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:

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

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

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

TAIR Portals

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!

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

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

Create a new profile

Step1: Begin the Registration process Enter personal and contact info Submit (but not done yet)

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

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 saying your account is active, you can then order stocks (if you are affiliated with a lab).

User’s ‘Personal Data' page

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 If your address has ALSO changed- you need to contact TAIR curators  Can't place order Not affiliated with a lab Account not activated yet

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

Searching for stocks

Searching seed stocks

Select seed stocks to order

Payment options New

Finding stock order history Click to find out YOUR order history

Browse ABRC stock catalog: Seed and DNA Stocks

IV. Gene Search

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

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) AT2G AT2G are splice variants

Gene Search Results (example 2)

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?

Functional annotation detail page: locus AT1G74960 Original publication

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

Keyword search results