Phenote

1
Phenote

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

2
Outline

• What Phenote does now
• What Phenote aspires to
• Demo

3
What is Phenote?

• A tool for annotating Phenotypes
• Curator reads about a phenotype in the literature
  related to taxonomy or genotype
• Curator enters genotype(or taxonomy)
• Curator enters genetic context (optional)
• Curator searches/enters Entity (e.g. Anatomy)
• Curator searches/enters PATO attribute/value

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Phenote
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Current Phenotype Character in Phenote

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

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Phenotype (clinical sign)
entity
value
attribute


eye
placement
hypoteloric


P1

midface
development
hypoplastic

P2

kidney
size
hypertrophied

P3
shh-/- (holoprosencephaly)
From M. Westerfield
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Phenotype (clinical sign)
entity
value
attribute


Anatomical ontology Cell tissue ontology
Developmental ontology Gene ontology
biological process molecular function
cellular component
PATO (phenotype and trait ontology)
From M. Westerfield
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Term Completion

• All possible terms displayed as you type

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Completion Search

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

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Term Info

• Mouse over terms in completion list gives more
  info
• Synonyms,Definition, Parent relationships, Child
  relationships, Whether obsolete
• Relationship terms are clickable

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Phenotype Character Table

• List of Phenotype Character instances
• Operations
• New, Delete, Copy

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Recent additions

• Web interface!
• Configuration
• Data adapter (FlyBase)
• Genetic context field
• Term info navigation
• Pheno xml writeback

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ToDo
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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

15
GUI for Ontology Browsing

• UVics Jambalaya
• DAG view
• Relationship views
• Parents/kids, level limits

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More aspirations

• Pheno XML reader
• Worn paths

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ZFIN integration
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ZFIN aspirations

• Make webby
• JavaScript/AJAX interface collaboration
• ZFIN data adapter
• Seamless generic
• Fish evolutionists (cToL)

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ZFIN Requirements

• Imitate Phenote or FX? K-Plan?
• Datablades -gt 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?

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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

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DEMO
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Download

• Webstart (0.6)
• http//toy.lbl.gov9010/phenote/phenote.html
• Nascent Webby Phenote
• http//reaper.lbl.gov/phenote/html/ncbo.html
• Sourceforge OBO
• http//sourceforge.net/projects/obo
• subversion for phenote sub project
• 0.7 release August/September (web)

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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