'Anna, Frederik Coppens, Mijke Jetten, Munazah Andrabi, Niclas Jareborg, Pinar Alper, Rob Hooft, Ulrike Wittig, Laura Portell Silva, Martin Cook"%} diff --git a/pages/contribute/copyright.md b/pages/contribute/copyright.md index b0f23e64a..5032c7f33 100644 --- a/pages/contribute/copyright.md +++ b/pages/contribute/copyright.md @@ -26,7 +26,7 @@ The great majority of images on the web are copyrighted. This includes images on If you are using an image with a [Creative Commons license](https://creativecommons.org/licenses/), remember you still need to attribute the creator in accordance with the license. -If you are using a stock image you have bought, or a royalty-free image, check the image license to make sure that you can use it on the RDMKit website. If you are using images provided by your institute or organisation, please also check that you can use them on this site. +If you are using a stock image you have bought, or a royalty-free image, check the image license to make sure that you can use it on the RDMkit website. If you are using images provided by your institute or organisation, please also check that you can use them on this site. You are welcome to create the images yourself, but please follow the [site style guide](style_guide), and bear in mind the image may be modified to better suite the style of the site. The content of the site is published under the [Creative Commons 4 license](https://creativecommons.org/licenses/by/4.0/). diff --git a/pages/contribute/github_way.md b/pages/contribute/github_way.md index e5ae69f95..67de88aa2 100644 --- a/pages/contribute/github_way.md +++ b/pages/contribute/github_way.md @@ -15,7 +15,7 @@ This guide tells you how you can easily request and edit a page on this website. --> ## Announce and discuss your proposal through GitHub "issues" -1. Go to the [RDMKit repo](https://github.com/elixir-europe/rdmkit){:target="_blank"} on GitHub. +1. Go to the [RDMkit repo](https://github.com/elixir-europe/rdmkit){:target="_blank"} on GitHub. 2. Click on "Issues" in the top menu bar and look at the existing issues. See if your idea or suggestion is already being discussed. * **If an issue exists**, add your comments. If you want to edit the content discussed, let people know through the comments. * **If no relevant issue exists**, create a new issue by clicking on the green "New issue" button on the right, and choose one of the issues templates. You can find more information on creating issues in the [GitHub documentation](https://docs.github.com/en/github/managing-your-work-on-github/creating-an-issue). @@ -23,14 +23,14 @@ This guide tells you how you can easily request and edit a page on this website. 3. Discuss your idea with the editors through comments in the issues. You will be notified when others comment on your issues. Read the comments and write your opinion/questions/answers in the "Leave a comment" box and click on the green "Comment" button on the right. 4. You can always return to your opened issue by going to the [issues section](https://github.com/elixir-europe/rdmkit/issues) of our GitHub repo. -{% include tip.html content="You can also get to the [RDMKit pages](https://github.com/elixir-europe/rdmkit) on GitHub using the 'GitHub' link in the header of this site" %} +{% include tip.html content="You can also get to the [RDMkit pages](https://github.com/elixir-europe/rdmkit) on GitHub using the 'GitHub' link in the header of this site" %} ## Write your content and make a pull request 1. When you and the editors have agreed on what you will do, go to the page you want to edit on the website. Click on "Edit me" pencil icon :pencil:, shown next to the page title. If you want to add a new page, the editors will give you the link to the page via comments in the issue you created. The page will come with a predefined template, based on the kind of content you want to contribute. 2. The "Edit me" pencil icon will take you to the GitHub repository, where you again click on the pencil icon, shown on the right, and start editing. {% include image.html class="mt-0 mb-0" file="raw_github.png" inline=true alt="Editing a page on GitHub" %} -3. You can now edit or add new text and images according to the provided template. GitHub provide a [guide for writing and formatting in GitHub](https://docs.github.com/en/github/writing-on-github/getting-started-with-writing-and-formatting-on-github). We also provide a [markdown cheat sheet](markdown_cheat_sheet) to show you how to write in this webpage. Make sure to read our [style guide](style_guide) before start writing. In general, try to avoid manual interlinking of RDMKit pages. +3. You can now edit or add new text and images according to the provided template. GitHub provide a [guide for writing and formatting in GitHub](https://docs.github.com/en/github/writing-on-github/getting-started-with-writing-and-formatting-on-github). We also provide a [markdown cheat sheet](markdown_cheat_sheet) to show you how to write in this webpage. Make sure to read our [style guide](style_guide) before start writing. In general, try to avoid manual interlinking of RDMkit pages. 