Merge branch 'master' into update_commcall_date

_data/live_deployments.json

@@ -1728,6 +1728,26 @@
           "highlight": "Over 1,500 ontologies, controlled vocabularies, and resources including their preferred prefix, name, description, homepage, mappings to other registries, and more."
         }
       ]
+    },
+    {
+      "name": "Metabolic Atlas",
+      "description": "A web platform integrating open-source genome scale metabolic models (GEMs) for easy browsing and analysis. ",
+      "url": "https://metabolicatlas.org",
+      "nodes": ["SE"],
+      "profiles": [
+        {
+          "profileName": "MolecularEntity",
+          "conformsTo": "0.5-RELEASE",
+          "exampleURL": "https://metabolicatlas.org/explore/Human-GEM/gem-browser/metabolite/MAM00217c",
+          "highlight": "Over 3'000 metabolites."
+        },
+        {
+          "profileName": "Gene",
+          "conformsTo": "1.0-RELEASE",
+          "exampleURL": "https://metabolicatlas.org/explore/Human-GEM/gem-browser/gene/ENSG00000078237",
+          "highlight": "Over 15'000 genes from multiple organisms."
+        }
+      ]
     }
   ]
 }

_data/type_versions.yaml

@@ -124,13 +124,13 @@ Study:
 Taxon:
     name: "Taxon"
     latest_publication: "0.4-DRAFT"
-    latest_release: "0.3-RELEASE-2019_11_18"
+    latest_release: "1.0-RELEASE"
     status: "active"
 
 TaxonName:
     name: "TaxonName"
     latest_publication: "0.1-DRAFT"
-    latest_release:
+    latest_release: "1.0-RELEASE"
     status: "active"
 
 ---

_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>

_layouts/person-details.html

@@ -24,16 +24,18 @@ <h3>Groups</h3>
 
 <ul>
   {% for group in site.groups %}
-  {% if group.lead contains person-id %}
-  <li>
-    <a href="{{group.url}}">{{group.name}}</p>
-  </li>
-  {% endif %}
-  {% if group.members contains person-id %}
-  <li>
-    <a href="{{group.url}}">{{group.name}}</p>
-  </li>
-  {% endif %}
+    {% for leader in group.lead %}
+      {% if leader.person == person-id %}
+      <li>
+        <a href="{{group.url}}">{{group.name}}</p>
+      </li>
+      {% endif %}
+    {% endfor %}
+    {% if group.members contains person-id %}
+      <li>
+        <a href="{{group.url}}">{{group.name}}</p>
+      </li>
+    {% endif %}
   {% endfor %}
 </ul>
 

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)*
+

pages/_groups/MachineLearning.md

@@ -0,0 +1,44 @@
+---
+layout: group-details
+identifier: machinelearning
+name: Machine Learning
+collection: groups
+active: true
+type: generic
+description: Specification for digital objects commonly used in machine learning solutions.
+lead: 
+  - person: LeylaGarcia
+  - person: FotisPsomopoulos
+  - person: DanSKatz
+email: [email protected]
+issues: https://github.com/BioSchemas/specifications/labels/group%3AMachineLearning
+folder: https://drive.google.com/drive/folders/1NGiDfc6WSCJNDheGhYApfEVN3-X6Uj6z?usp=sharing
+
+# Page attributes
+abstract: 'Machine Learning combines data, software, models and workflows. There is a need to harmonize and connect those different elements to have a full picture of a Machine Learning approach from the metadata perspective.'
+objectives:
+  [
+    'Describe training datasets including characterization of features and attributes that can be used for training (e.g., number of data points, classes, target variable).',
+    'Describe software used for training purposes including elements related to the optimization process.',
+    'Describe ML models together with their evaluation.',
+    'Describe links among the different elements involved in ML approaches clearly and explicitly.'
+  ]
+
+specifications:
+  [
+    'Dataset', 'ComputationalTool'
+  ]
+
+
+members:
+- AlbanGaignard
+- DietrichRebholzSchuhmann
+- IvanMicetic
+
+---
+
+<h2>Further Details</h2>
+
+<p>Machine Learning (ML) is nowadays a common path in data-driven research due to the amount of available data and the resources needed to process it and make sense out of it. In addition to data, software also plays and important role in ML. Models produced by an ML training process also become a thing on their own, a thing that could be seen as similar to software (e.g., prediction model that can be executed with some input and produce a prediction as output) or to data (e.g., clusters emerged from a clustering approach). Furthermore, the training software has to be tuned and optimized while the model has to be evaluted, either intrinsic or extrinsically. Ideally, all of this information should be reported and represented as metadata of the ML process. However, this is not always the case. This group, a joint effort across <a href="https://www.rd-alliance.org/groups/fair-machine-learning-fair4ml-ig" target="_blank">Research Data Alliance FAIR4ML Interest Group</a>, <a href="https://elixir-europe.org/focus-groups/machine-learning" target="_blank">ELIXIR Machine Learning Focus Group</a> and <a href="https://www.nfdi4datascience.de/" target="_blank">NFDI4DataScience</a>, aims at providing a common ground for the metadata necessary to describe ML approaches. </p>
+
+<p>To achieve its objectives, this group is using as a starting point <a href="https://research.google/pubs/pub48120/" target="_blank">Machine Learning Cards for models and datasets</a>. Other efforst will also be taken into account, e.g., <a href="https://www.nature.com/articles/s41592-021-01205-4" target="_blank">Data, Optimization, Model and Evaluation (DOME) recommendations</a>, <a href="https://doi.org/10.1038/s41592-021-01241-0" target="_blank">AIMe registry for artificial intelligence in biomedical research</a> and <a href="https://huggingface.co/" target="_blank">HuggingFace</a>.</p>

