Update human_pathogen_genomics.md by bianchini88 · Pull Request #1526 · elixir-europe/rdmkit

bianchini88 · 2024-09-13T12:01:51Z

Improving the page style (closes General curation of the human pathogen genomics page #1530)
Adding tools with the right syntax (closes add tools in Human pathogen genomics #1345)
Adding references to bibliography (closes Creating a bibliography for the human pathogen genomics domain page #1524)

* Improving the page style. * Adding tools with the right syntax

bedroesb · 2024-09-26T07:58:02Z

@bianchini88 do you want me still to do something for this?

bianchini88 · 2024-09-26T08:22:42Z

Hi @bedroesb, sorry it is a particularly busy period. I will finish this by the end of October, if it's ok with you,

Adding missing FAIRsharing ID to an ontology

Adding the Genomic Epidemiology Ontology (GenEpiO) to the table of resources

Genepio moved to tool syntax

general style-related improvements

Adding the Phenotypic QualiTy Ontology (PATO) to the table of resources

Adding Chemical Entities of Biological Interest (ChEBI) to the table of resources.

Adding UBER anatomy ONtology (UBERON) to the table of resources

_data/tool_and_resource_list.yml

Tools syntax for various ontologies.

Changing id for bio.tools to match the table

bianchini88 · 2024-10-21T14:45:53Z

@bedroesb I think we need to address the discussion points I raised above, and then we can possibly merge this as it is becoming long enough. The bibliography bit can safely be added as a future PR, I believe.

Removing "tool" syntax for projects and organisations.

Removing organisations and projects from the table of resources.

Minor style improvements

Adding missing author to the list of contributors (permission obtained via private communications with the author)

Improved affiliation of author (now matches main label on ROR)

bianchini88 · 2024-10-22T14:28:41Z

@bedroesb I had a bit of extra time and I ended up adding also the bibliography as part of this PR. I will be opening this for reviewers now.

Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com>

bianchini88 · 2024-10-23T10:13:32Z

Thank you @marikapop for going through this. I have committed all the suggestions but one (see above).

I am not sure I submit suggestions and comments as a single review but it looks huge at the end.

I am not sure why it looked the way it did (some suggestions were doubled somehow), but I would say this is the correct approach for reviewing a page.

Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com>

bedroesb · 2024-10-23T10:19:11Z

@bianchini88 this is really great! Maybe even enough to highlight it with a news item?

bianchini88 · 2024-10-23T10:22:56Z

@bianchini88 this is really great! Maybe even enough to highlight it with a news item?

Thank you @bedroesb. The content in itself did not really change, but adding a news item is always a good idea.

marikapop · 2024-10-23T12:07:04Z

Thank you @marikapop for going through this. I have committed all the suggestions but one (see above).

I am not sure I submit suggestions and comments as a single review but it looks huge at the end.

I am not sure why it looked the way it did (some suggestions were doubled somehow), but I would say this is the correct approach for reviewing a page.

Thank you Federico. Then I will continue making review this way :)

bedroesb · 2024-10-23T16:46:46Z

@diana-pilvar or @marikapop do you give an official approval? Because I think this one is ready to be merged. Accept if Federico wants to add the news item as part of this PR, otherwise we do it after.

marikapop

Please go on and merge it.

bianchini88 · 2024-10-24T11:06:40Z

@bedroesb Shall we merge?

bedroesb · 2024-10-24T13:37:06Z

Lets merge!

