Phenote
Mark Gibson
Berkeley 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 Phenotypes
1. Curator reads about a phenotype in the
literature related to taxonomy or genotype
2. 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
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•
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DB ID/genotype/taxonomy
Genetic Context
Anatomy Term (Entity)
PATO value
Phenotype
(clinical sign) =
entity
+ attribute
+ value
+ placement
+ hypoteloric
P1
= eye
P2
P3
= midface + development + hypoplastic
+ hypertrophied
= kidney + size
shh-/(holoprosencephaly)
From M. Westerfield
Phenotype
(clinical sign) =
entity
+ attribute
+ value
Anatomical ontology
Cell & tissue ontology
Developmental ontology
Gene ontology
+
PATO
(phenotype and trait ontology)
biological process
molecular function
cellular component
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
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•
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Configuration
Data adapter (FlyBase)
Genetic context field
Term info navigation
Pheno xml writeback
ToDo…
What Phenote aspires to…
•
Other Entities: GO, Cell Type…
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Entity chooser
Post Coordinated Term(cross product)
Relational Quality & Secondary Entity
More Character Fields:
Stage, Pub ID, Figure ID, Quantity/Units, other
“Qualifiers”?
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Tags/Modifiers: radio buttons
GUI Configuration
Term info: add, back & forward
GUI for Ontology Browsing
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UVic’s Jambalaya
DAG view
Relationship views
Parents/kids, level
limits
More aspirations…
• Pheno XML reader
• “Worn paths”
ZFIN integration
ZFIN aspirations
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•
•
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Make webby
JavaScript/AJAX interface collaboration
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
DEMO…
Download
• Webstart (0.5):
http://toy.lbl.gov:9010/phenote/phenote.html
• Sourceforge
Obo sourceforge
http://sourceforge.net/projects/obo
subversion for phenote sub project
• 0.6 release soon
Acknowledgement
• BBOP:
Suzanna Lewis, Chris Mungall, Sima Misra, Nicole
Washington, ShengQiang Shu, Seth John DayRichter, 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