June 16, 2010
I recently attended the 2010 Semantic Web Workshop in Santa Fe, hosted by the SSWAP project and iPlant, at St. John’s College. This was a two-day workshop, June 7-8, introducing semantic web technologies and applications to biological data and service integration. The first day was scheduled to be a whirlwind overview of semantic web technologies, beginning with a lecture on the foundations of web logic and reasoning in classic formal logic and moving through RDF, RDFS, and OWL. However, air travel problems led me to miss the entire first day of the workshop. Fortunately Damian Gessler, the workshop organizer, provided me with all the slides for the first day upon my arrival, and I was able to somewhat catch up before day 2. These slides are really a great overview of semantic web technologies and will be a useful resource.
The second day focused on applications to biological data and web services. A discussion on “taxonomic intelligence” was particularly illuminating. It provided an example of how different communities can share a set of identifiers for species, for example, yet provide their own set of statements about the taxonomy relating those species. Each community can draw conclusions relevant to its preferred taxonomy using data associated with the same species.
The afternoon focused on the SSWAP project, led by Damian Gessler. SSWAP is a protocol which uses OWL documents to describe the inputs and outputs relevant to a web service. Interestingly, users of these web services would submit their input in the very same OWL model used for service descriptions.
In Phenoscape, we are using OBO ontologies rather than RDF and OWL and storing our ontological annotations in OBD, a datastore tailored for OBO technologies which provides its own very effective reasoner. However, this workshop provided a great opportunity to stay up to date with semantic web standards and explore how to make our data compatible with and part of the global semantic web. In addition, St. John’s College was a great meeting location – it is a small college with a wonderful natural landscape in the hills outside of Santa Fe.
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Posted by Jim
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.
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Posted by Jim
February 23, 2010
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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Posted by Jim
February 23, 2010
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 »
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Posted by mtakai
December 4, 2009
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.
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Posted by pmabee
October 12, 2009
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 »
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Posted by tjvision
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.
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Posted by Jim
