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 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

4. Phenote

5. Current Phenotype Character in Phenote DB ID/genotype/taxonomy Genetic Context Anatomy Term (Entity) PATO value

6. eyeplacementhypoteloric++ entityvalueattribute++ midfacedevelopmenthypoplastic+ + kidneysizehypertrophied+ + Phenotype (clinical sign) = P 1 = P 2 = P 3 = shh -/- (holoprosencephaly) From M. Westerfield

7. entityvalueattribute++ 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

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. Phenotype Character Table List of Phenotype Character instances Operations: New, Delete, Copy

12. Recent additions Web interface! Configuration Data adapter (FlyBase) Genetic context field Term info navigation Pheno xml writeback

13. ToDo…

14. 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 UVic’s Jambalaya DAG view Relationship views Parents/kids, level limits

16. More aspirations… Pheno XML reader “Worn paths”

17. ZFIN integration

18. ZFIN aspirations Make webby JavaScript/AJAX interface collaboration ZFIN data adapter Seamless & generic Fish evolutionists (cToL)

19. 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?

20. 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

21. DEMO…

22. Download Webstart (0.6): http://toy.lbl.gov:9010/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)

23. 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