Celebrating 25 years of The Arabidopsis Information Resource
- Leonore Reiser
The Arabidopsis Information Resource (TAIR, www.arabidopsis.org) marked its 25th Anniversary on October 1, 2024. TAIR was launched in 1999, just before the public release of the genome sequence for the model plant Arabidopsis thaliana. TAIR quickly became an essential resource for the plant biology community and has since grown in popularity and importance with over 40,000 registered users across the globe. In 2023, TAIR served up over 3 million page views/month.
Evolution of TAIR’s data, tools and database
Over the years, TAIR has evolved to keep pace with the growth of the Arabidopsis research community and the increasing diversity and amount of data available. Initially focused on gene information, TAIR now integrates data on proteins, gene expression, alleles, mutant phenotypes, germplasms, clones, genetic markers, maps, publications, and the research community. TAIR curators systematically extract and organize experimental data from research publications using ontologies and evidence. This expert curation ensures high-quality annotations based on experimental evidence, which is crucial for accurate functional and comparative genomics studies. To facilitate and streamline literature curation,TAIR built a robust internal curation system that continues to support data integration. Early on,TAIR developed a number of in-house analytic research tools including the very popular SeqViewer genome browser, a Chromosome Map tool, and Pattern matching software that are still in use. TAIR has continued to integrate and maintain up-to-date versions of essential open source tools such as BLAST for sequence analysis and genome browsers starting with GBrowse, then JBrowse, and the most recent version, JBrowse2. Keeping up with the increasing volume and complexity of data has required frequent updates to internal systems and software. Since its inception, TAIR has transitioned database management systems from Sybase to Oracle, moved to the AWS cloud, and most recently adopted newer datastore technologies.
Community Engagement
TAIR is rooted in community and is driven by community needs. In the early days, TAIR’s scientific advisory board provided guidance and TAIR continues to seek input from the community to drive change. As a member of the broader database community, it has collaborated on the development of several essential resources including adaptation of the Gene Ontology for plants and integration of harmonization of plant development and anatomy terms into the Plant Ontologies. TAIR is a founding member of the AgBioData consortium of agricultural databases, and supports the FAIR (Findable, Accessible, Interoperable and Reusable) data principles of data management. Since its inception, TAIR has supported capacity building of its user community, providing user-friendly tools for data submission (e.g. TOAST and GOAT), educational resources (webinars, in person workshops at conferences, and video tutorials). Users have always been able to reach out to staff via email and can expect a response within 24 hours during the work week. In 25 years, TAIR curators have responded to tens of thousands of helpdesk requests.
Sustainability and the future of TAIR
TAIR, like many other community databases, experienced a decline of federal support for databases and ultimately faced closure. Rather than deprive the community of a much-needed resource, the remaining TAIR staff founded the non-profit Phoenix Bioinformatics in 2013, and transitioned TAIR into a user-backed funding model. That transition has allowed TAIR to not only survive over the past decade, but also to thrive.TAIR has continued its core activities, adding new data weekly, and made considerable investments into modernizing the resource. This includes updating the software infrastructure to enhance the speed of data retrieval and releasing a revamped, modern, and more accessible website. TAIR has also spearheaded a major community initiative to reannotate the Arabidopsis genome, the first new annotation since 2016. For 25 years TAIR has been an essential research resource for advancing plant genomic research. Continued development and support are essential to ensure it can do so for the next 25 years.