Phenote

Mark GibsonBerkeley Bioinformatics and Ontology Project (BBOP)

National Center for Biomedical Ontologies(NCBO)

Lawrence Berkeley National Lab

Outline

• What Phenote does now

• Demo

• What Phenote aspires to

What is Phenote?

A tool for annotating Phenotypes1. Curator reads about a phenotype in the

literature related to taxonomy or genotype

2. Curator enters taxonomy/genotype

3. Curator searches/enters Entity (Anatomy)

4. Curator searches/enters PATO attribute/value

Phenote

Current Phenotype Character in Phenote

• DB ID/genotype/taxonomy• Genetic Context• Anatomy Term (Entity)• PATO value

eye placement hypoteloric+ +

entity valueattribute+ +

midface development hypoplastic+ +

kidney size hypertrophied+ +

Phenotype(clinical sign) =

P1 =

P2 =

P3 =

shh-/- (holoprosencephaly)

From M. Westerfield

entity valueattribute+ +Phenotype(clinical sign) =

Anatomical ontology

Cell & tissue ontology

Developmental ontology

Gene ontology

biological process

molecular function

cellular component

+ PATO(phenotype and trait ontology)

From M. Westerfield

Term Completion

• All possible terms displayed as you type

Completion Search

• Can search on:Term, Synonym, Definition, Obsolete

Term Info

• Mouse over terms in completion list gives more info:Synonyms,Definition, Parent relationships, Child relationships,

Whether obsolete

• Relationship terms are clickable

Character Table

• List of Character instances• Operations:

New, Delete, Copy

Recently…

• Configuration

• Data adapter (FlyBase)

• Genetic context field

• Term info navigation

DEMO…

What Phenote aspires to…

• Other Entities: GO, Cell Type…– Entity chooser– Post Coordinated Term(cross product)– Relational Quality & Secondary Entity (& monadic

quality

• More Character Fields:Stage, Pub ID, Figure ID, Quantity/Units, other

“Qualifiers”?

• Tags: radio buttons• GUI Configuration • Term info: add, back & forward

GUI for Ontology Browsing

• UVic’s Jambalaya• DAG view• Relationship views• Parents/kids, level

limits

More aspirations…

• Shared selection

• “Worn paths”

ZFIN integration

ZFIN aspirations

• Make webby

• ZFIN data adapter

• Seamless & generic

• Fish evolutionists (cToL)

FlyBase aspirations

• Data adapter that talks to FB app proforma• Genotype maker• Genetic interactions• Seamless & generic integration• NLP - infer phenotypes from literature• Dump to OBD (zf & fb) via pheno-xml

Download

• Webstart (0.5): http://toy.lbl.gov:9010/phenote/phenote.html

• SourceforgeObo sourceforge

http://sourceforge.net/projects/obo

subversion for phenote sub project

• 0.6 release ~July

Acknowledgement• BBOP:

Suzanna Lewis, Chris Mungall, Sima Misra, John Day-Richter, ShengQiang Shu, Nomi Harris

• ZFIN:Monte Westerfield, Melissa Haendel, Erik Segerdell,

Sierra Taylor, Judy Sprague,Leyla Bayraktaroglu…

• FlyBase:Rachel Drysdale, Gillian Milburn, Michael Ashburner,

George Gkoutos, David Sutherland…

• University of Victoria:Chris Callendar, Margaret-Anne Storey, Sean

Falconer