%1 services

Brochure on ELIXIR Industry programme.

The objectives of ELIXIR’s Industry Strategy are to:

1. Increase industry usage of ELIXIR resources and ensure that name is synonymous with quality
2. Enable Open innovation by Europe’s SMEs
3. Build effective partnerships with key industry stakeholders and initiatives
4. Ensure effective communication between industry and ELIXIR
5. Support the bioinformatics training needs of industry 

Harnessing the strength of the ELIXIR Hub and Nodes structure, ELIXIR’s Industry Strategy also seeks to ensure complementarity with the industry programmes already being run by ELIXIR Nodes, adding value where possible and avoiding duplications.

This documents outlines ELIXIR’s position on the different business models for access and use of bioinformatics data. Reflecting its commitment to Open Data, Open Source and Open Science, ELIXIR's recommendation for the European Open Science Cloud is that non-depletable resources (such as data, tools and software and standards) developed through public funding should be provided to users without charge (i.e. a “public good”). Charging users for access to depletable resources (including HPC/cloud computing and data management consultancy support), however, is a necessary and legitimate business model that helps with efficient resource allocation. However, care must be taken such that cost-recovery models do not introduce costly overheads and complex management of micro transactions for users and home institutions (e.g. universities and other scientific or educational organisations).

This ELIXIR report describes companies whose business model is fundamentally based on selling services on top of public bioinformatics data. It presents the typical business model of these companies and the particular way in which they add value to public data through customisation, aggregation and through facilitating the discovery of public data. Furthermore, it describes the relationship these companies have with ELIXIR Core Data Resources, and the direct way in which they generate revenue, such as through consultancy services or developing bespoke software.

This Study's work will address the following themes:

1. Optimal CNV detection pipelines for research and diagnostics: to release a set of sensitive and reliable pipelines, optimized and validated to detect CNV from various high throughput datasets. These pipelines will be available either through the ELIXIR compute nodes and/or as stand-alone solutions.
2. Definition of reference datasets: to provide open reference datasets of fully validated somatic and germline CNVs representing a wide range of samples types and experimental technologies.
3. Improvement of community formats for CNV exchange: to improve the VCF format and identify other nomenclatures and widely used formats in other communities (in alignment with GA4GH and the ELIXIR Interoperability Platform)
4. Enabling CNV data discovery in diagnostic and phenotypic context: The hCNV Community will work towards enabling the ELIXIR Beacon Project for the envisioned patient discovery, through the support of extended clinical descriptions including enabling and testing of relevant annotation standards (e.g. HPO, NCIt and additional ontologies).
5. Functional annotation of CNVs
6. Combinatorial approaches to CNV interpretation
7. Identification of landmark genes in regions of interest
8. FAIRification of hCNV databases and datasets: The FAIR principles (Findable, Accessible, Interoperable, Reusable) will be applied to those systems to demonstrate the feasibility and utility of distributed CNV databases in order to allow interoperability (including resource and data discovery).
9. Dissemination:
   1. Training materials
   2. Train actors, patients and the general public
   3. Capacity Building training events across certain ELIXIR Nodes

This Study's work will address the following themes:

1. Optimal CNV detection pipelines for research and diagnostics: to release a set of sensitive and reliable pipelines, optimized and validated to detect CNV from various high throughput datasets. These pipelines will be available either through the ELIXIR compute nodes and/or as stand-alone solutions.
2. Definition of reference datasets: to provide open reference datasets of fully validated somatic and germline CNVs representing a wide range of samples types and experimental technologies.
3. Improvement of community formats for CNV exchange: to improve the VCF format and identify other nomenclatures and widely used formats in other communities (in alignment with GA4GH and the ELIXIR Interoperability Platform)
4. Enabling CNV data discovery in diagnostic and phenotypic context: The hCNV Community will work towards enabling the ELIXIR Beacon Project for the envisioned patient discovery, through the support of extended clinical descriptions including enabling and testing of relevant annotation standards (e.g. HPO, NCIt and additional ontologies).
5. Functional annotation of CNVs
6. Combinatorial approaches to CNV interpretation
7. Identification of landmark genes in regions of interest
8. FAIRification of hCNV databases and datasets: The FAIR principles (Findable, Accessible, Interoperable, Reusable) will be applied to those systems to demonstrate the feasibility and utility of distributed CNV databases in order to allow interoperability (including resource and data discovery).
9. Dissemination:
   1. Training materials
   2. Train actors, patients and the general public
   3. Capacity Building training events across certain ELIXIR Nodes

