Hello and welcome, this is our interactive hands-on course about efficient use of the ELIXIR TeSS platform.
We are using the interactive Open Educational Resource online/offline course infrastructure called LiaScript. It is a distributed way of creating and sharing educational content hosted on github. To see this document as an interactive LiaScript rendered version, click on the following link/badge:
The original publication of the protocols can be found here. We have reused the content to prepare this training material.
About ELIXIR Training Platform
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About VIB and VIB Technologies
VIB is an entrepreneurial non-profit research institute, with a clear focus on groundbreaking strategic basic research in life sciences and operates in close partnership with the five universities in Flanders – Ghent University, KU Leuven, University of Antwerp, Vrije Universiteit Brussel and Hasselt University.
As part of the VIB Technologies, the 12 VIB Core Facilities, provide support in a wide array of research fields and housing specialized scientific equipment for each discipline. Science and technology go hand in hand. New technologies advance science and often accelerate breakthroughs in scientific research. VIB has a visionary approach to science and technology, founded on its ability to identify and foster new innovations in life sciences.
The goal of VIB Technology Training is to up-skill life scientists in various topics like ...
Editorial team for this course
Authors: Alexander Botzki
Technical Editors: Alexander Botzki
License: 
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Many trainers and their organisations are passionate about sharing their training material. Sharing training material has several benefits like 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 facilitating to complement the training resource landscape by data-driven gap analysis from the bioinformatics community (see PLOS Computational Biology, 16(5), e1007854).
In this tutorial, we elaborate a series of protocols leading the TeSS users through the process of searching and filtering TeSS content (Protocol 1 to 3). Protocols 4 to 7 show how to register manually and automatically training events and material in the Training eSupport System (TeSS), ELIXIR’s training portal. More information about TeSS can be found in this publication.
TeSS provides a one-stop shop for trainers and trainees to discover online information and content, including training materials, events and interactive tutorials. Following these protocols, you will contribute to promote your 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 training specific BioSchemas specifications. Protocol 8 will teach you how to enrich your training resources to allow for more efficient sharing of the structured metadata like prerequisites, target audience, and learning outcomes using Bioschemas specification. Once more and more training events and material are aggregated in TeSS, searching the registry for specific events and material becomes crucial.
In the next section, you will find links where you can follow all protocols.
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Protocol 1: Searching for training events in TeSS
Protocol 2: Integrating TeSS widgets on your web site
Protocol 3: Searching for e-learning materials in TeSS
Protocol 4: Log into TeSS using an institutional account
Protocol 5: Manual registration of a training event in TeSS
Protocol 6: Manual registration of training material in TeSS
Protocol 7: Registration of a content provider in TeSS
Protocol 8: Automated harvesting of a training event in TeSS
During the ELIXIR-EXCELERATE project, the TeSS platform has been established as the key application for bioinformatics training events and material aggregation. During a period of further adoption of the TeSS platform as such on the international level e.g. in Australia and in 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 the content providers in a more prominent position since they are in turn responsible for a more structured delivery of more comprehensive metadata of their training events and material to TeSS as the aggregation platform. In the longer run, this will increase the quality level of the aggregated resources and its usefulness to TeSS user base.
Content providers looking to promote use of particular tools and databases via their course offering or the specific training material can find information about them in other ELIXIR registries, such as bio.tools for tools and web services and FAIRsharing.org for databases, standards and policies . Lately, such registries 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 material. Given that minting services by e.g. 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 to use 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, the 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 the courses as well as for training material. For more detailed information about our pedagogical model, please browse to the course material of the ELIXIR Train the Trainer course.
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Training resources (both events and materials) may be searched in TeSS in several ways. If you are on the main page of TeSS, 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. This 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. Be aware that by searching for events, the standard search returns only future events. If you want to include past events, you need to click the Show past event button.
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Please navigate to TeSS and follow the steps shown below.
- Select Events in the top menu.
- Click on the Show past events button.
- Enter ‘Single-cell’ as the keyword in the search text box on the right side of the page and click on the magnifier icon.
- On the side menu, scroll down to the Country facet. We will select the United Kingdom.