* ETT version update (#1516) * version update * less css needed * patch * update scroll to top button * make snakecase (#1519) * Implementing suggested edits on ArrayExpress and BioStudies (from EBI) (#1521) * Update tool_and_resource_list.yml * Update dm_coordination.md Implemented point 3 in #1520 + minor grammar/style fixes. * Update microbial_biotechnology.md Point 4 of #1520 + minor style/grammar fixes * Update dm_coordination.md * Update dm_coordination.md spelling (US to UK) * Automatic tool/resource-list update (#1522) * Update tool/resource_list.yaml * Better description for IDSM --------- Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Update (#1523) * Update tool_and_resource_list.yml (#1525) Improved title and descriptions os some metadata standards * Update tool/resource_list.yaml (#1531) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Move Martin as past editorial member (#1535) * add martin to past editorial members * no codeowner anymore * Update tool/resource_list.yaml (#1538) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Refactor of contribute pages (#1437) * Update google_doc_way.md improve readability and clarity * improve readibility and clarity * Improve readibility and clarity * Simplify how to contribute page * Create ways_to_contribute.md * Update contribute navigation * correct typos * correct typos * correct typos * correct typos * correct typos and remove toc * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/editors_checklist.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/google_doc_way.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/github_way.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/how_to_contribute.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/how_to_contribute.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/how_to_contribute.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/editors_checklist.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/github_way.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/google_doc_way.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/google_doc_way.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * start with ways of contributing tiles * some general improvements * relative url * Update pages/contribute/how_to_contribute.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Improve boxes * shorter sentence * text improvement * apply suggestion from Federico * Update contribute.yml * implement feedback * add Xenia * incorporate feedback * using MD * some minor improvements * strongly suggesting the ORCID * shorter --------- Co-authored-by: Xenia Perez Sitja <62298255+sitjart@users.noreply.github.com> Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update tool/resource_list.yaml (#1539) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Update news.yml (#1540) * Update news.yml * Update affilations of Marina and Pinar (#1537) * Update affilation of Marina * Update Pinar's affilation * improved contributors page * Martin is not an editor anymore * Add page on data discoverability (#1517) * Create data_discoverability.md * Update data_discoverability.md * Update tool_and_resource_list.yml * Add files via upload * Add content to data discoverability page * Update data_discoverability.md * Add tools to the tools table * Update tool_and_resource_list.yml * Add new tools in the text * improve size of pic + part of list * add to sidebar * typo * Add Aina to contributors * Update pages/your_tasks/data_discoverability.md Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Add related pages * Update data_discoverability.md replaced 'like' with 'such as' * Update data_discoverability.md Small updates in style and spelling * Add changes based on Nazeefa's comments * Update text based on Nazeefa's comments * Changes based on Nazeefa's comments * add news item * capital in title * adding acronym to tool snippet * no task page linkage * Remove B4OMOP documentation * Update links --------- Co-authored-by: bedroesb <bert.droesbeke@vib.be> Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> Co-authored-by: Nazeeefa <fatima.nazeefa@gmail.com> Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update tool/resource_list.yaml (#1544) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Update human_pathogen_genomics.md (#1526) * Update human_pathogen_genomics.md * Improving the page style. * Adding tools with the right syntax * start adding tools (#1527) * Update tool_and_resource_list.yml Adding missing FAIRsharing ID to an ontology * Update tool_and_resource_list.yml Adding the Genomic Epidemiology Ontology (GenEpiO) to the table of resources * Update human_pathogen_genomics.md Genepio moved to tool syntax * Update human_pathogen_genomics.md general style-related improvements * Update tool_and_resource_list.yml Adding the Phenotypic QualiTy Ontology (PATO) to the table of resources * Update tool_and_resource_list.yml Adding Chemical Entities of Biological Interest (ChEBI) to the table of resources. * Update tool_and_resource_list.yml Adding UBER anatomy ONtology (UBERON) to the table of resources * Update human_pathogen_genomics.md Tools syntax for various ontologies. * Update human_pathogen_genomics.md Changing id for bio.tools to match the table * Update human_pathogen_genomics.md Removing "tool" syntax for projects and organisations. * Update tool_and_resource_list.yml Removing organisations and projects from the table of resources. * Update human_pathogen_genomics.md Minor style improvements * Update CONTRIBUTORS.yaml Adding missing author to the list of contributors (permission obtained via private communications with the author) * Update CONTRIBUTORS.yaml Improved affiliation of author (now matches main label on ROR) * Adding bibliography for the human pathogen genomics domain page * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update human_pathogen_genomics.md * Added news item of revamped human pathogen page --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update tool/resource_list.yaml (#1551) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Update tool_and_resource_list.yml (#1552) Fixing wrong FAIRsharing ID for a resource (which currently brings up a 404) * Update tool_resource_update.md (#1554) Very minor style/grammar fixes * Update tool_and_resource_list.yml (#1555) Changing URL to the GitHub page instead of having a duplicate link to bio.tools. The GitHub page URL is taken from the bio.tool entry https://bio.tools/plant-3d * fix spelling (#1556) * Update tool/resource_list.yaml (#1557) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * enable affiliation filtering * Automatic tool/resource-list update (#1560) * Update tool/resource_list.yaml * Update tool_and_resource_list.yml --------- Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Update Portugal resources page (#1561) * Update metadata_management.md (#1565) * Update metadata_management.md added wikipedia