TAIR Bringing together data for the global plant

TAIR: Bringing together data for the global plant biology community kate dreher curator TAIR/PMN

Gene/protein function data at TAIR p Acquiring new gene/protein function data in TAIR n n p TAIR curators Research community Using gene function data n n n Searching by function Working with large datasets Connecting to other species

Capturing gene/protein function data at TAIR p Functional curation pipeline n ~200 papers about Arabidopsis show up in Pubmed each month p TAIR curators link papers to appropriate loci § Please help us and all researchers who read your paper. . . § Report the AGI locus code for every gene in the paper § ASA 1 is ambiguous § § ANTHRANILATE SYNTHASE ALPHA SUBUNIT 1? ATTENUATED SHADE AVOIDANCE 1? ATP SULFURYLASE ARABIDOPSIS 1? § AT 3 G 02260 is unique § p n Papers are prioritized for in-depth literature curation § First priority – Papers with data about unannotated / novel genes TAIR curators read primary literature to extract gene functional data

phy. A-201 Capturing gene/protein function data at TAIR p TAIR curators captures gene/protein function data using: n Free text p Gene descriptions p Gene names / symbols § Please help us by writing the full name of symbols, especially the first time that they are published § p GGT 2 = Glutamate: Glyoxylate aminotransferase 2 Mutant phenotype descriptions § We love to see ABRC stock numbers, SALK/SAIL/GABI-Kat IDs, etc. § Please check to see what allele numbers have already been used § Textpresso is a big help!

Free text functional data on TAIR locus pages Gene names / symbols Gene description

Free text functional data on TAIR locus pages Mutant phenotypes

Capturing gene/protein function data at TAIR p TAIR curators captures gene/protein function data using: n Controlled vocabularies p Gene Ontology terms § Molecular function (e. g. transcription factor activity) § Biological process (e. g. phosphate transport) § Cellular component (e. g. chloroplast) p Plant Ontology terms § Plant structure (e. g. endosperm) § Plant growth and development stages (e. g. root primordium formation)

GO and PO functional data on TAIR locus pages GO terms PO terms

Getting detailed functional data

Capturing gene/protein function data at TAIR p It’s 2010. . . n Do we know what every Arabidopsis protein does? p n 9024 genes (~30%) are linked to experimental functional data (3/2010) Is there more information out there? p ~32% of the Pub. Med Arabidopsis papers from 2009 were curated § ~68% were not curated p n Additional articles appear in plant journals not indexed by Pubmed How can we get closer to our 2010 goal? p p On-going TAIR curation Increased community annotation § Journal/author collaborations § NEW on-line gene functional data submission tool

Contributing new functional data – as you publish n Journal collaborations p n First started in March 2008 with Plant Physiology Current collaborators and methods p Submit at ASPB website: § Plant Physiology p Fill out a spreadsheet: § The Plant Journal p Use the NEW TAIR gene functional data submission tool § § § n Journal of Integrative Plant Biology Plant, Cell and Environment Journal of Experimental Botany Plant Science Environmental Botany Plant Physiology and Biochemistry But you can use the tool TODAY!

Contributing new functional data – anytime!

Given by publisher or found online

We welcome data from ALL your publications. . . but please add them one at a time

16753566 AT 2 G 01830 WOL Wooden Leg

Adding gene function annotations kinase But I actually know that it is a histidine kinase. . . Try entering a different search term

Adding gene function annotations histidine Is there an even more specific / appropriate term? Check TAIR Keywords

Choosing the best term

Providing an experimental method in vitro But what if my term or method do not appear?

Entering new terms and methods kinase sextuple mutant

Adding additional information kinase Do I have more molecular function data about THIS gene in THIS paper? Yes! Nope!

Adding additional information

Adding additional information in vitro assay

Adding additional information

What “Other” information can I add? • Mutant phenotype information • Identity of other loci in double/ triple / quadruple mutants, etc. • Description of gene • Any other free text information The wol-8 EMS mutant (CS 07856) has a point mutation in the first exon that introduces a premature stop codon. The roots of mutant plants fail to respond to the exogenous application of cytokinin.

