Merge branch 'master' into fairchecker-button-live-deploys

BioSchemas · Jun 26, 2023 · 2a578f2 · 2a578f2
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diff --git a/_data/live_deployments.json b/_data/live_deployments.json
@@ -375,6 +375,11 @@
           "profileName": "CourseInstance",
           "conformsTo": "1.0-RELEASE",
           "exampleURL": "https://www.sib.swiss/training/course/20221123_OPEMP"
+        }, 
+        {
+          "profileName": "TrainingMaterial",
+          "conformsTo": "1.0-RELEASE",
+          "exampleURL": "https://www.sib.swiss/training/course/20230426_DOCK"
         }
       ]
     },

diff --git a/_data/profile_versions.yaml b/_data/profile_versions.yaml
@@ -163,12 +163,12 @@ Study:
   status: active
 Taxon:
   latest_publication: 0.8-DRAFT
-  latest_release: 0.6-RELEASE
+  latest_release: 1.0-RELEASE
   name: Taxon
   status: active
 TaxonName:
   latest_publication: 0.2-DRAFT
-  latest_release: null
+  latest_release: 1.0-RELEASE
   name: TaxonName
   status: active
 TrainingMaterial:

diff --git a/_includes/navbar.html b/_includes/navbar.html
@@ -88,6 +88,7 @@
             <li><a class="dropdown-item" href="{{ '/people/' | relative_url }}">People</a></li>
             <li><a class="dropdown-item" href="{{ '/groups/' | relative_url }}">Groups</a></li>
             <li><a class="dropdown-item" href="{{ '/community/champions.html' | relative_url }}">Champions</a></li>
+            <li><a class="dropdown-item" href="{{ '/community/stories' | relative_url }}">Stories</a></li>
             <li><a class="dropdown-item" href="{{ '/community/related' | relative_url }}">Related Communities</a></li>
           </ul>
         </li>

diff --git a/index.html b/index.html
@@ -8,7 +8,7 @@
 title: Bioschemas
 # Community Call details
 call-minutes: https://docs.google.com/document/d/1kd5F97ogdiPNhLTnkei-RVR8TC8Ohpc5QSPX3KsfDrk
-call-date: 2023-04-24T15:00UTC
+call-date: 2023-06-26T15:00UTC
 ---
 <div id="landing" itemscope itemtype="http://schema.org/Organization">
    <meta itemprop="logo" content="http://bioschemas.org/assets/img/square_logo2.png"/>

diff --git a/pages/_community/stories.md b/pages/_community/stories.md
@@ -0,0 +1,19 @@
+---
+layout: default
+title: Bioschemas stories
+---
+# Bioschemas stories
+
+Here are some short stories where Bioschemas has been succesfully used by communities to progress on making their resources more findable and reusable. 
+
+## bio.tools
+*the 04th of April 2023*
+
+[Bio.tools](http://bio.tools) is a heavily used registry cataloguing more than 24.000 bioinformatics software, services  and tools. The listings can be searched based on authors, scientific topics or type of data processing entailed, which is underpinned by the [EDAM](http://edamontology.org) ontology. By automatically transforming the database content, it has been possible to produce Schema.org annotations that are nowadays embedded into each bio.tools web page for better findability. 
+
+These annotations can be used as the source for an RDF dataset, containing 550k+ triples, and  which is continuously updated at https://github.com/bio-tools/content/blob/master/datasets/bioschemas-dump.ttl. This dataset can be queried to retrieve useful information, such as the most used licences (GPL-3, MIT), or to identify the top-3 most represented data processing steps  (Visualisation, Standardisation/normalisation, Genotyping)
+
+In addition, bio.tools metadata is further enhanced by providing embedded Bioschemas annotations, which are an opinionated view on native schema.org, but focusing domain specific properties. Thus, the bio.tools registry has made significant progress in the FAIRification of hosted resources, since bioschemas enhances compliance with many of the FAIR principles, particularly concerning metadata. This improvement can be qualified using FAIR assessment tools (F-UJI, FAIR Evaluator, FAIR-Checker). Since workflow registries such as WorkflowHub and educational portals such as TeSS are following the same semantic annotation strategies, new cross-linking and querying opportunities are under active investigation. 
+
+*Further reading: [https://github.com/bio-tools/content/blob/master/doc/bioschemas.md](https://github.com/bio-tools/content/blob/master/doc/bioschemas.md)*
+
diff --git a/pages/_groups/Beacons.md b/pages/_groups/Beacons.md
@@ -4,7 +4,7 @@ identifier: beacons
 name: Beacons
 collection: groups
 active: true
-type: generic
+type: biological
 description: Specification for Beacon Type
 lead: 
 - person: SerenaScollen