This Study's work will address the following themes:

1. Optimal CNV detection pipelines for research and diagnostics: to release a set of sensitive and reliable pipelines, optimized and validated to detect CNV from various high throughput datasets. These pipelines will be available either through the ELIXIR compute nodes and/or as stand-alone solutions.
2. Definition of reference datasets: to provide open reference datasets of fully validated somatic and germline CNVs representing a wide range of samples types and experimental technologies.
3. Improvement of community formats for CNV exchange: to improve the VCF format and identify other nomenclatures and widely used formats in other communities (in alignment with GA4GH and the ELIXIR Interoperability Platform)
4. Enabling CNV data discovery in diagnostic and phenotypic context: The hCNV Community will work towards enabling the ELIXIR Beacon Project for the envisioned patient discovery, through the support of extended clinical descriptions including enabling and testing of relevant annotation standards (e.g. HPO, NCIt and additional ontologies).
5. Functional annotation of CNVs
6. Combinatorial approaches to CNV interpretation
7. Identification of landmark genes in regions of interest
8. FAIRification of hCNV databases and datasets: The FAIR principles (Findable, Accessible, Interoperable, Reusable) will be applied to those systems to demonstrate the feasibility and utility of distributed CNV databases in order to allow interoperability (including resource and data discovery).
9. Dissemination:
   1. Training materials
   2. Train actors, patients and the general public
   3. Capacity Building training events across certain ELIXIR Nodes

This Study's work will address the following themes:

1. Optimal CNV detection pipelines for research and diagnostics: to release a set of sensitive and reliable pipelines, optimized and validated to detect CNV from various high throughput datasets. These pipelines will be available either through the ELIXIR compute nodes and/or as stand-alone solutions.
2. Definition of reference datasets: to provide open reference datasets of fully validated somatic and germline CNVs representing a wide range of samples types and experimental technologies.
3. Improvement of community formats for CNV exchange: to improve the VCF format and identify other nomenclatures and widely used formats in other communities (in alignment with GA4GH and the ELIXIR Interoperability Platform)
4. Enabling CNV data discovery in diagnostic and phenotypic context: The hCNV Community will work towards enabling the ELIXIR Beacon Project for the envisioned patient discovery, through the support of extended clinical descriptions including enabling and testing of relevant annotation standards (e.g. HPO, NCIt and additional ontologies).
5. Functional annotation of CNVs
6. Combinatorial approaches to CNV interpretation
7. Identification of landmark genes in regions of interest
8. FAIRification of hCNV databases and datasets: The FAIR principles (Findable, Accessible, Interoperable, Reusable) will be applied to those systems to demonstrate the feasibility and utility of distributed CNV databases in order to allow interoperability (including resource and data discovery).
9. Dissemination:
   1. Training materials
   2. Train actors, patients and the general public
   3. Capacity Building training events across certain ELIXIR Nodes

This Study's work will address the following themes:

1. Optimal CNV detection pipelines for research and diagnostics: to release a set of sensitive and reliable pipelines, optimized and validated to detect CNV from various high throughput datasets. These pipelines will be available either through the ELIXIR compute nodes and/or as stand-alone solutions.
2. Definition of reference datasets: to provide open reference datasets of fully validated somatic and germline CNVs representing a wide range of samples types and experimental technologies.
3. Improvement of community formats for CNV exchange: to improve the VCF format and identify other nomenclatures and widely used formats in other communities (in alignment with GA4GH and the ELIXIR Interoperability Platform)
4. Enabling CNV data discovery in diagnostic and phenotypic context: The hCNV Community will work towards enabling the ELIXIR Beacon Project for the envisioned patient discovery, through the support of extended clinical descriptions including enabling and testing of relevant annotation standards (e.g. HPO, NCIt and additional ontologies).
5. Functional annotation of CNVs
6. Combinatorial approaches to CNV interpretation
7. Identification of landmark genes in regions of interest
8. FAIRification of hCNV databases and datasets: The FAIR principles (Findable, Accessible, Interoperable, Reusable) will be applied to those systems to demonstrate the feasibility and utility of distributed CNV databases in order to allow interoperability (including resource and data discovery).
9. Dissemination:
   1. Training materials
   2. Train actors, patients and the general public
   3. Capacity Building training events across certain ELIXIR Nodes

