1. Phenote
Mark Gibson
Berkeley Bioinformatics and Ontology Project (BBOP)
National Center for Biomedical Ontologies(NCBO)
Lawrence Berkeley National Lab
I work for Berkeley, telecommuting from NYC

2. Outline What Phenote does now Demo What Phenote aspires to
Phenote is in its very early stages - what it aspires to be is much bigger than what it is now.
Demo wil illustrate the state of things, before going into what I then hope to add to it.

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
To make a pheno instance its taxa + E + A/V. Phenote keeps a list of instances to update & delete.

4. Phenote
Need to make picture of current phenote - ideally with term comp list & term info & a few instances

5. Current Phenotype Character in Phenote
DB ID/genotype/taxonomy
Genetic Context
Anatomy Term (Entity)
PATO value
The first item is some handle to what the EAV will get associated.
The DB id is specific to a mod/group. For zf this includes environment. For FB this may include genetic interactions…
This is sometimes called a lump id - as the id can lump a few things together as with zfin genotype + environment
Currently the only entity is Anatomy - GO & CT coming…
No need for PATO attribute as the value implies the attribute - may use attribute for “worn paths”
More fields coming - later in talk…

6. shh-/- (holoprosencephaly)
Phenotype
(clinical sign) =
entity +
attribute +
value
P =
eye +
placement +
hypoteloric
P =
midface +
development +
hypoplastic
P =
kidney +
size +
hypertrophied
Nice slide stolen from monte
shh-/- (holoprosencephaly)
From M. Westerfield

7. + PATO Phenotype entity + attribute + value Anatomical ontology
(clinical sign) =
entity +
attribute +
value
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
This is for fields with ontologies - entity/anatomy & pato - not genotype
Uses containment not starts with.
Displays list of term nams - should it put syns in brackets?)

9. Completion Search Can search on: Term, Synonym, Definition, Obsolete
Searching on jaw - returns terms with no jaw in them, but have jaw as synonym - as can be seen in term info.
Is this confusing - should synonym be included parenthesized in the completion list?
Todo - put in both “just obsoletes” & “include obsoletes”

10. Term Info Mouse over terms in completion list gives more info:
Synonyms,Definition, Parent relationships, Child relationships, Whether obsolete
Relationship terms are clickable
Relationships: ISA - superclass/subclass, part of/superpart, develops-from
Todo: comments

11. Character Table List of Character instances Operations:
New, Delete, Copy
New just gives ya a blank one. Copy is the handy one here as often ya just wanna change one thing in the phenotype to get a new pheno - be it entity, value or genotype.
When selected populates pheno fields

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
Configure entity ontologies, fields to use, and everything else imaginable about the gui - need to be able to configure for different sites but not be hardwired to a site.
As I said Phenote is in its early stages - so the wish list is a mile long… Compund entities - 2 kinds? Chris? Entity w qualifier - and double entities?
Is qualifier a separate field or part of compound entities?
So theres composite terms & compound entities. Composite term is a term with a qualifier like a spatial qualifier - for instance dorsal fin - also called cross product or qualified term (not qualified entry)
Compound entity is more than one entity to make up and entity - like head fused to arm. Head & arm are 2 entities making up one entity. Brain fused with eye, sensitivity to red light -> relational attrib + 2ndary entity
“Qualifiers” is a fb catch all for a bunch of different ontologies.
Whats a good example for spatial qual? Anterior Notochord

15. GUI for Ontology Browsing
UVic’s Jambalaya
DAG view
Relationship views
Parents/kids, level limits
Uvic is working on gui using their jambalaya tools - DAG & tree views, Be able to filter views by relationship types - isa, part of, develops from. Also be able to filter on parents & children, also limit the amount of levels especially for kids
DAG view is similar to Quick GO - quik go just does parents, no limit on levels, no relationship filters. DAG is directed acyclic graph - can have more than one parent
Shared selection between all parts of the gui - table, fields, term info, & dag guis… at least optionally so
When term info lists parents & children terms make them clickable to go to that term - this will go a long way for navigation needs actually and its only text based. Also descriptions sometimes have links in them - make those clickable.
So can really navigate 3 ways - term completion, term info selecting parent/kids, & dag gui

16. More aspirations… Shared selection “Worn paths”
Worn paths are trying to discern what the user might do in the future from what they’ve done in the past - theres 2 different ways that could be implemented - gui worn path and data worn path - for data just observe what attributes are used for what entities and put those attributes &/or values up as suggestions for the user
For gui - take note of how user navigates through ontologies and highlight the parts of the ontology the user has been to, as well as even allow user to filter to just those they’ve been to.

17. ZFIN integration

18. ZFIN aspirations Make webby ZFIN data adapter Seamless & generic
Fish evolutionists (cToL)
Webby will be zf collaboration. Use phenote/oboedit stuff in backend servlet. Front end use combination of java server pages, java server faces, shale… java script/ajax, applet? Uvic stuff webby?
Need to get data in zfin database - might write straight into database - jdbc/hibernate - or might just write pheno-xml (cjm/cbio) and zfin would handle the xml - unclear at this point.
The goal is to work seamlessly in zfin environment and yet be generic to use elsewhere - there should be configurations for zfin specific stuff.
Ctol group also interested

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
FB currently uses text editor - going to a java app from NLP folk. Will
2 very different environments to integrate with - zf is webby, fb is not. More work but good for long run I suppose.
Configuration for fb specific stuff of course
NLP - Natural Language Processing - might scan papers for ontology items and even come up with phenotype annotations.
ZF and other groups may be interested in this as well - ideally make generic & reusable

20. Download Webstart (0.5): Sourceforge 0.6 release ~July
Sourceforge
Obo sourceforge
subversion for phenote sub project
0.6 release ~July
Webstart is a way to install java applications from a web page…
Theres a webstart link at that url - theres also troubleshooting for webstart issues - should work from windows & mac - linux & solaris might require some futzing. Also java 1.5 is required so download if you don’t have it. For mac this means you need to be on Tiger (is that problematic?)
I tend to put out releases every few weeks - up to 0.3? at the moment.
At this point its definitely alpha software.
Sourceforge coming soon - svn is the new hipper cvs (can track history of moved files!)
For now on Obo sourceforge site - if cbio puts up a sourceforge site will migrate there (would be nice)
Could do 0.4 earlier if desired, 0.5 probably in early July

21. Acknowledgement BBOP: ZFIN: FlyBase: University of Victoria:
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
Visited zf & fb - very helpful to watch curators in action
Uvic - gui