diff --git a/pages/_groups/BiologicalEntities.md b/pages/_groups/BiologicalEntities.md
@@ -4,7 +4,7 @@ identifier: biologicalentities
 name: Biological Entities
 collection: groups
 active: true
-type: generic
+type: bilogical
 description: Specification for biological entities
 lead: 
 - person: CarlosHorro

diff --git a/pages/_groups/Community.md b/pages/_groups/Community.md
@@ -3,7 +3,7 @@ layout: group-details
 identifier: community
 name: Community
 collection: groups
-active: true
+active: false
 type: other
 description: 'The objective of this workstream is to support this project and the involvement of the Bioschemas community.'
 lead: 

diff --git a/pages/_groups/Genes.md b/pages/_groups/Genes.md
@@ -4,7 +4,7 @@ identifier: genes
 name: Genes
 collection: groups
 active: true
-type: generic
+type: biological
 description: Specification for Beacon Type
 lead: 
 - person: LeylaGarcia

diff --git a/pages/_groups/LabProtocols.md b/pages/_groups/LabProtocols.md
@@ -4,7 +4,7 @@ identifier: labprotocols
 name: Laboratory Protocols
 collection: groups
 active: true
-type: generic
+type: biological
 description: Specification for biological laboratory protocol Type
 lead: 
 - person: OlgaXimenaGiraldo

diff --git a/pages/_groups/Standards.md b/pages/_groups/Standards.md
@@ -4,7 +4,7 @@ identifier: standards
 name: Standards
 collection: groups
 active: false
-type: generic
+type: other
 description: Specification for standards
 lead: 
 - person: PeterMcQuilton

diff --git a/pages/_groups/Studies.md b/pages/_groups/Studies.md
@@ -4,7 +4,7 @@ identifier: studies
 name: Studies
 collection: groups
 active: true
-type: generic
+type: biological
 description: Developing a profile and type to capture studies and their associated projects
 lead: 
 - person: To be determined

diff --git a/pages/_groups/Technical.md b/pages/_groups/Technical.md
@@ -4,8 +4,8 @@ layout: group-details
 identifier: technical
 name: Technical
 collection: groups
-active: true
-type: generic
+active: false
+type: other
 description:
 lead: 
 - person: JustinClark-Casey

diff --git a/pages/_groups/Tools.md b/pages/_groups/Tools.md
@@ -3,7 +3,7 @@ layout: group-details
 identifier: tools
 name: Tools
 collection: groups
-active: false
+active: true
 type: generic
 description: Specification for tools
 lead: 

diff --git a/pages/_groups/Validation.md b/pages/_groups/Validation.md
@@ -3,7 +3,7 @@ layout: group-details
 identifier: validation
 name: Validation
 collection: groups
-active: true
+active: false
 type: other
 description: Tools for validating markup against a specification
 lead: 