- On the side menu, scroll to the facet Target audience. Select ‘Graduate students’.
- As a result, you get the list of training events about single-cell data analysis available in the United Kingdom for Graduate students.
At any time you may remove any of the filters you applied to reduce stringency of your search.
TODO: enter summary/solution check on the solution via using API At the time of writing this protocol, you should find at least
Widgets are chunks of JavaScript code that can be copied into website source code to display TeSS content. There are several different styles and functionalities available from our configurable widget suite. Widgets can be used to enhance your site and offer your community lists of relevant events or training resources. There are examples of code on this page.
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For a tabular layout of events with filtering options, choose the specific widget type Events table with a sidebar. A working example is shown on the github pages from the ELIXIR TeSS team at https://elixirtess.github.io/TeSS_widgets. For training material, investigate the example for training materials on the same website.
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Manually annotate the HTML web site e.g. index.html with the code snippet for the TeSS widget. More specifically, enter the code snippet as shown below as a sibling of a div element.
<link rel="stylesheet" property="stylesheet" href="https://elixirtess.github.io/TeSS_widgets/css/tess-widget.css"/>
<div id="tess-widget-events-table" class="tess-widget tess-widget-faceted-table"></div>
<script>
function initTeSSWidgets() {
TessWidget.Events(document.getElementById('tess-widget-events-table'),
'FacetedTable',
{
opts: {
columns: [{name: 'Date', field: 'start'},
{name: 'Name', field: 'title'},
{name: 'Location', field: 'location'}],
allowedFacets: ['scientific-topics', 'country', 'city', 'target-audience'],
facetOptionLimit: 5
},
params: {
q: 'Python',
country: ['Belgium', 'United Kingdom']
}
});
}
</script>
<script async="" defer="" src="https://elixirtess.github.io/TeSS_widgets/js/tess-widget-standalone.js" onload="initTeSSWidgets()"></script> -
Save the HTML page and serve the HTML page for visual inspection.
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Validate visually that the rendered HTML page includes a table with the Events extracted from TeSS. It will show a filtered list according to the values in the params section (see snippet from step 2). In this case, all future courses aggregated in TeSS will be live filtered on the general search term ‘Python’ and display only the courses from ‘Belgium’ and ‘United Kingdom’.
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Remove the term ‘Python’ from the general search. Now, the table underneath should be updated with all the up-coming courses from Belgium and the United Kingdom. By adapting the other facets ‘Scientific Topics’ and ‘Target audience’, other filtering schemes can be established. At any time you may remove any of the filters you applied to reduce stringency of your search. If you would like to include past events in your search, click on the Show past events button.
TODO: show our implementation of the TeSS widget
E-learning resources are a specific type of training materials in TeSS which are displayed on the dedicated section E-learning on the main TeSS page. But you can also perform a specific search on the Materials page filtering on 'Resource type' and retrieve e-learning material by specifying the value 'e-learning'.
Please navigate to TeSS.
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Select Materials in the top menu.
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Enter a keyword in the search text box on the right side of the page. We will enter ‘Data retrieval’.
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On the side menu, select a difficulty level. We will select ‘Beginner’.
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Scroll to the facet ‘Resource type’ and select ‘e-learning’.
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You get the list of training materials about data retrieval intended for a beginner level audience whereby the resource has been tagged as e-learning material. At any time you may remove any of the filters you applied to reduce stringency of your search.
In order to be able to register resources in TeSS you need to log in the registry. The following steps are specific for the login procedure with the Life Sciences Account. Alternatively, you can use another existing account like Google, Apple or an ORCID. In this case you will be redirected to the respective login portal.
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Open your browser and go to TeSS.
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Click the “Log In” dropdown button on the top-right corner of the page.
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To log in using your institutional account, choose Log in with LS Login from the dropdown menu You will be redirected to the LifeScience RI authentication page (TODO Fig. 1).
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Start typing the name of your own institution, for instance ‘CNRS’, into the text box then choose the appropriate option that appears and proceed with your usual institutional login procedure (Fig. 2). You should now be logged into TeSS. Once successful, you should be taken to the TeSS Welcome page with a message stating “Logged in successfully.” You should also see your username in the top bar of the page, which you can click to view and edit your TeSS profile. There are also options to log in using Google, Apple, ORCID, etc. accounts, but we will not be able to provide a detail procedure for all the federated authentication mechanisms here.