4. If you have mentioned tools or resources in your text, make sure to add them to the [tool and resource list](tool_resource_update). 5. When you are happy with your first draft of the content, go to the “Propose changes” section at the end of the page and write a title and a brief explanation of your changes. 6. Click on “Propose changes”. diff --git a/pages/contribute/google_doc_way.md b/pages/contribute/google_doc_way.md index 91ceb28d5..e710508b6 100644 --- a/pages/contribute/google_doc_way.md +++ b/pages/contribute/google_doc_way.md @@ -7,7 +7,7 @@ toc: false ## Contribution process -RDMKit is hosted on GitHub. We understand, however, that many people may be unfamiliar or inexperienced with git. We therefore provide the Google doc option for contributing. +RDMkit is hosted on GitHub. We understand, however, that many people may be unfamiliar or inexperienced with git. We therefore provide the Google doc option for contributing. The steps are as follows: * Email the editorial team at [rdm-editors@elixir-europe.org](mailto:rdm-editors@elixir-europe.org) to propose a new page or a new section in an existing page. Make sure you keep other contributors in the CC of your email. The editors will create an issue in our GitHub repository to announce your contribution to others. diff --git a/pages/contribute/how_to_contribute.md b/pages/contribute/how_to_contribute.md index e11137449..4203e0a3c 100644 --- a/pages/contribute/how_to_contribute.md +++ b/pages/contribute/how_to_contribute.md @@ -1,5 +1,5 @@ --- -title: How to contribute to the RDMKit website +title: How to contribute to the RDMkit website sidebar: contribute toc: false --- diff --git a/pages/contribute/style_guide.md b/pages/contribute/style_guide.md index 21e910e40..11821d6a3 100644 --- a/pages/contribute/style_guide.md +++ b/pages/contribute/style_guide.md @@ -3,7 +3,7 @@ title: Style guide sidebar: contribute --- -In general, we follow the European Commission's [Web Writing Style Guide](https://wikis.ec.europa.eu/display/WEBGUIDE/02.+Web+writing+guidelines). Below are the points that you might find most useful, though, and that relate particularly to the RDMKit. +In general, we follow the European Commission's [Web Writing Style Guide](https://wikis.ec.europa.eu/display/WEBGUIDE/02.+Web+writing+guidelines). Below are the points that you might find most useful, though, and that relate particularly to the RDMkit. ## General style and tone * Keep the tone friendly rather than formal, and use "you". Imagine you were explaining something verbally to someone - how would you say it? diff --git a/pages/contribute/tool_resource_update.md b/pages/contribute/tool_resource_update.md index 338c55a18..ce4016345 100644 --- a/pages/contribute/tool_resource_update.md +++ b/pages/contribute/tool_resource_update.md @@ -1,12 +1,12 @@ --- title: Updating the tool and resource list sidebar: contribute -summary: How to add a tool or resource to RDMKit +summary: How to add a tool or resource to RDMkit --- ## Way of working -The tools or resources you will find on pages are a filtered set from a [bigger list](all_tools_and_resources). This filtering is done using tags. If a tool or resource is tagged with for example `researcher`, it will be automatically listed on the page where in the markdown file the code snippet {% raw %}`{% include toollist.html tag="researcher" %}`{% endraw %} is present. Since the Data Life Cycle pages are not listing tools, we do not allow these tags in the tool table, instead tag them with Your domain, Your role and Your problem tags (The tags can be found [here](https://github.com/elixir-europe/rdmkit/blob/master/_data/tags.yml)). The general tool/resource list is based on the [csv file](https://github.com/elixir-europe/rdmkit/blob/master/_data/main_tool_and_resource_list.csv) in the `_data` directory of the RDMKit repository. Tools and resources are manually linked to [FAIRsharing.org](https://fairsharing.org/). The