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.
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Curation Tools, Informatics, Phenex, Software | 
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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.
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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
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
Phenex 1.0-beta24 is now available for download.
This release has a few new features and a number of bug fixes:
Features:
Bugs fixed:
Leave a Comment » | Curation Tools, Informatics, Phenex | Permalink
Posted by Jim
We have set up a data repository on SourceForge to house the growing number of data files that are worked on daily by new curators and students. The repository uses Subversion (SVN) software to maintain current and all previous versions of each Phenex data file. Curators “update” the local copies of data files on their computers with the current versions from the repository, add their modifications, and “commit” their modified local copy to the repository at the end of their work session. We have been using ZigVersion as a friendly graphical client interface to SVN. Read the rest of this entry »
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Posted by wdahdul
After a summer of intensive development, at our recent Data Roundup we introduced curators to our new phenotype annotation software, Phenex. Phenex is an application for annotating character matrix files with ontology terms. Character states can be annotated using the Entity-Quality syntax for ontologically describing phenotypes. In addition, taxon entries can be annotated with identifiers from a taxonomy ontology. Phenex saves ontology annotations alongside traditional character matrix data using the new NeXML format standard for evolutionary data. Read the rest of this entry »
Leave a Comment » | Curation Tools, Informatics, Phenex, Phenote | Permalink
Posted by Jim
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