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).  


Released Phenote v2.0 update (PhenoScape beta 1664)

March 27, 2008

Released new Phenote version (Phenote-MacOSX.zipPhenote-Windows.zip). It has the following new features:

  • New feature – “Scratch lists” (see below)
  • Browse all the ontologies using a tree view, select terms, and drag them onto fields to use them as values
  • New, clean, interface look

You can open Scratch lists from the View menu. First you will see a blank table.  You can add rows to the table and give them whatever name you want.  Select a row and press the table-looking button in the component’s toolbar.  A character table will open somewhere with that name.  You can make new annotation rows in this table and then drag them into the main annotation table.  You might want to make a couple different scratch lists that have particular values pre-filled in that you want to use again and again.  This makes life a lot easier for Wasila, our data curator,  when particular species always use the same voucher evidence. The caveat is that right now the scratch tables aren’t saved. That will require data adapter work.


Released Phenote v2.0 update (PhenoScape beta 1535)

February 19, 2008

Released new Phenote version (Phenote-MacOSX.zipPhenote-Windows.zip). It has the following new features:

  • Museum collection code name completion when entering specimens for a taxon.
  • Separate editable table for entering specimens for a taxon.
  • Field for spatial ontology.
  • Post-composition enabled for PATO fields.

Released Phenote v2.0 update (PhenoScape beta 1468)

February 4, 2008

Released new Phenote version (Phenote-MacOSX.zipPhenote-Windows.zip). It has the following new features:

  • Taxon Comments field
  • Publication Name field
  • changed Taxon field to Valid Name
  • write out starter NEXUS file for Taxon List (in phylogeny window)
  • press Cmd-Return to enter current value and advance to next character while editing the same field
  • in-progress Save (Cmd-S)
  • simultaneous save of main document and taxon list files
  • lock layout of interface panels (look in the Settings menu – Nicole Washington added this, it’s really handy)