Celebrating 25 years of The Arabidopsis Information Resource

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.

Librarian Version 

Celebrating 25 Years of TAIR: A Key Resource for Plant Research

On October 1, 2024, The Arabidopsis Information Resource (TAIR) celebrated its 25th anniversary. Since its launch in 1999, just before the groundbreaking release of the Arabidopsis thaliana genome sequence, TAIR has been an invaluable tool for plant researchers. Today, TAIR supports over 40,000 registered users worldwide and remains essential for the plant biology community.

TAIR’s Growth Over the Years

TAIR has grown immensely since its early focus on genetics and genome sequence data. It now hosts a vast collection of information on gene functions, proteins, gene expression, alleles, mutant phenotypes, and much more. TAIR’s team of curators carefully organizes data from scientific studies to ensure high-quality, reliable annotations for genomic research. Over the years, TAIR developed and maintained numerous tools, like the popular SeqViewer genome browser, and kept essential open-source tools up to date, such as the BLAST sequence analysis software and the JBrowse2 genome browser.

Behind the scenes, TAIR has consistently modernized its technology to handle ever-growing data. From transitioning database systems to moving onto the AWS cloud, TAIR has invested in systems that allow researchers to access data quickly and easily.

Community at the Heart of TAIR

TAIR’s success is closely tied to its commitment to the research community. Feedback from users has continually shaped its growth, and collaborations with scientific organizations, like the Gene Ontology Consortium and AgBioData, have driven forward important resources, such as plant-specific adaptations of the Gene Ontology and data standards. TAIR also supports the FAIR data principles that make scientific data easy to find, access, and share.

TAIR’s dedication to its users goes beyond just data access. It provides educational resources through webinars, workshops, and video tutorials and offers personalized support to researchers, responding to thousands of helpdesk questions over the years.

Ensuring a Sustainable Future for TAIR

As funding for databases like TAIR began to wane, TAIR faced the threat of closure. Rather than letting this vital resource disappear, the remaining TAIR team founded Phoenix Bioinformatics, a nonprofit that shifted TAIR to a user-backed funding model in 2013. This move has kept TAIR thriving, allowing it to continue adding new data weekly and improving its infrastructure. Recently, TAIR relaunched with a new website and initiated a community-led project to re-annotate the Arabidopsis genome, marking the first major update since 2016.

For 25 years, TAIR has been a cornerstone for plant research, empowering discoveries in plant genomics. With continued support, TAIR is set to inspire and assist researchers for another 25 years and beyond.