Phenex 1.6 has been released. Updates:
- Support for entry of polymorphic values in matrix cells (documentation).
- Improvements to the tab-delimited export format.
Filed under: Data Curation, Phenex
The Phenoscape team has created a tutorial introduction to the Knowledgebase. The tutorial is designed to introduce users to exploring phenotypic data in the Phenoscape Knowledgebase, starting with searching for anatomical terms, browsing data using faceted browsing, and performing searches using the query panel. Let us know if you find it helpful in getting started with the KB.
In June I had the opportunity to attend DILS 2012 (Data Integration in the Life Sciences), at the University of Maryland in College Park. I presented a poster on Phenoscape, “The Phenoscape Knowledgebase: Integrating phenotypic data across taxonomy, from biodiversity to developmental genetics”. The poster highlighted some of the new directions the Phenoscape project is heading, such as broadening taxonomic coverage and adoption of semantic web technologies. DILS was a small conference but had several talks discussing the applications of ontologies to biological data. I’m looking forward to DILS 2013 in Montreal, in conjunction with ICBO and the Canadian Semantic Web conference.
A new bugfix release of Phenex is available. Phenex 1.4.2 addresses the following issues:
The NESCent Informatics group periodically holds “hack days”, one day mini-hackathons where we take a break from our usual schedule and push forward on a specific topic of interest. Most recently, the topic was support for the mobile web. I took a look at the Phenoscape Knowledgebase layout on the iPad and iPhone. In general the site did not adapt well to small screen sizes.
In order to avoid serving different layouts to specific devices, I applied techniques from the Responsive Web Design approach, which uses new functionality from CSS 3 to dynamically adjust the page layout based on the size of the browser window. In the new layout, when the window is small, controls move from the side to the top, allowing both the controls and the content table to use the full screen width.
The new layout works across most of the pages on the Knowledgebase site. In general, it is a big improvement on mobile devices. However, there are a few remaining glitches to address, such as controls that appear upon mouse hover: difficult to use on a touchscreen device, where there is no mouse.
We have recently released version 1.2.1 of our Phenex annotation software. This release adds some functionality for easier collaborative editing of data files. While our curators have used Subversion revision control software in the past, the new features make it more reliable to share Phenex data files with user-friendly file synchronization software such as Dropbox. While a NeXML document is open in Phenex, the application monitors for changes to the document file in the background. If the file is being shared via Dropbox and is simultaneously edited by someone else, Phenex will alert the user that the file has changed and offer to load the new version. If there are no unsaved edits then Phenex will reload the file automatically. Phenex 1.2 also provides an autosave feature which saves the document after every edit—this reduces the chance that the file might be edited elsewhere while one has unsaved changes, avoiding complicated file merges.
Last month, I (Jim Balhoff) and Hilmar Lapp attended the Biodiversity Information Standards meeting (TDWG 2011), in New Orleans. As a representative of both Phenoscape and the Hymenoptera Anatomy Ontology project, I presented a poster, with co-authors Matt Yoder and Andy Deans, detailing an OWL model showing the explicit semantics of linking an Entity–Quality (EQ) phenotype to evolutionary character matrix data and taxonomic specimens. While EQ can be thought of as simple ontological tags on descriptive data, modeling phenotypes within a more explicit logical framework allows us to make use of more powerful automated reasoning. It also provides a consistent interpretation for EQs across projects annotating phenotypes (for example, Phenoscape and HAO).
Of particular relevance to our poster was another presented by Cam Webb. Cam has created an OWL-compatible version of Darwin Core which can be used to describe specimen metadata in RDF. We made similar use of Darwin Core in our poster, but we are looking into adopting Cam’s Darwin-SW for this part of the model.
Overall there was a lot of interest in semantic technologies at TDWG, ranging from the initial meeting of an RDF/OWL working group to other projects that are not using semantic technologies but seem well suited for RDF.
I recently attended the Conference on Semantics in Healthcare and Life Sciences (CSHALS), in Cambridge, MA. The CSHALS meeting was a change for me in that it’s much more healthcare-oriented than other venues in which I’ve presented work from Phenoscape. This was a great opportunity to see how far the healthcare community has pushed semantic web technologies, and also to become more familiar with some of the more commercial packages which are available for storing and querying very large knowledgebases based on RDF (for example, AllegroGraph and Gruff from Franz, Inc., and Sentient Knowledge Explorer from IO Informatics). A particularly interesting talk was the keynote by Toby Segaran, of Metaweb Technologies, advocating semantic techniques as a more agile approach to data. Slideshows from the conference presentations are available for download here, including my own.
Phenoscape Knowledgebase 2.0 beta release 3 is now available at http://kb.phenoscape.org/. 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.
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.