Update tool_and_resource_list.yml (#1472)

* Automatic tool/resource-list update (#1396) * Update tool/resource_list.yaml * Update plant_phenomics_assembly.md * Update plant_sciences.md --------- Co-authored-by: bedroesb <[email protected]> Co-authored-by: Bert Droesbeke <[email protected]> * add editors to alumni (#1433) * Update csc_assembly.md (#1429) * Update csc_assembly.md We updated our tool assembly. We would also have a new picture, but I don't know how I can upload it. * New csc tool assembly picture New csc tool assembly picture * Update csc_assembly.md changed the picture name to fi_csc_assembly_v2.svg * Update csc_assembly.md * Update pages/tool_assembly/csc_assembly.md Co-authored-by: Federico Bianchini <[email protected]> * Update pages/tool_assembly/csc_assembly.md ok! Co-authored-by: Federico Bianchini <[email protected]> * Update pages/tool_assembly/csc_assembly.md Co-authored-by: Federico Bianchini <[email protected]> * Update pages/tool_assembly/csc_assembly.md Co-authored-by: Federico Bianchini <[email protected]> * Update pages/tool_assembly/csc_assembly.md Co-authored-by: Federico Bianchini <[email protected]> * delete old image * Update news.yml Adding news about the refreshed CSC tool assembly page. --------- Co-authored-by: Nazeeefa <[email protected]> Co-authored-by: Federico Bianchini <[email protected]> Co-authored-by: bedroesb <[email protected]> * Adding a bibliography (#1434) * Adding bibliography * Update style_guide.md (#1435) --------- Co-authored-by: Korbinian Bösl <[email protected]> * Update nels_assembly.md (#1436) Using a country keyword for a tool assembly might create undesired results when courses for other independent national resources/tools are registered into TeSS. With the current suggestion some results of the query get lost, but maybe the annotations on TeSS should be improved (e.g. including explicitly NeLS as a keyword or similar). * Fairtracks assembly (#1419) * first draft of FAIRtracks tool assembly * adding EMBL-EBI to affiliations * Update no_resources.md * Update no_resources.md * Update fairtracks_assembly.md Added description metadata * Update fairtracks_assembly.md minor text improvements * adding link to training events on TeSS * Adding TeSS to the omnipy tool entry * revision from Sveinung * cross-referencing domain pages * revision of FAIRtracks assembly * replacing figure with new version based on feedback from the editors * Update news.yml news item on FAIRtracks tool assembly page * Update news.yml fixing wrong indentation * adding newline * Update news.yml updated date of news item --------- Co-authored-by: bedroesb <[email protected]> * Slight clarification (#1438) * Update fi_resources.md (#1439) * Update fi_resources.md Filling out "instance_of" field for FEGA Finland (instance of EGA) * Update fi_resources.md --------- Co-authored-by: Nazeeefa <[email protected]> * Update se_resources.md (#1430) * Update se_resources.md Review of all links and resources, and update where necessary * Update se_resources.md * Add FEGA-SE to metadata * Update tool/resource_list.yaml (#1440) Co-authored-by: bedroesb <[email protected]> * Update style_guide.md (#1442) * Update style_guide.md make bibliography as header * Add suggestions * Add full stop --------- Co-authored-by: Bert Droesbeke <[email protected]> * fixing display of instructions for creating a bibliography (#1446) * fixing display of instructions for creating a bibliography * Update pages/contribute/style_guide.md Co-authored-by: Bert Droesbeke <[email protected]> --------- Co-authored-by: Bert Droesbeke <[email protected]> * Update news.yml (#1449) added news about RIR * Update tool/resource_list.yaml (#1451) Co-authored-by: bedroesb <[email protected]> * Ml domain (#1443) * Adding md file for domain page on machine-learning * Adding domain page for ML to the sidebar * Changing authir name to match the one recorded in the contributors file * Update machine_learning.md * Update tool_and_resource_list.yml * Update machine_learning.md * Update references.bib * Update machine_learning.md * Fixing syntax for bibliography * minor polishing of bib file * Update machine_learning.md * Adding missing authors based on information from the draft Google document * Update machine_learning.md Minor text polishing and fixed indentation for nested lists. * Update tool_and_resource_list.yml * Update tool_and_resource_list.yml * updating page metadata * adding news item about