phenote mark gibson berkeley bioinformatics and ontology project (bbop) national center for...

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