10.4. Main Content¶
We provide here detailed information on how to perform annotation on TeSS. All the annotation work is done on TeSS, although it is sometimes useful to visit the registry providing the identifier or the ontology portal for better clarity. All the annotations are performed by editing the form collecting information for TeSS entries. This applies to both training materials and events. Annotations using the three resources mentioned here can be done independently and without following any particular order.
Note
You need to be the resource creator of the page or have annotator privileges on TeSS to add these annotations on a previously generated pages
10.4.1. Annotating TeSS with FAIRsharing identifiers¶
Each FAIRsharing entry is assigned a human-readable, unique identifier.
These allow to trace resources and integrate FAIRsharing data with other resources. To annotate a TeSS entry with FAIRsharing identifiers, follow these steps:
Please select event or material you wish to annotate on TeSS or create a new one.
Click the EDIT button on the top right.
In this edit mode, scroll down to the “Suggested policies, standards and databases to associate with this resource” section and expand it.
Type the name of the standard/repository/policy to be associated with the TeSS entry. You have the option to choose one of the sub-registries from FAIRsharing.
Click on the “+” symbol to add the identifier to the page.
Scroll to the bottom and click the orange “update” button to publish your updates.
The annotation will appear on the materials page in the “External resources” section
This annotations can be used for filtered queries on TeSS using the syntax:
https://tess.elixir-europe.org/ + “TeSS SUBREGISTRY” + standard_database_or_policy= + “FAIRSHARING NAME”
where “TeSS SUBREGISTRY” is one of the subregistries of TeSS (e.g. “materials”) and “FAIRSHARING NAME” is the name (not the DOI) associated with the FAIRsharing entry.
In the case of training materials for the European Nucleotide Archive, for example, the query sting would be:
https://tess.elixir-europe.org/materials?standard_database_or_policy=European+Nucleotide+Archive
10.4.2. Annotating TeSS with bio.tools identifiers¶
Each bio.tools entry is assigned a human-readable, unique identifier.
These identifiers provide a reference to a “Tool Cards” of essential information. These allow to trace resources and integrate bio.tools data with other resources. To annotate a TeSS entry with bio.tools identifiers, follow these steps:
Please select event or material you wish to annotate on TeSS or create a new one.
Click the EDIT button on the top right.
In this edit mode, scroll down to the “Suggested tools to associate with this resource” section and expand it.
Type the name of the tool to be associated with the TeSS entry.
Click on the “+” symbol to add the identifier to the page.
Scroll to the bottom and click the orange “update” button to publish your updates.
The annotation will appear on the materials page in the “External resources” section
These annotations can be used for filtered queries on TeSS using the syntax:
https://tess.elixir-europe.org/ + “TeSS SUBREGISTRY” + ?tools= + “BIOTOOLS_NAME”
where “TeSS SUBREGISTRY” is one of the subregistries of TeSS (e.g. “materials”) and “BIOTOOLS_NAME” is the name (not the tool ID) associated with the bio.tools entry.
In the case of training materials for the Data Stewardship Wizard, for example, the query string would be:
https://tess.elixir-europe.org/materials?tools=Data+Stewardship+Wizard
10.4.3. Annotating TeSS with EDAM ontology¶
10.4.3.1. Annotating with EDAM main terms¶
TeSS pages can be annotated using two subregistries of EDAM: “Scientific topics” and “Operations”. These would need to be added separately. To annotate a TeSS entry using a main terms of EDAM, use the following procedure:
Please select event or material you wish to annotate on TeSS or create a new one.
Click the EDIT button on the top right.
In this edit mode, scroll down to the “Scientific topics” or to the “Operations” section.
Type the name of the main EDAM term to be associated with the TeSS entry. As you are typing, suggestions will be provided. If no relevant suggestions appear, follow the block of instructions below.
Click on the suggestion to add the annotation to the page.
Scroll to the bottom and click the orange “update” button to publish your updates.
The annotation will appear on the materials page in the “Scientific Topics” and “Operations” sections. Note that the terms are not clickable.
10.4.3.2. Browse through synonyms on EDAM to find the right class¶
In the current integration (Version: 1.4.1), TeSS only displays the main EDAM terms. Synonyms cannot be accessed. Instructions on how to browse this additional information are provided below:
1.Open the NCBO BioPortal 1.Under “Find an ontology”, start typing “EDAM” and click on “EDAM - The data analysis and management ontology”
Open the “Classes” tab and type your desired term. This will search also through synonyms and provide a better suggestion than the native TeSS implementation.
Use the “preferred name” as the main EDAM term when following the block of instructions above.
Note
EDAM supports a wide range on synonyms with various degrees of semantic proximity to the main term.
EDAM-annotated entries can be retrieved using filtered queries on TeSS with the syntax:
for EDAM’s Topics
https://tess.elixir-europe.org/+ “TeSS SUBREGISTRY” +?scientific_topic=+ “EDAM_NAME”for EDAM’s Operations
https://tess.elixir-europe.org/+ “TeSS SUBREGISTRY” +?operations=+ “EDAM_NAME”
where “TeSS SUBREGISTRY” is one of the subregistries of TeSS (e.g. “materials”) and “EDAM_NAME” is the name (not the ID) associated with the EDAM class.
In the case of training events with “data management” as a topic, for example, the query string would be:
https://tess.elixir-europe.org/events?scientific_topics=Data+management
