Celebrating 25 years of The Arabidopsis Information Resource

Leonore Reiser posted on Nov 19, 2024

infographic.jpeg Visual timeline and infographic The Arabidopsis Information Resource (TAIR, www.arabidopsis.org http://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,…

An Open Letter to the Arabidopsis Community from the New TAIR Director

Tanya Berardini posted on Dec 22, 2021

Dear Researcher, After many years of working behind the scenes at TAIR first as curator, then Director of Curation, and then Chief Scientific Officer after the founding of Phoenix Bioinformatics, I am honored to step into Eva Huala's shoes as TAIR Director. To plant biologists new and old, I look forward to continuing to grow and improve this shared community resource that has helped so many of us (me included!) advance our research. Long ago and far away, I too was working at the bench,…

Give GO annotation a go – Part III

Erica Bakker posted on Mar 24, 2019

In the previous blog about GO annotation we discussed how GO terms are assigned only based on supporting data in the paper. In this blog we will go into further detail for a specific type of supporting data: phenotypic data. Phenotypic data are mainly collected for mutants, either T-DNA insertion lines or mutants created through methods such as CRISPR or chemical mutagenesis. Based on the phenotype of the mutant, inferences are made about the function of the gene.…

Give GO annotation a go - Part II

Erica Bakker posted on Feb 22, 2019

GOPuzzleFigCropped.png The following is the second in a series of posts about how experiment based GO annotations are assigned to genes in TAIR. The manual process of assigning experimental GO annotations to genes starts with a prioritized list of papers describing genes for which no or limited GO information exists in TAIR (see our December 2018 blog post for more information).…

Give GO annotation a go - Part I

Erica Bakker posted on Jan 23, 2019

It was great to see so many participants at the functional annotation workshop at PAGXXVII (https://plan.core-apps.com/pag_2019/event/d42319e9aae3945c459f3e5e1526585a https://plan.core-apps.com/pag_2019/event/d42319e9aae3945c459f3e5e1526585a). Interestingly, many of you came to us expecting to learn how to mass annotate RNAseq data with Gene Ontology (GO) terms. I know the feeling: you have completed your awesome RNAseq experiment and have a long list of genes to analyze.…

Cool lncRNAs respond to cold

Erica Bakker posted on Dec 19, 2018

As a literature curator at TAIR, I see all kinds of papers on all kinds of different topics coming through. Recently I noticed a couple of papers in Nature Communications describing long non-coding RNAs and their role in cold tolerance and vernalization response. Since many of you are currently experiencing cold winter weather, this seemed like an appropriate topic to cover in December’s blog post.…

How a new article is curated in TAIR

Erica Bakker posted on Nov 13, 2018

We have come a long way in understanding gene function in plants since the first Arabidopsis mutant studies in the 1970s. The continuous global effort to elucidate the function of each gene in the Arabidopsis genome has resulted so far in 34,268 papers linked to 24,810 loci in TAIR. If you were ever curious how this information got into TAIR, keep reading for a glimpse behind the scenes.…

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