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http://phenotypercn.org/ Anatomy Ontologies from a MOD (Model Organism Database) perspective Model Organism Database (MOD) for Arabidopsis - focus on genes and their function http://phenotypercn.wordpress.com/ 21,000 registered users (9500 updated last 5 years) Academic researchers: • grad students • postdocs • PIs Heavy international usage 2010: 1,765,873 visits from 178 countries/territories http://phenotypercn.wordpress.com/ How does TAIR use phenotype ontologies now? Plant Ontology Expression pattern annotation http://phenotypercn.wordpress.com/ How would we like to use anatomy ontologies? standardized mutant phenotype descriptions! http://phenotypercn.wordpress.com/ Why? search, categorize, compare, infer Question: Which genes control seed size in Arabidopsis? Entity: Flower Seed Flowering time Disease resistance Drought resistance Cold tolerance … Quality: Normal size Decreased size Increased size Small Large Yellow Green Species: Data type: Soybean Tomato Arabidopsis Maize Rice Sorghum … Genes QTLs Regulatory networks Expression Mutant phenotypes Images … Arabidopsis genes Question: Is seed size controlled by the same mechanism in Arabidopsis, tomato and soybean? Entity: Flower Seed Flowering time Disease resistance Drought resistance Cold tolerance … Quality: Normal size Decreased size Increased size Small Large Yellow Green Species: Data type: Soybean Tomato Arabidopsis Maize Rice Sorghum … Genes QTLs Regulatory networks Expression Mutant phenotypes Images … Soybean genes Tomato genes Arabidopsis genes Question: Which tomato gene can I mutate to give me smaller seeds? Tomato phenotype Tomato mutant allele Tomato gene: may control seed size >SGN-P669913 (395 Aa) MDNSNRSYNRNADHLGVNKFGKNINKSPIHQPNFNNANSARQQPQ PQVYNINKNDFRSVVQQLTGSPSQEPPSKPPQNPSKPPEYEITKD SATAFDPINRPQIPMHPPAQILAPARPAGGVPYQNNIARPPPHYG QPSPPMLPPTPGDVWTNTTESPISVYMRYLQNSIIDSGPKQTQFQ GPGHFQAHPASSGLLPNPSMPPFPSPRXEWPASFPIVAENGPPPP LLSPRXEWPAASPIARLNGPPPRLLSPRMNGPPLLPSPRMNGPPP PLPSPGINGPPPLPSPTSQYLLPSPTGFLNLLSPRSPYPLLSPGM QHPPPLTPNFFFSPMAQPGGFGTGPQFPPSPGYGFPLSPSGFFAM SSQDGGVNSTTTNRAADLDGFFASSFXPGGRFPSN* Arabidopsis phenotype: decreased seed size Arabidopsis mutant allele: iku1-1 Arabidopsis gene: controls seed size 1 51 101 151 201 251 301 351 401 MDRPRQNDHL SKNDFRSIVQ PAVPLPSMAP VSEYMRYLQS PGNEQRPYIP PLQPNQYLPP SPRYNGFGPL NFSFSQIAQQ DY GVNRIGKNIR QLTGSPSRES PQSHPQFARQ SLGDSGPNAN GHEQRSYMPA PGLVPSPVPH QSPTSQFLQP GSLGPGAGPS KSPLHQSTFA LPRPPQNNSL PPHQPPFPQT QMQPGHEQRP QSQSQSQPQP NLPSPRFNAP SPTGYPNMFS QGPPQPPPSP ASTSNGAAPR RPQNTRLQRI TQQPMMGHRD YIPGHEQRPY QPQPQQHMMP VPVTPTQPSP PRSPYPLLSP GLMFPLSPSG LQTQPQVYNI RPSPLTQLNR QFWSNTAESP VPGNEQQPYM GPQPRMNMQG MFSQMYGGFP GVQYPQPLTP FFPMPSPRWN http://phenotypercn.wordpress.com/ What are the barriers? curation efficiency funding for curation lack of interoperability http://phenotypercn.wordpress.com/ What are the barriers? curation efficiency funding for curation lack of interoperability reading research articles and converting data into annotations is time consuming and expensive! Current status Phenotype data in TAIR is still free text 2238 sequenced genes with free text phenotypes Additional 1755 unsequenced mutant loci with phenotypes (total of 3993 loci) 4696 images http://phenotypercn.wordpress.com/ What are the barriers? curation efficiency / funding (also applies to GO) - let’s try getting data directly from authors/ funding lack of interoperability A Article Navigator B Full Text Frame C We crossed syp122-1 to the EMS-induced, null alleles of PEN1, pen1-1, and pen1-4 (Collins et al., 2003). For both allelic combinations, the double mutants (identified as described in Materials and Methods) grew on soil as severely dwarfed plants with necrotic rosettes (Figure 3, A-E). When plated on MS medium, double mutant seedlings grew well for the first 2 to 3 wk. Thereafter, necrotic lesions were seen on the rosette leaves, even though these were propagated in sterile tissue culture (Figure 3A). The lesions were more frequent under high light than under low light (compare Figure3C with 3D), suggesting an enhanced susceptibility to oxidative stress. In spite of their lesions, the double mutants yielded a small amount of seed and could be propagated as true breeding lines. Processes requiring polarized secretion such as root hair tip growth, trichome morphogenesis (Figure 3A), and transmission through the pollen did not appear to be perturbed in the pen1 Open PDF Select text E Genotype Ontology Browser Term: trichome (PO:0000282) Definition: A unicellular or multicellular plant structure that forms a non-sclerified outgrowth from the epidermis. D Pick Lists X Selected text Alleles: syp122-1 pen1-1 pen1-4 Anatomy: rosette seedling rosette leaf root hair trichome GO: secretion trichome morphogenesis SP term: dwarf Maps to: PATO: height reduced / PO: whole plant Whole article Quality: severe necrotic sterile small susceptible Curator-Composed Annotations Quality Entity syp122-1 pen1-1 height reduced whole plant syp122-1 pen1-1 necrotic rosette leaf 2nd term [opt] Synonym [opt] dwarf Add synonym Add synonym Add synonym Vision… Model organism biologists Plant breeders Explore: Systematists Leaf Shape Phenotypes (structured and interoperable) Ecologists Adaptation, genetic basis, evolution, effect on yield, classification, development, gene regulation…