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.
Phenoscape solicits feedback on new interfaces at AmphibAnat Kansas City meeting
December 4, 2009
Leave a Comment » | 
Anatomy Ontology, Data Curation, Ontology, Software, Workshops | Tagged: AmphibAnat, Data Curation, Software | 
Permalink
Posted by pmabee
ICBO Summary
August 12, 2009While 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
Joint Phenoscape and AmphibAnat Workshop at ASIH, July 25th in Portland, Oregon
May 28, 2009
Ontologies, controlled vocabularies with well-defined relations among terms, are a key tool in scientific data integration. By using ontologies, scientists from different disciplines can know when they are referring to the same entity by different names, and new discoveries are enabled by computer software being able to reason across disciplines and over large datasets. Already widely used in genomics, ontologies are of growing importance in systematics, ecology, behavior, genetics, morphology and physiology. This workshop aims to explore the utility of ontologies for ichthyology and herpetology, using the Teleost Anatomy Ontology and the Amphibian Anatomy Ontology as case studies of community resources that are being actively developed and used by members of ASIH. Read the rest of this entry »
1 Comment | Workshops | Tagged: AmphibAnat, ASIH, Outreach, Workshops | Permalink
Posted by tjvision
Meeting with Deep Fin and other fishy folk
April 17, 2009Phenoscapers met with Deep Fin and several associated fish groups in late February for ontology development, curation, web interface development and outreach. We had lots of good interactions with the 30+ ichthyologists attending. Read below for the details. Read the rest of this entry »
1 Comment | Workshops | Tagged: Outreach | Permalink
Posted by pmabee
Second “Evolutionary Biology & Ontologies” workshop
January 9, 2009Our second “Evolutionary Biology & Ontologies Workshop” was held at the Society of Integrative and Comparative Biology (SICB) meetings in Boston (January 5, 2009). It was organized by the Phenoscape PIs (Paula Mabee, Todd Vision, Monte Westerfield), NESCent and Barry Smith from the National Center for Biomedical Ontologies (NCBO). In our morning of talks, our speakers provided the audience with a solid introduction to ontologies, annotations, curation tools, databases, and examples of the integrative questions that can be answered using them. The speakers, titles, and slides for these talks are available through the links below, and they provide an instructive resource for the community. Read the rest of this entry »
Leave a Comment » | Workshops | Tagged: Outreach | Permalink
Posted by pmabee
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 »
1 Comment | Curation Tools, Data Curation, Informatics, Workshops | Tagged: Bison, Data Jamboree, Roundup | 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
