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.
1 Comment | 
Curation Tools, Informatics, Phenex, Software | 
Permalink
Posted by Jim
Hello all,
As an online student of Bioinformatics based in Nairobi, Kenya, I had a strong desire to undertake a project that would enhance my knowledge and skills in software development. Hence, after completing MSc. Course work at the University of Manchester, UK, I was happy to be awarded an internship from the Phenoscape project for an 11-week traineeship beginning September 21st, 2009 at the National Evolutionary Synthesis Center (NESCent). This project seeks to establish the developmental and genetic basis of the astonishing morphological heterogeneity across diverse species. In addressing this, a rich and rigorous knowledge base, PhenoscapeKB, constituting evolutionary variable characters across a clade of fishes connected to mutant phenotypes from ZFIN has been developed. Core to the PhenoscapeKB is the modeling of the character entities using ontologies thus facilitating the knowledge synthesis via logical/mathematical reasoning. Read the rest of this entry »
Leave a Comment » | Informatics, Ontology, Software | Permalink
Posted by mtakai
Phenex 1.0.2 is now available. This is a minor update which fixes an interface problem caused by a recent Mac OS X Java update. It also fixes a file loading bug which occurred on specific older versions of Mac OS X. Phenex can be downloaded from its homepage on the Phenoscape wiki.
Leave a Comment » | Phenex, Software | Permalink
Posted by Jim
In early November Wasila and I attended the AmphibAnat workshop in Kansas City, MO (Nov. 5-8) that was organized by Anne Maglia. As you may know, Phenoscape has a close relationship with this group, not only because they work on herps (ichthyologists and herpetologists have a long tradition of working together…), but because they are also developing ontologies to annotate the published comparative anatomical literature. I presented the status of our work in Phenoscape to the large group (~40) of amphibian development and anatomy experts who were present. As these folks added new terms, synonyms, and images to the amphibian ontologies over the course of the next few days, we solicited comments on the prototypes of three new interfaces for the Phenoscape Knowledgebase. Using both images and paper copies of these prototypes, we invited people to sit down with us on a one-on-one basis and describe in detail what worked and what was missing or unclear. The feedback was extremely useful, and we appreciated the AmphibAnat time. We have now gone over all the comments within Phenoscape and logged them individually to FogBugz, our internal tracking system. We’ll be generating new versions of these prototypes through early February, when we plan a formal round of usability testing.
Leave a Comment » | Anatomy Ontology, Data Curation, Ontology, Software, Workshops | Tagged: AmphibAnat, Data Curation, Software | Permalink
Posted by pmabee
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 »
Leave a Comment » | Curation Tools, Data Curation, Informatics, Phenex | Permalink
Posted by Jim
Last month I participated in an informal meeting for users and developers of the Phenotype and Trait Ontology (PATO), organized by Chris Mungall and Suzanna Lewis at the Lawrence Berkeley National Labs in Berkeley, California. PATO is the quality ontology used by many in the OBO community to annotate phenotypic variation. We are heavy-duty PATO users here at Phenoscape, so I was eager to meet with its developers and other users to discuss outstanding issues and hear about phenotype annotation from other projects. Read the rest of this entry »
Leave a Comment » | Data Curation | Permalink
Posted by wdahdul
We are pleased to announce the beta release of the Phenoscape Knowledgebase (KB) at http://kb.phenoscape.org/ and would like to solicit feedback.
Phenoscape KB integrates phenotypic data from genetic studies of zebrafish with evolutionarily variable phenotypes from the literature of fishes. It currently contains 333,987 phenotype statements about 2,310 taxa (mainly ostariophysan fishes), from 51 publications, and 11,267 phenotype statements about 2,953 genes retrieved from ZFIN (zfin.org). You can explore these data by searching for anatomical terms, taxa (by Latin name), or genes (by ZFIN gene symbol). Read the rest of this entry »
Leave a Comment » | Informatics, Knowledge Base, Science, Software | Tagged: knowledgebase | Permalink
Posted by tjvision
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
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
A recent publication on Megapiranha paranensis from Phenoscape curators Wasila Dahdul and John Lundberg is in the news!
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
Connotea Bookmarks NESCent