This Study's work will address the following themes:

1. Optimal CNV detection pipelines for research and diagnostics: to release a set of sensitive and reliable pipelines, optimized and validated to detect CNV from various high throughput datasets. These pipelines will be available either through the ELIXIR compute nodes and/or as stand-alone solutions.
2. Definition of reference datasets: to provide open reference datasets of fully validated somatic and germline CNVs representing a wide range of samples types and experimental technologies.
3. Improvement of community formats for CNV exchange: to improve the VCF format and identify other nomenclatures and widely used formats in other communities (in alignment with GA4GH and the ELIXIR Interoperability Platform)
4. Enabling CNV data discovery in diagnostic and phenotypic context: The hCNV Community will work towards enabling the ELIXIR Beacon Project for the envisioned patient discovery, through the support of extended clinical descriptions including enabling and testing of relevant annotation standards (e.g. HPO, NCIt and additional ontologies).
5. Functional annotation of CNVs
6. Combinatorial approaches to CNV interpretation
7. Identification of landmark genes in regions of interest
8. FAIRification of hCNV databases and datasets: The FAIR principles (Findable, Accessible, Interoperable, Reusable) will be applied to those systems to demonstrate the feasibility and utility of distributed CNV databases in order to allow interoperability (including resource and data discovery).
9. Dissemination:
   1. Training materials
   2. Train actors, patients and the general public
   3. Capacity Building training events across certain ELIXIR Nodes

This Study's work will address the following themes:

1. Optimal CNV detection pipelines for research and diagnostics: to release a set of sensitive and reliable pipelines, optimized and validated to detect CNV from various high throughput datasets. These pipelines will be available either through the ELIXIR compute nodes and/or as stand-alone solutions.
2. Definition of reference datasets: to provide open reference datasets of fully validated somatic and germline CNVs representing a wide range of samples types and experimental technologies.
3. Improvement of community formats for CNV exchange: to improve the VCF format and identify other nomenclatures and widely used formats in other communities (in alignment with GA4GH and the ELIXIR Interoperability Platform)
4. Enabling CNV data discovery in diagnostic and phenotypic context: The hCNV Community will work towards enabling the ELIXIR Beacon Project for the envisioned patient discovery, through the support of extended clinical descriptions including enabling and testing of relevant annotation standards (e.g. HPO, NCIt and additional ontologies).
5. Functional annotation of CNVs
6. Combinatorial approaches to CNV interpretation
7. Identification of landmark genes in regions of interest
8. FAIRification of hCNV databases and datasets: The FAIR principles (Findable, Accessible, Interoperable, Reusable) will be applied to those systems to demonstrate the feasibility and utility of distributed CNV databases in order to allow interoperability (including resource and data discovery).
9. Dissemination:
   1. Training materials
   2. Train actors, patients and the general public
   3. Capacity Building training events across certain ELIXIR Nodes

This Study's work will address the following themes:

1. Optimal CNV detection pipelines for research and diagnostics: to release a set of sensitive and reliable pipelines, optimized and validated to detect CNV from various high throughput datasets. These pipelines will be available either through the ELIXIR compute nodes and/or as stand-alone solutions.
2. Definition of reference datasets: to provide open reference datasets of fully validated somatic and germline CNVs representing a wide range of samples types and experimental technologies.
3. Improvement of community formats for CNV exchange: to improve the VCF format and identify other nomenclatures and widely used formats in other communities (in alignment with GA4GH and the ELIXIR Interoperability Platform)
4. Enabling CNV data discovery in diagnostic and phenotypic context: The hCNV Community will work towards enabling the ELIXIR Beacon Project for the envisioned patient discovery, through the support of extended clinical descriptions including enabling and testing of relevant annotation standards (e.g. HPO, NCIt and additional ontologies).
5. Functional annotation of CNVs
6. Combinatorial approaches to CNV interpretation
7. Identification of landmark genes in regions of interest
8. FAIRification of hCNV databases and datasets: The FAIR principles (Findable, Accessible, Interoperable, Reusable) will be applied to those systems to demonstrate the feasibility and utility of distributed CNV databases in order to allow interoperability (including resource and data discovery).
9. Dissemination:
   1. Training materials
   2. Train actors, patients and the general public
   3. Capacity Building training events across certain ELIXIR Nodes

