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. Users 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 Cant remember your username or password! Cant remember whether youve 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 PIs 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 receivesaying your account is active, you can then order stocks (if you are affiliated with a lab). Users 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 Cant login If your record is in TAIR but you forgot your password- you can request it byIf youraddress 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