diff --git a/pages/_groups/index.html b/pages/_groups/index.html
@@ -7,15 +7,84 @@ <h1>Bioschemas Groups
 <a target="_blank" href="mailto:[email protected]?subject=[Bioschemas] request to create a new group" class="btn btn-sm btn-primary float-end" role="button">
 Propose a new group</a>
 </h1>
-<p>The following groups, responsible for creating specifications within the project, are active within the Bioschemas community:</p>
-<ul>
 {%- assign sorted_groups = site.groups | sort: 'name' %}
-{%- for group in sorted_groups %}
+
+<h2>Bioschemas life sciences groups</h2>
+
+<h3>Active life sciences groups</h3>
+<p>The following groups, responsible for creating specifications in the Life Science domain, are active within the Bioschemas community:</p>
+<ul>
+{%- assign loop_groups = sorted_groups | where: 'active', true | where: 'type', 'biological' %}
+{%- for group in loop_groups %}
+{%- if group.name %}
+    <li><a href="{{group.url | relative_url}}">{{group.name}}</a> - {{group.abstract}}</li>
+{%- endif %}
+{%- endfor %}
+</ul>
+
+{%- assign loop_groups = sorted_groups | where: 'active', false | where: 'type', 'biological' %}
+{% if loop_groups.size > 0 %}
+
+<h3>Hibernated life sciences groups</h3>
+<p>The following groups, responsible for creating specifications in the Life Science domain,  
+    are currently hibernating as there has been no activity in at least 6 months. 
+    The hibernation could correspond to a maturity reached by all of the specifications supported by 
+    the group (i.e., stable types and profiles that have not requrired updates for at least 6 months):</p>
+<ul>
+
+    {%- for group in loop_groups %}
+    {%- if group.name %}
+        <li><a href="{{group.url | relative_url}}">{{group.name}}</a> - {{group.abstract}}</li>
+    {%- endif %}
+    {%- endfor %}
+</ul>
+{% endif %}
+
+
+<h2>Cross-domain groups</h2>  
+
+<h3>Active cross-domain groups</h3>
+<p>The following groups, responsible for creating corss-domain specifications, are active within the Bioschemas community:</p>
+<ul>
+{%- assign loop_groups = sorted_groups | where: 'active', true | where: 'type', 'generic' %}
+{%- for group in loop_groups %}
 {%- if group.name %}
     <li><a href="{{group.url | relative_url}}">{{group.name}}</a> - {{group.abstract}}</li>
 {%- endif %}
 {%- endfor %}
 </ul>
+
+{%- assign loop_groups = sorted_groups | where: 'active', false | where: 'type', 'generic' %}
+{% if loop_groups.size > 0 %}
+
+<h3>Hibernated cross-domain groups</h3>
+<p>The following groups, responsible for creating corss-domain specifications, 
+    are currently hibernating as there has been no activity in at least 6 months.
+    The hibernation could correspond to a maturity reached by all of the specifications supported by 
+    the group (i.e., stable types and profiles that have not requrired updates for at least 6 months):</p>
+<ul>
+    {%- assign loop_groups = sorted_groups | where: 'active', false | where: 'type', 'generic' %}
+    {%- for group in loop_groups %}
+    {%- if group.name %}
+        <li><a href="{{group.url | relative_url}}">{{group.name}}</a> - {{group.abstract}}</li>
+    {%- endif %}
+    {%- endfor %}
+</ul>
+{% endif %}
+
+<h2>Supporting groups</h2>
+<p>These groups provided supporting functions early in the Bioschemas effort. These functions have been
+    now transitioned to the steering commitee. We keep the informatoin here for attribution and legacy
+    purposes:</p>
+    <ul>
+        {%- assign loop_groups = sorted_groups | where: 'type', 'other' %}
+        {%- for group in loop_groups %}
+        {%- if group.name %}
+            <li><a href="{{group.url | relative_url}}">{{group.name}}</a> - {{group.abstract}}</li>
+        {%- endif %}
+        {%- endfor %}
+        </ul>
+
 <a target="_blank" href="mailto:[email protected]?subject=[Bioschemas] request to create a new group" class="btn btn-sm btn-primary float-end" role="button">
-Propose a new group</a>
-<br/>
+    Propose a new group</a>
+    <br/>
diff --git a/pages/_groups/tags.md b/pages/_groups/tags.md
@@ -0,0 +1,9 @@
+Hidden page documenting the tags used to categorize groups.
+Such tags are used in the index.md to filter and create subgroups depending on their status and type
+
+Tags:
+* 'collection' = groups (always the same value)
+* 'active' = true or false (used to established the status active or hibernating)
+* 'type' = generic or biological or other (used to establish the domain)
+
+
diff --git a/pages/_news/2023-05-10-BH2022-DDE-Profiles.md b/pages/_news/2023-05-10-BH2022-DDE-Profiles.md
@@ -0,0 +1,15 @@
+---
+layout: post
+title: "BioHackathon 2022 preprint DDE & Profiles"
+tags:
+- Profile
+- Tooling
+- Community
+---
+We are pleased to announce that our preprint from [BioHackathon 2022](https://2022.biohackathon-europe.org/) is available [here](https://doi.org/10.37044/osf.io/3b9gp)
+
+Abstract:
+
+Bioschemas is a grassroots community effort to improve FAIRness of resources in the Life sciences by defining specific Life Science metadata schemas and exposing that metadata from resources that have adopted it. Now that some initial types have been adopted directly into schema.org, an improved mechanism is required to reignite community engagement and encourage profile development. The current process for creating or updating Bioschemas profiles and types is technical and convoluted which creates accessibility issues that can hamper community participation. As adoption of Bioschemas grows and more of the Life Science community considers contributing specific types and profiles, a more accessible creation/modification process is necessary to avoid a loss in engagement. To address this issue, and to drive further Bioschemas adoption, the community has exploited the Data Discovery Engine (DDE) for profile and type development. DDE provides a schema registry and user-friendly tools for creating and editing schemas. The goal of this project is to update existing Bioschemas community profiles in a targeted and crowd-sourced manner, add new profiles as required, and to ensure the documentation is fit for purpose to enable further Bioschemas contributions, at scale.
