Phenex 1.0.3 released

February 23, 2010

Phenex 1.0.3 is now available.  This release fixes a serious bug which caused Phenex to append modified phenotype annotations within files, instead of replacing the previous data. Phenex will now read and write NeXML files correctly. It should also automatically recover the latest data from files saved with older versions of Phenex.

All Phenex users should replace their current copy of Phenex with the latest release. It can be downloaded from the Phenex homepage on the Phenoscape wiki.


Announcing Phenex 1.0

November 25, 2009

Phenoscape is proud to announce the immediate availabiity of Phenex 1.0, the first public release of our platform-independent desktop application for annotating character-by-taxon matrices with ontology terms.  Phenex has been in development and available in beta form for over a year, while we used it to curate more than 50 publications for inclusion in the Phenoscape Knowledgebase. Read the rest of this entry »


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.

New Phenoscape data repository

November 6, 2008

We have set up a data repository on SourceForge to house the growing number of data files that are worked on daily by new curators and students. The repository uses Subversion (SVN) software to maintain current and all previous versions of each Phenex data file.  Curators “update” the local copies of data files on their computers with the current versions from the repository, add their modifications, and “commit” their modified local copy to the repository at the end of their work session.  We have been using ZigVersion as a friendly graphical client interface to SVN. Read the rest of this entry »


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 »


Report from the Phenoscape Data Roundup

October 24, 2008

“…where the buffalo roam and the data are rounded up-up all day….”

A few weeks ago, from Sep 27 to Oct 1, we met in the Black Hills of South Dakota with a group of guest data curators and outside advisors to curate high priority papers, refine the curation workflow and Phenex interface, and evaluate the first prototypes for the web-based user interface to the database. Not only did the workshop end up highly productive (see below), we also had a chance to observe the annual roundup of the largest herd of buffalo in North America, swim in cold Sylvan lake, and see Mount Rushmore one evening. Read the rest of this entry »


Evolutionary Biology & Ontologies Workshop report

July 11, 2008

Our first educational and outreach event “Evolutionary Biology & Ontologies Workshop” was held at the Evolution meetings in Minneapolis, Minnesota (June 20, 2008), and we felt it was a big success.  We had lots of enthusiasm and over 50 attendees for this all day workshop, which was organized by the Phenoscape PIs (Paula Mabee, Todd Vision, Monte Westerfield), NESCent and Barry Smith from the National Center for Biomedical Ontologies (NCBO). 

We need to especially thank all our speakers for their excellent presentations, They not only gave the audience a varied introduction to ontologies, but also a set of examples of the integrative questions that can be answered using them.   The slideshows for all of these talks are on our wiki but I thought I would provide a brief overview of each one right below as a summary of the workshop. The use of ontologies is just emerging in evolutionary biology, and it is an exciting time to be involved in this field.  As we move forward to use ontologies in evolutionary biology, we discover new requirements and challenges — for example, the challenge of how we create ontologies that are interoperable — so that we can ask big questions that span not only taxonomic groups (such as bees and fishes and mouse and fly) but different knowledge domains (such as phenotype, evolution, and genetics, genomics, medicine). Read the rest of this entry »


Released Phenote update (v1.6-beta4)

April 15, 2008

Released new Phenote version (download). It has the following new features:

  • Changed version scheme again, hopefully for the last time
  • Bug fixes to in-table editing
  • Added TAO to the Quality field for use in post-composition
  • Included built-in Phenoscape interface layout
  • Re-ordered input fields to better match curation workflow

Released Phenote update (v1.6 beta 1699)

April 8, 2008

Released new Phenote version (download). It has the following new features:

  • Annotations can now be edited directly in the table

Released Phenote update (v1.6 beta 1692)

April 4, 2008

Released new Phenote version (download). It has the following new features:

  • Changed version back to 1.6 beta to be inline with NCBO versioning
  • Term info panel now shows information for terms selected in Complete Ontology Tree View
  • Window close button now works on specimen picker window
  • User can turn off table sorting by clicking again on a reverse-sorted table column
  • Rows can be dragged from Taxon list into any other table
  • Dropped rows are selected in target table
  • Fixed bug where dragged rows were not being copied as new rows (editing would screw up original)
  • Editor fields no longer grow wider than the panel they’re in
  • Selected rows attempt to stay visible when table is re-sorted
  • Added updated collection code ontology

This is also the first release uploaded to and downloadable from the OBO SourceForge site as a file release, and can therefore be linked to indefinitely. Previously we were putting up the updated downloads on the Phenoscape wiki, which had the nasty effect that upon every update all earlier links no longer pointed to the correct version (but simply always to the latest).