# Making Bioinformatics Training Events and Material More Discoverable Using TeSS, the ELIXIR Training Portal

Finn Bacall, Aitor Apaolaza, Munazah Andrabi, Chris Child, Carole Goble, Olivier Sand, Alexander Botzki

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To cite this version:

Finn Bacall, Aitor Apaolaza, Munazah Andrabi, Chris Child, Carole Goble, et al. Making Bioinformatics Training Events and Material More Discoverable Using TeSS, the ELIXIR Training Portal. Current Protocols, 2023, 3 (2), pp.e682. 10.1002/cpz1.682. hal-05130610

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# Making Bioinformatics Training Events and Material More Discoverable Using TeSS, the ELIXIR Training Portal

Finn Bacall,<sup>1,2</sup> Aitor Apaolaza,<sup>1,2</sup> Munazah Andrabi,<sup>1,2</sup> Chris Child,<sup>1,2</sup> Carole Goble,<sup>1,2</sup> Olivier Sand,<sup>3,4,7</sup> and Alexander Botzki<sup>5,6,7</sup>

Published in the Bioinformatics section

Many trainers and organizations are passionate about sharing their training material. Sharing training material has several benefits, such as providing a record of recognition as an author, offering inspiration to other trainers, enabling researchers to discover training resources for their personal learning path, and improving the training resource landscape using data-driven gap analysis from the bioinformatics community. In this article, we present a series of protocols for using the ELIXIR online training registry Training eSupport System (TeSS). TeSS provides a one-stop shop for trainers and trainees to discover online information and content, including training materials, events, and interactive tutorials. For trainees, we provide protocols for registering and logging in and for searching and filtering content. For trainers and organizations, we also show how to manually or automatically register training events and materials. Following these protocols will contribute to promoting training events and add to a growing catalog of materials. This will concomitantly increase the FAIRness of training materials and events. Training registries like TeSS use a scraping mechanism to aggregate training resources from many providers when they have been annotated using Bioschemas specifications. Finally, we describe how to enrich training resources to allow for more efficient sharing of the structured metadata, such as prerequisites, target audience, and learning outcomes using Bioschemas specification. As increasing training events and material are aggregated in TeSS, searching the registry for specific events and materials becomes crucial. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.

**Basic Protocol 1:** Searching for training events and materials in TeSS

**Support Protocol:** Integrating TeSS widgets on your website

**Basic Protocol 2:** Logging in to TeSS using an institutional account

**Alternate Protocol:** Creating and logging in to a TeSS account

**Basic Protocol 3:** Manual registration of training events in TeSS

**Basic Protocol 4:** Manual registration of training materials in TeSS

**Basic Protocol 5:** Registration of a content provider in TeSS

**Basic Protocol 6:** Automated harvesting of training events and materials in TeSS

**Keywords:** bioinformatics training • Bioschemas annotation • TeSS • training catalog • training event • training material

<footnote n="1"><sup>1</sup>Department of Computer Science, University of Manchester, Manchester, United Kingdom</footnote>

<footnote n="2"><sup>2</sup>ELIXIR-UK, Norwich, United Kingdom</footnote>

<footnote n="3"><sup>3</sup>Institut Français de Bioinformatique, Villeneuve d'Ascq, France</footnote>

<footnote n="4"><sup>4</sup>ELIXIR-FR, Institut Français de Bioinformatique, Évry, France</footnote>

<footnote n="5"><sup>5</sup>VIB Technology Training, Vlaams Instituut voor Biotechnologie, Ghent, Belgium</footnote>

<footnote n="6"><sup>6</sup>ELIXIR-BE, VIB, Ghent, Belgium</footnote>

<footnote n="7"><sup>7</sup>Corresponding authors: olivier.sand@cnrs.fr; alexander botzki@vib.be</footnote>
**How to cite this article:**

Bacall, F., Apaolaza, A., Andrabi, M., Child, C., Goble, C., Sand, O., & Botzki, A. (2023). Making bioinformatics training events and material more discoverable using TeSS, the ELIXIR training portal.

*Current Protocols*, 3, e682. doi: 10.1002/cpz1.682

INTRODUCTION

The Training eSupport System (TeSS) is an ELIXIR online training registry (Beard et al., 2020) that provides a one-stop shop for trainers and mostly (but not only) graduate-level trainees to discover online information and content, including training materials, events, and interactive tutorials. TeSS provides opportunities to promote training events and news and to contribute to a growing catalog of materials. For trainers, the portal offers an environment for sharing materials and event information; for trainees, it offers a convenient gateway to identify relevant training events and resources. Thanks to our search-engine optimization and widgets, registering an event on TeSS will allow it to appear in more searches and be seen across all websites that display site resources.

The ELIXIR training platform promotes sharing of training materials and exchange of training best practices. Many trainers are passionate about providing open-access training material. Such sharing has several benefits, including providing a record of recognition as an author, offering inspiration to other trainers, enabling researchers to discover training resources for their personal learning path, and improving the training resource landscape using data-driven gap analysis from the bioinformatics community (Garcia et al., 2020).

Now that you are convinced you should register your events and training materials in TeSS, let's see how it is done. Registration can be performed manually or automatically. In either case, it is important to describe and annotate training resources using relevant keywords from controlled vocabularies, taxonomies, thesauruses, or ontologies. This reduces ambiguity and facilitates discovery and retrieval of information by improving the efficacy of metadata filtering. An example ontology is EDAM (Ison et al., 2013), which includes terms for data types, data identifiers, data formats, operations, and topics. Other ontologies can be found in resources like FAIRsharing (Sansone et al., 2019), the Ontology Lookup Service (Jupp et al., 2015), or BioPortal (Whetzel et al., 2011).

