myFAIR

1. Resource facilitation to scientific research

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

Clinical and translational research generates and utilises multi-sample multi-platform “OMICS” data that has a significant monetary cost to generate and to store. We have implemented a secure and easy to use “end-to-end” FAIR data point and analysis architecture that is applicable to any translational or clinical research project. myFAIR was developed to access to provide users with integrated analysis across EU RDF Services in combination with secure EGA access and analysis. myFAIR Analysis will be delivered as cloud based service that can be executed using the advanced INDIGO PaaS services on-top of any ELIXIR Compute Platform. 

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 current solutions for FAIR data management fall into two themes, (1) FAIR data developed programmatically and (2) FAIR data for large resources (e.g. EBI services) that have been made FAIR for use by research scientists. There is a need for tools that allow researchers to support FAIR data management themselves if GO-FAIR is to be a scalable and viable option. 

myFAIR encompasses both these solutions and provides the end user with a simple solution for personal FAIR data management and analysis to the research and clinical scientists (https://github.com/ErasmusMC-Bioinformatics/myFAIR). 
No similar application to myFAIR exist and the tranSMART the open source standard for data management and analysis requires data to be managed by a bioinformatician and the data structure needs to be modified prior to loading and analysis resulting in additional overhead to the process. 

FAIR data storage and management in myFAIR are provided by two existing platform, EUDAT (https://eudat.eu/) and SEEK (https://fair-dom.org/platform/seek/), and the inbuilt myFAIR triple store. 
myFAIR uses Galaxy as the workflow service and we have implemented a secure access and analysis application Galaxy European Genome Archive (GEGA) to support EU researchers accessing the EGA. 
Integrative analysis from EU resources (e.g EBI services, wikiPathways, etc…) is provided by the SPARQL query implementation included in myFAIR. This functionality can be combined with local data analysis and that from EGA with GEGA to deliver a cross platform FAIR data analysis.

c. Resource url

https://myfair.erasmusmc.nl

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)

In the Netherlands myFAIR has been adopted by HealthRI (https://www.health-ri.org/) and Lygature (https://www.lygature.org/) and presented as part of their training programme for FAIR data management (https://events.lygature.org/myfair-workshop-2017/). 

myFAIR has been adopted by the ELIXIR programme and will be funded in September 2018 as part of the Galaxy IS and as an implementation study in it own right as The development of myFAIR has been integrated into two H2020 proposals (CINECA, MEDiCate) and a ZonMw FAIR NGS Standardisation application to provide a FAIR data management and analysis solution. 

To extend the functionality of myFAIR beyond the use of EUDAT and Galaxy we have partnered with the FAIRdom community to incorporate their concepts and applications to unify these two FAIR applications. Currently the SEEK application is being incorporated as an alternative to EUDAT file storage, to deliver Investigation-Study Assay (ISA) and extend the use of ontologies beyond EDAM and DisGeNet that are part of myFAIR. 

2. Community

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

myFAIR is a new resource and is only now being prepared for publication and as the first in class for this type of application so the complete metrics about the community impact are limited currently. However, our myFAIR team and colleagues in our group are responsible for the implementation of several public Galaxy services. These include Galaxian (Erasmus MC central server for all published Galaxy tools ), ARGlaxy (for Immune disorders), MYcrobiota (for metagenomics and host-pathogen response) and the choosegalaxy.nl (Dutch ELIXIR Galaxy) in collaboration with Dr Leon Mei (LUMC, Leiden, NL). The Erasmus MC Galaxy server (Galaxian) has been available for public use for 5 years, MYcrobiota for 3 years, ARgalaxy for 2 years, choosegalaxy.nl for 1 year and all supported by the Clinical Bioinformatics Unit, Department of Pathology, Erasmus MC. Theses web services have delivered 10 peer review publications and have been cited 78 times for utilizing these applications.

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

myFAIR was developed to address the challenge outlined by EU to support FAIR data in all H2020 project applications. FAIR data analysis for cancer biomarker discovery with myFAIR will be developed to use federated data from the Catalog of FAIR data. Secure access to these data will be managed with the ELIXIR AAI service delivered in federated workflows used to analyse these data are part of existing Galaxy services for cancer genomics including fusion gene detection. Thus myFAIR will provide clinical research scientists with secure electronic notebook of their bioinformatics analysis with complete provenance of both the data, the methods and the parameters. In summary myFAIR is a unique application for FAIR data analysis used by researchers involved with clinical and translational research projects.

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 source code for myFAIR is available from https://github.com/ErasmusMC-Bioinformatics/myFAIR and the overall project and user documentation are also available.

Training material for myFAIR analysis was presented at Lygature Partnerships MeetUp 2016 (http://www.ctmm-trait.nl/training/partnership-meetup-utrecht-15-nov-201…). 
Dissemination of myFAIR which was as a poster at GCC 2017: P07: myFAIR Analysis: Personal FAIR Data. (https://gcc2017.sched.com/event/B8Rc/p07-myfair-analysis-personal-fair-…)..
In addition Scalable OMICS Analysis and Reporting (SOAR), incorporates the use of myFAIR as a central component, was accepted as an invited presentation at the Molecular Tri-conference in San Francisco, USA (http://www.triconference.com/Genomic-NGS-Knowledgebases/17)

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.

myFAIR Contribute to the Digital Single Market through piloting IT health research solutions. Federated analysis are in development ted methods it develops in real world research, SME and translational contexts. These will be in biobanking, disease associated biomarker/variant analysis, molecular pathology diagnostics and treatment planning. These services will all be available within a GDPR-compliant technical and legal framework to advance a patient-centred healthcare system by supporting a) cross-border sharing and access to healthcare data for citizens and b) cross-border data and analytics infrastructure.

myFAIR will support a research-enabling legal and ethical framework. The ability to process genomic and phenotypic data in the cloud, connect it to cohort meta data records, and use those discoveries in a systematic way to design a holistic solution for applying genomic medicine in healthcare can enable longer healthy lifespans and improved quality of life for patients. This can only be realised if the challenge of transferring expertise effectively from the research domain to healthcare is resolved with established and trusted data access mechanisms that are both appropriate to research applications and respectful of the rights of the individuals to whom the data pertain. 

This will be demonstrated by proof of concept studies demonstrating healthcare applications and will promote uptake by SMEs, contract research organisations (CROs) and academic researchers. We will embed our findings in the wider ELSI landscape using our network comprising primarily BBMRI-ERIC, ELIXR, GA4GH.

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.

The development server has been running internally and now we are waiting to get the production online https://myfair.erasmusmc.nl. Support via email is available 8 hours per working day? "Service is currently run on best effort base on our own cluster (with hardware redundancy?), when more projects will be making use of it, we will....." Update frequency for the tools/content/systems?Trackable response to uses feedback would come from email reports for code or application failure.

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.

myFAIR has been developed as a standalone virtual machine (VM) and a web resource (https://myfair.erasmusmc.nl) that is deployed from the same VM which is available for download from the project home page (https://github.com/ErasmusMC-Bioinformatics/myFAIR). Since the code is open source and on github this guarantees the uptime for code access to be 24/7 . myFAIR will be coupled to the ELIXIR-AAI in the ELIXIR-Human Data Implementation study myFAIR CLOUD https://docs.google.com/document/d/11ik0fl1fQus4pEWS7FrZsVVJeZATrZm5Dim…) starting 1st September 2018. The data contented in myFAIR is the responsibility of the user this content. We will ensure that the application and service comply with GDPR guidelines.

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).

The maintenance of myFAIR plan has been partially developed to to comply with the guidelines for sustainable software as defined by the Software Sustainability Institute using their criteria based evaluation form from 2011. The Usability has been partially outlined in our open code repository and associated training material (Section 2c) which provides users and developers with the adequate information to install, manage and use myFAIR application in a linux platform. 

To address sustainability and maintainability then the basic questions relating to the project identity, the application licencing and ownership are clearly outlined on the myFAIR project page (https://erasmusmc-bioinformatics.github.io/#projectsModal1).

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.

Ticketing is available via github for issues relating to use of the application or code and e-mail support for the moment. If myFAIR grows in usage as we expect then as a bigger service ELIXIR should embrace Topdesk, that can be done although most tools, even the very mature ones, only have a (volunteer) mail help desk.

Tutorial will be made available on the TeSS platform and currently the user manual is available from https://github.com/ErasmusMC-Bioinformatics/myFAIR#run-the-myfair-analy…

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.

The licence attached to myFAIR is an Academic Free License version 3.0. which offers the most comprehensive freedom to operate for both academics and companies and can facilitate Open Science. Since myFAIR accesses the users EUDAT storage and Galaxy service then the limitation for data size is only restricted by the users storage and compute allowance.

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.

The public myFAIR public service is maintained as a self-contained virtual machine (VM) in which no personal data is stored on the server and the local VM is restricted to PC’s for which the owner is responsible for that data. The GDPR policy will be added to the public myFAIR test service but the stand alone VM with have the same service for the user. The GDPR relating to data is the responsibility of the end user. We do not have and ELSI policy in place but plan to comply with ELSI guidelines by the end of 2018.

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

myFAIR is development and implementation is funded by several EU projects and has also been included as the cornerstone FAIR data management and analysis application if two H2020 grant applications for 2019. myFAIR has been supported as part of the EUROSTARS iKnowIT project (https://www.eurostars-eureka.eu/project/id/10959) which is supported until October 2019. In addition my FAIR is a part of the ELIXIR Galaxy Implementation plan for 2018 (https://docs.google.com/document/d/1chM85YPmoU0X_w9oPkjuG8_C2AyNdtHgpW2…) and for myFAIR application development in the EOSC as an ELIXIR Human Implementation Study (2018). These grants are available until myFAIR has been included in two H2020 grants (CINECA and MEDiCaTe) that will use this application as the de facto standard for FAIR data management and analysis. 

We believe that whilst we have secured funding for the further development myFAIR as an ELIXIR cloud service it is the maintenance of myFAIR over the next five years that need to be addressed. 

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

Quality assurance will be added to myFAIR at the end 2018 to have a similar QA/QC process to that used by Galaxy which we use already and includes continuous integration (e.g. Travis and Jenkins). 

As an ELIXIR-NL service, myFAIR is subject to regular review by the ELIXIR-NL strategy board, who, as described in the ELIXIR-NL Service Delivery Plan, work with the myFAIR team to optimize 5 criteria: Openness, FAIRness, Quality, Fit (to the node goals) and Plan (for the future). We formally do not have a scientific advisory board. However several members of the myFAIR team in Rotterdam have regular meetings with representatives from different user communities (such as, but not limited to ....). In these meetings we collect feedback on how to proceed with myFAIR both on a strategic level as well as for development of the software.