TAIR: Bringing together data for the global plant biology community

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

2. 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

3. 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

4. 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

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

6. Free text functional data on TAIR locus pages Mutant phenotypes

7. 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

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

9. Getting detailed functional data

10. 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

11. 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

12. Contributing new functional data – anytime!

15. Given by publisher or found online

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

18. 16753566 AT2G01830 WOL Wooden Leg

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

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

21. Choosing the best term

22. Choosing the best term

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

24. Entering new terms and methods kinase sextuple mutant

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

26. Adding additional information

27. Adding additional information in vitro assay

28. Adding additional information

29. Adding additional information

30. Adding additional information

31. 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.

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

33. 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

34. 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

35. 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 Vandepoele et al, 2009 BAR TAIR Tips for gene function data submission

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

37. 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 . . .

38. 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 . . .

39. 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 . . .

40. Putting gene/protein functional data to use

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

42. 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

43. Adding information to data sets

45. Adding information to data sets

46. Finding “related” genes in other species Connecting to other species

47. Connecting to other species

48. Connecting to other species

49. Connecting to other species

50. Connecting to other species save as text file