Poster at the Evolution Meetings

April 30, 2008

Aside from the Evolutionary Biology and Ontologies Workshop that we organize together with the NCBO at the Evolution Meeting 2008 in Minneapolis, we will also be presenting a poster. For your advance pleasure, here is the abstract that we wrote, only to realize that registration for a poster presentation actually did not require or even offer any abstract submission.

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Posted by Hilmar

Phenoscape project set up on SourceForge

April 29, 2008

We finally set up a Phenoscape project on SourceForge.net. At this moment there isn’t much there in the code repository, but within the next days we’ll deposit some scripts that we had to develop for OBO-format ontology generation (for example, for initiating the TTO from the Catalog of Fishes) and for massaging the tracker messages auto-generated by the OBO term request trackers to be more user-friendly. The source code repository will also be the home for some controlled vocabularies that (only?) we need for our project (such as the one for museum codes).

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Posted by Hilmar

Our first Data Jamboree is beginning

April 18, 2008

The first Phenoscape Data Jamboree (we are scheduled to have one each year) is starting today at NESCent. The event brings three fish morphologists external to the project (Miles Coburn, Kevin Conway, Mário de Pinna) together with our morphologist, ontology, and informatics personnel. In addition, Nicole Washington (NCBO) and Martin Ringwald (Jackson Laboratory), two experts from communities that have made considerable strides in bringing ontology-driven and semantically explicit approaches to bear on annotating gene function and mouse phenotypes and gene expression, respectively, are here to serve in an advisory role.

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Posted by Hilmar

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

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Posted by Jim

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

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Posted by Jim

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).  

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Posted by Jim