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Check all the fields in your user profile are correct and click the “Update Profile” button. You will also see a button to log out of TeSS.
An event in TeSS is a link to a single training event sourced by a provider along with description and related meta information (e.g. date, location, audience, ontological categorization, keywords, etc.). Training events can be added manually or automatically harvested from a provider's website. Here is the procedure to register for training events manually.
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Login to TeSS at https://tess.elixir-europe.org following Protocol 3.
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To register for a training event, click on the Events menu.
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Click on “+ Register event”. As an example, we use an RNAseq training event. You will be directed to a form type of page.
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Select that Type at the beginning of the form since we enter a face-to-face event. If your event is online, choosing the option Online will modify the form to fit that type of event i.e. no address field has to be filled in.
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In the Title field, enter the Title of the event, which is “Bulk RNASeq: from counts to differential expression” in our example.
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The optional Subtitle field can be filled in case you’d like to specify more context on the event, like “Spring edition” of a regularly repeated course
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In the URL field, enter the URL where the announcement and registration of the training event can be found. In our example: “https://training.vib.be/all-trainings/bulk-rnaseq-counts-differential-expression-2”
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In the subsequent field Description, provide general information and relevant context about the training event in the form of short text, like in our example: “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.
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Specify the start date and door time of the event in the field Start via the pop-up Date and Time Picker. In our example, the event starts on the 29th of September 2022.
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Specify the end date of the event in the field End via the pop-up Date and Time Picker. Our example event will end on the 4th of October 2022.
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In the field Timezone, enter the time zone of the location where the event will occur and pick the one that applies. In our example, we select ‘(GMT:+01:00) Amsterdam’ since the event takes place in Leuven, Belgium.
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In the field Duration, indicate how long the event will last in hours, days, whatever applies best. Enter ‘2 days’ for our example.
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In the field Prerequisites, enter which prerequisites are necessary to follow the training event. For example, write “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.
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In the field Learning objectives, list the learning objectives of the training event like ○ Learn how RNA-seq reads are converted into counts ○ Understand QC steps that can be performed on RNA-seq reads ○ Generate interactive reports to summarise 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 to the course material of the ELIXIR Train the Trainer course https://github.com/TrainTheTrainer/ELIXIR-EXCELERATE-TtT This field supports markdown syntax.
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For the Address and related fields, enter the relevant information as ○ Address: fill in the address by starting 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 ○ Venue: the venue of the event e.g. street ○ City: the city where the venue is located ○ Region: the region where the city is located ○ Country: the country where the event will take place ○ Postcode: the postcode of the venue In our example, these are ○ Herestraat 49 ○ Campus Gasthuisberg ○ Leuven ○ Flemish region ○ Belgium ○ 3000
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For the Eligibility field, there are three options you can choose from: First come first served, Registration of interest, By invitation. You could provide more than one eligibility type, if applicable. In our example, we enter First come, first serve.
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Enter for example ELIXIR-Belgium in the Organiser field. This field is a free text field.
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Enter the name of the training coordinator in the contact field. Since this is also a free text field, one or more contact persons preferably with an email address can be added.
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Start typing ‘VIB’ as the name of the host institution(s) in the ‘Host institutions’ field. You will get a dropdown menu to choose from. If your institution is not present in the menu, add it. Add as many as you’d like.
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Enter ‘transcriptomics’ in the Keywords field. You can start typing keyword(s) and you will get a list to choose from. Add as many as you want.
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Enter ‘Life scientists researchers’ as Target audience. Start typing target audience types and you will get a list to choose from. Add as many as you want.
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In the field Scientific topics, enter ‘RNA-Seq, Sequencing’. You can enter the appropriate scientific topics according to the EDAM ontology. In case you do not have a matching entry, you could use the keywords field.
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Enter ‘Differential gene expression profiling’ in the Operations field. you can enter the appropriate operations according to the EDAM ontology. In case you do not have a matching entry, you could use the keywords field.
