2006 ICAR: TAIR workshop

1. 2006 ICAR: TAIR workshop Organizers: Katica Ilic and Peifen Zhang Location: Reception Room, 4th floor A general overview of TAIR website and demonstration of how to use some of the common features at TAIR The Arabidopsis Information Resource URL: www.arabidopsis.org

2. 2006 ICAR: TAIR workshop, Part I • Navigation of the TAIR website • User registration • Search and order stocks • Gene search and gene functional annotations • Keyword browser

3. 2006 ICAR - TAIR workshop, Part II • TAIR genome browser – SeqViewer • AraCyc biochemical pathways • Help Central

4. I. Navigation of TAIR web site • Searches • Tools • Stocks • Arabidopsis Info • FTP site • Portals New

5. TAIR Portals

7. II. User’s registration at TAIR: Why register? • To order stocks from ABRC • To add comments about genes • To submit data to TAIR • To update your contact /personal information • To view your order history TAIR registration is NOT the same as registration to access Cereon datasets!

9. Login Can’t remember whether you’ve already registered at TAIR? Can’t remember your username or password! No Problem! Search People/Labs

10. Before you start registration process, the New User Search page shows up To avoid duplicated entries

11. Create a new profile

12. Step1: Begin the Registration process 1. Enter personal and contact info 2. 3. Submit (but not done yet)

13. Step 2: Affiliate yourself to a lab/add papers Required to order stocks If you are PI Add your PI’s name Commit changes to complete your registration

14. Step 3: Wait for account activation • Before you can order , your account needs to be activated. This normally takes less than 24 hours. Once you receive email saying your account is active, you can then order stocks (if you are affiliated with a lab).

15. User’s ‘Personal Data' page

16. Common problems with registration/ordering • Can't register • Check that you have enabled cookies in your browser • Registration not complete • Forgot to commit changes to the database • Can’t login • If your record is in TAIR but you forgot your password- you can request it by email • If your email address has ALSO changed- you need to contact TAIR curators (curator@arabidopsis.org) • Can't place order • Not affiliated with a lab • Account not activated yet

17. III. Finding and ordering stocks from the ABRC • Search for stocks • Browse ABRC Catalog • Search order histories

18. Searching for stocks

19. Searching seed stocks

20. Select seed stocks to order

21. Payment options New

22. Finding stock order history Click to find out YOUR order history

23. Browse ABRC stock catalog: Seed and DNA Stocks

24. IV. Gene Search

25. Gene search options fatty acid biosynthesis genes Example 1 Example 2 Example 3

26. Gene Search Results TAIR locus - a mapped element that corresponds to a transcribed region on the Arabidopsis genome (AGI locus, ATxGxxxxx) or a genetic locus. A locus can have multiple gene models such as alternatively spliced variants. TAIR gene model- an annotated AGI gene model (ATxGxxxxx.x) or a published gene symbol (fab1) AT2G43710.1 AT2G43710.2 are splice variants

27. Gene Search Results (example 2)

28. Locus detail page What is known about the locus/gene: - Functional annotations - Gene expression - cDNA/EST clones - Sequences - Protein - Map/Chr. location - Gene structure - Polymorphisms - Publications What is functional annotation?

29. Functional annotation detail page: locus AT1G74960 Original publication

30. V. TAIR Keywords: Search and browse TAIR Keywords are controlled vocabulary terms (ontologies) silique Gene Ontology Plant Ontology

31. Keyword search results

32. www.geneontology.org www.plantontology.org