link with [Bio.tools](https://bio.tools) is done manually in the scenarios that the automatic lookup fails. Finally, the link with [TeSS](https://tess.elixir-europe.org/) is fully automatic and weekly updated. If changes to this file are pushed to GitHub, a GitHub Bot will generate a Pull Request (PR) with the changes of the csv file applied to the main data file of the website (a yaml file). +The tools or resources you will find on pages are a filtered set from a [bigger list](all_tools_and_resources). This filtering is done using tags. If a tool or resource is tagged with for example `researcher`, it will be automatically listed on the page where in the markdown file the code snippet {% raw %}`{% include toollist.html tag="researcher" %}`{% endraw %} is present. Since the Data Life Cycle pages are not listing tools, we do not allow these tags in the tool table, instead tag them with Your domain, Your role and Your problem tags (The tags can be found [here](https://github.com/elixir-europe/rdmkit/blob/master/_data/tags.yml)). The general tool/resource list is based on the [csv file](https://github.com/elixir-europe/rdmkit/blob/master/_data/main_tool_and_resource_list.csv) in the `_data` directory of the RDMkit repository. Tools and resources are manually linked to [FAIRsharing.org](https://fairsharing.org/). The link with [Bio.tools](https://bio.tools) is done manually in the scenarios that the automatic lookup fails. Finally, the link with [TeSS](https://tess.elixir-europe.org/) is fully automatic and weekly updated. If changes to this file are pushed to GitHub, a GitHub Bot will generate a Pull Request (PR) with the changes of the csv file applied to the main data file of the website (a yaml file). {% include important.html content="The link with TeSS and Bio.tools is automatically done using GitHub actions and is weekly updated. These automatic links are not seen in the table. The search query to TeSS or the Bio.tools ID for a tool or resource can be overwritten in the registry column of the main csv tool table. If no Bio.tools ID or TeSS Query is available for a source, you can overwrite the automatic linking by adding 'NA' as registry." %} diff --git a/pages/tools_assembly/nels_assembly.md b/pages/tools_assembly/nels_assembly.md index f73c87e5f..7956de32f 100644 --- a/pages/tools_assembly/nels_assembly.md +++ b/pages/tools_assembly/nels_assembly.md @@ -16,7 +16,7 @@ NeLS and the underlying infrastructure are accessible for researchers in Norway ## For what can you use the NeLS data management tool assembly? -{% include image.html file="NeLS_toolkit.svg" caption="Figure 1. The Norwegian e-Infrastructure for Life Sciences (NeLS) Data Management tool assembly." alt="NeLS RDMKit" %} +{% include image.html file="NeLS_toolkit.svg" caption="Figure 1. The Norwegian e-Infrastructure for Life Sciences (NeLS) Data Management tool assembly." alt="NeLS RDMkit" %} You can access all tools in NeLS using the the national solution for secure login and data sharing in the educational and research sector [FEIDE](https://www.feide.no/), when coupled with [ELIXIR AII](https://elixir-europe.org/services/compute/aai). The NeLS Data Management tool assembly can support you with [Data Management Planning](planning) through an [instance of the Data Steward Wizard](https://elixir-no.ds-wizard.org) with a dedicated knowledge model referring to national infrastructure, resources, laws and regulations. Soon you will be able to submit storage request forms for [Data Storage](storage) in NeLS with defined access roles through the Data Steward Wizard. diff --git a/pages/your_domain/TEMPLATE_your_domain.md b/pages/your_domain/TEMPLATE_your_domain.md index 279c79820..cdf140a36 100644 --- a/pages/your_domain/TEMPLATE_your_domain.md +++ b/pages/your_domain/TEMPLATE_your_domain.md @@ -22,7 +22,7 @@ For problems that are fully domain-specific, a detailed description is merited. For detailing the domain-specific challenges of a problem that is generic, please link to the corresponding generic Problem page before going into the domain-specific challenges. ---> ### Considerations - + ### Solutions diff --git a/pages/your_domain/microbial_biotechnology.md b/pages/your_domain/microbial_biotechnology.md index 5b0d6755a..17a9c98ca 100644 --- a/pages/your_domain/microbial_biotechnology.md +++ b/pages/your_domain/microbial_biotechnology.md @@ -22,7 +22,7 @@ For problems that are fully domain-specific, a detailed description is merited. For detailing the domain-specific