phenote mark gibson berkeley bioinformatics and ontology project (bbop) national center for...
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Phenote
Mark GibsonBerkeley Bioinformatics and Ontology Project (BBOP)
National Center for Biomedical Ontologies(NCBO)
Lawrence Berkeley National Lab
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
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 Info
• Mouse over terms in completion list gives more info:Synonyms,Definition, Parent relationships, Child relationships,
Whether obsolete
• Relationship terms are clickable
Recent additions
• Web interface!
• Configuration
• Data adapter (FlyBase)
• Genetic context field
• Term info navigation
• Pheno xml writeback
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
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
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