TAIR: Bringing together data for the global plant biology community kate dreher curator TAIR/PMN.
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Transcript of TAIR: Bringing together data for the global plant biology community kate dreher curator TAIR/PMN.
TAIR: Bringing together data for the global plant biology community
kate dreher
curator
TAIR/PMN
Acquiring new gene/protein function data in TAIR TAIR curators Research community
Using gene function data Searching by function Working with large datasets Connecting to other species
Gene/protein function data at TAIR
Functional curation pipeline ~200 papers about Arabidopsis show up in Pubmed each month
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
ASA1 is ambiguous ANTHRANILATE SYNTHASE ALPHA SUBUNIT 1? ATTENUATED SHADE AVOIDANCE 1? ATP SULFURYLASE ARABIDOPSIS 1?
AT3G02260 is unique
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
Capturing gene/protein function data at TAIR
TAIR curators captures gene/protein function data using: Free text
Gene descriptions
Gene names / symbols Please help us by writing the full name of symbols, especially the first time
that they are published GGT2 = 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!
Capturing gene/protein function data at TAIR phyA-201
Free text functional data on TAIR locus pages
Gene description
Gene names / symbols
Free text functional data on TAIR locus pages
Mutant phenotypes
TAIR curators captures gene/protein function data using:
Controlled vocabularies Gene Ontology terms
Molecular function (e.g. transcription factor activity) Biological process (e.g. phosphate transport) Cellular component (e.g. chloroplast)
Plant Ontology terms Plant structure (e.g. endosperm) Plant growth and development stages (e.g. root primordium formation)
Capturing gene/protein function data at TAIR
GO and PO functional data on TAIR locus pages
GO terms
PO terms
Getting detailed functional data
It’s 2010 . . . Do we know what every Arabidopsis protein does?
9024 genes (~30%) are linked to experimental functional data (3/2010)
Is there more information out there? ~32% of the PubMed Arabidopsis papers from 2009 were curated
~68% were not curated Additional articles appear in plant journals not indexed by Pubmed
How can we get closer to our 2010 goal? On-going TAIR curation Increased community annotation
Journal/author collaborations NEW on-line gene functional data submission tool
Capturing gene/protein function data at TAIR
Journal collaborations First started in March 2008 with Plant Physiology
Current collaborators and methods Submit at ASPB website:
Plant Physiology
Fill out a spreadsheet: The Plant Journal
Use the NEW TAIR gene functional data submission tool 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 – as you publish
Contributing new functional data – anytime!
Given by publisheror found online
We welcome data fromALL your publications . . .but please add them one at a time
AT2G01830 WOL Wooden Leg
16753566
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
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
Do I have more molecular function data about THIS gene in THIS paper?
kinase
Yes!Nope!
Adding additional information
Adding additional information
in vitro assay
Adding additional information
Adding additional information
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 (CS07856) 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:
Something is better than nothing . . . 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 . . . As complete as possible
e.g. If it’s a kinase, also add that it’s involved in biological process of phosphorylation
As specific as possible e.g. use potassium transporter instead of transporter.
Benefits of good annotation Better understanding of individual gene functions
Tips for gene function data submission
Something is better than nothing . . . 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 . . . As complete as possible
e.g. If it’s a kinase, also add that it’s involved in biological process of phosphorylation
As specific as possible e.g. use potassium transporter instead of transporter.
Benefits of good annotation Better understanding of individual gene functions Better categorization / analysis of large-scale data sets Better functional predictions for newly sequenced genomes
Tips for gene function data submission
Vandepoele et al, 2009
BAR
TAIR
Contributing new functional data – anytime!
Many other data
types still
welcome!
How can all thisgene/protein function information
be put to good use?
Use Gene Search to find genes . . .
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 . . .
Use Gene Search to find genes . . .
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
Finding the gene(s) you want . . .
Use Gene Search to find genes . . .
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
Finding the gene(s) you want . . .
Putting gene/protein functional data to use
Adding value to community-generated gene families Over 150 gene families have been submitted by researchers
Working with large data sets
Adding value to community-generated gene familes Over 150 gene families have been submitted by researchers
Attach data to your favorite protein family:
Adding information to data sets
Generate a .txt file of AGI locus codes
Adding information to data sets
Adding information to data sets
Finding “related” genes in other species
Connecting to other species
Connecting to other species
Connecting to other species
Connecting to other species
Connecting to other species
save as text file
Connecting to other species
Connecting to other species
We are here to help: www.arabidopsis.org Please use the data we provide
Please use the tools we provide
Please use TAIR to help improve your research!
Please contact us if we can be of any help! 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
www.arabidopsis.org
www.twitter.com/tair_news
http://www.facebook.com/tairnews
(432 fans so far . . . )
AcknowledgementsTAIR
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)
Eva Huala (Director) Sue Rhee (Co-PI)
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 Please use the data we provide
Please use the tools we provide
Please use TAIR to help improve your research!
Please contact us if we can be of any help! 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
www.arabidopsis.org
www.twitter.com/tair_news
http://www.facebook.com/tairnews