Merge branch 'main' of github.com:elixir-europe/infectious-diseases-t…

…oolkit into pathogen-data-analysis

_config.yml

@@ -4,12 +4,13 @@ title: Infectious Diseases Toolkit
 description: "Find tools and guidelines to help you access, analyse and share infectious disease data, and respond quickly to disease outbreaks."
 # Metadata description of the website
 
-remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@3.0.0
+remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@3.2.0
 
 gtag: G-TNT17YGXQ4
 
 theme_variables:
   privacy_statement_url: /about/privacy
+  dev-info-banner: true
   theme_color: 457B9D
   headings:
     resource-table-all-collapse: true

_data/CONTRIBUTORS.yaml

@@ -276,4 +276,18 @@ Carola Schulz:
   email: Carola.Schulz@empirica.com
   orcid: 0009-0005-9577-9647
   affiliation: empirica
+Pierluca Piselli:
+  git: pierlucapis
+  email:
+  orcid: https://orcid.org/0000-0002-7342-0263 
+  affiliation: Clinical Epidemiology Unit, INMI Lazzaro Spallanzani IRCCS, Roma
+Isabel Kemmer:
+  orcid: https://orcid.org/0000-0002-8799-4671
+  affiliation: EuroBioImaging
+Reagon Karki:
+  git: jrkarki
+  email: reagon.karki@itmp.fraunhofer.de
+  orcid: https://orcid.org/0000-0002-1815-0037
+  affiliation: Fraunhofer ITMP/EU-OpenScreen
+
 

_data/affiliations.yml

@@ -106,3 +106,25 @@
   expose: true
   type: institution
   url: https://uni-freiburg.de/
+- name: Euro-BioImaging
+  image_url: /images/infrastructures/eurobioimaging-logo.svg
+  pid: https://ror.org/05d78xc36
+  expose: true
+  type: infrastructure
+  url: https://www.eurobioimaging.eu/
+- name: ISIDORe
+  image_url: /images/infrastructures/isidore-logo.png
+  pid: https://cordis.europa.eu/project/id/101046133
+  expose: true
+  type: funder
+  url: https://isidore-project.eu/
+- name: Fraunhofer ITMP
+  type: institution
+  image_url: /images/institutions/fraunhofer_ITMP_institute_logo.png
+  expose: true
+  url: https://www.itmp.fraunhofer.de/en.html
+- name: EU-OpenScreen
+  type: institution
+  image_url: /images/infrastructures/eu-openscreen.png
+  expose: true
+  url: https://www.eu-openscreen.eu/

_data/news.yml

@@ -126,3 +126,15 @@
   date: 2024-05-30
   linked_pr: 317
   description: A page with general information about Ethical, Legal, and Social Issues was added. [Discover the page here](/ethical-legal-and-social-issues/)
+- name: "New page: Data description of Human clinical health data"
+  description: Content was added to the Human clinical health data page in the Data Description section. [Discover the page here](/data-description/human-clinical-and-health-data)
+  date: 2024-08-08
+  linked_pr: 327
+- name: "New page: An automated pipeline for analysing brain autoradiography images"
+  date: 2024-08-13
+  linked_pr: 329
+  description: A showcase page was added about an automated pipeline for analysing brain autoradiography images, in the Showcase section. [Discover the page here](/showcase/brain-autoradiography)
+- name: "New page: Knowledge Graph Generator (KGG) - A fully automated workflow for creating disease-specific KGs"
+  date: 2024-09-05
+  linked_pr: 339
+  description: A showcase page was added about an open source workflow, integrating biological databases for FAIR data compliant Knowledge Graphs, in the Showcase section. [Discover the page here](/showcase/knowledge-graph-generator)

_data/sidebars/main.yml

@@ -26,6 +26,8 @@ subitems:
     description: Finding (meta)data standards and documentation
     image_url: /assets/img/section-icons/list-timeline-duotone.svg
     subitems:
+      - title: Human clinical and health data
+        url: /data-description/human-clinical-and-health-data
       - title: Pathogen characterisation
         url: /data-description/pathogen-characterisation
 
