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Phenote

Phenote is a tool for annotating phenotypes based on genetic context, anatomy terms, and PATO attributes. It aids curators in categorizing and organizing clinical signs, using various ontologies for data completion and analysis.

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Phenote

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  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

  4. Phenote

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

  6. Phenotype (clinical sign) = entity + attribute + value P1 = eye + placement + hypoteloric + P2 = midface + development hypoplastic + P3 = kidney + size hypertrophied shh-/-(holoprosencephaly) From M. Westerfield

  7. Phenotype (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

  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

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