The preferred and hence primary mechanism for collecting training metadata in TeSS is to collect data from content providers automatically. This involves the use of a “scraper” that extracts information from a variety of trusted websites. In this case, describing digital objects with structured metadata is fundamental (not to mention that it will also make them FAIR). Regardless of the type of object, adding appropriate standardized metadata will help make it both machine- and human-readable.

What is the most recommended mechanism to increase the FAIRness of training events announcements and training materials? By using metadata schemas for structured data from the collaborative project Schema.org, adding structured metadata to web pages has been greatly facilitated (Guha, Brickley, & MacBeth, 2015). The community has developed annotation schemas for a vast variety of data types, including creative works, non-text objects, organizations, and products, all described by extensive lists of properties such as author, audience, and context. Search engines like Google crawl the internet to index those annotated websites and provide snippets of information via linked data objects. To make life science resources more discoverable, the Bioschemas community initiative (Gray, Goble, & Jiménez, 2017) builds upon the foundation of the Schema.org
standard. For automatic registration of training resources, the recently released and first official version of the specifications for Course (a training course), CourseInstance (an event of said training course), and TrainingMaterial (Castro et al., 2022) are used in the automatic collection of structured metadata. Those three standards are community-endorsed, which facilitates a broader and more homogeneous adoption of the standard through life sciences content providers. The Bioschemas specification offers guidance to content providers on how to enrich their training resources to allow for more efficient sharing of structured metadata like prerequisites, target audience, and learning outcomes. Training registries like TeSS use a scraping mechanism to aggregate training resources from many providers when they have been annotated using Bioschemas specifications.

In this article, we describe how to search for specific training events and material in TeSS (Basic Protocol 1 and Support Protocol), gain access to TeSS (Basic Protocol 2 and Alternate Protocol), manually and automatically register training events and materials (Basic Protocols 3, 4, and 6), and register a content provider (Basic Protocol 5).

## SEARCHING FOR TRAINING EVENTS AND MATERIALS IN TeSS

Training resources (both events and materials) may be searched in TeSS in several ways. A general search can be performed based on keywords, which will return separate lists of events and materials. Alternatively, events or materials can be searched for independently of each other. The second approach allows more precise filtering on several parameters (e.g., event type, country, and target audience) alone or in combination. In this protocol, we provide examples of searches for specific events or materials.

### Necessary Resources

- Desktop or a laptop computer or a mobile device with fast Internet connection

- Up-to-date web browser such as Google Chrome, Mozilla Firefox, Apple Safari, or Microsoft Edge

### Search for specific events

1a. Select “Events” in the top menu.

2a. Enter “Single-cell” as the keyword in the search text box and click on the magnifier icon.

3a. In the side menu, scroll down to the “Country” facet. Select “United Kingdom”.

4a. In the side menu, scroll to the “Target audience” facet. Select “Graduate students”.

*The result is a list of training events about single-cell data analysis available in the United Kingdom for graduate students.*

### Search for specific materials

1b. Select “Materials” in the top menu.

2b. Enter a keyword in the search text box. We will enter “Data retrieval”.

3b. In the side menu, select a difficulty level. We will select “Beginner”.

4b. Scroll to the “Resource type” facet and select “e-learning”.

*The result is a list of training materials about data retrieval intended for a beginner level audience and tagged as e-learning material.*

*Whether searching for event or materials, any of the filters can be removed at any time to reduce the stringency of the search. Past events can also be included by clicking the “Show past events” button.*
5. Remove the term “Python” from the general search.

The table should now be updated with all upcoming courses from Belgium and the United Kingdom. By adapting other facets such as “Scientific Topics” and “Target audience”, other filtering schemes can be established.

## LOGGING IN TO TeSS USING AN INSTITUTIONAL ACCOUNT

In order to be able to register resources in TeSS, you need to log in to the registry. The following steps are specific for the login procedure using a Life Science RI account. Alternatively, you can use another existing account like Google, Apple, or ORCID. In this case, you will be redirected to the respective login portal, but we cannot provide a detailed procedure for all the federated authentication mechanisms involved.

### Necessary Resources

- Desktop or a laptop computer or a mobile device with fast Internet connection

- Up-to-date web browser such as Google Chrome, Mozilla Firefox, Apple Safari, or Microsoft Edge

- Access to an email account

1. Open your browser and go to https://tess.elixir-europe.org/.

<figure><img src="image_3.png" /><figcaption>**Figure 1** Screenshot of the Life Science RI login portal.</figcaption></figure>
<figure><img src="image_4.png" /><figcaption>**Figure 2** Screenshot of the TeSS training portal welcome page.</figcaption></figure>

2. Click the “Log In” dropdown button on the top-right corner of the page.

3. Choose “Log in with LS Login” from the dropdown menu.

*This will redirect you to the Life Science RI authentication page (Fig. 1).*

4. Start typing the name of your institution (e.g., “CNRS”) into the text box, choose the appropriate option when it appears, and proceed with your usual institutional login procedure.

*You should be taken to the TeSS homepage. In the top-right corner of the page you should see your username (Fig. 2), which you can click to view and edit your TeSS profile. You will also see a button to log out of TeSS.*

ALTERNATE
PROTOCOL

## CREATING AND LOGGING IN TO A TeSS ACCOUNT

In order to register resources in TeSS as a unaffiliated provider, you can create a local account that will allow you to log in to the registry. The following steps show how this is done.