page on minimum information standards * Update metadata_management.md * Update tool_and_resource_list.yml (#1567) added wiki page on min info standards * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Improve machine actionability page (#1566) * Better intro * Update machine_actionability.md * ELN additions (#1562) * Add eLabFTW and ELN-finder * Update tool_and_resource_list.yml syntax fix for TeSS query on the resource. (ref. https://rdmkit.elixir-europe.org/tool_resource_update#the-main-yaml-file) * Grammar fixes Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Fix typo the in ELN Finder's description --------- Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Fix links (#1569) * start setting up lychee * 2 link fixes * add action * add link checker * Delete .github/workflows/link-checker.yml * Delete .lycheeignore * draft of data workflow diagram task (#1528) * draft of data workflow diagram task * add sidebar and news item * addressing comments of #1528 * resolving comments from Nazeefa * fixing name of creating data workflow page in different places * fixing name of page in news --------- Co-authored-by: bedroesb <bert.droesbeke@vib.be> * fix url * order sidebar * add tools to toolstable * betetr description * add 2 licensed packages * typos * Create link-check.yml (#1571) * Create link-check.yml * Update .github/workflows/link-check.yml Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Update link-check.yml * Update link-check.yml * Update link-check.yml * Update link-check.yml --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * no token * bring back token * personal github token * Mmp2 (#1572) * Create link-check.yml * Update .github/workflows/link-check.yml Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Update link-check.yml * Update link-check.yml * Update link-check.yml * Update link-check.yml * marine_metagenomics_assembly.md * Update no_resources.md * tool_and_resource_list.yml --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * fix version + exclude github (#1573) * Update tool/resource_list.yaml (#1576) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * lychee-action 2.1.0 * correct version syntax lychee * lychee version format (#1575) * Change title to Creating a data workflow diagram (#1574) * Creating a data workflow diagram * some small changes * change to data-flow * space * second space * Link update no_resources (#1577) * Link update no_resources * Update pages/national_resources/no_resources.md * Update pages/national_resources/no_resources.md * Update no_resources.md (#1578) Fixing broken link + minor grammar/style changes * Add IDTk in the corresponding pages (#1559) * Add IDTk in the corresponding pages Add IDTk link in: - Human pathogen data - COVID-19 Data Portal * Update COVID-19 Data Portal page Update COVID-19 Data Portal page with IDTk link * Update human_pathogen_genomics.md * Update pages/tool_assembly/covid19_data_portal.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update covid19_data_portal.md --------- Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update tool/resource_list.yaml (#1579) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Update ES resources page (#1580) Update ES resources page with more information about initiatives and resources that were missing. * Update tool/resource_list.yaml (#1583) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Create a CITATION.cff (#1543) * Add new link to template slides * fix aspect ratio * more spacing * Create CITATION.cff * Update CITATION.cff * Update CITATION.cff * Update CITATION.cff * Update CITATION.cff Co-authored-by: Vilem Ded <51602017+vildead@users.noreply.github.com> * Update CITATION.cff Co-authored-by: Vilem Ded <51602017+vildead@users.noreply.github.com> * Update CITATION.cff Co-authored-by: Vilem Ded <51602017+vildead@users.noreply.github.com> * Update CITATION.cff Co-authored-by: Vilem Ded <51602017+vildead@users.noreply.github.com> * update about * attempt to fix * attempt without author * add back ELIXIR * Update CITATION.cff * Update about.md --------- Co-authored-by: Vilem Ded <51602017+vildead@users.noreply.github.com> * Update ee_resources.md (#1582) * removed redcap Estonia (#1586) * Upgrading to ETT V4.0.0 (#1581) * update to latest version * homepage sizing * consistent search * Replacing outdate form of FAIRsharing IDs (#1587) * Replacing outdate form of FAIRsharing IDs * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml These both refer to https://fairsharing.org/3527. I think we want to use these 4 digits only to refer to FAIRsharing collections. * Update tool_and_resource_list.yml Duplicate, it was bringing to the same entry, not to a collection * Update tool_and_resource_list.yml --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Automatic tool/resource-list update (#1591) * Update tool/resource_list.yaml * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml --------- Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Improve the concept of "resources" in the RDMkit (#1532) * start improving resources * betetr box * new variations * describing what a tool or resource is in the RDMkit * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update tool_resource_update.md * Update tool_resource_update.md (#1590) updates on documentation of FAIRsharing IDs * Update tool_resource_update.md * update icon * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> --------- Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update tool/resource_list.yaml (#1596) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Update jekyll.yml (#1599) * Update tool/resource_list.yaml (#1601) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Update built dependencies * lock versions * Update tool/resource_list.yaml (#1602) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Update FWO logo as funder (#1603) * update FWO logo * bigger logo * Licensing Statement (#1594) * Update about.md updated statement on licensing * Update about.md * Standardisation of affiliations and other reccomendations for persistent identifiers (#1597) * Update tool_and_resource_list.yml Adding ROR as a resource. * Update how_to_contribute.md Added recommendation to look into ROR * Update jekyll.yml (#1599) (#1600) * Update identifiers.md minor fixes in grammar, typos, style * Update identifiers.md Adding ROR, ORCID, and OFR. (ORCID and OFR will need to be added in the table of resources as well). * Update tool_and_resource_list.yml Adding ORCID and OFR to the list * Update tool_and_resource_list.yml * Update pages/contribute/how_to_contribute.md Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Updating TSD Tools Assembly page (#1606) * Update tsd_assembly.md Updated "What can you use the TSD data management tools assembly for?" with DSW link and minor fixes in text. * Update tsd_assembly.md * Update about.md updated statement on licensing * Update pages/tool_assembly/tsd_assembly.