ML domain page * minor tweaks of ML domain page * shortening title to avoid splitting in two lines * polishing list of tools * Update machine_learning.md * Update pages/your_domain/machine_learning.md * shortening long title, splitting wall of text in smaller paragraphs, adding again list that were lost in the conversion from Google document * polishing bib file * Update data_management.yml * Update news.yml * removed duplicate entry for Schema.org * removing license from tools and resources list * Update machine_learning.md --------- Co-authored-by: Stella Fragkouli <[email protected]> * improved bibtex entries for ML domain page (#1455) * Replaced broken links in National page of Estonia (#1452) * Update ee_resources.md, changed broken links * Update ee_resources.md * Update ee_resources.md * Update ee_resources.md * Update ee_resources.md minor fix --------- Co-authored-by: Nazeeefa <[email protected]> * Improved bibliography (#1448) * take away and * Update references.bib (#1454) --------- Co-authored-by: Korbinian Bösl <[email protected]> * Update news.yml (#1453) Added linked PR to new item * Update tool/resource_list.yaml (#1459) Co-authored-by: bedroesb <[email protected]> * Update email Bert Droesbeke * Update email Bert Droesbeke * Adding Daniel to past editors (#1460) * Take Daniel out of the CODEOWNERS * Update tool/resource_list.yaml (#1461) Co-authored-by: bedroesb <[email protected]> * Update tool/resource_list.yaml (#1462) Co-authored-by: bedroesb <[email protected]> * changing bibliography style to nature (#1456) * changing bibliography style to nature * custom nature bib tex style --------- Co-authored-by: bedroesb <[email protected]> * Adding metadata standards to the table of tools and resources (#1463) * Update existing_data.md (#1465) * Update no_resources.md (#1444) * Update no_resources.md * added VID resources * added normen chapter on privacy in research * Update no_resources.md * Update tool/resource_list.yaml (#1467) Co-authored-by: bedroesb <[email protected]> * Adding rss feed to track RDMkit news (#1466) * adding rss feed for news * fix xml * add ixon * Rounded video * Update tool/resource_list.yaml (#1468) Co-authored-by: bedroesb <[email protected]> * Update nl_resources.md (#1469) * Update nl_resources.md Added cBioPortal as a Dutch National Resource, requested by Lygature/EOSC4Cancer * Update nl_resources.md fixed the faulty URL for cBioPortal --------- Co-authored-by: Diana Pilvar <[email protected]> * Improve navigation by aligning the related pages with navigation tiles (#1366) * same graphics * fix type config * with icons * better theming * fix assembly * less css * variables * fix white * gray background * absolute path * relative link * variable for white * anchor fix * with shadow * smaller anchor * fix popping shadow * no shadow * smaller font * add new version * default shadow * different sizes * replace fix * replace fix * latest evrsion * primary color buttons * add news item * Update _data/news.yml Co-authored-by: Marina Popleteeva <[email protected]> * Update news.yml --------- Co-authored-by: Marina Popleteeva <[email protected]> * Adding Gil Poiares-Oliveira as an editorial member (#1471) * add @GilOliveira * Change Gil's email to BioData.pt --------- Co-authored-by: Gil Poiares-Oliveira <[email protected]> * Update tool_and_resource_list.yml Added the tools for the health data page. --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: bedroesb <[email protected]> Co-authored-by: Bert Droesbeke <[email protected]> Co-authored-by: Siiri Fuchs <[email protected]> Co-authored-by: Nazeeefa <[email protected]> Co-authored-by: Federico Bianchini <[email protected]> Co-authored-by: bedroesb <[email protected]> Co-authored-by: Korbinian Bösl <[email protected]> Co-authored-by: Sveinung Gundersen <[email protected]> Co-authored-by: YvonneKallberg <[email protected]> Co-authored-by: floradanna <[email protected]> Co-authored-by: wittigue <[email protected]> Co-authored-by: Stella Fragkouli <[email protected]> Co-authored-by: Diana Pilvar <[email protected]> Co-authored-by: bedroesb <[email protected]> Co-authored-by: MijkeJetten <[email protected]> Co-authored-by: Marina Popleteeva <[email protected]> Co-authored-by: Gil Poiares-Oliveira <[email protected]>
elixir-europe · Mar 26, 2024 · 89b6250 · 89b6250
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diff --git a/CODEOWNERS b/CODEOWNERS
@@ -5,17 +5,17 @@
 *       @bedroesb
 
