Toxicology data management tutorials automatically collected by European training portal TeSS

A team including Egon Willighagen from Maastricht University, Niall Beard from ELIXIR’s TeSS team, and Oana Florean from Douglas Connect (coordinator of OpenRiskNet) has used BioSchemas to create a system that automatically pulls toxicology-related training materials from the eNanoMapper project into the European training portal TeSS.

TeSS is ELIXIR’s training portal. It provides trainers and trainees with training materials, events and interactive tutorials in the field of life sciences. Egon Willighagen: “The toxicology training materials that we have now added to TeSS originate from the eNanoMapper project. This FP7 project developed a computational infrastructure for toxicology data management of engineered nanomaterials. Within eNanoMapper, we developed many tutorials. In the beginning, we put these online in Microsoft Word format. At a certain point, our Programme Technical Officer Cedric Notredame from Spain pushed us to make the training resources available in a more sustainable, machine-readable format. However, we did not have enough time to do this within the eNanoMapper project.”

Machine-readable
Willighagen continues: “Now, we have started two new European toxicology projects (OpenRiskNet and NanoCommons). In addition, we are developing a proposal for an ELIXIR Toxicology Community. So, I really wanted to make the tutorials available to a larger audience. I asked on Twitter if people knew how to use BioSchemas to this end. Niall Beard from ELIXIR’s TeSS team replied that he had some ideas. That same afternoon, he sent me a pull request on Github with BioSchemas annotations.”

The TeSS team can write scripts (‘scrapers’) to automatically register resources from target websites such as the eNanoMapper website. The scrapers run each night, adding new resources to TeSS or updating any that have changed. The team can create a scraper as long as the target site contains structured data. “So, we used Bioschemas to structure the data about the tutorials,” says Willighagen.

Bioschemas
Bioschemas encourages people to use schema.org to structure the information on their websites. Schema.org provides an extensive library of simple, lightweight schemas that webmasters can use to explicitly define their website content in order to improve search engine visibility and interoperability. It describes ‘types’ of information, which then have ‘properties’. For instance, ‘Event’ is a type that has properties like ‘startDate’, ‘endDate’ and ‘description’. The Bioschemas community has created schema.org extensions with life science-specific vocabularies, which add additional fields relevant to the life sciences. This all makes it easier to discover, collate and analyse distributed data.

Willighagen: “Niall, Oana, and me have now converted several eNanoMapper tutorials into the Markdown format with BioSchemas annotations. We also installed a sitemap.xml that allows us to select which tutorials we want TeSS to update automatically. Niall has created a TeSS script that regularly checks for changes. The result can be found here: https://tess.elixir-europe.org/content_providers/enanomapper .” Niall Beard adds: “I would like to invite people to contact us if they would like their training events or materials to be included in the TeSS portal. We can then discuss a similar automatic solution. You may also want to have a look at the TeSS help pages.”

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