Our summer of code project

August 27, 2009

Phenoscape has mentored, under the auspices of NESCent, another Google Summer of Code student this year.  Kasia Hayden developed a plugin package for Mesquite that allows users to view character matrices and EQ (ontology-based) annotations produced using the Phenex tool.  The primary purpose was to allow curators to share their annotation work with others in the context of a more familiar tool.  Users can select cells in a Mesquite character matrix and, using two new cell tools, see EQ annotations either as text in the bottom pane of the matrix window, or as a graph in a separate pop-up window. Read the rest of this entry »

Leave a Comment » | Informatics, Phenex, Software, Source Code | Permalink
Posted by pmidford

Phenex 1.0-beta24 released

August 14, 2009

Phenex 1.0-beta24 is now available for download.

This release has a few new features and a number of bug fixes:

Features:

  • The Search panel from OBO-Edit is now available in Phenex, under the View > Ontology menu.  This allows the user to do a textual search of all loaded terms, and view a results list.
  • There is a “quick editing” mode for the character matrix interface.  The user can type the name of a state symbol, without first double-clicking the cell, and Tab or Return to the next cell to edit.
  • If the quality “count” has been used in a phenotype for any state for a character, it will be auto-filled for subsequent states.
  • Open/Save panel starts at the previously visited directory.

Bugs fixed:

  • Copy and paste of terms in the Phenotypes table works consistently now.
  • The post-composition editor no longer disappears after tabbing out of the genus field when running on Java 6.
  • The menubar no longer disappears after using the post-composition editor.

Leave a Comment » | Curation Tools, Informatics, Phenex | Permalink
Posted by Jim

Introducing Phenex

October 30, 2008

After a summer of intensive development, at our recent Data Roundup we introduced curators to our new phenotype annotation software, Phenex. Phenex is an application for annotating character matrix files with ontology terms. Character states can be annotated using the Entity-Quality syntax for ontologically describing phenotypes. In addition, taxon entries can be annotated with identifiers from a taxonomy ontology. Phenex saves ontology annotations alongside traditional character matrix data using the new NeXML format standard for evolutionary data. Read the rest of this entry »

Leave a Comment » | Curation Tools, Informatics, Phenex, Phenote | Permalink
Posted by Jim

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