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
• Demo
• What Phenote aspires to

3
What is Phenote?

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

4
Phenote
5
Current Phenotype Character in Phenote

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

6
Phenotype (clinical sign)
entity
value
attribute


eye
placement
hypoteloric


P1

midface
development
hypoplastic

P2

kidney
size
hypertrophied

P3
shh-/- (holoprosencephaly)
From M. Westerfield
7
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
8
Term Completion

• All possible terms displayed as you type

9
Completion Search

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

10
Term Info

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

11
Character Table

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

12
Recently

• Configuration
• Data adapter (FlyBase)
• Genetic context field
• Term info navigation

13
DEMO
14
What Phenote aspires to

• Other Entities GO, Cell Type
• Entity chooser
• Post Coordinated Term(cross product)
• Relational Quality Secondary Entity ( monadic
  quality
• More Character Fields
• Stage, Pub ID, Figure ID, Quantity/Units, other
  Qualifiers?
• Tags radio buttons
• GUI Configuration
• Term info add, back forward

15
GUI for Ontology Browsing

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

16
More aspirations

• Shared selection
• Worn paths

17
ZFIN integration
18
ZFIN aspirations

• Make webby
• ZFIN data adapter
• Seamless generic
• Fish evolutionists (cToL)

19
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

20
Download

• Webstart (0.5)
• http//toy.lbl.gov9010/phenote/phenote.html
• Sourceforge
• Obo sourceforge
• http//sourceforge.net/projects/obo
• subversion for phenote sub project
• 0.6 release July

21
Acknowledgement

• BBOP
• Suzanna Lewis, Chris Mungall, Sima Misra, John
  Day-Richter, ShengQiang Shu, 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