 # Contribute
-/pages/contribute       @floradanna @pinarpink @bedroesb
+/pages/contribute       @floradanna @bedroesb
 /pages/contribute/copyright.md       @martin-nc
 /pages/contribute/style_guide.md       @martin-nc
-CONTRIBUTING.md       @floradanna @pinarpink
+CONTRIBUTING.md       @floradanna
 
 # Different Sections
-/pages/your_tasks       @DanFaria @floradanna @nazeeefa @marikapop @diana-pilvar
-/pages/your_role       @smza @pinarpink
+/pages/your_tasks       @floradanna @nazeeefa @marikapop @diana-pilvar
+/pages/your_role       @smza @GilOliveira
 /pages/data_life_cycle       @wittigue @floradanna @smza @marikapop
 /pages/tool_assembly       @korbinib @bianchini88
-/pages/your_domain       @DanFaria @pinarpink @bianchini88 @lauportell
+/pages/your_domain       @bianchini88 @lauportell @GilOliveira
 /pages/national_resources       @lauportell @nazeeefa @diana-pilvar
 
 #About

diff --git a/Gemfile b/Gemfile
@@ -1,6 +1,6 @@
 source 'https://rubygems.org'
 
-gem 'elixir-toolkit-theme-plugins', '~> 0.1.9'
+gem 'elixir-toolkit-theme-plugins', '~> 0.1.10'
 gem 'webrick', '~> 1.7'
 gem 'jekyll', '~> 4.3.1'
 gem 'jemoji', '~> 0.13.0'
@@ -13,6 +13,7 @@ group :jekyll_plugins do
   gem 'jekyll-github-metadata', '~> 2.15'
   gem 'jekyll-relative-links', '~> 0.6'
   gem 'jekyll-seo-tag', '~> 2.8'
+  gem 'jekyll-scholar', '~> 7.1.3'
   gem 'jekyll-remote-theme'
 end
 
