Phenote Mark Gibson Berkeley Bioinformatics and Ontology Project (BBOP) National Center for Biomedical Ontologies(NCBO) Lawrence Berkeley National Lab.

Phenote

Mark GibsonBerkeley Bioinformatics and Ontology Project (BBOP)

National Center for Biomedical Ontologies(NCBO)

Lawrence Berkeley National Lab

Outline

• What Phenote does now

• What Phenote aspires to

• Demo

What is Phenote?

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

literature related to taxonomy or genotype2. Curator enters genotype(or taxonomy)3. Curator enters genetic context (optional)4. Curator searches/enters Entity (e.g.

Anatomy)5. 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

Phenotype Character Table

• List of Phenotype Character instances• Operations:

New, Delete, Copy

Recent additions

• Web interface!

• Configuration

• Data adapter (FlyBase)

• Genetic context field

• Term info navigation

• Pheno xml writeback

ToDo…

What Phenote aspires to…

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

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

“Qualifiers”?

• Tags/Modifiers: 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…

• Pheno XML reader

• “Worn paths”

ZFIN integration

ZFIN aspirations

• Make webby

• JavaScript/AJAX interface collaboration

• ZFIN data adapter

• Seamless & generic

• Fish evolutionists (cToL)

ZFIN Requirements

• Imitate Phenote or FX? K-Plan?

• Datablades -> Java migration

• Bulk edit: FX vs bulk copy/edit

• Components(ajax) or full web app?

• EQ Maker? Character table?

• Separate web page or same page?

• Post composed? Relational qualities?

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

DEMO…

Download

• Webstart (0.6): http://toy.lbl.gov:9010/phenote/phenote.htmlNascent Webby Phenote:http://reaper.lbl.gov/phenote/html/ncbo.html

• Sourceforge OBOhttp://sourceforge.net/projects/obosubversion for phenote sub project

• 0.7 release ~August/September (web)

Acknowledgement• BBOP:

Suzanna Lewis, Chris Mungall, Sima Misra, Nicole Washington, ShengQiang Shu, Seth John Day-Richter, 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