November 6, 2008
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.
This is a great improvement to our system of file management. We previously used a server for file sharing, which limited us to saving only the current version of each file. Aside from version control, SVN has other nice features such as automatic file merging if a curator checks in a different version of a file (which might happen if the file on the repository has been updated by another user since the curator first updated their local copy). Curators also utilize commit comments to document the edits made on a data file.
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Curation Tools, Data Curation, Informatics | 
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Posted by wdahdul
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 »
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Curation Tools, Data Curation, Informatics, Workshops | Tagged: Bison, Data Jamboree, Roundup | 
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Posted by pmabee
July 11, 2008
Our 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 »
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Posted by pmabee
April 18, 2008
The 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.
Read the rest of this entry »
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Posted by Hilmar
Posted by pmabee
