Phenote: new developments and new communities

A basic screen shot Entries are sorted by 'entity'

A close-up of the sort entry

New post-composition display. can do n-levels of specificity

New 'filter' featureOnly displays EQ matches

Initial “request a term” interface

BiologicalProcess

(2/2)

Sensory perception of mechanical stimulus

(0/2)

Sensory perception of soundHearing [syn]

(2/2)

Person(5/5)

FMA(5/5)

Ear(0/2)

Right_Ear(2/2)

Hair(1/1)

Kidney(2/2)

Is_a

Is_a

towards

towards

Is_a

Located_in

Part_ofPart_ofPart_of

Inheres_in

Inheres_in

EYA1E=Person Q=lacking_process_of( hearing)PMID:0000002

E=KidneyQ=Dysplastic

EYA1 PMID:0000001EYA1.1 PMID:0000003

EYA1.1E=hair located_in( right_ear ) Q=Short PMID:0000005

Inheres_in

Inheres_in

EYA1.1E=right_ear Q=reduced_process_of(hearing)PMID:0000004

Annotations

Inferred relationships

Relationships (btwn E & Q)

KEY

General Annotation(1 annot/row)

Table (current)(1 annot/row)

Matrix (BIRN)(1 annot/cell)

Tree

Subject (Genotype) Relation Object (Phenotype) Pub Property Value

Property Val (Prop+val pair)

EYA1 influences Dysplastic inheres_in(kidney) PMID:0000001 Key=Desc; Val="some description"Key=Name; Val="NLW"

EYA1 influences lacking_process_of(hearing) inheres_in (person) PMID:0000002 Key="Desc; Val="loss of hearing"Key=Name; Val="NLW"

EYA1.1 influences Dysplastic inheres_in(kidney) PMID:0000003 Key=Desc; Val="some description"Key=Name; Val="CJM"

EYA1.1 influences reduced_process_of(hearing) inheres_in (right_ear) PMID:0000004Key="Desc; Val="reduction in hearing in right ear"

Key=Name; Val="CJM"

EYA1.1 influences (short inheres_in(hair)) located_in right_ear PMID:0000005Key="Desc; Val="short ear hairs in right ear"

Key=Name; Val="NLW"

Entity Quality Desc NameEYA1 PMID:0000001 Kidney Q=Dysplastic "some description" "NLW"

EYA1 PMID:0000002 PersonQ=lacking_process_of E2=hearing "loss of hearing" "NLW"

EYA1.1 PMID:0000003 Kidney Dysplastic "some description" "CJM"

EYA1.1 PMID:0000004 Right_earQ=reduced_process_of E2=hearing

"reduction in hearing in right ear" "CJM"

EYA1.1 PMID:0000005Hair located_in (right_ear) Q=short

"short ear hairs in right ear; this should be class level quality to this instance of a person" "NLW"

Genotype Phenotype1 Phenotype2 Phenotype3Kidney hearing Hair

EYA1Displastic (PMID:0000001)

E=person Q=lacks_proces_of (PMID:0000002) -

EYA1.1Displastic (PMID:0000003)

E=right_ear Q=has_reduced_process_of (PMID:0000004)

Q=short E=located_in(right_ear) (PMID:0000005)

EYA1

PMID:0000001Person lacks_process_of(hearing)

PMID:0000002EYA1.1

Kidney DysplasticPMID:0000003

Right_ear reduced_process_of(hearing)PMID:0000004

Hair located_in right_ear shortPMID:0000005

Kidney Dysplastic

KidneyDysplastic (EYA1)Dysplastic (EYA1.1)

HearingRight_ear has_reduced_process_of (EYA1.1)Person lacks_process_of (EYA1)

HairShort located_in(right_ear) (EYA1.1)

Right_earEYA1.1

Short hair located_in(_)has_reduced_process_of(hearing)

NESCENT & Phenote

• Use EQ model to curate phenotypic diversity data published in phylogenetics literature

• Integrate with mutant phenotype data from ZFIN to investigate genetic basis of evolutionary change

Integration and Ontology Intersection

• Adding interface features to support efficient workflow for curation from taxonomic literature

• Using new teleost taxonomic ontology and teleost anatomy ontology

Enter a pre-defined list of specimens from which to repeatedly create different EQ

(character) statements.

A user may want to view a phylogenetic tree relating the specimens, and then simply select a node containing all the specimens to use. This functionality is available in an accessory window within Phenote.

You can paste Newick-format tree text into the "Newick Tree" field at the bottom of the window. When the taxonomy ontology is available for inclusion within Phenote, your Newick tree should be composed of ontology IDs from the taxonomy ontology. The tree view will automatically display the actual taxon name from the ontology.

Enabling the community

The various communities controls the actual data (i.e. instances)

We provide support for describing these data with ontologies

We must provide simple, non-intrusive ways of integrating into each community’s environment Customized plug-ins to manipulate the instance

data Simple communications channels

Leads for future work

• Cornell Plant Consortium

• Rheumatology and Autoimmune Disease at The University ofMinnesota

• J.Craig Venter Institute

• Encyclopedia of Life

• K. White, U of Chicago - modENCODE

• The greater zebra fish community