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/tool_assembly/tsd_assembly.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update tsd_assembly.md Updated "What is the Norwegian TSD Data Management Tools Assembly?" and "Who can use the TSD data management tools assembly?" sections. * Update tsd_assembly.md Updated training links, and first two sections of the pages. * Update about.md * Update pages/tool_assembly/tsd_assembly.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/tool_assembly/tsd_assembly.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> --------- Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update gr_resources.md (#1568) * Update gr_resources.md First test for adding content in the page * Update gr_resources.md * Update gr_resources.md Edits and one additional tool "ARGOS" * Update gr_resources.md Removed twitter account mention * fix build * Update gr_resources.md Followed reviewers latest suggestions * Update gr_resources.md * Update gr_resources.md Added contributors and coordinators * Update gr_resources.md Added argos id * add greece to sidebar * add news article * Update CONTRIBUTORS.yaml Added Eleni, Thanasis and Alexandros as contributors * Update gr_resources.md Added Funders, Policies and one additional national resource. * Update gr_resources.md added tool assembly in related paged of the Greek covid-19 portal * Update gr_resources.md rephrased hypatia description * Update gr_resources.md elixir greece titles * Update gr_resources.md Removed the DMP submission requirement from HFRI * Update gr_resources.md Added 2 training Zenodo inputs * Update gr_resources.md GDI updates, Zenodo training edits * Update gr_resources.md HFRI DMP requirement clarification and minor zenodo publication edit. * Update gr_resources.md Added related pages to HYPATIA and GDI * update date * fix url * Update gr_resources.md Corrected the related pages categories and ids in hypatia and gdi * Update gr_resources.md * some formatting * Update gr_resources.md Fixed GDI link to hyperlink * Update news.yml fixed news description * Update news.yml --------- Co-authored-by: bedroesb <bert.droesbeke@vib.be> Co-authored-by: Bert Droesbeke <bertdroesbeke@hotmail.com> Co-authored-by: Nazeeefa <fatima.nazeefa@gmail.com> * Update editorial board members (#1609) * Update CODEOWNERS Removing Laura from CODEOWNERS * Taking out Martin specific lines * Update editorial_board.md Removing Laura from the carousel, small grammar/style fixes. * Update editorial_board.md Adding Laura to the list of former members of the editorial board. * Update CONTRIBUTORS.yaml --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Update tool/resource_list.yaml (#1613) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * add domain placeholder (#1619) * Update plant_sciences.md (#1608) Punctuation and style improvement, tools syntax for EVA * Automatic tool/resource-list update (#1621) * Update tool/resource_list.yaml * Update tool_and_resource_list.yml --------- Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Fix url to VIB institute (#1615) * add vib * Update affiliations.yaml * Update data_publication.md (#1611) * Update data_publication.md include paragraph about datasets accession numbers in pre-prints * Update data_publication.md added space * Update pages/your_tasks/data_publication.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_tasks/data_publication.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_tasks/data_publication.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_tasks/data_publication.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_tasks/data_publication.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_tasks/data_publication.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_tasks/data_publication.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update data_publication.md * Update data_publication.md add contributors * Update pages/your_tasks/data_publication.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> --------- Co-authored-by: Diana Pilvar <125961725+diana-pilvar@users.noreply.github.com> Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update news.yml (#1623) * Update news.yml add news * adding page + link to paragraph --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Update CODEOWNERS (#1610) Redistributing roles * Removed acronyms from headings in Portugal National Resources (#1607) * Removed acronyms from headings in Portugal National Resources * Update pt_resources.md fixed typos in "Institutional policies on research data in Portugal" * Changed Portuguese Research Data Management Forum title * Changed INCD to RNCA INCD recently rebranded to RNCA. For now, they're keeping the incd.pt domain, so keeping that. --------- Co-authored-by: Nazeeefa <fatima.nazeefa@gmail.com> * Update bioimaging_data.md (#1627) * Update bioimaging_data.md * Update bioimaging_data.md * Update tool/resource_list.yaml (#1629) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Update CONTRIBUTORS.yaml (#1631) * Update CONTRIBUTORS.yaml Added contributors for the Cancer DM domain page * Update CONTRIBUTORS.yaml Corrected errors to the contributor information added * Update CONTRIBUTORS.yaml deleted unwanted space * Update CONTRIBUTORS.yaml Corrected an author listed twice (Fotis) * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml made corrections to the tools and resources added from Cancer DM page * Update tool_and_resource_list.yml corrections to the T&R for Cancer DM page * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml Removing duplicate * Update tool_and_resource_list.yml Fixing misclick * Update tool_and_resource_list.yml Momentarily removed item that does not seem to be parsed * Update tool_and_resource_list.yml Bringing back element (there was a copy/paste artefact that revealed itself when pasted in a plain text editor) * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml swap test * Update tool_and_resource_list.yml ids should be lowercase * Update tool_and_resource_list.yml minor style/grammar fixes --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> Co-authored-by: Xenia Perez Sitja <62298255+sitjart@users.noreply.github.com> Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> Co-authored-by: Laura Portell Silva <74184187+lauportell@users.noreply.github.com> Co-authored-by: bedroesb <bert.droesbeke@vib.be> Co-authored-by: Nazeeefa <fatima.nazeefa@gmail.com> Co-authored-by: Justin Clark-Casey <justinccdev@gmail.com> Co-authored-by: Gil Poiares-Oliveira <gpo@biodata.pt> Co-authored-by: Diana Pilvar <125961725+diana-pilvar@users.noreply.github.com> Co-authored-by: Vilem Ded <51602017+vildead@users.noreply.github.com> Co-authored-by: Korbinian Bösl <korbinian.bosl@uib.no> Co-authored-by: Eleni Adamidi <eleni.adamidi@athenarc.gr> Co-authored-by: Bert Droesbeke <bertdroesbeke@hotmail.com> Co-authored-by: floradanna <51486716+floradanna@users.noreply.github.com>

