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

Summer Curation Drive

August 24, 2009

On March 29, 2009, we initiated an ambitious goal (informally dubbed the ‘5K Karacters Kuration Goal’) to curate over 5,000 characters for 3,500 species from 50 papers by June 15. The reason for this annotation push was the planned beta release of the Phenoscape Knowledgebase at the Joint Meeting of Ichthyologists and Herpetologists (22-27 July 2009) in Portland, Oregon. We formed a curator team including Jeff Engeman, Terry Grande, Eric Hilton, John Lundberg, and Paula Mabee, and we each took on a significant chunk (either 500 or 1000 characters) of the ichthyological literature.   Read the rest of this entry »

Leave a Comment » | Anatomy Ontology, Data Curation | Permalink
Posted by wdahdul

New fossil tells how piranhas got their teeth

August 16, 2009

A recent publication on Megapiranha paranensis from Phenoscape curators Wasila Dahdul and John Lundberg is in the news!

click for full-zise image

DURHAM, N.C. — How did piranhas — the legendary freshwater fish with the razor bite — get their telltale teeth? Researchers from Argentina, the United States and Venezuela have uncovered the jawbone of a striking transitional fossil that sheds light on this question. Named Megapiranha paranensis, this previously unknown fossil fish bridges the evolutionary gap between flesh-eating piranhas and their plant-eating cousins. Read the rest of this entry »

3 Comments | Data Curation, Morphology, Publications, Science, Teleosts | Permalink
Posted by tjvision

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

ICBO Summary

August 12, 2009
While the rest of Phenoscape was at ASIH running the ontology workshop and announcing the database and website release, I was across the country, representing Phenoscape at the International Conference on Biomedical Ontologies in Buffalo, NY.
ICBO covered 2-3/4 days (July 24-26) of presentations with two evening poster sessions.  There were
also software demos during the lunch breaks, and two panel discussions.
Although there were several sessions devoted to ontologies of disease and clinical practice, there
were a number of talks of interest to Phenoscapers.  Among these were several alignment talks, including
one from the BGEE group on Homonto and Chris Mungall’s on cross products and Uberon.  There were also sessions
on annotation and natural language processing (NLP), including Mike Bada’s talk on developing a corpus for testing NLP based annotation.
There were also two talks specifically about ontologies and physiology, one by John Gennari focused on integrating
existing anatomy ontologies (e.g., FMA) with physiological simulations, though he specifically ducked ontological
modeling of physiology as process.  The other was an ‘old school AI’ simulation of a patient, that includes models of
physiology, cognition, and NLP.
There was also some promising activity on behavior ontologies, including a poster by Tim Beck, a postdoc from the UK on a mammalian behavior ontology
and a ‘behavior lunch’ on the second day, with Tim, Judy Blake, David Shotton (ABO collaborator from Oxford), Mary Shimoyama (RGD), and several others.
There is a European plan to develop a new OWL-based general behavior ontology, and Chris Mungall has recently established an OBO-behavior list ().
There was also a lot of discussion generated by the proposed ontology of homology relations (the 1.0 version; 1.1 released recently(http://bgee.unil.ch/bgee/download/homology_ontology_v1.1.obo)), although the consensus from the numerous people I discussed
it with was that it needed more work (which is happening).
Other interesting ontologies included an ontology of Evolutionary processes presented in a poster by Adam Goldstein (Iona University).  He’s since been in
contact with Hilmar, and I believe with representatives of CDAO and Dryad.  Phenoscape was also represented by a poster.
There were two panels, one focussing on Ontology and Publishing.  Although the lineup, which included
a representative from Elsevier (Jabe Wilson) and Alan Ruttenberg from Science Commons suggested a discussion
on open publishing, the Elsevier representation was quiet restrained, and it was Larry Hunter who made the strongest argument that publishers currently
provide little value to academics.  David Shotton discussed his semantic annotation of a randomly selected paper on an infectous disease.
The second panel was on the Future (and past) of ontologies and knowledge representation.  I think the two memorable claims from this discussion
were the call to expand the A-box (since the T-box is really less than most people think) and Barry Smith’s claim that in 25 years consulting ontologies
will be as common in biology and medical departements as statisticians are today.
The text from all the presentations and posters will be made available at Nature Proceedings (http://precedings.nature.com/collections/icbo-2009).  There was
also an ICBO group on FriendFeed (http://friendfeed.com/icbo) with other attendee’s tweets from the conference and preceeding tutorial sessions.  Finally, I will
be posted a more detailed report on my personal blog (http://ontethology.blogspot.com).

While the rest of Phenoscape was at the ASIH meeting, involved with the ontology workshop and the release of the database and website, I was across the country, representing Phenoscape at the International Conference on Biomedical Ontologies (ICBO) in Buffalo, NY.  ICBO covered 2-3/4 days (July 24-26) of presentations with two evening poster sessions. There were also software demos during the lunch breaks, and two panel discussions.

Although many of the sessions were devoted to ontologies of disease and clinical practice, there were a number of talks of interest to Phenoscapers. Read the rest of this entry »

2 Comments | Data Curation, Ontology, Workshops | Tagged: , | Permalink
Posted by pmidford