diff --git a/_bibliography/nature_custom.csl b/_bibliography/nature_custom.csl
@@ -0,0 +1,168 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-GB">
+  <info>
+    <title>Nature</title>
+    <id>http://www.zotero.org/styles/nature</id>
+    <link href="http://www.zotero.org/styles/nature" rel="self"/>
+    <link href="http://www.nature.com/nature/authors/gta/index.html#a5.4" rel="documentation"/>
+    <link href="http://www.nature.com/srep/publish/guidelines#references" rel="documentation"/>
+    <author>
+      <name>Michael Berkowitz</name>
+      <email>[email protected]</email>
+    </author>
+    <category citation-format="numeric"/>
+    <category field="science"/>
+    <category field="generic-base"/>
+    <issn>0028-0836</issn>
+    <eissn>1476-4687</eissn>
+    <updated>2022-07-01T16:03:34+00:00</updated>
+    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+  </info>
+  <macro name="title">
+    <choose>
+      <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
+        <text variable="title" font-style="italic" text-case="title"/>
+      </if>
+      <else>
+        <text variable="title"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="author">
+    <names variable="author">
+      <name sort-separator=", " delimiter=", " and="symbol" initialize-with=". " delimiter-precedes-last="never" name-as-sort-order="all"/>
+      <label form="short" prefix=", "/>
+      <et-al font-style="italic"/>
+    </names>
+  </macro>
+  <macro name="access">
+    <choose>
+      <if variable="volume" type="article dataset software" match="any"/>
+      <else-if variable="DOI">
+        <text variable="DOI" prefix="doi:"/>
+      </else-if>
+    </choose>
+  </macro>
+  <macro name="access-data">
+    <choose>
+      <if type="dataset software" match="any">
+        <text variable="DOI" prefix="https://doi.org/"/>
+      </if>
+    </choose>
+  </macro>
+  <macro name="issuance">
+    <choose>
+      <if type="bill book graphic legal_case legislation motion_picture song thesis chapter paper-conference" match="any">
+        <group delimiter="; " suffix=".">
+          <group delimiter=", " prefix="(" suffix=")">
+            <text variable="publisher" form="long"/>
+            <text variable="publisher-place"/>
+            <date variable="issued">
+              <date-part name="year"/>
+            </date>
+          </group>
+        </group>
+      </if>
+      <else-if type="article">
+        <group delimiter=" ">
+          <choose>
+            <if variable="genre" match="any">
+              <text variable="genre" text-case="capitalize-first"/>
+            </if>
+            <else>
+              <text term="article" text-case="capitalize-first"/>
+            </else>
+          </choose>
+          <text term="at"/>
+          <choose>
+            <if variable="DOI" match="any">
+              <text variable="DOI" prefix="https://doi.org/"/>
+            </if>
+            <else>
+              <text variable="URL"/>
+            </else>
+          </choose>
+          <date date-parts="year" form="text" variable="issued" prefix="(" suffix=")"/>
+        </group>
+      </else-if>
+      <else-if type="dataset software" match="any">
+        <group delimiter=" ">
+          <text variable="publisher"/>
+          <text macro="access-data"/>
+          <date date-parts="year" form="text" variable="issued" prefix="(" suffix=")"/>
+        </group>
+      </else-if>
+      <else-if type="report webpage post post-weblog" match="any">
+        <group delimiter=" ">
+          <text variable="URL"/>
+          <date date-parts="year" form="text" variable="issued" prefix="(" suffix=")"/>
+        </group>
+      </else-if>
+      <else>
+        <date variable="issued" prefix="(" suffix=")">
+          <date-part name="year"/>
+        </date>
+      </else>
+    </choose>
+  </macro>
+  <macro name="container-title">
+    <choose>
+      <if type="article-journal">
+        <text variable="container-title" font-style="italic" form="short"/>
+      </if>
+      <else>
+        <text variable="container-title" font-style="italic"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="editor">
+    <choose>
+      <if type="chapter paper-conference" match="any">
+        <names variable="editor" prefix="(" suffix=")">
+          <label form="short" suffix=" "/>
+          <name and="symbol" delimiter-precedes-last="never" initialize-with=". " name-as-sort-order="all"/>
+        </names>
+      </if>
+    </choose>
+  </macro>
+  <macro name="volume">
+    <choose>
+      <if type="article-journal" match="any">
+        <text variable="volume" font-weight="bold" suffix=","/>
+      </if>
+      <else>
+        <group delimiter=" ">
+          <label variable="volume" form="short"/>
+          <text variable="volume"/>
+        </group>
+      </else>
+    </choose>
+  </macro>
+  <citation collapse="citation-number">
+    <sort>
+      <key variable="citation-number"/>
+    </sort>
+    <layout vertical-align="sup" delimiter=",">
+      <text variable="citation-number"/>
+    </layout>
+  </citation>
+  <bibliography et-al-min="6" et-al-use-first="1" second-field-align="flush" entry-spacing="0" line-spacing="2">
+    <layout suffix=".">
+      <group delimiter=" ">
+        <text macro="author" suffix="."/>
+        <text macro="title" suffix="."/>
+        <choose>
+          <if type="chapter paper-conference" match="any">
+            <text term="in"/>
+          </if>
+        </choose>
+        <text macro="container-title"/>
+        <text macro="editor"/>
+        <text macro="volume"/>
+        <text variable="page"/>
+        <text macro="issuance"/>
+        <text macro="access"/>
+      </group>
+    </layout>
+  </bibliography>
+</style>