* Create cancer_data_management.md * Update cancer_data_management.md * Update cancer_data_management.md * Update tool_and_resource_list.yml (#1633) * ETT version update (#1516) * version update * less css needed * patch * update scroll to top button * make snakecase (#1519) * Implementing suggested edits on ArrayExpress and BioStudies (from EBI) (#1521) * Update tool_and_resource_list.yml * Update dm_coordination.md Implemented point 3 in #1520 + minor grammar/style fixes. * Update microbial_biotechnology.md Point 4 of #1520 + minor style/grammar fixes * Update dm_coordination.md * Update dm_coordination.md spelling (US to UK) * Automatic tool/resource-list update (#1522) * Update tool/resource_list.yaml * Better description for IDSM --------- Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Update (#1523) * Update tool_and_resource_list.yml (#1525) Improved title and descriptions os some metadata standards * Update tool/resource_list.yaml (#1531) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Move Martin as past editorial member (#1535) * add martin to past editorial members * no codeowner anymore * Update tool/resource_list.yaml (#1538) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Refactor of contribute pages (#1437) * Update google_doc_way.md improve readability and clarity * improve readibility and clarity * Improve readibility and clarity * Simplify how to contribute page * Create ways_to_contribute.md * Update contribute navigation * correct typos * correct typos * correct typos * correct typos * correct typos and remove toc * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/editors_checklist.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/google_doc_way.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/github_way.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/how_to_contribute.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/how_to_contribute.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/how_to_contribute.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/editors_checklist.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/github_way.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/google_doc_way.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/google_doc_way.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * start with ways of contributing tiles * some general improvements * relative url * Update pages/contribute/how_to_contribute.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Improve boxes * shorter sentence * text improvement * apply suggestion from Federico * Update contribute.yml * implement feedback * add Xenia * incorporate feedback * using MD * some minor improvements * strongly suggesting the ORCID * shorter --------- Co-authored-by: Xenia Perez Sitja <62298255+sitjart@users.noreply.github.com> Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update tool/resource_list.yaml (#1539) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Update news.yml (#1540) * Update news.yml * Update affilations of Marina and Pinar (#1537) * Update affilation of Marina * Update Pinar's affilation * improved contributors page * Martin is not an editor anymore * Add page on data discoverability (#1517) * Create data_discoverability.md * Update data_discoverability.md * Update tool_and_resource_list.yml * Add files via upload * Add content to data discoverability page * Update data_discoverability.md * Add tools to the tools table * Update tool_and_resource_list.yml * Add new tools in the text * improve size of pic + part of list * add to sidebar * typo * Add Aina to contributors * Update pages/your_tasks/data_discoverability.md Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Add related pages * Update data_discoverability.md replaced 'like' with 'such as' * Update data_discoverability.md Small updates in style and spelling * Add changes based on Nazeefa's comments * Update text based on Nazeefa's comments * Changes based on Nazeefa's comments * add news item * capital in title * adding acronym to tool snippet * no task page linkage * Remove B4OMOP documentation * Update links --------- Co-authored-by: bedroesb <bert.droesbeke@vib.be> Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> Co-authored-by: Nazeeefa <fatima.nazeefa@gmail.com> Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update tool/resource_list.yaml (#1544) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Update human_pathogen_genomics.md (#1526) * Update human_pathogen_genomics.md * Improving the page style. * Adding tools with the right syntax * start adding tools (#1527) * Update tool_and_resource_list.yml Adding missing FAIRsharing ID to an ontology * Update tool_and_resource_list.yml Adding the Genomic Epidemiology Ontology (GenEpiO) to the table of resources * Update human_pathogen_genomics.md Genepio moved to tool syntax * Update human_pathogen_genomics.md general style-related improvements * Update tool_and_resource_list.yml Adding the Phenotypic QualiTy Ontology (PATO) to the table of resources * Update tool_and_resource_list.yml Adding Chemical Entities of Biological Interest (ChEBI) to the table of resources. * Update tool_and_resource_list.yml Adding UBER anatomy ONtology (UBERON) to the table of resources * Update human_pathogen_genomics.md Tools syntax for various ontologies. * Update human_pathogen_genomics.md Changing id for bio.tools to match the table * Update human_pathogen_genomics.md Removing "tool" syntax for projects and organisations. * Update tool_and_resource_list.yml Removing organisations and projects from the table of resources. * Update human_pathogen_genomics.md Minor style improvements * Update CONTRIBUTORS.yaml Adding missing author to the list of contributors (permission obtained via private communications with the author) * Update CONTRIBUTORS.yaml Improved affiliation of author (now matches main label on ROR) * Adding bibliography for the human pathogen genomics domain page * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_domain/human_pathogen_genomics.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update human_pathogen_genomics.md * Added news item of revamped human pathogen page --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update tool/resource_list.yaml (#1551) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Update tool_and_resource_list.yml (#1552) Fixing wrong FAIRsharing ID for a resource (which currently brings up a 404) * Update tool_resource_update.md (#1554) Very minor style/grammar fixes * Update tool_and_resource_list.yml (#1555) Changing URL to the GitHub page instead of having a duplicate link to bio.tools. The GitHub page URL is taken from the bio.tool entry https://bio.tools/plant-3d * fix spelling (#1556) * Update tool/resource_list.yaml (#1557) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * enable affiliation filtering * Automatic tool/resource-list update (#1560) * Update tool/resource_list.yaml * Update tool_and_resource_list.yml --------- Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Update Portugal resources page (#1561) * Update metadata_management.md (#1565) * Update metadata_management.md added wikipedia page on minimum information standards * Update metadata_management.md * Update tool_and_resource_list.yml (#1567) added wiki page on min info standards * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Improve machine actionability page (#1566) * Better intro * Update machine_actionability.md * ELN additions (#1562) * Add eLabFTW and ELN-finder * Update tool_and_resource_list.yml syntax fix for TeSS query on the resource. (ref. https://rdmkit.elixir-europe.org/tool_resource_update#the-main-yaml-file) * Grammar fixes Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Fix typo the in ELN Finder's description --------- Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Fix links (#1569) * start setting up lychee * 2 link fixes * add action * add link checker * Delete .github/workflows/link-checker.yml * Delete .lycheeignore * draft of data workflow diagram task (#1528) * draft of data workflow diagram task * add sidebar and news