Bioschemas

Goal: To encourage the use of schema.org markup within life sciences web resources to improve discoverability of information.

Leader: Carole Goble (ELIXIR UK), Alasdair Gray (ELIXIR UK)

Activities:

• Developing specifications for content types relevant to the life science community e.g. Dataset, Protein, Sample, Standard (see the Bioschemas website for the current list of specifications).
• Creating tools that facilitate the validation and the discovery of web resources that use schema.org markup
• Meetings, hackathons, training in adoption - see the events section for upcoming events or the Bioschemas meetings page.

Get involved: join the ELIXIR Bioschemas group and the broader Bioschemas community.

Identifiers

Goal: To harmonise existing practice in identifier assignment and resolution, to support resources in implementing community standards and to promote the creation of identifier services.

Leader: Carole Goble (ELIXIR UK)

Activities:

• Working with the Rare Diseases Community to assess and support their needs for identifier best practices, resolution, citation and mapping.
• Engaged with NIH BD2K and BioCADDIE/DCIP on identifier service harmonisation and data citation infrastructure.
• Implementation Study on Data Identification and Interoperability: a project to establish Identifiers.org as a stable ELIXIR system for uniform identifier resolution to major bioinformatics resources.
• Holding Bring Your Own Data workshops to support best practices and adoption of identifier services.
• For more information see the Identifiers group page.

Get involved: join the Identifiers group.

Metadata and ontology tooling

Goal: To design, test and implement a metadata strategy for ELIXIR using the Plant Sciences Community as a driver.

Leader: Helen Parkinson (EMBL-EBI), Alasdair Gray (ELIXIR UK), Carole Goble (ELIXIR UK), Susanna-Assunta Sansone and Philippe Rocca-Serra (ELIXIR UK)

Activities:

• Working with the ELIXIR Communities to assess their complex requirements for metadata both for archival and added value resources.
• Developing a metadata strategy for ontology services, semantic services and best practice examples for the ELIXIR Plant Sciences Community.
• Implementing a BRAPI 2 ISA conversion with ISA Tools to comply to the MIAPPI requirements.
• Providing training for ELIXIR-affiliated developers in the use of metadata (ontology) standards and existing ontology tools.
• Working with the international ontology user community to promote interoperable ontologies and services international biomedical interoperability.
• Delivery of ELIXIR candidate ontology services comprising the Ontology Lookup Service, Ontology Cross Reference Service (OxO), and the data annotation service (Zooma).
• Service Benchmarking to improve performance and usability.
• Providing training for ELIXIR-affiliated developers in the use of metadata (ontology) standards and existing ontology tools.

Linked Data

Goal: To deliver best practice for implementation and use of Linked Data in ELIXIR Communities and inform future development, deployment and sustainable production of linked data resources as ELIXIR resources. Not all ELIXIR Linked Data will be Linked Open Data (LOD); instead we will focus on technologies for Linked Data to help make data FAIR, resulting in what we call "Linked FAIR Data".

Leader: Chris Evelo (ELIXIR Netherlands), Marco Roos (ELIXIR Netherlands)

Activities:

• Developing the FAIR Service Suite.
• Engaged with the Linked (Open) Data Community to define best practices.
• The Rare Disease Use Case has developed a data linkage plan that allows it to test the tools, models, and protocols to standardise data services in the rare disease domain conform to FAIR data principles (See a summary of practical FAIRification guidelines).
• Use-case collaborators include RD-Connect, BBMRI-NL, FAIR-dICT, and ODEX4ALL.

Workflow and Tool interoperability

Goal: To create specifications that enable data scientists to describe analysis tools and workflows to make them interoperable across Communities.

Leader: Carole Goble (ELIXIR UK)

Activities:

• Enabling the reuse, extension, scaling, and reproducibility of scientific workflows, an Implementation Study working with the Marine Metagenomics Community on using the Common Workflow Language (CWL).
• Promoting industry standards for API documentation.
• Engaged with the Common Workflow Language (CWL) community group and BioExcel Centre of Excellence for BioMolecular Simulation.

Interoperability Knowledge Hub

Goal: To create an online knowledge hub where infrastructure and tool developers can be informed about current ELIXIR Interoperability Platform activities, assess current best practice and determine which interoperability services and standards to implement under specific circumstances. This will build upon the initial description of activities as described on this page above.

Leaders: Sirarat Sarntivijai (ELIXIR Hub)

Activities:

• Work with the community to develop the ELIXIR Interoperability Service guideline and best practices.
• In support of the project activities detailed above an ELIXIR Interoperability Knowledge Hub will be developed in collaboration with the ELIXIR Hub.

Implementation Studies

The Interoperability Platform is involved in a number of short-term, technical projects called Implementation Studies. These are currently:

• Capacity Building
• FAIR Service Architecture
• Interoperability Services for the Cloud
• Interoperability with a Purpose
• A Scalable approach to Personal FAIR Data
• Data Validation
• Increasing Interoperability of protein resources 
• Annotation and curation of human genomic variations
• Metabolite Identification  

For completed studies see the Implementation Studies page.