### Necessary Resources

- Desktop or a laptop computer or a mobile device with fast Internet connection

- Up-to-date web browser such as Google Chrome, Mozilla Firefox, Apple Safari, or Microsoft Edge

- Access to an email account

1. Open your browser and go to https://tess.elixir-europe.org/.

2. Click the “Log In” dropdown button on the top-right corner of the page.

3. Click the “Register” option.

4. Fill out the username, email, and password fields, complete the captcha if present, and click the data processing consent checkbox after reading the privacy policy.

5. Wait for a confirmation email to arrive, then click the “Confirm my account” link.

*You should be taken to the TeSS homepage (Fig. 2) with a message stating “Your email address has been successfully confirmed”.*
6. Click the “Log In” dropdown button on the top-right corner of the page and then choose the “Login” option.

7. Fill out your username (or email address) and password, then click the “Log in” button.

*You should be taken to the TeSS homepage. In the top-right corner of the page you should see your username (Fig. 2), which you can click to view and edit your TeSS profile. You will also see a button to log out of TeSS.*

# MANUAL REGISTRATION OF TRAINING EVENTS IN TeSS

An event in TeSS is a link to a single training event sourced by a provider along with a description and related meta information (e.g., date, location, audience, ontological categorization, keywords). Training events can be added manually or harvested automatically from a provider's website. Here is the procedure to register training events manually.

## Necessary Resources

Desktop or a laptop computer or a mobile device with fast Internet connection

Up-to-date web browser such as Google Chrome, Mozilla Firefox, Apple Safari, or Microsoft Edge

1. Log in to TeSS at https://tess.elixir-europe.org.

2. Click on the “Events” menu.

3. Click on “Register event” to be directed to the form.

*As an example, we use an RNAseq training event in all of the following steps.*

4. In the “Type” field, select “Face-to-face” for a face-to-face event.

*If your event is online, choose the option “Online” to modify the form for that type of event (for instance, no address field is needed).*

5. In the “Title” field, enter the title of the event: “Bulk RNASeq: from counts to differential expression”.

6. In the optional “Subtitle” field, enter any additional information for the event, such as “Spring edition” for a regularly repeated course.

7. In the “URL” field, enter the URL where the announcement and registration for the event can be found: “https://training.vib.be/all-trainings/bulk-rnaseq-counts-differential-expression-2”.

8. In the “Description” field, provide general information and relevant context about the event in the form of short text:

> “The course consists of introductory online material on producing count matrices and two face-to-face sessions on differential expression analysis in R and all the questions that arise when trying the analysis on your own data.”

*This field supports markdown syntax.*

9. Specify the start date and door time of the event in the “Start” field via the pop-up “Date and Time Picker” (in our case, 29 September, 2022).

10. Specify the end date in the “End” field via the pop-up Date and Time Picker (4 October, 2022).

11. In the “Timezone” field, choose the time zone of the location where the event will occur: “(GMT:+01:00) Amsterdam” for our event in Leuven, Belgium.

BASIC
PROTOCOL 3
12. In the “Duration” field, indicate how long the event will last in hours, days, or whatever applies best. In our example: “2 days”.

13. In the “Prerequisites” field, enter the necessary prerequisites for the training event:
“Background knowledge of NGS data formats and the first steps in the analysis workflow (fastqc -> bam files). If you are a newbie in the field, you have to follow the NGS introduction training first. Experience in R programming is highly recommended. If you never worked with R, you should attend the R introduction training first.”

This field supports markdown syntax.

14. In the “Learning objectives” field, list the learning objectives of the event, such as:
* Learn how RNA-seq reads are converted into counts
* Understand QC steps that can be performed on RNA-seq reads
* Generate interactive reports to summarize QC information with MultiQC
* Use the Galaxy Rule-based Uploader to import FASTQs from URLs
* Create a Galaxy Workflow that converts RNA-seq reads into counts

We recommend applying the Bloom hierarchy of cognitive skills to formulate the learning objectives. For more detailed information about our pedagogical model, please browse the course material of the ELIXIR Train the Trainer course at https://github.com/TrainTheTrainer/ELIXIR-EXCELERATE-TiT.

This field supports markdown syntax.

15. In the “Address” and related fields, start to type the address. Once you select an address, the Google maps view will be shown and the fields Venue, City, Region, Country, and Postcode will be filled in automatically. For our example:

<table><tr><td>Address:</td><td>Herestraat 49</td></tr><tr><td>Venue:</td><td>Campus Gasthuisberg</td></tr><tr><td>City:</td><td>Leuven</td></tr><tr><td>Region:</td><td>Flemish region</td></tr><tr><td>Country:</td><td>Belgium</td></tr><tr><td>Postcode:</td><td>3000</td></tr></table>

16. In the “Eligibility” field, enter “First come first served”.

The other two options are “Registration of interest” and “By invitation”. More than one type can be provided, if applicable.

17. In the “Organiser” field, enter the organizer of the event: “ELIXIR-Belgium”.

This is a free text field.

18. In the “Contact” field, enter the name of the training coordinator.

This is also a free text field, and one or more contact persons can be added, preferably with an email address.

19. In the “Host institutions” field, start typing “VIB” to bring up a dropdown menu to choose from.

In steps 19-21, if your institutions, keywords, or target audiences are not listed in the menu, you can add them. You may add and select as many as you like.