pages/_groups/Tools.md

@@ -5,8 +5,10 @@ name: Tools
 collection: groups
 active: true
 type: generic
-description: Specification for tools
+description: Specification for computational tools, e.g., software applications, software releases and software source code
 lead: 
+- person: FotisPsomopoulos
+- person: EvaMartin
 - person: RicardoArcila
 - person: JustinClark-Casey
 - person: LeylaGarcia
@@ -18,7 +20,8 @@ folder: https://drive.google.com/open?id=0BzDhyOWTnRNTYkdQNHppUjZ3U2M
 abstract: 'The Tools Group develops and maintains a community specification for describing life science tools.'
 objectives:
   [
-    'This group investigates the required extensions to <a href="http://schema.org">schema.org</a> to support such use case.'
+    'This group investigates the required extensions to <a href="http://schema.org">schema.org</a> to support the description of software tools, applications, releases and source code.',
+    'A specific use case is supporting machine-actionable Software Management Plans (maSMPS)'
   ]
 
 specifications:
@@ -28,6 +31,11 @@ specifications:
 
 
 members:
+    - JoseMFernandez
+    - AllegraVia
+    - DimitriosBampakalis
+    - OlgaXimenaGiraldo
+    - DietrichRebholzSchuhmann
     - GiuseppeProfiti
     - NiallBeard
     - PhilippeRocca-Serra
@@ -55,3 +63,9 @@ members:
     - StianSoiland-Reyes
     - SaharFrikha
 ---
+
+<h2>Further Details</h2>
+
+<p>Research software is a fundamental element in research. Research software recognition and citation, together with software management plans will improve reproducibility in science.</p>
+
+<p>For the specific use case around machine-actionable software management plans, this group has taken as a starting point the <a href="https://doi.org/10.4126/FRL01-006444988" target="_blank">metadata schemas</a> produced as part of the maSMPs project lead by the Semantic Technologies group at <a href="https://www.zbmed.de/en" target="_blank">ZB MED</a>, with funding from RDA/EOSC-Future horizon 2020 Framework Programme (no. 101017536) and Deutsche Forschungsgemeinschaft DFG (project no. 460234259 corresponding to the <a href="https://www.nfdi4datascience.de/" target="_blank">NFDI4DataScience consortium</a>). Such metadata schemas were created taking as basis the <a href="https://doi.org/10.37044/osf.io/k8znb" target="_blank">ELIXIR SMPs</a> created by the <a href="https://elixir-europe.org/platforms/tools/software-best-practices" target="_blank">ELIXIR Software Best Practices group</a>, and later aligned to other related efforts (e.g., <a href="https://rdm.mpdl.mpg.de/2022/12/09/smp-template-available/" target="_blank">SMPs in RDMO</a>, <a href="https://doi.org/10.5281/zenodo.7589725" target="_blank">SMPs by eScience Center Netherlands</a>). The maSMPs also take into account the <a href="https://github.com/RDA-DMP-Common/RDA-DMP-Common-Standard" target="_blank">maDMPs</a> produced by the <a href="https://www.rd-alliance.org/groups/dmp-common-standards-wg" target="_blank">RDA-DMP-Common-Standard</a>.</p>

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! 

pages/_people/AllegraVia.md

@@ -0,0 +1,9 @@
+---
+layout: person-details
+id: AllegraVia
+first-name: Allegra
+last-name: Via
+collection: people
+affiliation: 
+orcid: 0000-0002-3398-5462
+---

pages/_people/DanSKatz.md

@@ -0,0 +1,11 @@
+---
+layout: person-details
+id: DanSKatz
+first-name: Daniel S.
+last-name: Katz
+collection: people
+affiliation:
+homepage:
+github_username: 
+orcid: 0000-0001-5934-7525
+---

pages/_people/DimitriosBampalikis.md

@@ -0,0 +1,9 @@
+---
+layout: person-details
+id: DimitriosBampalikis
+first-name: Dimitrios
+last-name: Bampalikis
+collection: people
+affiliation: 
+orcid: 
+---

pages/_people/EvaMartin.md

@@ -0,0 +1,9 @@
+---
+layout: person-details
+id: EvaMartin
+first-name: Eva
+last-name: Martin del Pico
+collection: people
+affiliation: 
+orcid: 0000-0001-8324-2897
+---

pages/_people/FotisPsomopoulos.md

@@ -0,0 +1,11 @@
+---
+layout: person-details
+id: FotisPsomopoulos
+first-name: Fotis E.
+last-name: Psomopoulos
+collection: people
+affiliation:
+homepage:
+github_username: fpsom
+orcid: 0000-0002-0222-4273
+---

pages/_profiles/Dataset/1.0-RELEASE.html

@@ -49,7 +49,7 @@
      "alternateName": "MetaboLights dataset",
       "alternateName": "Automated Label-free Quantification of Metabolites from Liquid Chromatography",
       "alternateName": "Mass Spectrometry Data (Plasma) Automated Label-free Quantification of Metabolites from Liquid Chromatography",
-      "alternateName": “Mass Spectrometry Data (Plasma)"
+      "alternateName": "Mass Spectrometry Data (Plasma)"
     }
 - property: citation
   expected_types:

pages/_profiles/TrainingMaterial/1.1-DRAFT.html

@@ -253,7 +253,7 @@
 - bsc_description: ''
   cardinality: MANY
   controlled_vocab: ''
-  description: URL of additional sources for the dataset
+  description: URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.
   example: ''
   expected_types:
   - URL
@@ -452,4 +452,4 @@
 spec_type: Profile
 status: revision
 use_cases_url: /useCases/TrainingMaterial
----
+---