item * addressing comments of #1528 * resolving comments from Nazeefa * fixing name of creating data workflow page in different places * fixing name of page in news --------- Co-authored-by: bedroesb <bert.droesbeke@vib.be> * fix url * order sidebar * add tools to toolstable * betetr description * add 2 licensed packages * typos * Create link-check.yml (#1571) * Create link-check.yml * Update .github/workflows/link-check.yml Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Update link-check.yml * Update link-check.yml * Update link-check.yml * Update link-check.yml --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * no token * bring back token * personal github token * Mmp2 (#1572) * Create link-check.yml * Update .github/workflows/link-check.yml Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Update link-check.yml * Update link-check.yml * Update link-check.yml * Update link-check.yml * marine_metagenomics_assembly.md * Update no_resources.md * tool_and_resource_list.yml --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * fix version + exclude github (#1573) * Update tool/resource_list.yaml (#1576) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * lychee-action 2.1.0 * correct version syntax lychee * lychee version format (#1575) * Change title to Creating a data workflow diagram (#1574) * Creating a data workflow diagram * some small changes * change to data-flow * space * second space * Link update no_resources (#1577) * Link update no_resources * Update pages/national_resources/no_resources.md * Update pages/national_resources/no_resources.md * Update no_resources.md (#1578) Fixing broken link + minor grammar/style changes * Add IDTk in the corresponding pages (#1559) * Add IDTk in the corresponding pages Add IDTk link in: - Human pathogen data - COVID-19 Data Portal * Update COVID-19 Data Portal page Update COVID-19 Data Portal page with IDTk link * Update human_pathogen_genomics.md * Update pages/tool_assembly/covid19_data_portal.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update covid19_data_portal.md --------- Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update tool/resource_list.yaml (#1579) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Update ES resources page (#1580) Update ES resources page with more information about initiatives and resources that were missing. * Update tool/resource_list.yaml (#1583) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Create a CITATION.cff (#1543) * Add new link to template slides * fix aspect ratio * more spacing * Create CITATION.cff * Update CITATION.cff * Update CITATION.cff * Update CITATION.cff * Update CITATION.cff Co-authored-by: Vilem Ded <51602017+vildead@users.noreply.github.com> * Update CITATION.cff Co-authored-by: Vilem Ded <51602017+vildead@users.noreply.github.com> * Update CITATION.cff Co-authored-by: Vilem Ded <51602017+vildead@users.noreply.github.com> * Update CITATION.cff Co-authored-by: Vilem Ded <51602017+vildead@users.noreply.github.com> * update about * attempt to fix * attempt without author * add back ELIXIR * Update CITATION.cff * Update about.md --------- Co-authored-by: Vilem Ded <51602017+vildead@users.noreply.github.com> * Update ee_resources.md (#1582) * removed redcap Estonia (#1586) * Upgrading to ETT V4.0.0 (#1581) * update to latest version * homepage sizing * consistent search * Replacing outdate form of FAIRsharing IDs (#1587) * Replacing outdate form of FAIRsharing IDs * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml These both refer to https://fairsharing.org/3527. I think we want to use these 4 digits only to refer to FAIRsharing collections. * Update tool_and_resource_list.yml Duplicate, it was bringing to the same entry, not to a collection * Update tool_and_resource_list.yml --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Automatic tool/resource-list update (#1591) * Update tool/resource_list.yaml * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml --------- Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Improve the concept of "resources" in the RDMkit (#1532) * start improving resources * betetr box * new variations * describing what a tool or resource is in the RDMkit * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update tool_resource_update.md * Update tool_resource_update.md (#1590) updates on documentation of FAIRsharing IDs * Update tool_resource_update.md * update icon * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/contribute/tool_resource_update.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> --------- Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update tool/resource_list.yaml (#1596) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Update jekyll.yml (#1599) * Update tool/resource_list.yaml (#1601) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Update built dependencies * lock versions * Update tool/resource_list.yaml (#1602) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Update FWO logo as funder (#1603) * update FWO logo * bigger logo * Licensing Statement (#1594) * Update about.md updated statement on licensing * Update about.md * Standardisation of affiliations and other reccomendations for persistent identifiers (#1597) * Update tool_and_resource_list.yml Adding ROR as a resource. * Update how_to_contribute.md Added recommendation to look into ROR * Update jekyll.yml (#1599) (#1600) * Update identifiers.md minor fixes in grammar, typos, style * Update identifiers.md Adding ROR, ORCID, and OFR. (ORCID and OFR will need to be added in the table of resources as well). * Update tool_and_resource_list.yml Adding ORCID and OFR to the list * Update tool_and_resource_list.yml * Update pages/contribute/how_to_contribute.md Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Updating TSD Tools Assembly page (#1606) * Update tsd_assembly.md Updated "What can you use the TSD data management tools assembly for?" with DSW link and minor fixes in text. * Update tsd_assembly.md * Update about.md updated statement on licensing * Update pages/tool_assembly/tsd_assembly.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/tool_assembly/tsd_assembly.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update tsd_assembly.md Updated "What is the Norwegian TSD Data Management Tools Assembly?" and "Who can use the TSD data management tools assembly?" sections. * Update tsd_assembly.md Updated training links, and first two sections of the pages. * Update about.md * Update pages/tool_assembly/tsd_assembly.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/tool_assembly/tsd_assembly.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> --------- Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update gr_resources.md (#1568) * Update gr_resources.md First test for adding content in the page * Update gr_resources.md * Update gr_resources.md Edits and one additional tool "ARGOS" * Update gr_resources.md Removed twitter account mention * fix build * Update gr_resources.md Followed reviewers latest suggestions * Update gr_resources.md * Update gr_resources.md Added contributors and coordinators * Update gr_resources.md Added argos id * add greece to sidebar * add news article * Update CONTRIBUTORS.yaml Added Eleni, Thanasis and Alexandros as contributors * Update gr_resources.md Added Funders, Policies and one additional national resource. * Update gr_resources.md added tool assembly in related paged of the Greek covid-19 portal * Update gr_resources.md rephrased hypatia description * Update gr_resources.md elixir greece titles * Update gr_resources.md Removed the DMP submission requirement from HFRI * Update gr_resources.md Added 2 training Zenodo inputs * Update gr_resources.md GDI updates, Zenodo training edits * Update gr_resources.md HFRI DMP requirement clarification and minor zenodo publication edit. * Update gr_resources.md Added related pages to HYPATIA and GDI * update date * fix url * Update gr_resources.md Corrected the related pages categories and ids in hypatia and gdi * Update gr_resources.md * some formatting * Update gr_resources.md Fixed GDI link to hyperlink * Update