20. In the “Keywords” field, enter “transcriptomics”.

21. In the “Target audience” field, enter “Life Science Researchers”.

22. In the “Scientific topics” field, enter “RNA-Seq, Sequencing”.

Scientific topics can be added according to the EDAM ontology (www.edamontology.org). If you do not see a matching entry, you can use the keywords field.
23. In the “Operations” field, enter “Differential gene expression profiling”.

Operations can also be added according to the EDAM ontology. If you do not see a matching entry, you can use the keywords field.

24. In the “Capacity” field, enter the maximum number of attendants (e.g., 20).

25. In the “Event type” field, choose “Workshops and courses”.

The other three options are “Awards and prizegivings”, “Meetings and conferences”, and “Reception and networking”. More than one event type can be provided, if applicable.

26. In the “Tech requirements” field, enter “R, Rstudio, various R packages”.

Any technical requirements can be added. Ideally, a link to installation instructions should also be provided.

This field supports markdown syntax.

27. For the type of credit or recognition of attendance that will be delivered, enter “Certificate of attendance recognized by Doctoral School”.

Other types of recognition can be entered as free text.

28. In the “External resources” field, search for “DESeq2” in the tools section. Once the tool has been found in `bio.tools`, click on the “+” sign to add it to the entry.

You can associate policies, standards, and databases (provided by `FAIRsharing`) with your training event. In each case, a list of existing resources will be listed when you start typing keywords (click on the “+” sign to select).

29. In the “Cost basis” field, select “Cost to non-members”.

The other two options are “Free to all” and “Cost incurred by all”.

30. In the “Content Provider” field, enter “VIB Training”.

If you do not see your organization, register it first as a Provider in TeSS.

31. In the “Materials search” box, search for “Transcriptomics data analysis made easy” and select suggested training materials to associate with the course.

Start typing keywords and a list of existing training materials will be listed to select from (click on the “+” sign to select).

32. Select the “Node” the organizer belongs to from the dropdown list: “ELIXIR Belgium”.

A node is a country or EMBL-EBI in the ELIXIR context.

33. Enter the Sponsors/Funders of your training event: “VIB”.

34. Click the “Add event” button to finalize the registration.

# MANUAL REGISTRATION OF TRAINING MATERIALS IN TeSS

In the context of TeSS, a training material is a link to a single online training material sourced by a content provider (such as text on a webpage, presentation, video, etc.) along with a description and related meta information (e.g., ontological categorization, keywords). Materials can be added manually or harvested automatically from a provider's website. Here is the procedure to register training materials manually.

## Necessary Resources

- Desktop or a laptop computer or a mobile device with fast Internet connection

- Up-to-date web browser such as Google Chrome, Mozilla Firefox, Apple Safari, or Microsoft Edge

BASIC
PROTOCOL 4

Bacall et al.
1. Log in to TeSS at https://tess.elixir-europe.org.

2. Click on the “Material” menu.

3. Click on “Register training material” to be directed to the form.

As an example, the following steps use training material about the use of AlphaFold for structure prediction of proteins and binary protein complexes.

4. In the “Title” field, enter “How to use AlphaFold for prediction of single proteins or protein complexes using the HPC”.

5. In the “URL” field, enter “https://elearning.bits.vib.be/courses/alphafold/”.

6. In the “Description” field, enter:

"Architectural details, code and trained AlphaFold models were released by Deep-Mind in 2021. Given the high computational cost of deep learning algorithms, specialized hardware and software are required. Online solutions are available but come with considerable disadvantages. Therefore, the Flemish Supercomputer Center (VSC) provides high performance computing facilities, on which AlphaFold is installed and fully operational. This course gives a solid introduction on how AlphaFold can be easily and swiftly accessed using the HPC.

This tutorial material was created by Jasper Zuallaert (VIB-UGent), with the help of Alexander Botzki (VIB) and Kenneth Hoste (UGent). For questions and remarks, feel free to contact jasper.zuallaert@vib-ugent.be or training@vib.be."

This field supports markdown syntax

7. In the “Keywords” field, enter “Structure prediction”, “AlphaFold Database”, and “Protein complex prediction”.

A list will be displayed when you start typing keyword(s). If your desired keywords are not listed, you can add them. You may add and select as many as you like.

8. In the “License” field, select “Creative Commons Attribution Non commercial Share Alike 4.0 International”.

The dropdown list includes an option for “License not specified” in case you do not hold a license for your material.

9. In the “Status” field, select “Active”.

The three options are Active, Under development, and Archived.

10. In the “Contact” field, enter “training@vib.be”.

As this is a free text field, one or more contact persons can be added, preferably with an email address.

11. In the “DOI” field, enter the URL of the DOI if you have created one for your training material.

In our example, we do not provide a DOI.

12. In the “Version” field, enter “1.0”.

You can provide a version number for the material, if available.

13. In the “Content Provider” field, select the content provider from the dropdown list: “VIB Training”.

14. In the “Authors” field, enter the name(s) of the author(s) of the material: “Jasper Zuallaert” and “Alexander Botzki”.
15. In the “Contributors” field, enter the name(s) of contributor(s) to the material: “Kenneth Hoste”.

Preferentially, specify your ORCID.

16. In the “Events” field, select “Structural Prediction of Proteins using AlphaFold on the HPC” from the dropdown list.

We recommend doing the linking from the event side (when the event is registered) according to Basic Protocol 3, step 30.

