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Phenote: new developments and new communities

Phenote: new developments and new communities. A basic screen shot Entries are sorted by 'entity'. A close-up of the sort entry. New post-composition display. can do n-levels of specificity. New 'filter' feature Only displays EQ matches. Initial “ request a term ” interface. KEY.

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Phenote: new developments and new communities

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  1. Phenote: new developments and new communities

  2. A basic screen shot Entries are sorted by 'entity'

  3. A close-up of the sort entry

  4. New post-composition display. can do n-levels of specificity

  5. New 'filter' featureOnly displays EQ matches

  6. Initial “request a term” interface

  7. KEY Annotations Inferred relationships Relationships (btwn E & Q) FMA (5/5) Biological Process (2/2) Is_a Sensory perception of mechanical stimulus (0/2) Person (5/5) Is_a Part_of Part_of Part_of Sensory perception of sound Hearing [syn] (2/2) Ear (0/2) Kidney (2/2) Hair (1/1) Inheres_in E=Kidney Q=Dysplastic EYA1 PMID:0000001 EYA1.1 PMID:0000003 Is_a Right_Ear (2/2) Inheres_in towards Inheres_in Located_in towards Inheres_in

  8. General Annotation (1 annot/row) Table (current) (1 annot/row) Matrix (BIRN) (1 annot/cell) Tree

  9. NESCENT & Phenote • Use EQ model to curate phenotypic diversity data published in phylogenetics literature • Integrate with mutant phenotype data from ZFIN to investigate genetic basis of evolutionary change

  10. Integration and Ontology Intersection • Adding interface features to support efficient workflow for curation from taxonomic literature • Using new teleost taxonomic ontology and teleost anatomy ontology

  11. Enter a pre-defined list of specimens from which to repeatedly create different EQ (character) statements.

  12. A user may want to view a phylogenetic tree relating the specimens, and then simply select a node containing all the specimens to use. This functionality is available in an accessory window within Phenote. You can paste Newick-format tree text into the "Newick Tree" field at the bottom of the window. When the taxonomy ontology is available for inclusion within Phenote, your Newick tree should be composed of ontology IDs from the taxonomy ontology. The tree view will automatically display the actual taxon name from the ontology.

  13. Enabling the community • The various communities controls the actual data (i.e. instances) • We provide support for describing these data with ontologies • We must provide simple, non-intrusive ways of integrating into each community’s environment • Customized plug-ins to manipulate the instance data • Simple communications channels

  14. Leads for future work • Cornell Plant Consortium • Rheumatology and Autoimmune Disease at The University ofMinnesota • J.Craig Venter Institute • Encyclopedia of Life • K. White, U of Chicago - modENCODE • The greater zebra fish community

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