news.yml fixed news description * Update news.yml --------- Co-authored-by: bedroesb <bert.droesbeke@vib.be> Co-authored-by: Bert Droesbeke <bertdroesbeke@hotmail.com> Co-authored-by: Nazeeefa <fatima.nazeefa@gmail.com> * Update editorial board members (#1609) * Update CODEOWNERS Removing Laura from CODEOWNERS * Taking out Martin specific lines * Update editorial_board.md Removing Laura from the carousel, small grammar/style fixes. * Update editorial_board.md Adding Laura to the list of former members of the editorial board. * Update CONTRIBUTORS.yaml --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Update tool/resource_list.yaml (#1613) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * add domain placeholder (#1619) * Update plant_sciences.md (#1608) Punctuation and style improvement, tools syntax for EVA * Automatic tool/resource-list update (#1621) * Update tool/resource_list.yaml * Update tool_and_resource_list.yml --------- Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Fix url to VIB institute (#1615) * add vib * Update affiliations.yaml * Update data_publication.md (#1611) * Update data_publication.md include paragraph about datasets accession numbers in pre-prints * Update data_publication.md added space * Update pages/your_tasks/data_publication.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_tasks/data_publication.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_tasks/data_publication.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_tasks/data_publication.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_tasks/data_publication.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_tasks/data_publication.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update pages/your_tasks/data_publication.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update data_publication.md * Update data_publication.md add contributors * Update pages/your_tasks/data_publication.md Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> --------- Co-authored-by: Diana Pilvar <125961725+diana-pilvar@users.noreply.github.com> Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Update news.yml (#1623) * Update news.yml add news * adding page + link to paragraph --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Update CODEOWNERS (#1610) Redistributing roles * Removed acronyms from headings in Portugal National Resources (#1607) * Removed acronyms from headings in Portugal National Resources * Update pt_resources.md fixed typos in "Institutional policies on research data in Portugal" * Changed Portuguese Research Data Management Forum title * Changed INCD to RNCA INCD recently rebranded to RNCA. For now, they're keeping the incd.pt domain, so keeping that. --------- Co-authored-by: Nazeeefa <fatima.nazeefa@gmail.com> * Update bioimaging_data.md (#1627) * Update bioimaging_data.md * Update bioimaging_data.md * Update tool/resource_list.yaml (#1629) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * Update CONTRIBUTORS.yaml (#1631) * Update CONTRIBUTORS.yaml Added contributors for the Cancer DM domain page * Update CONTRIBUTORS.yaml Corrected errors to the contributor information added * Update CONTRIBUTORS.yaml deleted unwanted space * Update CONTRIBUTORS.yaml Corrected an author listed twice (Fotis) * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml made corrections to the tools and resources added from Cancer DM page * Update tool_and_resource_list.yml corrections to the T&R for Cancer DM page * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml Removing duplicate * Update tool_and_resource_list.yml Fixing misclick * Update tool_and_resource_list.yml Momentarily removed item that does not seem to be parsed * Update tool_and_resource_list.yml Bringing back element (there was a copy/paste artefact that revealed itself when pasted in a plain text editor) * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml swap test * Update tool_and_resource_list.yml ids should be lowercase * Update tool_and_resource_list.yml minor style/grammar fixes --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> Co-authored-by: Xenia Perez Sitja <62298255+sitjart@users.noreply.github.com> Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> Co-authored-by: Laura Portell Silva <74184187+lauportell@users.noreply.github.com> Co-authored-by: bedroesb <bert.droesbeke@vib.be> Co-authored-by: Nazeeefa <fatima.nazeefa@gmail.com> Co-authored-by: Justin Clark-Casey <justinccdev@gmail.com> Co-authored-by: Gil Poiares-Oliveira <gpo@biodata.pt> Co-authored-by: Diana Pilvar <125961725+diana-pilvar@users.noreply.github.com> Co-authored-by: Vilem Ded <51602017+vildead@users.noreply.github.com> Co-authored-by: Korbinian Bösl <korbinian.bosl@uib.no> Co-authored-by: Eleni Adamidi <eleni.adamidi@athenarc.gr> Co-authored-by: Bert Droesbeke <bertdroesbeke@hotmail.com> Co-authored-by: floradanna <51486716+floradanna@users.noreply.github.com> * Cancer DM patient journey stages (#1630) * Update tool_and_resource_list.yml removed some tools which were guidelines and corrected typos * Update cancer_data_management.md added the tool snippets and corrected style, typos. * Update data_management.yml Added the cancer data management page info the side bar * Update cancer_data_management.md * Update cancer_data_management.md style correction * Update cancer_data_management.md corrected tool name * Update cancer_data_management.md corrected tool id * Update cancer_data_management.md corrected tool id * Update cancer_data_management.md corrected typo in tool id * Update pages/your_domain/cancer_data_management.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update _data/sidebars/data_management.yml Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/your_domain/cancer_data_management.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/your_domain/cancer_data_management.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/your_domain/cancer_data_management.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/your_domain/cancer_data_management.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/your_domain/cancer_data_management.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/your_domain/cancer_data_management.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/your_domain/cancer_data_management.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/your_domain/cancer_data_management.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update tool_and_resource_list.yml deleted tools with no-context in the text and corrected misleading names and ids * Update cancer_data_management.md corrected tool snippets * Update cancer_data_management.md corrected typo * Update cancer_data_management.md corrected typos and grammar * Update cancer_data_management.md replaced e.g., with e.g. to follow the British system * shuffle cancer prevention headings * aligned headings * Update pages/your_domain/cancer_data_management.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/your_domain/cancer_data_management.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * add news item * rename to cancer data * news update --------- Co-authored-by: Martin Cook <martin.cook@elixir-europe.org> Co-authored-by: Munazah <munazaha@gmail.com> Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> Co-authored-by: Xenia Perez Sitja <62298255+sitjart@users.noreply.github.com> Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> Co-authored-by: Laura Portell Silva <74184187+lauportell@users.noreply.github.com> Co-authored-by: bedroesb <bert.droesbeke@vib.be> Co-authored-by: Nazeeefa <fatima.nazeefa@gmail.com> Co-authored-by: Justin Clark-Casey <justinccdev@gmail.com> Co-authored-by: Gil Poiares-Oliveira <gpo@biodata.pt> Co-authored-by: Diana Pilvar <125961725+diana-pilvar@users.noreply.github.com> Co-authored-by: Vilem Ded <51602017+vildead@users.noreply.github.com> Co-authored-by: Korbinian Bösl <korbinian.bosl@uib.no> Co-authored-by: Eleni Adamidi <eleni.adamidi@athenarc.gr> Co-authored-by: Bert Droesbeke <bertdroesbeke@hotmail.com> Co-authored-by: floradanna <51486716+floradanna@users.noreply.github.com>