17. In the “Target audience” field, select “Life scientists with programming skills” from the dropdown list.

Add as many applicable options as you want

18. In the “Prerequisites” field, add:

> “You are encouraged to use your own laptop. For those who do not have a laptop, the YASARA software can be run in a remote Linux environment (access to cloud via web browser). Knowledge of command line and basic Python skills are recommended.”

This field supports markdown syntax.

19. For “Competency” level, select “Intermediate”.

The other options are “Beginner” and “Advanced”.

20. For “Learning Objectives”, enter:

> “Understand the technical methodology of AlphaFold2, Understand the technical setup at the Flemish SuperComputer, Predict three-dimensional protein models with AlphaFold2 using the HPC at the VSC UGent.”

We recommend applying the Bloom hierarchy of cognitive skills to formulate the learning objectives. For more detailed information about our pedagogical model, please browse the course material of the ELIXIR Train the Trainer course at https://github.com/TrainTheTrainer/ELIXIR-EXCELERATE-TiT.

This field supports markdown syntax.

21. Enter the “Date created” (1 April, 2022).

22. Enter “no value” in “Date modified”.

If applicable, enter the date the material was last modified.

23. Enter the “Date published” (28 April, 2022).

24. In the “Resource types” field, enter “Tutorial” and “Slides” from the dropdown menu.

Other options include video, slides, pdf, etc.

25. In the “Scientific topics” field, select “Structure prediction, Protein Structure Analysis, Machine Learning”.

Scientific topics can be added according to the EDAM ontology (www.edamontology.com). If you do not see a matching entry, you can use the keywords field.

26. In the “External resources” field, click on “Suggested tools to associate with this resource”. In the “Search” field, enter “AlphaFold”. Wait a couple of seconds until the result from the request to the ELIXIR Tools and Services Registry is shown. Select the entry “AlphaFold 2” by clicking on the “+” sign.
You can associate policies, standards, and databases (provided by FAIRsharing) or tools (provided by bio.tools) with your training event. In each case, a list of existing resources will be listed when you start typing relevant words (click on the "+" sign to select).

27. In the “Nodes” field, use the dropdown list to select “Belgium” as the node to which the authors and contributors belong.

28. In the “Operations” field, select “Multiple Sequence Alignment, Structure Visualization”.

Operations can be added according to the EDAM ontology. If you do not see a matching entry, you can use the keywords field.

29. Click on “Register training material” to finalize the registration.

## REGISTRATION OF A CONTENT PROVIDER IN TeSS

TeSS features content providers, which are entities such as academic institutions, non-profit organizations, or portals that provide training materials of relevance to the life sciences and ELIXIR. In order to have a training event automatically harvested in TeSS (see Basic Protocol 6), a content provider must first be registered. This also adds visibility for content providers. Here is the procedure to register a new content provider in TeSS.

### Necessary Resources

- Desktop or a laptop computer or a mobile device with fast Internet connection

- Up-to-date web browser such as Google Chrome, Mozilla Firefox, Apple Safari, or Microsoft Edge

1. Log in to TeSS at https://tess.elixir-europe.org.

2. Under “Directory”, click on the “Providers” menu.

3. Click on “Register content provider” to be directed to the form.

As an example, we create the content provider NanoCommons.

4. In the “Title” field, enter “NanoCommons”.

5. In the “URL” field, enter the URL of the content provider: “https://www.nanocommons.eu/”.

6. In the “Contact” field, enter “Jean Dupont” as the contact person.

7. In the “Description” field, provide general information and relevant context about the content provider in the form of short text:

> “NanoCommons will deliver a sustainable and openly accessible nanoinformatics framework (knowledgebase and integrated computational tools, supported by expert advice, data interpretation and training), for assessment of the risks of NMs, their products and their formulations. NanoCommons combines Joint Research Activities to implement the nanoinformatics Knowledge Commons, Networking Activities to facilitate engagement with the research community, industry and regulators, and provision of funded Access to the nanoinformatics tools via funded calls for Transnational Access.”

This field supports markdown syntax.

8. To provide a logo for the Content Provider, in the “Image” field under “or enter the URL”, enter the URL of the image location: https://www.nanocommons.eu/wp-content/uploads/2018/04/NanoCommons-Logo-Sphere-Trans-White-circle-512px.png

Upload an image by choosing an image file if you cannot provide a URL where the image file is located.
9. In the “Type” field, enter “Project” as type of content provider.

*Alternative options are Organisation or Portal.*

10. In the “Approved Editors” field, enter “Alexander” and select “alexander botzki@vib.be (Alexander Botzki)”.

*If approved editors are not listed, they must first be registered as in the Alternate Protocol and acknowledged by the TeSS team. More than one registered user can be added as an approved editor. Selected users can be removed by clicking on the cross.*

11. In the “Keywords” field, enter “nanotechnology”, “commons”, “product safety”, and “toxicology”.

12. In the “Nodes” field, select an associated ELIXIR node, if applicable.

*In our example, there is no direct association with ELIXIR nodes, so it is left empty.*

13. Click on “Register content provider” to confirm the creation of the content provider.

## AUTOMATED HARVESTING OF TRAINING EVENTS AND MATERIALS IN TeSS

BASIC
PROTOCOL 6

TeSS features several options for automatically harvesting resources from external sources. This can be helpful if you maintain a large collection of events and materials that changes frequently. To register resources in TeSS automatically, data must be able to be reliably extracted from target sources. To this end, it is helpful if the data are structured according to a globally used standardized format. The following are examples of the kinds of structured data that are compatible with TeSS.