This Study's work will address the following themes:

1. Optimal CNV detection pipelines for research and diagnostics: to release a set of sensitive and reliable pipelines, optimized and validated to detect CNV from various high throughput datasets. These pipelines will be available either through the ELIXIR compute nodes and/or as stand-alone solutions.
2. Definition of reference datasets: to provide open reference datasets of fully validated somatic and germline CNVs representing a wide range of samples types and experimental technologies.
3. Improvement of community formats for CNV exchange: to improve the VCF format and identify other nomenclatures and widely used formats in other communities (in alignment with GA4GH and the ELIXIR Interoperability Platform)
4. Enabling CNV data discovery in diagnostic and phenotypic context: The hCNV Community will work towards enabling the ELIXIR Beacon Project for the envisioned patient discovery, through the support of extended clinical descriptions including enabling and testing of relevant annotation standards (e.g. HPO, NCIt and additional ontologies).
5. Functional annotation of CNVs
6. Combinatorial approaches to CNV interpretation
7. Identification of landmark genes in regions of interest
8. FAIRification of hCNV databases and datasets: The FAIR principles (Findable, Accessible, Interoperable, Reusable) will be applied to those systems to demonstrate the feasibility and utility of distributed CNV databases in order to allow interoperability (including resource and data discovery).
9. Dissemination:
   1. Training materials
   2. Train actors, patients and the general public
   3. Capacity Building training events across certain ELIXIR Nodes

This Study's work will address the following themes:

1. Optimal CNV detection pipelines for research and diagnostics: to release a set of sensitive and reliable pipelines, optimized and validated to detect CNV from various high throughput datasets. These pipelines will be available either through the ELIXIR compute nodes and/or as stand-alone solutions.
2. Definition of reference datasets: to provide open reference datasets of fully validated somatic and germline CNVs representing a wide range of samples types and experimental technologies.
3. Improvement of community formats for CNV exchange: to improve the VCF format and identify other nomenclatures and widely used formats in other communities (in alignment with GA4GH and the ELIXIR Interoperability Platform)
4. Enabling CNV data discovery in diagnostic and phenotypic context: The hCNV Community will work towards enabling the ELIXIR Beacon Project for the envisioned patient discovery, through the support of extended clinical descriptions including enabling and testing of relevant annotation standards (e.g. HPO, NCIt and additional ontologies).
5. Functional annotation of CNVs
6. Combinatorial approaches to CNV interpretation
7. Identification of landmark genes in regions of interest
8. FAIRification of hCNV databases and datasets: The FAIR principles (Findable, Accessible, Interoperable, Reusable) will be applied to those systems to demonstrate the feasibility and utility of distributed CNV databases in order to allow interoperability (including resource and data discovery).
9. Dissemination:
   1. Training materials
   2. Train actors, patients and the general public
   3. Capacity Building training events across certain ELIXIR Nodes

This ELIXIR report presents the different ways in which ELIXIR Nodes support industry . It features a series of success stories highlighting industry-academia collaboration across ELIXIR.

The success stories are grouped into four categories: 

1. Engagement and collaboration: Strategic partnerships and bespoke collaboration
2. Service provision: Services with high industry relevance
3. Outreach, dissemination and brokering
4. Seeking advice: Membership programmes and advisory bodies

Each category represents the different ways ELIXIR Nodes, and the services they run,  interact with and are used by companies. The report shows that While some companies look for bespoke collaborations with ELIXIR Nodes to help them to find an optimal solution to their research activities, others simply want to learn more about the existing bioinformatics services and provide feedback on how they can better meet the needs of industry.