Output from the Common Language Task Force

This webpage includes the glossary of the terms that are relevant to the VHP4Safety Project.

The (current development version of) the glossary can be found here. The OWL version is also available.

Metadata

This work is licensed under the CC-BY 4.0 International.

New content?

To make new entry queries, please create an issue here using the issue template. Experienced GitHub users are encouraged to submit pull requests adding new terms to the template.tsv tables.

For other issues, suggestions, or problems, please create an issue here.

Data format

The Glossary is mainly presented under https://glossary.vhp4safety.nl/ in the HTML rendering of a Markdown file with HTML bits and RDFa annotation.

New terms are added under the adequate template in /templates, and the Markdown gets updated automatically via a GitHub action.

The Glossary terms are listed in a set of HTML tables, where each row describes a single term. Here, we take advantage of the HTML+RDFa standard, and embed the OWL data. Because OWL is just RDF, we effectively specify RDF triples:

<tr about="https://vhp4safety.github.io/glossary#VHP0000086" typeof="owl:Class">
  <td property="rdfs:label">Task Force</td>
  <td property="ncit:C42610">TF</td>
  <td property="dc:description">Cross work package effort to reach some goal.</td>
</tr>

RDFa uses the HTML attribute about to specify of the subject and the property attribute to specify the predicate. The object can be specified in different ways, and the above example shows how the Literal is given.

Adding new sections

To add any new section or edit the text in index.md, we won't use the actual index.md but add a new template under .github/index.md. After adding the table with the right columns:

• Go to .github/index.md and add the section header and placeholder (see below):

  glossary/.github/index.md

  Lines 26 to 28 in 43df600

  	## Chemicals
  	${chemicals}

• Go to the script and add the {placeholder, filename} key-value pair (e.g., {'chemicals', 'chemicals.tsv',}:

  glossary/templateToMarkdown.py

  Lines 23 to 32 in 43df600

  	sections = {
  	"toxicology": "toxicology.tsv",
  	"risk_assessment": "risk_assessment.tsv",
  	"adverse-outcome": "adverse_outcome.tsv",
  	"server": "server.tsv",
  	"tools": "tools.tsv",
  	"projects": "projects.tsv",
  	"organizations": "organizations.tsv",
  	"chemicals": "chemicals.tsv",
  	}

Extract OWL triples

With the extractOWL.groovy tool this can be extracted into a stand-alone OWL files (in Notation3) with:

groovy extractOWL.groovy > glossary.owl

This is done by a GitHub Action.

Funding

VHP4Safety – the Virtual Human Platform for safety assessment project NWA 1292.19.272 is part of the NWA research program ‘Research along Routes by Consortia (ORC)’, which is funded by the Netherlands Organization for Scientific Research (NWO). The project started on June 1, 2021 with a budget of over 10 million Euros and will last for the duration of 5 years.