If your website currently includes no structured data and you want your resources added to TeSS, we recommend using Bioschemas to structure your site. Schema.org is a project run by a consortium of search engines. Schema.org has created an extensive library of schemas that webmasters can use to explicitly mark up website content in order to improve search engine visibility and interoperability. Bioschemas is an initiative to supplement the work of Schema.org to help improve the findability of online resources in the life sciences. TeSS supports the following Bioschemas profiles: (1) CourseInstance and Course for events that are courses, (2) Event for other events, and (3) TrainingMaterial for training materials. Figure 3 provides a schematic overview of the protocol steps.

### Necessary Resources

- Desktop or a laptop computer or a mobile device with fast Internet connection

- Up-to-date web browser such as Google Chrome, Mozilla Firefox, Apple Safari, or Microsoft Edge

<figure><img src="image_5.png" /><figcaption>**Figure 3** Schematic overview of steps for automatic harvesting of training events and materials.</figcaption></figure>
1. Select the profile Learning resource https://bioschemas.org/profiles/TrainingMaterial/1.0-RELEASE for the automated harvesting of a specific training material from the NanoCommons initiative (https://nanocommons.github.io/user-handbook/) located at https://nanocommons.github.io/tutorials/enteringData/index.html.

For training events, select Course/CourseInstance by using the profile described at https://bioschemas.org/profiles/CourseInstance.

2. Manually annotate the HTML website containing the training material (here, index.html; https://nanocommons.github.io/tutorials/enteringData/index.html) using JSON-LD markup. More specifically, enter a JSON object as shown below in a script element with the attribute type="application/ld+json". This script element needs to be placed as a child of the head element of the HTML page. This results in the following script HTML element.

<script type="application/ld+json">
{
    "@context": "https://schema.org/",
    "@type": "LearningResource",
    "http://purl.org/dc/terms/conformsTo": { "@type": "CreativeWork", "@id": "https://bioschemas.org/profiles/TrainingMaterial/1.0-RELEASE" },
    "name": "Adding nanomaterial data",
    "version": "0.9.3",
    "description": "This tutorial describes how nanomaterial data can be added to an eNanoMapper server using an RDF format.",
    "license": "https://creativecommons.org/licenses/by/4.0/",
    "keywords": "ontologies, enanomapper, RDF",
    "url": "https://nanocommons.github.io/tutorials/enteringData/",
    "provider": {
        "@type": "Organization",
        "name": "NanoCommons",
        "url": "https://www.nanocommons.eu/"
    },
    "audience": {
        "@type": "EducationalAudience",
        "educationalRole": "Graduates"
    },
    "inLanguage": {
        "@type": "Language",
        "name": "English",
        "alternateName": "en"
    },
    "author": [
        {
            "@context": "https://schema.org",
            "@type": "Person",
            "name": "Egon Willighagen",
            "identifier": "https://orcid.org/0000-0001-7542-0286",
            "orcid": "https://orcid.org/0000-0001-7542-0286"
        }
    ]
}
</script>
<figure><img src="image_6.png" /><figcaption>**Figure 4** Screenshot of the Schema.org validator that checks whether you have used non-existing properties of the Bioschemas profile.</figcaption></figure>

3. Validate the individual page with the Schema.org validator at https://validator.schema.org by pasting the URL https://nanocommons.github.io/tutorials/enteringData/index.html into the Fetch URL tab (Fig. 4).

*The validation procedure will indicate if you have used non-existing properties of the Bioschemas profile. If error messages are returned, see Troubleshooting below.*

4. Create a sitemap listing the material page URL and save it as sitemap.xml. The sitemap.xml file needs to be publicly browsable on the internet. In our example, the manually created sitemap.xml is published at https://nanocommons.github.io/sitemap.xml.

*More complex mechanisms for sitemap creation are available by using content management systems such as Drupal and using specific sitemap plugins.*

5. Enter “NanoCommons” as the “Content Provider”.

*If the provider is not already registered in TeSS, this should be done first as described above (see Basic Protocol 5).*

6. Make note of the Content Provider's exact Title and URL. In our example, this is NanoCommons and https://www.nanocommons.eu/.

7. Go to https://github.com/ElixirTeSS/bioschemas.sources/edit/main/sources.yml to edit the sources.yml file and add your Content Provider details along with the URL to your sitemap:

```
title: NanoCommons
url: https://www.nanocommons.eu/
source: https://nanocommons.github.io/sitemap.xml
```

8. To commit your change, click the button to open a pull request, which will then be reviewed. After review, the new training material will appear in TeSS.

*Your content should appear in TeSS the following day. Each source will be scraped once per day at ~3 AM UTC.*

# COMMENTARY

## Background Information

During the ELIXIR-EXCELERATE project, the TeSS platform was established as the key application for bioinformatics training events and material aggregation. During

further adoption of the TeSS platform as such on the international level (e.g., in Australia and the Netherlands), it became obvious that the implementation of individual automatic content scrapers for more than 30 content
providers lead to an enormous diversity of the code base and finally to a maintenance challenge. Therefore, during the last two to three years, a strategic reorientation of the automated harvesting procedure has been proposed and implemented in TeSS using the Bioschemas profiles for Course, CourseInstance, and TrainingMaterial. This approach will put content providers in a more prominent position, since they are in turn responsible for more structured delivery of more comprehensive metadata of their training events and materials to TeSS as the aggregation platform. In the long run, this will increase the quality level of aggregated resources and their usefulness to the TeSS user base.

