Phenotype RCN

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http//phenotypercn.org/
Anatomy Ontologies from a MOD (Model Organism
Database) perspective
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http//phenotypercn.wordpress.com/
Model Organism Database (MOD) for Arabidopsis -
focus on genes and their function
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
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http//phenotypercn.wordpress.com/
How does TAIR use phenotype ontologies now?
Expression pattern annotation
Plant Ontology
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How would we like to use anatomy ontologies?
http//phenotypercn.wordpress.com/
standardized mutant phenotype descriptions!
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Why?
http//phenotypercn.wordpress.com/
search, categorize, compare, infer
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Question Which genes control seed size in
Arabidopsis?
Entity
Species
Data type
Quality
Flower Seed Flowering time Disease
resistance Drought resistance Cold tolerance
Soybean Tomato Arabidopsis Maize Rice Sorghum
Genes QTLs Regulatory networks Expression Mutant
phenotypes Images
Normal size Decreased size Increased
size Small Large Yellow Green
Arabidopsis genes
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Question Is seed size controlled by the same
mechanism in Arabidopsis, tomato and soybean?
Entity
Species
Data type
Quality
Flower Seed Flowering time Disease
resistance Drought resistance Cold tolerance
Soybean Tomato Arabidopsis Maize Rice Sorghum
Genes QTLs Regulatory networks Expression Mutant
phenotypes Images
Normal size Decreased size Increased
size Small Large Yellow Green
Soybean genes
Tomato genes
Arabidopsis genes
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Question Which tomato gene can I mutate to give
me smaller seeds?
Tomato phenotype
Tomato mutant allele
Tomato gene may control seed size
gtSGN-P669913 (395 Aa) MDNSNRSYNRNADHLGVNKFGKNINKSP
IHQPNFNNANSARQQPQPQVYNINKNDFRSVVQQLTGSPSQEPPSKPPQN
PSKPPEYEITKD SATAFDPINRPQIPMHPPAQILAPARPAGGVPYQNNI
ARPPPHYGQPSPPMLPPTPGDVWTNTTESPISVYMRYLQNSIIDSGPKQT
QFQ GPGHFQAHPASSGLLPNPSMPPFPSPRXEWPASFPIVAENGPPPPL
LSPRXEWPAASPIARLNGPPPRLLSPRMNGPPLLPSPRMNGPPP PLPSP
GINGPPPLPSPTSQYLLPSPTGFLNLLSPRSPYPLLSPGMQHPPPLTPNF
FFSPMAQPGGFGTGPQFPPSPGYGFPLSPSGFFAM SSQDGGVNSTTTNR
AADLDGFFASSFXPGGRFPSN
Arabidopsis mutant allele iku1-1
Arabidopsis gene controls seed size
Arabidopsis phenotype decreased seed size
  1 MDRPRQNDHL GVNRIGKNIR KSPLHQSTFA ASTSNGAAPR LQ
TQPQVYNI 51 SKNDFRSIVQ QLTGSPSRES LPRPPQNNSL RPQN
TRLQRI RPSPLTQLNR101 PAVPLPSMAP PQSHPQFARQ PPHQPP
FPQT TQQPMMGHRD QFWSNTAESP151 VSEYMRYLQS SLGDSGPN
AN QMQPGHEQRP YIPGHEQRPY VPGNEQQPYM201 PGNEQRPYIP
 GHEQRSYMPA QSQSQSQPQP QPQPQQHMMP GPQPRMNMQG251 P
LQPNQYLPP PGLVPSPVPH NLPSPRFNAP VPVTPTQPSP MFSQMYG
GFP301 SPRYNGFGPL QSPTSQFLQP SPTGYPNMFS PRSPYPLLS
P GVQYPQPLTP351 NFSFSQIAQQ GSLGPGAGPS QGPPQPPPSP 
GLMFPLSPSG FFPMPSPRWN401 DY
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What are the barriers?
http//phenotypercn.wordpress.com/
curation efficiency funding for curation lack of
interoperability
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What are the barriers?
http//phenotypercn.wordpress.com/
curation efficiency funding for curation lack of
interoperability
reading research articles and converting data
into annotations is time consuming and expensive!
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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
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What are the barriers?
http//phenotypercn.wordpress.com/
curation efficiency / funding (also applies to
GO) - lets try getting data directly from
authors/ funding lack of interoperability
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Ontology Browser
Article Navigator
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Full Text Frame
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
Term trichome (PO0000282) Definition A
unicellular or multicellular plant structure that
forms a non-sclerified outgrowth from the
epidermis.
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Pick Lists
Selected text
Whole article
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Alleles Anatomy GO Quality syp122-1
rosette secretion severe pen1-1
seedling trichome morphogenesis
necrotic pen1-4 rosette leaf sterile root
hair small trichome susceptible

SP term Maps to dwarf PATO height reduced /
PO whole plant
Select text
Open PDF
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Curator-Composed Annotations
Genotype
Quality
Entity
2nd term opt
Synonym opt
Add synonym
dwarf
syp122-1 pen1-1
height reduced
whole plant
Add synonym
rosette leaf
necrotic
syp122-1 pen1-1
Add synonym
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Vision
Model organism biologists
Systematists
Leaf Shape Phenotypes (structured and
interoperable)
Plant breeders
Ecologists
Explore
Adaptation, genetic basis, evolution, effect on
yield, classification, development, gene
regulation