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Add e.g. 20 as maximum number of attendants to the event in the field Capacity.
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Enter ‘Workshops and courses’ as Event type. There are four options for the event type: Workshops and courses, Awards and prizegivings, Meetings and conferences, Reception and networking. You could provide more than one event type if applicable.
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As Tech requirements, enter “R, Rstudio, various R packages”. You can list here any technical requirement needed to follow the training event. Ideally, you also provide a link to the installation instructions. This field supports markdown syntax.
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Enter ‘Certificate of attendance recognised by Doctoral School’ as the type of credit or recognition of attendance that will be delivered.
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In the field External resources, 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 also associate policies, standards and databases (provided by FAIRsharing) with your training event. In each case, start typing keywords and a list of existing resources will be listed to select from (click on the “+” sign).
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Select ‘Cost to non-members’ as Cost basis. There are three choices: Free to all, Cost to non-members, Cost incurred by all.
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Select ‘VIB Training’ as Content Provider. In case you do not find your organisation, please register it first as a Provider in TeSS.
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Search for ‘transcriptomics data analysis made easy’ in the Materials search box and select suggested training materials to associate with this course. Start typing keywords and a list of existing training materials will be listed to select from (click on the “+” sign).
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Select ‘ELIXIR Belgium’ as a node from the downtown list. Select the node the organiser(s) belong(s) to.
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Enter ‘VIB’ as Sponsors/Funders of your training event.
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Click on the Add event button to finalize the manual registration.
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The resulting course can be visited here.
In the context of TeSS, a training material is a link to a single online training material sourced by a content provider (such as a text on a Web page, presentation, video, etc.) along with description and related meta information (e.g. ontological categorization, keywords, etc.). Materials can be added manually or automatically harvested from a provider's website. Here is the procedure to register training materials manually.
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As outlined in Protocol 4, in order to register for training material in TeSS, login first.
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To register for training material, click on the Material menu.
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Click on “+ Register training material”. You will be directed to a form. We will use training material about the use of AlphaFold for structure prediction of proteins and binary protein complexes.
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Enter ‘How to use AlphaFold for prediction of single proteins or protein complexes using the HPC ’ as Title of the training material.
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Enter ‘https://elearning.bits.vib.be/courses/alphafold/’ as the URL of the training material in the field URL.
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As Description, enter “Architectural details, code and trained AlphaFold models were released by DeepMind 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 [email protected] or [email protected].“ This field supports markdown syntax -
In the field Keywords, enter ‘Structure prediction’, ‘AlphaFold Database’, ‘Protein complex prediction’. Start typing keyword(s) and you will get a list to choose from. Add as many as you want. New ones can also be added.
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Select ‘Creative Commons Attribution Non commercial Share Alike 4.0 International’ in the License field. From the dropdown list, choose the one that applies. It includes “License not specified” in case you do not hold one for your material.
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Select ‘Active’ as Status. Select the status that fits the material you’d like to register. There are three stati available: Active, Under development, Archived.
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Enter ‘[email protected]’ in the Contact field. Enter one of more contact persons preferably with an email address.
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Enter DOI if available. In our example, we do not provide a DOI. Add the URL of the DOI in this field if you have created a DOI for your training material.
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Enter ‘1.0’ as in the Version field. You can provide a version number for the material, if available.
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Enter ‘VIB Training’ as Content Provider. Please select the content provider from the dropdown list.
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Enter ‘Jasper Zuallaert’ and ‘Alexander Botzki’ in the Authors field. Enter the name of authors of the material.
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Enter ‘Kenneth Hoste’ in the Contributors field. Enter the name of contributors to the material. Preferentially, specify your ORCID.
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Enter Events ‘Structural Prediction of Proteins using AlphaFold on the HPC’ from the dropdown list of events. We recommend doing the linking from the event side (when the event is registered) according to Basic Protocol 4 step 30.