@@ -76,6 +78,10 @@ subitems:
     subitems:
       - title: An automated SARS-CoV-2 genome surveillance system built around Galaxy
         url:  /showcase/covid19-galaxy
+      - title: An automated pipeline for analysing brain autoradiography images
+        url:  /showcase/brain-autoradiography
+      - title: Knowledge Graph Generator
+        url: /showcase/knowledge-graph-generator
       - title: Linked Cohort Data
         url: /showcase/linked-cohort-data
       - title: "Prevalence study of SARS-CoV-2 in Estonia: lessons learned"

_data/tool_and_resource_list.yml

@@ -368,7 +368,7 @@
   id: gitlab
   name: GitLab
   registry:
-    fairsharing: 530e61
+    fairsharing: 5.3e+63
     tess: GitLab
   url: https://about.gitlab.com/
 - description: GO is to perform enrichment analysis on gene sets.
@@ -462,6 +462,7 @@
   name: matplotlib
   registry:
     biotools: matplotlib
+    tess: matplotlib
   url: https://github.com/matplotlib/matplotlib
 - description: MetaboAnalyst is a comprehensive platform dedicated for metabolomics data analysis via user-friendly, web-based interface.
   id: metaboanalyst
@@ -959,6 +960,64 @@
   registry:
     tess: Webin-CLI
   url: https://github.com/enasequence/webin-cli
+- description: Interface to query on the EGA data through Beacon v2
+  id: ega-beacon
+  name: EGA Beacon
+  url: https://beacon.ega-archive.org/
+- description: Beacon from UNottingham to query a backend OMOP database of synthetic COVID-19 patient EHRs (electronic health records).
+  id: unott-beacon
+  name: UNottingham Beacon
+  url: https://beacon.nottingham.ac.uk
+- description: The Bento platform enables the research community to explore the BQC19 cohort aggregate data.
+  id: bento-platform
+  name: Bento platform
+  url: https://bqc19.bento.sd4h.ca/#/en/
+- description: SARS-CoV-2 whole genome sequencing circuit of Andalusia
+  id: andalusia-beacon
+  name: SARS-COV-2 outbreak in Andalucia
+  url: https://nextstrain.clinbioinfosspa.es/SARS-COV-2-latest
+- description: The COVID-19 Beacon is a searchable platform for SARS-CoV-2 genomic variants conforming to the Beacon specifications of the Global Alliance for Genomics and Health but adjusted for viral genome searches.
+  id: covid19-beacon
+  name: COVID-19 BEACON
+  url: https://d2eqg84un4jpac.cloudfront.net/
+- description: A global network for genomic surveillance and infectious disease research
+  id: viral-ai
+  name: Viral AI
+  url: https://viral.ai/collections
+- description: EMBL-EBI's web portal for finding ontologies
+  id: ols
+  name: Ontology Lookup Service
+  registry:
+    biotools: ols
+    fairsharing: Mkl9RR
+    tess: Ontology Lookup Service
+  url: https://www.ebi.ac.uk/ols/index
+- description: A comprehensive repository of biomedical ontologies
+  id: bioportal
+  name: BioPortal
+  registry:
+    biotools: bioportal
+    fairsharing: 4m97ah
+    tess: BioPortal
+  url: https://bioportal.bioontology.org
+- description: Collaborative effort to develob interoperable ontologies for the biological sciences
+  id: the-open-biological-and-biomedical-ontology-foundry
+  name: The Open Biological and Biomedical Ontology (OBO) Foundry
+  registry:
+    fairsharing-coll: bsg-d001083
+  url: http://obofoundry.org
+- description: Semi-automated processing of autoradiography (ARG) images from mouse brain tissue. This project includes a Napari-based user interface where ARG slides can be preprocessed and registered to Allen Brain Atlas regions.
+  id: mbat
+  name: Mouse Brain Alignment Tool (MBAT)
+  url: https://github.com/Turku-BioImaging/mouse-brain-alignment-tool
+- description: Pure Python package for parsing and handling biological networks encoded in the Biological Expression Language (BEL).
+  id: pybel
+  name: PyBEL
+  url: https://github.com/pybel/pybel
+- description: The OpenBEL Framework is an open-platform technology for managing, publishing, and using biological knowledge represented using the Biological Expression Language (BEL).
+  id: openbel
+  name: OpenBEL
+  url: https://github.com/OpenBEL/openbel-framework
 - description: Velvet is an algorithm package that has been designed to deal with de novo genome assembly and short read sequencing alignments.  
   id: velvet
   name: Velvet
@@ -1060,4 +1119,4 @@
   id: beauti
   name: BEAUti
   url: https://beast.community/beauti.html
-  regsitry:
+  regsitry:

_sass/_custom_classes.scss

@@ -309,24 +309,3 @@ section#search-section {
     }
 }
 
-/*-----Accordion styles-----*/
-
-// Add a bottom border to the last accordion.
-a.info-collapse[aria-expanded="false"]:last-of-type, 
-a.info-collapse[aria-expanded="true"]:last-of-type + .show {
-    border-bottom: 1px solid $border-color;
-}
-
-// Remove border hover effect.
-.info-collapse:hover, .info-collapse[aria-expanded="true"] {
-    border-color: $border-color !important;
-}
-
-// Add hover effect to accordion header text.
-a.info-collapse h3 {
-    transition: color .2s ease-in-out;
-}
-
-a.info-collapse:hover h3 {
-    color: rgba($link-color, .8) !important;
-}

attributing-credit/index.md

@@ -1,5 +1,6 @@
 ---
 title: Attributing credit
+toc: false
 ---
 
 

contribute/google-doc-way.md

@@ -10,7 +10,11 @@ Infectious Diseases Toolkit is hosted on GitHub. We understand, however, that ma
 
 The steps are as follows:
 * Email the editorial team at [idtk-editors@elixir-europe.org](mailto:idtk-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.  
-* Use [our google doc template](https://docs.google.com/document/d/1kAYZaimOG6UR9wvTUn2Tzi-0pSO8eOarO-Kxpmg2HRM/edit?usp=sharing) to write the page and notify the editorial team when you are finished.
+* Use our section specifc Google Doc templates to write your page:
+  * [General guideline template](https://docs.google.com/document/d/1Jd71fAKdJBax0ZVg2IkQUJ8e21jRoHjl48jytOGT5_c/edit?usp=sharing)
+  * [Showcase template](https://docs.google.com/document/d/1uS5inLcy2UA0casGR1cYABq8xqAjgm6j_POI4ylOM0o/edit?usp=sharing)
+  * [National resources template](https://docs.google.com/document/d/165-r9VzCu-ZfhJlKy-7QWabkMMp9KIEzEBRvQcmijmA/edit?usp=sharing)
+* Notify the editorial team when you are finished.
 * The editors will assign reviewers to your page, who will provide feedback as comments on the shared google doc.
 * Address the reviewers' comments and let the editorial team know, again by mail, that you're finished with revisions.
 * The editors will transfer your page to GitHub and let you know when it is published on the website.

data-analysis/index.md

@@ -1,5 +1,6 @@
 ---
 title: Data analysis
+toc: false
 ---
 
 Data analysis involves employing workflows tailored to different types of data, such as epidemiological, clinical, or molecular data. These workflows can include steps like data collection, cleaning, integration, and analysis, and use statistical and computational methods to uncover trends, associations, and patterns. Systematic data analysis helps researchers and health professionals to understand disease dynamics, assess intervention strategies, and improve disease prevention and control measures based on robust, data-driven insights.