Communication and Documentation Standards at Biocuration 2019

Posted By: Marina DiStefano, PhD, ASHG Communications Committee

I recently returned from the ISB Biocuration 2019 conference in Cambridge, UK. To me, this year’s conference focused on two of the core goals of the International Society for Biocuration (ISB): one, to promote communication and exchanges between curators and two, to encourage best practices by providing documentation on standards and annotation procedures.

Biocuration2019_Group
The group at the 2019 ISB Conference (photo courtesy of: George Georghiou)

Communication and Exchanges between Curators

Many presenters encouraged sharing of database resources and curation materials so as not to duplicate efforts and to facilitate transparency. For example, Rolf Apweiler, director of EMBL-EBI, discussed the Alliance of Genome resources, an effort to locate all curations of model organisms on the same website in a standardized format. The Alliance is founded by FlyBase, Mouse Genome Database, the Gene Ontology Consortium, Saccharomyces Genome Database, Rat Genome Database, WormBase, and the Zebrafish Information Network and contains information about six model organisms. In a related vein, Niklas Blomberg, director of ELIXIR, pointed out that many of the curation resources used by the entire scientific community are reliant on grant funding, making their future existence unstable. He discussed how resources should be defined as Core Data Resources to potentially solicit permanent stable funding.

There were also interactive workshops each afternoon that further supported this idea of communication between curators. One workshop, in which I presented, discussed the efforts of the Gene Curation Coalition (GenCC). This Coalition is an international group of gene curation resources with the goal of harmonizing the terms for defining clinical validity of gene:disease relationships. Three GenCC member groups (ClinGen, Genomics England PanelApp, and Orphanet) each took turns presenting their gene curation strategies. Participants were able to discuss the similarities and differences between the approaches. The workshop ended with survey results from the scientific community about the gene:disease validity terms.

Documentation and Standards

The more time I spend as a curator, the more I understand the value of consistent curation language. This idea was heartily supported by presenters at the conference who encouraged use of ontologies and the idea that each curation resource should strive to abide by FAIR (Findable, Accessible, Interoperable, and Reusable) data standards. Varsha Khodiyar, data curation editor at the journal Scientific Data, discussed how Springer Nature is trying to support FAIR data sharing to help reduce irreproducible experiments. Sirarat Sarntivijai, ELIXIR interoperability platform coordinator, spoke about recommended interoperability resources, tools that could be used by curators, creators of websites, or even authors to make data FAIR.

Many talks about specific resources, such as SIGNOR/DISNOR, SwissLipids, and the BioGRID Interaction database, cemented the idea that resources are most useful when they use ontologies to categorize terms.

The four days of this conference were a fascinating and important glimpse into the world of curation resources. After attending, it is quite clear that many of these resources are critical to the scientific community and keep research moving forward, thanks to the hard work of all the biocurators. The poster sessions were intimate and allowed for thoughtful discussion, useful suggestions, and hopefully the start of budding collaborations. Workshops were very interactive, and it was clear that the curators harbor a passion for their field of work and the work of their fellow curators.

If you have ever done or are planning on doing any curation, I highly recommend you attend this conference. The 13th International Biocuration Conference takes place in Bar Harbor, Maine from May 17-20, 2020.

Marina DiStefano, PhD, is a member of the ASHG Communications Committee and a postdoc at Harvard Medical School. She has been a member of ASHG since 2018.

Returning Individual Research Results to Participants: New NASEM Report

Posted By: Jillian Galloway, MS, Science Policy Analyst, ASHG

As you may recall, last year, the National Academies of Sciences, Engineering, and Medicine (NASEM) was asked by the Centers for Medicare & Medicaid Services (CMS), the Food and Drug Administration (FDA), and the National Institutes of Health (NIH) to evaluate the many issues and perspectives surrounding ‘the return of individual-specific research results generated in research laboratories’.

In recent years, there has been significant discussion among scientists about the return of results to research participants. As geneticists and genomicists discover information of potential clinical benefit to participants, they are considering when it is appropriate to share such information with participants.

Consensus Study Report
NASEM Report: Returning Individual Research Results to Participants: Guidance for a New Research Paradigm

In keeping with the trend towards greater participant inclusion, the recently launched All of Us program promises to share individual-level data with participants. By signaling greater involvement in the research process and dubbing All of Us participants as ‘partners’, NIH hopes to make participation more valuable and equitable.

Given this context, the NASEM committee was charged with evaluating the ethical, social, regulatory, and operational issues associated with returning results to participants. With many members involved in such research, ASHG submitted comments to the committee that focused on the complexity of returning individual-specific results of genomics research, outlining areas of consensus and contention within the genomics community.

The NASEM committee’s report, released last month, aligns with ASHG’s comments in some ways as well as revealing meaningful differences of perspective. For example, ASHG recommended that research funding include financial support for returning results to participants to make the task more viable. However, the NASEM report calls for research institutions and funding agencies to “develop and provide access to the resources and infrastructure needed to ensure that investigators conducting testing…can meet the necessary standards for quality”. Overall, NASEM’s report emphasizes addressing the quality of results over the burden to researchers in operationalizing their return.

The committee recommends placing greater responsibility on researchers returning individual-specific research results. It also proposes several guiding principles for researchers: chiefly, that the return of results be considered from the inception of the study, through its design and development, and that laboratories that plan to return results adopt high-quality standards.

However, the committee acknowledges that the diversity in size, funding, and scale of research laboratories makes CLIA certification, the clinically required regulation for laboratories issuing any test results to individuals, at times inappropriate or unnecessary for returning results not intended to inform clinical care. To address the financial, logistical, and operational hurdles of returning high-quality laboratory analyses with confidence, the committee suggests the creation of an accepted quality management system for research laboratories as an alternative to CLIA certification.

The NASEM report also outlines the many scenarios and variables determining whether laboratory quality is sufficient for investigators to return individual research results. In addition, the committee calls for the continued assessment of participant preferences and values, echoing ASHG’s comments.

In summary, while the committee’s recommendations may increase the frequency of returning results, and thereby enlarge the demands upon researchers, they are in keeping with the general scientific move  towards increasing researcher responsibility for the respect, trust, and needs of research participants.

ASHG will continue to monitor the activities of the various agencies to see how and to what extent they will adopt the recommendations set forth by the NASEM committee.

Jillian Galloway, MS, is a Science Policy Analyst at ASHG. For more information on ASHG’s policy priorities and activities, visit the Policy & Advocacy website.