Content providers looking to promote the use of particular tools and databases via their course offerings or specific training materials can find information in other ELIXIR registries, such as bio.tools (https://bio.tools) for tools and web services and FAIRsharing.org (https://fairsharing.org) for databases, standards, and policies. Lately, such registries have started to track training relating to the resources they list. Therefore, it is mutually beneficial that TeSS provides the relevant links (allowing users to search for resource-specific training) and the resource pages in bio.tools and FAIRsharing that contain reciprocal links for users to discover relevant training in TeSS.

Related to the provisioning of persistent identifiers, TeSS provides the Digital Object Identifier (DOI) as a unique means to identify training materials. Given that minting services by, for example, university libraries are not yet broadly available for teaching and learning material in contrast to research datasets and collections, associated workflows, software, and models, we recommend using services like OSF or Zenodo to get own unique, persistent URLs and DOIs.

Given the engagement of the ELIXIR Train the Trainer instructor's community to create a vibrant environment for reciprocal support and exchange of experiences via the ELIXIR Train the Trainer Programme, TeSS content providers are encouraged to follow best-practice guidance on course and training material development (Via et al., 2020). Therefore, we recommend applying the Bloom hierarchy of cognitive skills to formulate the learning objectives for courses and training materials. For more detailed information about our pedagogical model, please browse the course material of the ELIXIR Train the Trainer course (https://github.com/TrainTheTrainer/ELIXIR-EXCELERATE-TiT).

# Critical Parameters

## Curation of manual content for automatically harvested events or training materials

In Basic Protocols 3 and 4, it is important to note that much of the content in TeSS is retrieved and kept up to date via automated scrapers (see Basic Protocol 6) that pull information from public webpages and application programming interfaces (APIs) in regular intervals. To prevent TeSS from overwriting a field you have just changed, click the “locker” icon to lock the field. Fields marked as locked will not be overwritten by an automatic procedure.

For training events and materials, mandatory fields are marked with an * symbol. Unmarked fields are optional.

## Automated harvesting of training events

In step 2 of Basic Protocol 6, we recommend following the guidelines from the Bioschemas community on strategies for marking up your internet sites by using this tutorial: https://bioschemas.org/tutorials/howto/howto_add_markup. If your website is hosted on GitHub, you can follow https://bioschemas.org/tutorials/howto/howto_add_github instead.

In step 3, if you get an error during the validation procedure by the Schema.org validator, consult the properties definitions in the respective profile on Schema.org and Bioschemas.org.

In step 7, you must have a GitHub account to edit the sources.yml file. It is important to make sure the title and URL exactly match the Content Provider's title and URL on TeSS. You will make changes in the GitHub project ElixirTeSS/bioschemas.sources, for which you do not have write access. Submitting a change will write it to a new branch in your fork <your github user name>/bioschemas.sources, so that you can send a pull request afterwards.

If you have implemented Bioschemas markup on your website and would like your content to appear in TeSS, see our “Bioschemas sources” repository for detailed information on how to proceed: https://github.com/ElixirTeSS/bioschemas.sources#readme.

# Troubleshooting

See Table 1 for troubleshooting if you experience issues with missing concepts in the EDAM ontology, potentially new properties in the form on the TeSS website, a missing
<table><caption>**Table 1** Sources and Solutions to Potential Errors</caption><thead><tr><td>Problem</td><td>Possible cause</td><td>Solution</td></tr></thead><tbody><tr><td>Missing concept in the EDAM ontology</td><td>EDAM does not cover all scientific topics</td><td>Select a closely related term or submit a request to add new concepts, if appropriate</td></tr><tr><td>There are new properties in the TeSS interface for events or material</td><td>Sometimes new properties are added to the TeSS interface</td><td>Browse the documentation on the TeSS website</td></tr><tr><td>Your host institution is missing when you go to register an event or material</td><td>The dropdown of host institutions is a fixed list</td><td>Enter a new host organisation in the field</td></tr><tr><td>After using the automated harvesting protocol, your training material does not appear in TeSS the following day</td><td>The title and/or URL did not exactly match the Content Provider's title and URL on TeSS<br>You have provided a validated Bioschemas markup, but the harvesting procedure in TeSS did not recognize all the properties correctly</td><td>Double check that the title and URL match exactly the Content Provider's title and URL on TeSS<br>Submit an issue on the ELIXIR-T eSS/BioschemasSources GitHub repository</td></tr></tbody></table>

hosting institution, or synchronizations issues with the automated procedure.

## Understanding Results

As a content provider in TeSS, it is important to realize that adding training events or materials manually will take roughly 10-15 min per item if all properties are filled in. Given that this can be a considerable time investment, we strongly encourage content providers to implement the automated harvesting procedure based on Bioschemas annotation. While this can also be very time consuming, depending on the nature of the content provider's technical platform, the upfront investment of the technical setup will pay back in the long run. From a consumers' perspective of the TeSS content, a high annotation level is very much appreciated. The higher the annotation level, the more useful the search experience will be for the TeSS audience. In particular, this greatly facilitates the filtering process after an initial search using facets, e.g., for country, difficulty level, resource type, or audience.

## Acknowledgments

The fundamental work for building TeSS as a platform was part of the ELIXIR-EXCELERATE project 2014-2018 and we are grateful for the efforts provided from across the ELIXIR Nodes and ELIXIR Platforms. We are also grateful for support and funding of this work by the ELIXIR Scientific Programme 2019-2023 (https://elixir-europe.org/about-

us/what-we-do/elixir-programme). Furthermore, we would like to acknowledge Christof De Bo (ELIXIR-BE, VIB Bioinformatics Core) for his support creating the illustration in Figure 3.