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Enter ‘Life scientists with programming skills’ as Target audience. Start typing target audience types and you will get a list to choose from. Add as many as you want
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Add the following text as Prerequisites in the field: ‘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.’ If prerequisites are necessary to follow the training event, list them here. We recommend applying the Bloom hierarchy of cognitive skills to formulate the Learning objectives. For more detailed information about our pedagogical model, please browse to the course material of the ELIXIR Train the Trainer course https://github.com/TrainTheTrainer/ELIXIR-EXCELERATE-TtT. This field supports markdown syntax.
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Select ‘Intermediate’ as Competency level. You can choose between three levels: Beginner, Intermediate, Advanced.
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Enter the following text as Learning Objectives: ‘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 UGhent’ This field supports markdown syntax.
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Pick the 1st of April 2022 as Date created.
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Enter no value in Date modified. Pick the date the material was last modified, if applicable.
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Pick 28th of April as Date published.
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Enter ‘Tutorial’ and ‘Slides’ as Resource types. The media used for your material (e.g. video, slides, pdf…). Start typing a media type and you will get a list to choose from.
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Select ‘Structure prediction, Protein Structure Analysis, Machine Learning’ as Scientific topics. You can enter the appropriate scientific topics according to the EDAM ontology. In case you do not have a matching entry, you could use the keywords field (see above).
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Click on ‘Suggested tools to associate with this resource’ in the External resources field. Enter ‘AlphaFold’ in the search field. 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, start typing relevant words and a list of existing resources will be listed to select from (click on the “+” sign).
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Select ‘Belgium’ in the Nodes field. Select the node(s) from which the organiser(s) belong(s) to from the dropdown list.
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Select ‘Multiple Sequence Alignment, Structure Visualisation’ in the field Operations. You can enter the appropriate scientific topics according to the EDAM ontology. In case you do not have a matching entry, you could use the keywords field (see above).
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Click on ‘Register training material’.
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The resulting training material can be visited here.
Images:
Training resources (events and materials) may be added to TeSS to reach bigger audiences, increase impact and bolster event attendance. Registering events and training materials makes them more findable in a variety of ways to various user bases. TeSS features content providers which are entities (such as academic institutions, non-profit organisations, portals etc.) that provide training materials of relevance to life sciences and ELIXIR. In order to have a training event automatically harvested in TeSS, as described in Protocol 7, a content provider has to be registered first. It also adds visibility to content providers. Here is the procedure to register a new content provider in TeSS.
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Login to TeSS at https://tess.elixir-europe.org following Protocol 4.
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To register a content provider, click on the Providers menu.
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Click on “+ Register content provider”. You will be directed to a form type of page.
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As an example, we will create the content provider NanoCommons. Enter “NanoCommons“ in the Title field.
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In the URL field, enter the URL of the content provider, which is “https://www.nanocommons.eu/” in our example.
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Enter “Jean Dupont” as a contact person in the Contact field.
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In the subsequent field Description, provide general information and relevant context about the content provider in the form of short text, like in our example: “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.
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Enter the URL of the image location in the field under “or enter the URL”: https://www.nanocommons.eu/wp-content/uploads/2018/04/NanoCommons-Logo-Sphere-Trans-White-circle-512px.png Upload an image if you cannot provide a URL where the image file is located.
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Enter ‘Project’ as Type of the content provider in the Type field. Alternatively, you can select Organisation or Portal.
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In the field Approved Editors, enter ‘Alexander’ and select the name ‘[email protected] (Alexander Botzki)’. You can add more than one registered user as Approved Editor. Selected users can be removed by clicking on the red cross.
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In the field Keywords, enter the keywords “Nanotechnology”, “commons”, “Product safety”, and “toxicology”.
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Select an associated ELIXIR node if applicable. In this example, there is no direct association with ELIXIR nodes, so we leave it empty.
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Confirm the creation of the content provider by clicking on ‘Register content provider’.
