ELIXIR Interoperability - Frequently Asked Questions

The ELIXIR Interoperability Platform frequently asked questions are answered by a community-support mechanism. If you cannot find the answer to your question, please submit your question via  "Ask Interoperability a question" form.

What is the purpose of the ELIXIR Interoperability Platform (EIP)?

The goal of the Interoperability Platform is to help people and machines to discover, access, integrate and analyse biological data. It encourages the life science community to adopt standardised file formats, metadata, vocabularies and identifiers and works internationally to achieve its goals. In other words, we hope to generally increase the sum of human happiness and reduce the sum of human frustration via a much more valid-ly interconnected data-verse.

Where can I find information of the past EIP F2F meetings?

What is an RIR?

A Recommended Interoperability Resource (RIR) is a resource that has been reviewed through a selection process by linked-data and interoperability technical experts as suitable to perform a specific FAIRification task. The tasks are based on the activities in the EIP FAIR Service Architecture. For more information please see https://elixir-europe.org/platforms/interoperability/rirs

How does a service become an RIR?

The call for the ELIXIR RIR selection applications happens annually. The applicant service must be an ELIXIR service (indicated in the Node Service Delivery Plan) to be eligible for the consideration. The call is announced via the ELIXIR Weekly Brief newsletter, and other ELIXIR communications. The submission period generally remains open for 6-8 weeks. All applications are subject to reviews by semantics/ linked-data/ interoperability experts based on the selection criteria that is published with the call.

Where can I find information on ELIXIR data management and open science strategy?

As an organisation that stands for Open Science, ELIXIR has been referenced in key documentations [for grantees] such as the European Research Council Open Research Data and Data Management Plans.Information on ELIXIR's stance on open sceince strategy and data manangement policies can also be found in some [of] ELIXIR's response[s] to consultation[s] below.

It is also highlighted that ELIXIR-CONVERGE is a project funded by the European Commission to help standardise life science data management across Europe via the data management expert network equipped with the common data management toolkit for life scientists.

How do I FAIRify my data?

The FAIRplus Project (https://fairplus-project.eu/) aims to develop tools and guidelines for making life science data FAIR (Findable, Accessible, Interoperable, Reusable). The FAIRplus FAIR Cookbook provides the recipes to FAIRify data of various data types with different FAIRification tasks. The overview of the FAIRification steps and setup is described on FAIRplus - Making the data FAIR webpage.

How can I use Bioschemas?

Bioschemas is an extension of the schema.org technology that search engines use to understand web pages the way humans do naturally. Bioschemas can be used to exchange information between its services and its own search engines. Bioschemas makes life sciences resources more ‘F’indable on the Web by using Search Engine Optimisation approaches. Bioschemas provides guidelines for embedding schema.org markup within your web resource so that it becomes more discoverable. See https://bioschemas.gitbook.io/training-portal/ for additional information.

What is BrAPI?

The Breeding API (https://brapi.org). This is a way to get standardized metadata exchange for resources with plant breeding data.

How do I get advice on ontologies?

Depending on what specific part of “advice on ontologies” you are looking for, here are a few common things that we can think of:

  1. How to select an ontology - see Malone, James, et al. "Ten Simple Rules for Selecting a Bio-ontology." PLoS Computational Biology 12.2 (2016): e1004743-e1004743. (PMID:26867217 PMCID:PMC4750991).
  2. Where to find / browse an ontology of interest - we recommend the use of our RIR Ontology Lookup Service (OLS).
  3. How to contact the author(s) of a specific ontology - you can navigate to the author information of your ontology of interest via the OLS ontology listing page. By selecting an ontology, it will take you to the browsing page at the top level of the ontology. If the information of the authors is available, it will appear there.
  4. How to request a new term from an ontology - each ontology is managed differently. Some take requests via Github issue tracker, others communicate via direct e-mails or other channels. The common practice is to identify the developer(s) of the ontology of your interest, and enquire with the ontology developers.

Is there a repository of ontology mappings I can donate my mappings to and/or reuse previously mapped identifiers?

The EBI Ontology Xref Service (OxO) is a service for finding mappings (or cross-references) between terms from ontologies, vocabularies and coding standards. OxO imports mappings from a variety of sources including the Ontology Lookup Service and a subset of mappings provided by the UMLS. Please get in touch with the OxO developers if you have a set of curated identifier mappings you would like to share.

How can FAIRsharing help me?

FAIRsharing (https://fairsharing.org)  guides consumers to discover, select and use standards for data and metadata (reporting guidelines, models, formats, terminologies, identifiers schemas), repositories (databases, knowledgebases), data policies (by journals and funders)  with confidence. FAIRsharing assists producers of these resources to make them more discoverable, more widely adopted and cited. If you are a producer, ensure your resource is in FAIRsharing, by registering it or claiming its record (https://fairsharing.org/new).

How can I get in touch with a specific Interoperability Platform service support team and learn how to use it?

All ELIXIR Interoperability services (e.g., RIRs service) have a service page on https://elixir-europe.org/services. You can find the documentation and the contact details via these pages.

What is the phone number to speak to an Interoperability Human?

We fully understand that not being able to speak to another human is very frustrating. Here is the solution to that. Every second Friday of the month, all Interoperability Humans get together on a monthly Platform call. Please join our platform to receive the call-in information to talk to us human-to-human.

Can the Interoperability Platform get a Core Data Resource to change its metadata model?

The Core Data Resources (CDRs - https://elixir-europe.org/platforms/data/core-data-resources) are selected in a very careful selection process. There will be possibilities for new submissions in the future. The Interoperability Platform is working together with the Data Platform on the interoperability between the CDRs. Should there be a specific request, please do not hesitate to let the Data/Interoperability coodinators know.