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32 changes: 26 additions & 6 deletions _data/live_deployments.json
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Expand Up @@ -1175,17 +1175,17 @@
"url": "https://massbank.eu/MassBank/",
"nodes": "DE",
"sitemap": "https://massbank.eu/MassBank/sitemapindex.xml",
"datadump": "https://msbi.ipb-halle.de/~sneumann/MassBank-2006.06.jsonld",
"datadump": "https://github.com/MassBank/MassBank-data/releases/latest/download/MassBank.json",
"profiles": [
{
"profileName": "MolecularEntity",
"conformsTo": "0.5",
"exampleURL": "https://massbank.eu/MassBank/RecordDisplay?id=LQB00001&dsn=RIKEN_IMS"
"profileName": "ChemicalSubstance",
"conformsTo": "0.4-RELEASE",
"exampleURL": "https://massbank.eu/MassBank/RecordDisplay?id=MSBNK-RIKEN_IMS-LQB00001"
},
{
"profileName": "Dataset",
"conformsTo": "0.3",
"exampleURL": "https://massbank.eu/MassBank/RecordDisplay?id=LQB00001&dsn=RIKEN_IMS"
"conformsTo": "1.0-RELEASE",
"exampleURL": "https://massbank.eu/MassBank/RecordDisplay?id=MSBNK-RIKEN_IMS-LQB00001"
}
]
},
Expand Down Expand Up @@ -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."
}
]
}
]
}
3 changes: 2 additions & 1 deletion _data/presentations.csv
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Expand Up @@ -5,4 +5,5 @@ Bioschemas for the IDP Community,AlasdairGray,https://docs.google.com/presentati
(Bio)schemas – Making (not only life science) data resources more interoperable and discoverable on the Web,AlasdairGray,https://docs.google.com/presentation/d/1TqvYpZVBvq_nhUkfzrzar6n87lDkryS-KYBf5bBH7bI/edit#slide=id.p1,2022-04_NFDI-InfraTalk,,,
Contributing to EOSC Research Graphs: the role of FAIRsharing and Bioschemas,SusannaSansone,https://docs.google.com/presentation/d/1lwm-452v-pyfd7egfmh4APbX3CHXe9xu/edit#slide=id.g12f39d505fa_0_535,2022-06_ELIXIRAllHands2022,,,
(Bio)schemas: Making data resources more Interoperable and Discoverable on the Web,AlasdairGray,https://docs.google.com/presentation/d/1MDWzlx4Mm1dpHOVnRlZcQqAIQuaOrvOfRVSLvArQBug/edit#slide=id.p1,2022-09_Ont4Chem,,,
Bioschemas: Marking up biodiversity websites to improve data discovery and web-scale integration,FranckMichel,https://docs.google.com/presentation/d/15HB6ldOSN5C_H10w9chwWyPt_CNh8AlM/edit#slide=id.p1,,,"NFDI4Biodiversity All Hands Conference, Workshop on Data Standards & Common Language",12-14 October 2022
Bioschemas: Marking up biodiversity websites to improve data discovery and web-scale integration,FranckMichel,https://docs.google.com/presentation/d/15HB6ldOSN5C_H10w9chwWyPt_CNh8AlM/edit#slide=id.p1,,,"NFDI4Biodiversity All Hands Conference, Workshop on Data Standards & Common Language",12-14 October 2022
Improving findability on chemical resources with Bioschemas,EgonWillighagen,https://doi.org/10.5281/zenodo.8369861,,https://www.acs.org/meetings/acs-meetings/fall-2023.html,"ACS Fall 2023",13-17 August 2023
4 changes: 2 additions & 2 deletions _data/type_versions.yaml
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Expand Up @@ -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"

---
22 changes: 12 additions & 10 deletions _layouts/person-details.html
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Expand Up @@ -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>

