Third beta release of Phenoscape Knowledgebase 2.0

February 7, 2011

Phenoscape Knowledgebase 2.0 beta release 3 is now available at This version includes an enhanced publication info interface [example] which displays the original character matrix, as well as a list of taxa including the taxonomic names and museum specimens used in the dataset. Other recent developments in the KB are global term info popups and hierarchical browsing of ontology terms on their info pages [example].

We have also improved our software and data release processes so that the public Knowledgebase can easily keep up with new developments and the latest data updates from our curators. Looking forward, the next major feature to be added to the Knowledgebase is a faceted browsing interface which is currently under development. This interface should help provide an overview of how the data are organized within the various ontologies used in the Knowledgebase.

Lapp gives NCBO webinar for Phenoscape

November 17, 2010

Hilmar Lapp gave a great overview today of the ongoing work in the Phenoscape project to 29 participants in the NCBO Webinar series.  This series showcases new projects, technologies and ideas in biomedical ontology, many of which use ontologies for interoperability.  Hilmar presented the biological context (evolution, conservation, development, etc.) into which our work fits, and the challenges involved in representing phenotype.  A videorecording of his talk will be posted in case you missed it.

Update: The slides are also posted on Slideshare

Revising the Knowledgebase interface

March 24, 2010

We have been developing mockup versions of new web interfaces for the Phenoscape Knowledgebase.  In order to design an updated interface which is both more powerful and easier to use than the existing one, in February I presented a series of mockups to faculty, post-docs, and graduate students at the University of Oregon, the home of ZFIN.  Following user-testing expertise at ZFIN, I met with the researchers in pairs and recorded their feedback on newly designed interfaces for viewing anatomical and taxonomic terms within the ontology hierarchy, configurable queries for phenotype annotations, and data visualization on phylogenetic trees.  The feedback proved to be extremely valuable and has led to several modifications to the planned interface revisions.

Taxonomy as ontology: opening up the debate

May 15, 2008

We have created a new mailing list, obo-taxonomy, under the OBO (Open Biomedical Ontologies) umbrella. Our motivation for this new forum is to really open up the discussion surrounding the issues of what should be a proper ontological representation of taxonomy and phylogeny, for example proper semantics of the relationship between taxonomic groups, and between specimens and species. If you care about or have thoughts or opinions on these and related questions, we encourage you to subscribe to this new list.

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Phenoscape project set up on SourceForge

April 29, 2008

We finally set up a Phenoscape project on 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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