FAIDARE FAIR Data-finder for Agronomic Research

1. Resource facilitation to scientific research

a. Interoperability Resource: Briefly describe the function of the Interoperability Resource

FAIDARE is a data portal that enables and increases dataset findability and accessibility in open international federations of information systems for research on plants. It increases interoperability by using, promoting and implementing established standards and in particular the Minimum Information About a Plant Phenotyping Experiment (MIAPPE) and the Breeding API. FAIDARE is proposed as a service by the ELIXIR Plant Science community through Elixir-fr (https://urgi.versailles.inra.fr/faidare) and as a software for any community wishing to build its own portal. It consists in a web portal (https://github.com/elixir-europe/plant-faidare ) and a a system for harvesting and indexing metadata from BrAPI endpoints (https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis).

b. Scope statement: describe the scope , and the users of the resource. How is the Interoperability Resource positioned with respect to other similar Interoperability Resources? Include the base URL and, if relevant, the introductory or “about” page URL.

The objective of the FAIDARE web portal and metadata harvester tools are to facilitate the development of national and international federations of information systems.

The FAIDARE Data finder and access service allows to index any international plant data repository and provides a one stop portal to access currently scattered data sets. For the data repository manager, FAIDARE’s originality lies in its ability to provide access to many data repositories with a low data integration effort. Indeed, to join the FAIDARE federation, it is only required to implement the relevant BrAPI calls that, on the top of improving data access, interoperability and visibility through the portal, enables interoperability with data visualization and exchange tools(https://brapi.org/brapps, …). For the researchers seeking interesting datasets, it allows a one stop search across well known and less reknowned data repositories.

FAIDARE implements the Breeding API (www.brapi.org, BrAPI) standard, an implementation of the MIAPPE and MCPD standards of the Plant research community respectively for plant phenotyping experiments and for germplasm. This enables, a deeper data interoperability between the information systems of a federation dedicated to research on plants. It is an extension of the successful WheatIS.org.

FAIDARE About Section : https://urgi.versailles.inra.fr/faidare/about

c. Resource url

https://urgi.versailles.inra.fr/faidare/

d. Inter-organisational recognition: does the Interoperability Resource have community recognition? (e.g. demonstrated through a collaboration, geographical diversity in the source of the submissions, international diversity of delivery partners and/or funders)

The FAIDARE data findability service has been so far developed in the frame of two major distributed infrastructures, to which it provides today data discoverability:

• the information system of the French National Phenotyping Network, Phenome (https://www.phenome-fppn.fr/), which is the French node of the European Plant Phenotyping infrastructure, EMPHASIS (https://emphasis.plant-phenotyping.eu/),
• and the ELIXIR portal of the plant community (/use-cases/plant-sciences) in collaboration with the interoperability and the compute platform.

Currently the FAIDARE federation includes endpoints from the Elixir Community: EMBL-EBI, Elixir-fr (INRAE, CIRAD), Elixir-be (VIB), Elixir-nl (WUR), Elixir-pt (IBET), Elixir-sl (NIB).

It also has attracted interest from US DOE TerraREF.org.

2. Community

a. Community impact: If applicable, provide documented evidence of community impact (e.g., publication citations, API calls, projects using the resource, etc.)

The adoption of the system is growing fast starting from the Elixir Plant community and outreaches toward the WheatIS, the Consultative Group for International Agricultural Research (CGIAR) and Emphasis. Elixir implemented 7 BrAPI endpoints in 2019 that allowed to validate the harvester and to test the interface. For instance, the Terraref.org phenotyping platform was also interested and joined the federation, hence showing the interest of that system beyond Elixir.

Elixir-de contributed to the library of federation enabling tools through the publication of a BrAPI endpoint validation tool, BRAVA (https://github.com/plantbreeding/IPK-BrAPI-Validator ), that is used to test the quality of the web services. It is important to note that these federation enabling tools are part of the formal discussions between ELIXIR and EMPHASIS ESFRIs and that PHIS (www.phis.inra.fr ) and PIPPA, Emphasis phenotyping databases, are connected to FAIDARE.

The interoperability specifications are managed through BrAPI. FAIDARE is in this case aims at being one of the applications demonstrating an international coordination between the CGIAR and Elixir communities.

A scientific paper describing FAIDARE will be written in 2020. It is implicitly present in federation perspectives of the GnpIS Phenomic paper (https://doi.org/10.34133/2019/1671403 ) and one of the BrAPI paper use cases (https://doi.org/10.1093/bioinformatics/btz190 ).

b. Potential usage: Describe other systems that could use this candidate resource, but currently do not.

The connection with Elixir Data repositories is being actively improved, in particular in the frame of Plant Community Lead Implementation Study (FONDUE IS) for the EMBL-EBI genomic and genotyping databases. Several other data repositories will be soon added, including CGIAR databases, using the github pull request mechanism (https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis/pulls?utf8=✓&q=is%3Apr+label%3A%22endpoint+managment%22+). Several other endpoints will be added to FAIDARE in Europe, including but not limited to major genetic resources data repositories.

To connect Findability and Workflows environment, FAIDARE will be added as a standard data source in galaxy.

There is a complementarity on data discovery between Beacons and FAIDARE that has been discussed in the frame of BrAPI and Ga4GH meetings that we coordinated.

