http://phenotypercn.org/ anatomy ontologies from a mod (model organism database) perspective
Post on 19-Dec-2015
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http://phenotypercn.org/
Anatomy Ontologies from a MOD (Model Organism Database)
perspective
http://phenotypercn.wordpress.com/
2010: 1,765,873 visits from 178 countries/territories
21,000 registered users (9500 updated last 5 years)
Academic researchers:• grad students• postdocs• PIs
Model Organism Database (MOD) for Arabidopsis- focus on genes and their function
Heavy international usage
http://phenotypercn.wordpress.com/
How does TAIR use phenotype ontologies now?
Expression pattern annotationPlant Ontology
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How would we like to use anatomy ontologies?
standardized mutant phenotype descriptions!
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Why?
search, categorize, compare, infer
Entity:
FlowerSeed Flowering timeDisease resistanceDrought resistanceCold tolerance…
Species:
SoybeanTomatoArabidopsisMaizeRiceSorghum…
Data type:
GenesQTLsRegulatory networksExpressionMutant phenotypesImages…
Question: Which genes control seed size in Arabidopsis?
Quality:
Normal sizeDecreased sizeIncreased sizeSmallLargeYellowGreen
Arabidopsisgenes
Entity:
FlowerSeed Flowering timeDisease resistanceDrought resistanceCold tolerance…
Species:
SoybeanTomatoArabidopsisMaizeRiceSorghum…
Data type:
GenesQTLsRegulatory networksExpressionMutant phenotypesImages…
Soybeangenes
Tomatogenes
Arabidopsisgenes
Quality:
Normal sizeDecreased sizeIncreased sizeSmallLargeYellowGreen
Question: Is seed size controlled by the same mechanism in Arabidopsis, tomato and soybean?
Arabidopsis phenotype: decreased seed size
Arabidopsis gene: controls seed size
1 MDRPRQNDHL GVNRIGKNIR KSPLHQSTFA ASTSNGAAPR LQTQPQVYNI 51 SKNDFRSIVQ QLTGSPSRES LPRPPQNNSL RPQNTRLQRI RPSPLTQLNR101 PAVPLPSMAP PQSHPQFARQ PPHQPPFPQT TQQPMMGHRD QFWSNTAESP151 VSEYMRYLQS SLGDSGPNAN QMQPGHEQRP YIPGHEQRPY VPGNEQQPYM201 PGNEQRPYIP GHEQRSYMPA QSQSQSQPQP QPQPQQHMMP GPQPRMNMQG251 PLQPNQYLPP PGLVPSPVPH NLPSPRFNAP VPVTPTQPSP MFSQMYGGFP301 SPRYNGFGPL QSPTSQFLQP SPTGYPNMFS PRSPYPLLSP GVQYPQPLTP351 NFSFSQIAQQ GSLGPGAGPS QGPPQPPPSP GLMFPLSPSG FFPMPSPRWN401 DY
Tomato gene: may control seed size
>SGN-P669913 (395 Aa)MDNSNRSYNRNADHLGVNKFGKNINKSPIHQPNFNNANSARQQPQPQVYNINKNDFRSVVQQLTGSPSQEPPSKPPQNPSKPPEYEITKDSATAFDPINRPQIPMHPPAQILAPARPAGGVPYQNNIARPPPHYGQPSPPMLPPTPGDVWTNTTESPISVYMRYLQNSIIDSGPKQTQFQGPGHFQAHPASSGLLPNPSMPPFPSPRXEWPASFPIVAENGPPPPLLSPRXEWPAASPIARLNGPPPRLLSPRMNGPPLLPSPRMNGPPPPLPSPGINGPPPLPSPTSQYLLPSPTGFLNLLSPRSPYPLLSPGMQHPPPLTPNFFFSPMAQPGGFGTGPQFPPSPGYGFPLSPSGFFAMSSQDGGVNSTTTNRAADLDGFFASSFXPGGRFPSN*
Arabidopsis mutant allele:
iku1-1
Tomatomutant allele
Tomatophenotype
Question: Which tomato gene can I mutate to give me smaller seeds?
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What are the barriers?
curation efficiency funding for curationlack of interoperability
http://phenotypercn.wordpress.com/
What are the barriers?
curation efficiency funding for curationlack of interoperability
reading research articles and converting data into annotations is time consuming and expensive!
Current statusPhenotype data in TAIR is still free text
2238 sequenced genes with free text phenotypes
Additional 1755 unsequenced mutant loci with phenotypes
4696 images
(total of 3993 loci)
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What are the barriers?curation efficiency / funding (also applies to GO)- let’s try getting data directly from authors/ fundinglack of interoperability
Alleles: Anatomy: GO: Quality:syp122-1 rosette secretion severe pen1-1 seedling trichome morphogenesis necroticpen1-4 rosette leaf sterile
root hair smalltrichome susceptible
Full Text FrameWe 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
Pick Lists
Curator-Composed Annotations
Ontology Browser
Genotype Quality
necrotic rosette leaf
Entity 2nd term [opt]
Term: trichome (PO:0000282)
Definition: A unicellular or multicellular plant structure that forms a non-sclerified outgrowth from the epidermis.
B
C
D
ESelect textOpen PDF
Article NavigatorA
Synonym [opt]
X Selected text Whole article
dwarf Add synonymsyp122-1 pen1-1
syp122-1 pen1-1
height reduced whole plant
SP term: Maps to:dwarf PATO: height reduced / PO: whole plant
Add synonym
Add synonym
Vision…
Model organism biologists
Plant breeders
Systematists
EcologistsLeaf Shape Phenotypes
(structured and interoperable)
Explore: Adaptation, genetic basis, evolution, effect on yield, classification, development, gene regulation…