Human data: tools not mentioned in in text

[bedroesb]

Page: Human data

In pull request #1249, we are implementing changes to how we handle tools, resulting in different rules for rendering the tools table at the bottom of pages. Going forward, only tools referenced in the text will be included in the bottom table of the page. Some of the tools have been tagged with the page_id of this page, and we are currently exploring how to incorporate these tools into the text.

Tools that are not mentioned in the text:

• ~BIONDA - BIONDA is a free and open-access biomarker database, which employs various text mining methods to extract structured information on biomarkers from abstracts of scientific publications~
• ~ChIPSummitDB - ChIPSummitDB is a database of transcription factor binding sites and the distances of the binding sites relative to the peak summits.~
• [x] Consent Clauses for Genomic Research - A resource for researchers when drafting consent forms so they can use language matching cutting-edge GA4GH international standards
• [x] DPIA Knowledge Model - A DSW knowledge model guiding users through a set of questions to collect information necessary for a research project Data Protection Impact Assessment (DPIA).
• [x] ERPA - Web-based tool allowing users to create and manage a register of personal data processing activities (ROPA).
• [x] EU General Data Protection Regulation - Regulation (eu) 2016/679 of the european parliament and of the council on the protection of natural persons with regard to the processing of personal data and on the free movement of such data, and repealing directive 95/46/ec (general data protection regulation).
• [x] GA4GH Genomic Data Toolkit - Open standards for genomic data sharing.
• [x] HumanMine - HumanMine integrates many types of human data and provides a powerful query engine, export for results, analysis for lists of data and FAIR access via web services.
• [x] International Compilation of Human Research Standards - The International Compilation of Human Research Standards enumerates over 1,000 laws, regulations, and guidelines (collectively referred to as standards) that govern human subject protections in 133 countries, as well as standards from a number of international and regional organizations
• [x] OTP - One Touch Pipeline (OTP) is a data management platform for running bioinformatics pipelines in a high-throughput setting, and for organising the resulting data and metadata.
• PAA - PAA is an R/Bioconductor tool for protein microarray data analysis aimed at biomarker discovery.

Would you kindly review these tools and determine if they should be mentioned (as a link) in the text? If necessary, please propose changes to the text through a pull request on this temporary instance of the RDMkit by clicking on the pencil icon next to the title and following the instructions in this guide. @nicjar, @BioDataAdmin, @pinarpink, @lauportell, @wna-se, @Nazeeefa, @TeresaDAltri

[bedroesb]

We will move to the new system in the week of the 24th of Juli, so please make sure changes are comments are made before this date. Thanks a lot in advance!

[lauportell]

Hi @bedroesb, I reviewed the tools and the following tools are in the text so that they shouldn't be in the list: Consent Clauses for Genomic Research, EU General Data Protection Regulation, International Compilation of Human Research Standards.

Also, I added HumanMine in the text.

[bedroesb]

@lauportell I unchecked them again so we can use the checklist for tools that have been converted to the new system :)

[bedroesb]

Thanks for looking into the mentioned tools! I can help out where needed.

[lauportell]

Added using the new system!

[lauportell]

I tried adding the rest of the tools in the text and I am missing 3 tools which I wouldn't know where to add them, as they are about biomarkers and transcription factor binding sites, which it is something not included in the page in any section.

[bedroesb]

@nicjar, @BioDataAdmin, @pinarpink, @wna-se, @Nazeeefa, @TeresaDAltri are others also ok with not adding the 3 tools in the list that are unchecked/scratched? Than this page can be called finished. Preview here: https://bedroesb.github.io/rdmkit/human_data

[bedroesb]

We will move to the new system soon, so I suggest we have a second look at the page when it is live!