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 »
Announcing Phenex 1.0
November 25, 2009
Leave a Comment » | 
Curation Tools, Data Curation, Informatics, Phenex | 
Permalink
Posted by Jim
PATO Users Meeting
November 20, 2009Last 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
Summer Curation Drive
August 24, 2009On 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, 2009A 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
ICBO Summary
August 12, 2009While 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: Conference, ICBO | Permalink
Posted by pmidford
New Phenoscape data repository
November 6, 2008We 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 »
Leave a Comment » | Curation Tools, Data Curation, Informatics | Permalink
Posted by wdahdul
Report from the Phenoscape Data Roundup
October 24, 2008“…where the buffalo roam and the data are rounded up-up all day….”
A few weeks ago, from Sep 27 to Oct 1, we met in the Black Hills of South Dakota with a group of guest data curators and outside advisors to curate high priority papers, refine the curation workflow and Phenex interface, and evaluate the first prototypes for the web-based user interface to the database. Not only did the workshop end up highly productive (see below), we also had a chance to observe the annual roundup of the largest herd of buffalo in North America, swim in cold Sylvan lake, and see Mount Rushmore one evening. Read the rest of this entry »
2 Comments | Curation Tools, Data Curation, Informatics, Workshops | Tagged: Bison, Data Jamboree, Roundup | Permalink
Posted by pmabee
Curation from Summer ’08
August 30, 2008Curation of evolutionary phenotypes from the systematic evolutionary literature of fishes is central to accomplishing our goal, which is to prototype an ontology-based informatics system to integrate evolutionary, anatomical, developmental, and genetics data. This summer we accomplished a fair chunk of curation, and I’m summarizing this here (see graph below). Read the rest of this entry »
Leave a Comment » | Data Curation | Permalink
Posted by pmabee
Evolutionary Biology & Ontologies Workshop report
July 11, 2008Our first educational and outreach event “Evolutionary Biology & Ontologies Workshop” was held at the Evolution meetings in Minneapolis, Minnesota (June 20, 2008), and we felt it was a big success. We had lots of enthusiasm and over 50 attendees for this all day workshop, which was organized by the Phenoscape PIs (Paula Mabee, Todd Vision, Monte Westerfield), NESCent and Barry Smith from the National Center for Biomedical Ontologies (NCBO).
We need to especially thank all our speakers for their excellent presentations, They not only gave the audience a varied introduction to ontologies, but also a set of examples of the integrative questions that can be answered using them. The slideshows for all of these talks are on our wiki but I thought I would provide a brief overview of each one right below as a summary of the workshop. The use of ontologies is just emerging in evolutionary biology, and it is an exciting time to be involved in this field. As we move forward to use ontologies in evolutionary biology, we discover new requirements and challenges — for example, the challenge of how we create ontologies that are interoperable — so that we can ask big questions that span not only taxonomic groups (such as bees and fishes and mouse and fly) but different knowledge domains (such as phenotype, evolution, and genetics, genomics, medicine). Read the rest of this entry »
Leave a Comment » | Curation Tools, Data Curation, Ontology, Workshops | Tagged: Evolution Conference, Outreach, RCN | Permalink
Posted by pmabee
Our first Data Jamboree is beginning
April 18, 2008The first Phenoscape Data Jamboree (we are scheduled to have one each year) is starting today at NESCent. The event brings three fish morphologists external to the project (Miles Coburn, Kevin Conway, Mário de Pinna) together with our morphologist, ontology, and informatics personnel. In addition, Nicole Washington (NCBO) and Martin Ringwald (Jackson Laboratory), two experts from communities that have made considerable strides in bringing ontology-driven and semantically explicit approaches to bear on annotating gene function and mouse phenotypes and gene expression, respectively, are here to serve in an advisory role.
1 Comment | Data Curation, Workshops | Tagged: Data Curation, Jamboree, Workshop | Permalink
Posted by Hilmar
Phenoscape 