challenges of a problem that is generic, please link to the corresponding generic Problem page before going into the domain-specific challenges. ---> ### Considerations - + ### Solutions diff --git a/pages/your_domain/structural_bioinformatics.md b/pages/your_domain/structural_bioinformatics.md index c2cf78136..4179698c6 100644 --- a/pages/your_domain/structural_bioinformatics.md +++ b/pages/your_domain/structural_bioinformatics.md @@ -22,7 +22,7 @@ For problems that are fully domain-specific, a detailed description is merited. For detailing the domain-specific challenges of a problem that is generic, please link to the corresponding generic Problem page before going into the domain-specific challenges. ---> ### Considerations - + ### Solutions diff --git a/pages/your_problem/data_transfer.md b/pages/your_problem/data_transfer.md index 853b5514a..04a02d64c 100644 --- a/pages/your_problem/data_transfer.md +++ b/pages/your_problem/data_transfer.md @@ -22,7 +22,7 @@ There are many aspects to consider when dealing with data transfer, but the most Data size and bandwidth are tightly linked since transferring large volumes of data on a low bandwidth network will be so time consuming that it could be simpler to send the data on a hard drive through carrier services. -If you intend to transfer sensitive data to another location, you have to check the regulation and security measures on the remote site. You can interact with the IT departments at both locations in order to establish your strategy. Do not forget to check the [Human Data](human_data) pages of the RDMKit. +If you intend to transfer sensitive data to another location, you have to check the regulation and security measures on the remote site. You can interact with the IT departments at both locations in order to establish your strategy. Do not forget to check the [Human Data](human_data) pages of the RDMkit. Since data transfer involves so many technical aspects, it is a good idea to interact with your technical/IT team in order to avoid any problem if you want to transfer large amounts of data. diff --git a/pages/your_role/researcher.md b/pages/your_role/researcher.md index ca859dfa4..213f7d537 100644 --- a/pages/your_role/researcher.md +++ b/pages/your_role/researcher.md @@ -8,7 +8,7 @@ contributors: [Mijke Jetten, Federico Bianchini, Gregoire Rossier, Erik Hjerde, PhD candidates, research grant applicants, project managers, group leaders, PIs ## Scenario -The funding organisation I am applying to requires a data management plan (DMP). I have little experience in writing a DMP, and I am not sure of the level of detail I am required to provide. I have limited access to data management experts within my institution. I am considering using the RDMKit for my data management needs. I also hope to find useful references to local training about data management requirements, data archives and DMP tools. +The funding organisation I am applying to requires a data management plan (DMP). I have little experience in writing a DMP, and I am not sure of the level of detail I am required to provide. I have limited access to data management experts within my institution. I am considering using the RDMkit for my data management needs. I also hope to find useful references to local training about data management requirements, data archives and DMP tools. I know the types and the approximate amount of data I will generate, but I have not thought about how to share data with my collaborators and how to store data securely. Initially, my plan was to buy a powerful computer and portable hard drive, but I am now thinking that I need to use a national computing infrastructure. The field I work in has well defined data and curation standards, for example, capturing information (metadata) about how to collect and sample my data. However, I am not yet familiar with the importance of storing provenance data, such as tool and database versions used in analysis. diff --git a/var/style_checker.py b/var/style_checker.py index 99f93bbee..14e1ba7c1 100644 --- a/var/style_checker.py +++ b/var/style_checker.py @@ -2,7 +2,7 @@ import re pagesdir = 'pages' -white_list= ['Google', 'Research Data Management Kit', 'Data Management Plan', 'Data Management Planning', 'DMP', 'RDMKit', 'I ', 'NeLS', 'ELIXIR', 'GitHub'] +white_list= ['Google', 'Research Data Management Kit', 'Data Management Plan', 'Data Management Planning', 'DMP', 'RDMkit', 'I ', 'NeLS', 'ELIXIR', 'GitHub'] for subdir, dirs, files in os.walk(pagesdir): for file_name in files: