The TE Hub Consortium recently posted a comment for Mobile DNA on the TE Hub, an open and collaborative platform that provides an entry point and reference page for researchers interested in the diversity, identification, and annotation of Transposable Elements (TE). While we are eagerly awaiting publication in our journal, the authors took part in a sneak preview Q&A on the project.
Image by PublicDomainPictures from Pixabay
Can you tell us a bit about the background and initiation of TE Hub?
Hadi Quesneville: In May 2019, during the FASEB Mobile DNA Conference, some of us met informally and started discussing the congestion we face with people who asked for our help in commenting on TEs and storing TE annotations and ask for their reference sequences. We have found that we have reached a point where neither of us is able to fully meet this growing demand. We had to do something for the community to overcome the bottleneck of TE annotation and bioinformatic analysis. We suggested engaging TE’s bioinformatics community to organize their expertise, knowledge, and tools on a collaborative platform that would help the TE community navigate the growing maze of tools, methods, and resources. After we sent out some emails, Slack messages, and tweets, an initial video meeting was organized to discuss how we could set it up.
When and why did you make lists of iterative databases and iterative tools?
Tyler A. Elliott: I’ve been interested in the resources available on TEs for a long time, and like many others, I’m sure it would be useful to have a single point of reference for all of this information. The first step, however, was to understand what databases and tools are available. Some of my team members at the CBG helped to create an initial list, which I then expanded a lot in my free time. Most of this work happened in 2019 when I first published the lists in a publicly available document.
I also wanted to compile information about the various systems used to classify TEs, as well as the references for those systems, in addition to a list of various named elements and when researchers suggested larger groupings of elements. I wanted people to be more aware of this, hoping that when new elements are discovered, they can be put in that larger context.
What were the key milestones and roadblocks in setting up TE Hub?
Travis J. Wheeler: After we started the bimonthly meeting in June 2020, we quickly worked out a vision and created a concrete plan for developing and populating the website. This required setting up the technology stack (a heavily expanded version of the wiki.js package) followed by extensive content posts to prepare the site for its first release. We have finally reached the part that motivated the work: Inviting others to get involved!
A key challenge was defining the scope of TE Hub – what role will it serve (and most importantly, not) in the TE community. It is really easy to expand the scope of a project beyond the limits of what is manageable; We have worked hard to clearly define the purpose of TE Hub in supporting access to TE resources, tools, and annotation methods.
How can I stay up to date with news and announcements in TE Hub?
Alexander Suh: Please follow us on Twitter @hub_te for TE Hub announcements, join the #te-hub channel on TransposonsWorldwide Slack for written communications, and we also have our “Hub Updates” (announced on the channels above) which are bimonthly Video calls for news and open discussions.
How can experts and newbies get involved in TE Hub?
Robert Hubley: Implementing TE Hub as a wiki-based site serves two key goals: it supports decentralized, community-driven growth and provides opportunities for contributors with a wide variety of expertise. The current subject areas are only a starting point from which the page will develop further with the interests of the individual contributors. In addition, many of the resources currently on the site benefit directly from the continued assistance of inexperienced and experienced editors. If someone is unsure how best to support the effort, please get in touch.
Where do you see the development of TE Hub in the short, medium and long term?
Tony Heitkam: We are currently communicating TE Hub’s mission and inviting researchers to join our efforts. One of our communication efforts is the upcoming Mobile DNA Comment; another is a poster at the FASEB conference.
In the short to medium term, we want to expand the wiki widely. To ensure safe and reliable maintenance, we are planning secure core funding for the scaling of TE Hub. In the long term, we want to create a framework for the translation and integration of tools and databases. Ideally, we hope to go beyond listing databases and tools and provide translations from one system / tool / classification scheme to another. We believe this will open up the PD field further, making it easier for both beginners and experts to source PD annotations.