Covering all the data Do I have any more information to add about OTHER genes in THIS paper? Yes!

Entering the data into the database Nope, no information about OTHER genes in THIS paper? Please e-mail us with any questions or problems during or after submitting your data: curator@arabidopsis. org

Tips for gene function data submission n Something is better than nothing. . . p n If you don’t have time to hunt around for the perfect term or method, please just give us what you can But, if possible, please try to be. . . p As complete as possible § e. g. If it’s a kinase, also add that it’s involved in biological process of phosphorylation p As specific as possible § e. g. use potassium transporter instead of transporter. n Benefits of good annotation p Better understanding of individual gene functions

Vandepoele et al, 2009 BAR Tips for gene function data submission n Something is better than nothing. . . p n If you don’t have time to hunt around for the perfect term or method, please just give us what you can But, if possible, please try to be. . . p As complete as possible TAIR § e. g. If it’s a kinase, also add that it’s involved in biological process of phosphorylation p As specific as possible § e. g. use potassium transporter instead of transporter. n Benefits of good annotation p p p Better understanding of individual gene functions Better categorization / analysis of large-scale data sets Better functional predictions for newly sequenced genomes

Contributing new functional data – anytime! How can all this gene/protein function information be put to good use? Many other data types still welcome!

Finding the gene(s) you want. . . n Use Gene Search to find genes. . . p p involved in a specific biological process with a particular molecular function found in a specific compartment expressed in a particular place and/or during a specific developmental phase § Enter keywords for GO or PO terms § Can limit by evidence codes

Finding the gene(s) you want. . . n Use Gene Search to find genes. . . p p involved in the same biological process with the same molecular function found in the same compartment expressed in the same place and/or at the same time § Enter keywords for GO or PO terms § Can limit by evidence codes § Enter search terms / keywords for gene descriptions § Enter search terms / keywords for mutant phenotype

Putting gene/protein functional data to use

Working with large data sets n Adding value to community-generated gene families p Over 150 gene families have been submitted by researchers

Adding information to data sets n Adding value to community-generated gene familes p Over 150 gene families have been submitted by researchers p Attach data to your favorite protein family: Generate a. txt file of AGI locus codes

Adding information to data sets

Adding information to data sets

Connecting to other species n Finding “related” genes in other species

Connecting to other species

Connecting to other species save as text file

Connecting to other species

We are here to help: www. arabidopsis. org p Please use the data we provide p Please use the tools we provide p Please use TAIR to help improve your research! p Please contact us if we can be of any help! n n n Make an appointment to meet with us during the conference Please come visit our exhibitor booth – 219 – Plant Genome Resources! Please stop by poster 14022 tomorrow night curator@arabidopsis. org www. twitter. com/tair_news www. arabidopsis. org http: //www. facebook. com/tairnews (432 fans so far. . . )

Acknowledgements TAIR Eva Huala (Director) Sue Rhee (Co-PI) Current Curators: - Tanya Berardini (lead curator – functional annotation) - David Swarbreck (lead curator – structural annotation) - Peifen Zhang (Director and lead curator- metabolism) - Philippe Lamesch (curator) - Donghui Li (curator) - Debbie Alexander (curator) - A. S. Karthikeyan (curator) - Marga Garcia (curator) - Leonore Reiser (curator) Tech Team Members: - Bob Muller (Manager) - Larry Ploetz (Sys. Administrator) - Raymond Chetty - Cynthia Lee - Shanker Singh - Chris Wilks Recent Past Contributors: - Anjo Chi (tech team) - Vanessa Kirkup (tech team) -Tom Meyer (tech team) - Rajkumar Sasidharan (curator)

Department of Plant Biology

We are here to help: www. arabidopsis. org p Please use the data we provide p Please use the tools we provide p Please use TAIR to help improve your research! p Please contact us if we can be of any help! n n n Make an appointment to meet with us during the conference Please come visit our exhibitor booth – 219 – Plant Genome Resources! Please stop by poster 14022 tomorrow night curator@arabidopsis. org www. twitter. com/tair_news www. arabidopsis. org http: //www. facebook. com/tairnews