+
+This work was done in collaboration with [Scripps Institute](https://www.scripps.edu/).
diff --git a/pages/_news/2023-05-10-Schema-Playground.md b/pages/_news/2023-05-10-Schema-Playground.md
@@ -0,0 +1,22 @@
+---
+layout: post
+title: "Schema Playground publication"
+tags:
+- Profile
+- Tooling
+- Community
+---
+We are pleased to announce that the Schema Playground publication from [BMC Bioinformatics](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05258-4) is available. 
+
+Abstract:
+
+Background
+Biomedical researchers are strongly encouraged to make their research outputs more Findable, Accessible, Interoperable, and Reusable (FAIR). While many biomedical research outputs are more readily accessible through open data efforts, finding relevant outputs remains a significant challenge. Schema.org is a metadata vocabulary standardization project that enables web content creators to make their content more FAIR. Leveraging Schema.org could benefit biomedical research resource providers, but it can be challenging to apply Schema.org standards to biomedical research outputs. We created an online browser-based tool that empowers researchers and repository developers to utilize Schema.org or other biomedical schema projects.
+
+Results
+Our browser-based tool includes features which can help address many of the barriers towards Schema.org-compliance such as: The ability to easily browse for relevant Schema.org classes, the ability to extend and customize a class to be more suitable for biomedical research outputs, the ability to create data validation to ensure adherence of a research output to a customized class, and the ability to register a custom class to our schema registry enabling others to search and re-use it. We demonstrate the use of our tool with the creation of the Outbreak.info schema—a large multi-class schema for harmonizing various COVID-19 related resources.
+
+Conclusions
+We have created a browser-based tool to empower biomedical research resource providers to leverage Schema.org classes to make their research outputs more FAIR.
+
+This work was done by [Scripps Institute](https://www.scripps.edu/).
diff --git a/pages/_news/2023-05-20-ETL-Pipeline.md b/pages/_news/2023-05-20-ETL-Pipeline.md
@@ -0,0 +1,23 @@
+---
+layout: post
+title: "BioHackathon 2022 preprint ETL for Knowledge Graph"
+tags:
+- Knowledge Graph
+- JSON-LD
+- SPARQL
+- Community
+---
+We are pleased to announce, belatedly, that our preprint from [BioHackathon 2022](https://2022.biohackathon-europe.org/) is available [here](https://doi.org/10.37044/osf.io/7f95d)
+
+Abstract:
+
+Schema.org and Bioschemas are lightweight vocabularies that aim at making the contents of web pages machine-readable so that software agents can consume that content and understand it in an actionable way. Due to the time needed to process each page, extracting markup by visiting each page of a site is not practical for huge sites. This approach imposes processing requirements on the publisher and the consumer. The Schema.org community proposed a method for exchanging markup from various pages as a DataFeed published at a recognized address in February 2022. This would ease publisher and customer processing requirements and accelerate data collection. In this work, we report on the implementation of a JSON-LD consumer ETL (Extract-Transform-Load) pipeline that enables data dumps to be ingested into knowledge graphs (KG). The pipeline loads scraped JSON-LD from the three sources, converts it to RDF, applies SPARQL construct queries to map the source RDF to a unified Bioschemas-based model and stores the resulting KG as a turtle file. This work was conducted during the one-week Biohackathion Europe 2022 in Paris France, under Project 23 titled, “Publishing and Consuming Schema.org DataFeeds.”
+
+
+
+
+
+
+
+
+
diff --git a/pages/_news/2023-06-24-BioHackathon-Europe-2023.md b/pages/_news/2023-06-24-BioHackathon-Europe-2023.md
@@ -0,0 +1,19 @@
+
+---
+layout: post
+title: "Projects Accepted at BioHackathon-Europe 2023"
+tags:
+- Community
+- Event
+---
+
+We are pleased to announce that the Bioschemas community have had three projects accepted at this year's [BioHackathon-Europe event](https://biohackathon-europe.org/) beginning 30th October.
+
+The projects are:
+- [Bioschemas resource index for chem and plants](https://github.com/elixir-europe/biohackathon-projects-2023/tree/main/7)
+- [Enabling FAIR Digital Objects with RO-Crates, Signposting and Bioschemas](https://github.com/elixir-europe/biohackathon-projects-2023/tree/main/15)
+- [Improving Bioschemas creation and community adoption through process improvements and tool development, and advancing compliance to FAIR standards](https://github.com/elixir-europe/biohackathon-projects-2023/tree/main/23)
+
+These projects should give us the opportunity to engage with the wider community, target specific domains, as well as improving our tooling for users.
+
+Please come and join - virtual participation is highly encouraged! 
diff --git a/pages/_profiles/ComputationalTool/1.1-DRAFT.html b/pages/_profiles/ComputationalTool/1.1-DRAFT.html
@@ -401,21 +401,13 @@
 parent_type: SoftwareApplication
 previous_release: 1.0-RELEASE
 previous_version: ''
-redirect_from: '- "devSpecs/Tool/specification"
-
+redirect_from: 
+  - "devSpecs/Tool/specification"
   - "devSpecs/Tool/specification/"
-
   - "/devSpecs/Tool/"
-
   - "/specifications/drafts/Tool"
-
   - "/profiles/Tool/"
-
   - "/profiles/ComputationalTool/"
-
-  - "/profiles/ComputationalTool/0.5-DRAFT/"
-
-  - "/profiles/Tool/0.5-DRAFT/"'
 spec_info:
   description: The Life Science Tools specification provides a way to describe bioscience
     tools and software on the World Wide Web. It defines a set of metadata and vocabularies,