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7 changes: 1 addition & 6 deletions index.html
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Expand Up @@ -8,7 +8,7 @@
title: Bioschemas
# Community Call details
call-minutes: https://docs.google.com/document/d/1kd5F97ogdiPNhLTnkei-RVR8TC8Ohpc5QSPX3KsfDrk
call-date: 2023-06-26T15:00UTC
call-date: 2023-09-25T15:00UTC
---
<div id="landing" itemscope itemtype="http://schema.org/Organization">
<meta itemprop="logo" content="http://bioschemas.org/assets/img/square_logo2.png"/>
Expand Down Expand Up @@ -131,11 +131,6 @@ <h3>Latest Presentation</h3>
</div>
<small>See more <a href="{{ '/about/publications' | relative_url }}">presentations and publications</a>.</small>
</section>
<hr>
<section>
<a class="twitter-timeline" data-height="450" data-theme="light" data-chrome="noborders"data-link-color="#2BB673" href="https://twitter.com/Bioschemas?ref_src=twsrc%5Etfw">Tweets by Bioschemas</a>
<script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
</section>
</div>
</div>
</div>
2 changes: 1 addition & 1 deletion pages/_developer/liveDeploys.html
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Expand Up @@ -13,7 +13,7 @@
<!-- This count is used to provide a unique ID -->
{%- assign count = 0 %}
<h1>{{ page.title }}</h1>
<p>Below we list the sites that use <a href="/">Bioschemas</a> markup to describe what they are offering. We provide a direct link to the site, an example deployment page, a link to test the markup syntax using the Schema.org Markup Validation tool (<a href="https://validator.schema.org/">SMV</a>), and also a link to the results of using the Bioschemas Markup Scraper and Extractor tool (<a href="https://github.com/HW-SWeL/BMUSE">BMUSE</a>). The links to the Schema.org Markup Validation tool and BMUSE show one example page from the site; however, many more may exist.</p>
<p>Below we list the sites that use <a href="/">Bioschemas</a> markup to describe what they are offering. We provide a direct link to the site, an example deployment page and a link to test the markup syntax using the Schema.org Markup Validation tool (<a href="https://validator.schema.org/">SMV</a>).</p>

<p>Note that when using the Schema.org Markup Validator, you may encounter some error warnings for types and properties. These should correspond to the types and properties that are being proposed by Bioschemas as extensions to the Schema.org vocabulary.</p>

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44 changes: 44 additions & 0 deletions pages/_groups/MachineLearning.md
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---
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>
18 changes: 16 additions & 2 deletions pages/_groups/Tools.md
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Expand Up @@ -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
Expand All @@ -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:
Expand All @@ -28,6 +31,11 @@ specifications:


members:
- JoseMFernandez
- AllegraVia
- DimitriosBampakalis
- OlgaXimenaGiraldo
- DietrichRebholzSchuhmann
- GiuseppeProfiti
- NiallBeard
- PhilippeRocca-Serra
Expand Down Expand Up @@ -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>
9 changes: 9 additions & 0 deletions pages/_people/AllegraVia.md
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---
layout: person-details
id: AllegraVia
first-name: Allegra
last-name: Via
collection: people
affiliation:
orcid: 0000-0002-3398-5462
---
2 changes: 0 additions & 2 deletions pages/_people/ChrisChild.md
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Expand Up @@ -5,7 +5,5 @@ first-name: Chris
last-name: Child
collection: people
affiliation: The University of Manchester
homepage: https://hardcopy.dev/
github_username: christopherchild
orcid: 0000-0003-0758-6908
---
11 changes: 11 additions & 0 deletions pages/_people/DanSKatz.md
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---
layout: person-details
id: DanSKatz
first-name: Daniel S.
last-name: Katz
collection: people
affiliation:
homepage:
github_username:
orcid: 0000-0001-5934-7525
---
9 changes: 9 additions & 0 deletions pages/_people/DimitriosBampalikis.md
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---
layout: person-details
id: DimitriosBampalikis
first-name: Dimitrios
last-name: Bampalikis
collection: people
affiliation:
orcid:
---
9 changes: 9 additions & 0 deletions pages/_people/EvaMartin.md
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---
layout: person-details
id: EvaMartin
first-name: Eva
last-name: Martin del Pico
collection: people
affiliation:
orcid: 0000-0001-8324-2897
---
11 changes: 11 additions & 0 deletions pages/_people/FotisPsomopoulos.md
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---
layout: person-details
id: FotisPsomopoulos
first-name: Fotis E.
last-name: Psomopoulos
collection: people
affiliation:
homepage:
github_username: fpsom
orcid: 0000-0002-0222-4273
---
2 changes: 1 addition & 1 deletion pages/_profiles/Dataset/1.0-RELEASE.html
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Expand Up @@ -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:
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4 changes: 2 additions & 2 deletions pages/_profiles/TrainingMaterial/1.1-DRAFT.html
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Expand Up @@ -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
Expand Down Expand Up @@ -452,4 +452,4 @@
spec_type: Profile
status: revision
use_cases_url: /useCases/TrainingMaterial
---
---
2 changes: 1 addition & 1 deletion pages/_tutorials/what_why_bioschemas.md
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Expand Up @@ -49,7 +49,7 @@ Using schema.org markup on web pages enables the generation of 'info box' summar

Imagine an insulin summary appearing within search results, but rather than pointing to Wikipedia, that summary would direct one to specialized resources such as Orphanet or CATH as seen in Figure 1. In this way you would get a quick overview while also being provided links to relevant resources, all in one search.

{% include image.html file="/tutorials/images/ilustration_life_sciences_event.png" caption="Figure 1. Insulin summary on a search engine" alt="Insulin summary on a search engine" %}
{% include image.html file="/tutorials/images/insulin.png" caption="Figure 1. Insulin summary on a search engine" alt="Insulin summary on a search engine" %}


## 2. What are the benefits of Bioschemas?
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