bianchini88 and others added 2 commits September 13, 2024 14:01

Update human_pathogen_genomics.md

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* Improving the page style. * Adding tools with the right syntax

start adding tools (#1527)

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This was linked to issues Sep 16, 2024

Creating a bibliography for the human pathogen genomics domain page #1524

Closed

General curation of the human pathogen genomics page #1530

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bianchini88 self-assigned this Sep 16, 2024

bedroesb linked an issue Sep 26, 2024 that may be closed by this pull request

add tools in Human pathogen genomics #1345

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bianchini88 and others added 8 commits October 10, 2024 14:25

Update tool_and_resource_list.yml

7897af7

Adding missing FAIRsharing ID to an ontology

Update tool_and_resource_list.yml

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Adding the Genomic Epidemiology Ontology (GenEpiO) to the table of resources

Update human_pathogen_genomics.md

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Genepio moved to tool syntax

Update human_pathogen_genomics.md

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general style-related improvements

Update tool_and_resource_list.yml

731e43b

Adding the Phenotypic QualiTy Ontology (PATO) to the table of resources

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Adding Chemical Entities of Biological Interest (ChEBI) to the table of resources.

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Adding UBER anatomy ONtology (UBERON) to the table of resources

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bianchini88 added 2 commits October 21, 2024 16:34

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Tools syntax for various ontologies.

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Changing id for bio.tools to match the table

bianchini88 and others added 6 commits October 22, 2024 09:16

Update human_pathogen_genomics.md

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Removing "tool" syntax for projects and organisations.

Update tool_and_resource_list.yml

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Improved affiliation of author (now matches main label on ROR)

Adding bibliography for the human pathogen genomics domain page

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bianchini88 marked this pull request as ready for review October 22, 2024 14:28

bianchini88 and others added 7 commits October 23, 2024 12:05

Update pages/your_domain/human_pathogen_genomics.md

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bianchini88 requested a review from marikapop October 23, 2024 10:13

bianchini88 and others added 8 commits October 23, 2024 12:14

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marikapop approved these changes Oct 24, 2024

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bianchini88 and others added 2 commits October 24, 2024 12:52

Update human_pathogen_genomics.md

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bedroesb merged commit 6a39718 into master Oct 24, 2024

bedroesb deleted the bianchini88-human_pathogen_genomics branch October 24, 2024 13:37

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