2006 ICAR TAIR workshop A general overview of

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

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 – Seq. Viewer Ara. Cyc biochemical pathways Help Central

I. Navigation of TAIR web site Searches Tools Stocks Arabidopsis Info FTP site Portals 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 Can’t remember your Can’t remember username whether you’ve or already password! registered at TAIR? No Problem! Search People/Labs

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

Create a new profile

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

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

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).

User’s ‘Personal Data' page

Common problems with registration/ordering Can't register Registration not complete Forgot to commit changes to the database Can’t login Check that you have enabled cookies in your browser 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

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 Example 3 fatty acid biosynthesis genes

Gene Search Results TAIR locus - a mapped element that corresponds to a transcribed region on the Arabidopsis genome (AGI locus, ATx. Gxxxxx) or a genetic locus. A locus can have multiple gene models such as alternatively spliced variants. TAIR gene model - an annotated AGI gene model (ATx. Gxxxxx. x) or a published gene symbol (fab 1) AT 2 G 43710. 1 AT 2 G 43710. 2 are splice variants

Gene Search Results (example 2)

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

Functional annotation detail page: locus AT 1 G 74960 Original publication

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

Keyword search results

www. geneontology. org www. plantontology. org