Finally, Bioschemas.org has a huge potential impact on FAIDARE by allowing to index and therefore give access to non BrAPI compliant datasets in FAIDARE, hence dramatically increasing the quantity of available data (Bioschemas Elixir Implementation Study).

c. Outreach & support: Provide resource support publication(s)/user documentation(s) describing the Interoperability Resource (e.g. scientific journal publications, community preprints, resource user’s documentations etc.), resource dissemination plan (e.g. workshops, conference presentations), and other equal-opportunity research support (if applicable).

The FAIDARE tool is being actively promoted in international conferences : Plant and Animal Genome San Diego 2019 & 2020, ISMB 2019, Integrative Bioinformatic symposium 2018 & 2019, Breeding API hackathon 2017-2020. A dedicated paper will be written in 2020.

The user documentation is embedded in the application. All the developer documentation is embedded in the github repository.

d. Dependency of other resources: How is this resource critical to the user(s)? Do other resources depend on the resource described here to provide downstream service? Please list, or provide a link to a diagram.

FAIDARE address the findability and programmatic access problem. It is therefore important for researchers and data providers, but there is no strong coupling to downstream analysis resources.

3. Quality of resource

a. Uptime: Average percentage uptime/month during the last 12 months, response time of the resource. In case of ontology/standards production, interval of update/release, adaptability of ontology design patterns to evolving data. Provide information where applicable: uptime of resource, software release cycle (please state week/month etc), update frequency.

FAIDARE has an average uptime of 96,7 % measured with Nagios.org since its public availability in July 2019. It is currently very actively developed, with continuous delivery of new versions every 1 to 3 months using the public INRAE Gitlab continuous integration infrastructure accessible from the github FAIDARE repository (https://github.com/elixir-europe/plant-faidare).

The FAIDARE underlying data standard, BrAPI, is regularly updated, with a new version at least each year.

b. Accessibility: what are resource retrieval mechanisms? Does the resource provide web-based user interface, application programmable interface (API), containers, and/or other channels? Please list resource access mechanism, provide URLs as applicable.

FAIDARE provide web based user interface as well as an OpenAPI documented using swagger (https://urgi.versailles.inra.fr/faidare/swagger-ui.html ).

c. Maintenance quality: Is there a maintenance SOP or plan, reflecting sustainability and scalability? Does it align with guidelines for sustainable software development? Please include a resource commitment statement (description text or URL).

There is no maintenance SOP. There is a plan in progress to improve genotyping data indexing and interoperability with phenotyping in the frame of FONDUE. This includes the set up of an alignment and a complementarity between BrAPI and GA4GH. Providing services to data federation are part of the platform objectives (https://urgi.versailles.inra.fr/About-us) which is fully supported by INRAE through the INRAE objective 2025 #OpenScience.

FAIDARE is aligned with the guidelines for sustainable software development:

Usability

• built with user committees and the interface is continuously improved. “Users help” documentation is embedded.
• the README available in the github repository gives extensive instruction on Buildability, Instability, and Learnability.

Sustainability and maintainability

• The identity, copyright and licensing are documented through the BSD license. The governance is for now minimal (URGI Platform with user committee : Elixir Plant community plus the WheatIS community) and will be extended if requested.
• The software is publicly accessible in Github and on the URGI platform website.
• Extensive test suites (unit, integration, interface, coverage coding standards) are run daily in INRAE gitlab continuous integration environment. This gitlab is automatically synchronized with github.
• FAIDARE uses portable frameworks (Java, Angular), dependencies management frameworks (Graddle, NPM) and containers (Docker, embedded tomcat) for easy installation and development on any modern operating system (Windows, Linux/*nix, MacOS).
• Support and analysis are good, therefore easily maintainable including by junior developers.
• The interoperability of FAIDARE is ensured by embedding established standards (BrAPI, Bioschemas, MIAPPE, Bioschemas, wheatIS federation, …).

d. Support quality: Please list support mechanisms (e.g., point of contact, request ticketing, resource’s response time where a solution is identified, etc.), and methods to collect user feedback. If available, list tutorial documentations or tutorial materials and format, including linking on the ELIXIR’s Training Portal (TeSS) (or other training platforms) where applicable.

FAIDARE support can be obtained through email, the elixir plant community list, and github and gitlab issues. Support to join FAIDARE federation is provided through pull requests (https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis/pulls).

4. Legal framework, funding, and governance

a. Legal framework: What are the resource’s license/terms of use? Can the license facilitate Open Science? Please include the url for the license the resource uses.

FAIDARE source code is open source (BSD). The data licensing is under the responsibility of the data repositories that are joining the FAIDARE federation.

b. Privacy/Ethics policy: If applicable, is there a publicly available privacy policy in which use and security around personal data are described (e.g. the EU General Data Protection Regulation (GDPR), ELIXIR Ethics Policy, other relevant ELIXIR Policies)? Please include the url of the privacy/ethics policy, if applicable.

N/A

c. Funding & sustainability plan: List of funding sources supporting the resource, and sustainability plan.

The French national institute for Agricultural Research and Environment (INRAE) is fully funding the URGI bioinformatic platform which main mission is to enable open science using in particular FAIDARE. Non-permanent staff will be hired to work on this technology through national and European projects such as the recently granted H20

d. Governance: Describe the Resource’s QA/QC plan that guarantees similar quality governance to that of ELIXIR. Please link SAB members, if applicable.

We will follow the experience of MIAPPE. The code and discussion or for now fully opened and anybody can reach out and contact us directly or through the Elixir Plant community. The user community will eventually be big enough to deem necessary the creation of a steering committee representing the main stakeholders.