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Phenote

Phenote. Mark Gibson Berkeley Bioinformatics and Ontology Project (BBOP) National Center for Biomedical Ontologies(NCBO) Lawrence Berkeley National Lab. Outline. What Phenote does now What Phenote aspires to Demo. What is Phenote?. A tool for annotating Phenotypes

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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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