## Author Contributions

**Finn Bacall:** Conceptualization, investigation, methodology, software, validation, writing review and editing; **Aitor Apaolaza:** Investigation, methodology, software; **Mu-nazah Andrabi:** Investigation, writing review and editing; **Chris Child:** Investigation, methodology, software; **Carole Goble:** Methodology, project administration, supervision, writing review and editing; **Olivier Sand:** Conceptualization, project administration, supervision, validation, writing original draft, review and editing; **Alexander Botzki:** Conceptualization, project administration, supervision, visualization, writing original draft, review and editing.

## Conflict of Interest

The authors declare no conflict of interest.

## Data Availability Statement

The data that support the findings of this study are openly available in the ELIXIR TeSS GitHub repository at https://github.com/ElixirTeSS/bioschemas.sources.

## Literature Cited

Beard, N., Bacall, F., Nenadic, A., Thurston, M., Goble, C. A., Sansone, S.-A., & Attwood, T. K. (2020). TeSS: A platform for
discovering life-science training opportuni-
ties. *Bioinformatics*, 36(10), 3290–3291. doi:
10.1093/bioinformatics/btaa047

Garcia, L., Batut, B., Burke, M. L., Kuzak, M., Pso-
mopoulos, F., Arcila, R., ... Palagi, P. M. (2020).
Ten simple rules for making training materi-
als FAIR. *PLoS Computational Biology*, 16(5),
e1007854. doi: 10.1371/journal.pcbi.1007854

Castro, L., Palagi, P. M., Beard, N., Bioschemas Training Profiles Group Members, ELIXIR FAIR Training Focus Group, The GOBLET Foundation, ... Brazas, M. (2022). Bioschemas Training Profiles: A set of specifications for standardizing training information to facilitate the discovery of training programs and resources. *bioRxiv*, 2022.11.24.516513. doi: 10.1101/2022.11.24.516513

Gray, A. J., Goble, C., & Jiménez, R. C. (2017). Bioschemas: From potato salad to protein annotation. International Semantic Web Conference; Berlin. Accessed 2019 Mar 11. Retrieved from https://pdfs.semanticscholar.org/74ec/a9c89622bff731b21b03acb4f2400a0f00fa.pdf

Guha, R. V., Brickley, D., & MacBeth, S. (2015). Schema.org: Evolution of structured data on the web: Big data makes common schemas even more necessary. *Queue*, 13(9), 10–37. doi: 10.1145/2857274.2857276

Ison, J., Kalas, M., Jonassen, I., Bolser, D., Uludag, M., McWilliam, H., ... Rice, P. (2013). EDAM: An ontology of bioinformatics operations, types of data and identifiers, topics and formats. *Bioinformatics*, 29(10), 1325–1332. doi: 10.1093/bioinformatics/btt113

Jupp, S., Burdett, T., Malone, J., Leroy, C., Pearce, M., McMurry, J., & Parkinson, H. (2015). A new ontology lookup service at EMBL-EBI. In J. Malone, R. Stevens, K. Forsberg, & A. Splendiani (Eds.), *Proceedings of the 8th SWAT4LS International Conference, Cambridge, UK, December 7-10, 2015*.

Sansone, S.-A., McQuilton, P., Rocca-Serra, P., Gonzalez-Beltran, A., Izzo, M., ... the FAIR-sharing Community. (2019). FAIRsharing as a community approach to standards, repositories and policies. *Nature Biotechnology*, 37(4), 358–367. doi: 10.1038/s41587-019-0080-8

Via, A., Palagi, P. M., Lindvall, J. M., Tractenberg, R. E., Attwood, T. K., & The GOBLET Foundation. (2020). Course design: Considerations for trainers – A professional guide. *F1000Res*, 9, 1377. doi: 10.7490/f1000research.1118395.1

Whetzel, P. L., Noy, N. F., Shah, N. H., Alexander, P. R., Nyulas, C., Tudorache, T., & Musen, M. A. (2011). BioPortal: Enhanced functionality via new web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. *Nucleic Acids Research*, 39, (suppl), W541–W545. doi: 10.1093/nar/gkr469

Internet Resources

http://edamontology.org/

Main information site for EDAM, the ontology of bioscientific data analysis and data management. EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within bioscientific data analysis and data management (including computational biology, bioinformatics, and bioimage informatics).

https://schema.org/

Schema.org is a collaborative community activity with a mission to create, maintain, and promote schemas for structured data on the internet, on web pages, in email messages, and beyond. On this website, you can find https://bioschemas.org/, the homepage of the Bioschemas community. Bioschemas aims to improve the findability on the web of life sciences resources such as datasets, software, and training materials. Information about the three Bioschemas profiles implemented in this protocol can be found at https://bioschemas.org/profiles. Various tutorials can be found at https://bioschemas.org/tutorials.

https://validator-schema.org

Site for easy validation of websites that have been
marked up with structured data as, e.g., a JSON-
LD object.

https://github.com/ElixirTeSS/bioschemas_ sources#readme

This is the README file of the GitHub repository bioschemas.sources for the TeSS portal hosted in the ELIXIR TeSS GitHub organization.

https://github.com/TrainTheTrainer/ELIXIR-EXCELERATE-TiT

GitHub repository hosted by ELIXIR-EXCELERATE-TiT in the TrainTheTrainer GitHub organization.

https://elixirtess.github.io/TeSS_widgets

GitHub repository for TeSS widgets where several
implementation scenarios are documented.