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Anatomy Ontologies from a MOD (Model Organism Database)

perspective

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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

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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

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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…