Registering events and training materials makes them more findable in a variety ways to various user bases. TeSS features several options for automatically "harvesting" resources from external sources. This can be helpful if you are maintaining a large collection of events and materials that changes frequently. To register resources in TeSS automatically, we need to be able to extract data from target sources reliably. To this end, it is helpful if the data is structured according to a globally used standardized format. The following are examples of the kinds of structured data that TeSS can work with. If your website currently includes no structured data, and you’d like your resources added to TeSS, we recommend using Bioschemas to structure your site. Schema.org is a project running by a consortium of search engines. Schema.org has created an extensive library of schemas that web-masters can use to explicitly mark-up their websites 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: for events that are courses CourseInstance and Course, for other events Event, for training materials TrainingMaterial. Fig. 3 displays a schematic overview of the protocol steps.
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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 for training by using the profile described at https://bioschemas.org/profiles/CourseInstance.
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Manually annotate the HTML web site containing the training material, here index.html (https://nanocommons.github.io/tutorials/enteringData/index.html) with 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 a 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>-
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, have a look at the troubleshooting section below.
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Create a sitemap listing the material page URL and save it as sitemap.xml. This 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 like Drupal and using specific sitemap plugins.
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Register a Content Provider in TeSS following the basic protocol 6. Use ‘NanoCommons’ as a provider.
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Make note of your Content Provider's exact Title and URL referring to the properties Title and URL mentioned in basic protocol 6. In our example, it is ‘NanoCommons’ as Title and ‘https://www.nanocommons.eu/’ as URL.
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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, e.g.
- title: NanoCommons url: https://www.nanocommons.eu/ source: https://nanocommons.github.io/sitemap.xml
- 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 ~3AM UTC.
In protocols 4 or 5 about manual provisioning of the information, it is important to note that much of the content in TeSS is retrieved and kept up-to-date via automated scrapers (see protocol 8 Registering events/materials automatically) that pull information from public web pages and 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 the training event, several mandatory fields have to be filled in, marked with the “” symbol. There are also a number of optional fields. For training material, several mandatory fields have to be filled in, marked with the “” symbol. There are also a number of optional fields.
In step 2 of Protocol 8, we recommend to follow the guidelines from the BioSchemas community on strategies on how to markup 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, in the case that you get an error during the validation procedure by the validator from schema.org, consult the properties definitions in the respective profile on schema.org and bioschemas.org. In step 7, you need to have an account on github.com 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 don’t have write access to. Submitting a change will write it to a new branch in your fork /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
In case, you experience issues with missing concepts in the EDAM ontology, potentially new properties in the form on the TeSS website, a missing hosting institution or synchronizations issues with the automated procedure, please refer to entries in the Table 1 for troubleshooting.
| Header 1 | Header 2 |
|---|---|
| Item 1 | Item 2 |
Table 1. Sources and Solutions to Potential Errors Problem Possible Cause Solution Missing concept in the EDAM ontology. The EDAM ontology does not cover all scientific topics. Select a term which is closely related or submit a request to add new concepts in the EDAM ontology if appropriate. There are new properties in the TeSS interface for events or material. Sometimes new properties are added to the interface in TeSS. Browse to the documentation on the TeSS web site. Your host institution is missing when you are registering an event or a material. The dropdown of the host institutions is a fixed list. Enter a new host organisation in the field. By using the automated harvesting protocol, your training material does not appear in TeSS on the next day. The title and url don’t exactly match the Content Provider's title and URL on TeSS. Double check that the title and url exactly match the Content Provider's title and URL on TeSS. By using the automated harvesting protocol, your training material does not appear in TeSS on the next day. You might have provided a validated Bioschemas markup but the harvesting procedure in TeSS did not recognise all the properties correctly. Submit an issue on the ELIXIRTeSS/Bioschemas_sources github repository.
http://edamontology.org/: This is the main information site about the EDAM ontology, the ontology of bioscientific data analysis and data management. It 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 web site, 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. Here you can find all the information about the three Bioschemas Profiles implemented in this protocol at https://bioschemas.org/profiles as well as various tutorials at https://bioschemas.org/tutorials. https://validator.schema.org: This is the site where you can easily validate web sites which 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 organisation. https://github.com/TrainTheTrainer/ELIXIR-EXCELERATE-TtT: This is the github repository ELIXIR-EXCELERATE-TtT hosted in the TrainTheTrainer github organisation. https://elixirtess.github.io/TeSS_widgets. This is the github repository for TeSS widgets where several implementation scenarios are documented.
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