diff --git a/pages/_profiles/ComputationalWorkflow/1.1-DRAFT.html b/pages/_profiles/ComputationalWorkflow/1.1-DRAFT.html
@@ -484,7 +484,17 @@
 parent_type: ComputationalWorkflow
 previous_release: 1.0-RELEASE
 previous_version: ''
-redirect_from: '- "/profiles/Workflow/0.1-DRAFT-2019_02_08/"'
+redirect_from: 
+  - "/devSpecs/ComputationalWorkflow/specification/"
+  - "/devSpecs/ComputationalWorkflow/specification"
+  - "/devSpecs/ComputationalWorkflow/"
+  - "/devSpecs/ComputationalWorkflow"
+  - "/specifications/drafts/ComputationalWorkflow/"
+  - "/specifications/drafts/ComputationalWorkflow"
+  - "/specifications/ComputationalWorkflow/"
+  - "/specifications/ComputationalWorkflow"
+  - "/profiles/ComputationalWorkflow/"
+  - "/profiles/ComputationalWorkflow"
 spec_info:
   description: "A computational workflow consists of an orchestrated and repeatable\
     \ pattern of activity enabled by the systematic organization of resources into\

diff --git a/pages/_profiles/Dataset/1.1-DRAFT.html b/pages/_profiles/Dataset/1.1-DRAFT.html
@@ -289,7 +289,7 @@
   example: ''
   expected_types:
   - CreativeWork
-  - Trip
+  - Thing
   marginality: Optional
   property: hasPart
   type: ''