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.
No Comments » | 
Curation Tools, Data Curation, Informatics | 
Permalink
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 »
1 Comment | 
Curation Tools, Data Curation, Informatics, Workshops | Tagged: Bison, Data Jamboree, Roundup | 
Permalink
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 »
No Comments » | Curation Tools, Data Curation, Ontology, Workshops | Tagged: Evolution Conference, Outreach, RCN | Permalink
Posted by pmabee
April 4, 2008
Released new Phenote version (download). It has the following new features:
- Changed version back to 1.6 beta to be inline with NCBO versioning
- Term info panel now shows information for terms selected in Complete Ontology Tree View
- Window close button now works on specimen picker window
- User can turn off table sorting by clicking again on a reverse-sorted table column
- Rows can be dragged from Taxon list into any other table
- Dropped rows are selected in target table
- Fixed bug where dragged rows were not being copied as new rows (editing would screw up original)
- Editor fields no longer grow wider than the panel they’re in
- Selected rows attempt to stay visible when table is re-sorted
- Added updated collection code ontology
This is also the first release uploaded to and downloadable from the OBO SourceForge site as a file release, and can therefore be linked to indefinitely. Previously we were putting up the updated downloads on the Phenoscape wiki, which had the nasty effect that upon every update all earlier links no longer pointed to the correct version (but simply always to the latest).
No Comments » | Curation Tools, Informatics, Phenote | Tagged: Curator resources, Releases | Permalink
Posted by Jim
March 27, 2008
Released new Phenote version (Phenote-MacOSX.zip, Phenote-Windows.zip). It has the following new features:
- New feature - “Scratch lists” (see below)
- Browse all the ontologies using a tree view, select terms, and drag them onto fields to use them as values
- New, clean, interface look
You can open Scratch lists from the View menu. First you will see a blank table. You can add rows to the table and give them whatever name you want. Select a row and press the table-looking button in the component’s toolbar. A character table will open somewhere with that name. You can make new annotation rows in this table and then drag them into the main annotation table. You might want to make a couple different scratch lists that have particular values pre-filled in that you want to use again and again. This makes life a lot easier for Wasila, our data curator, when particular species always use the same voucher evidence. The caveat is that right now the scratch tables aren’t saved. That will require data adapter work.
No Comments » | 
Curation Tools, Informatics, Phenote | Tagged: Curator resources, Releases | 
Permalink
Posted by Jim
February 4, 2008
Released new Phenote version (Phenote-MacOSX.zip, Phenote-Windows.zip). It has the following new features:
- Taxon Comments field
- Publication Name field
- changed Taxon field to Valid Name
- write out starter NEXUS file for Taxon List (in phylogeny window)
- press Cmd-Return to enter current value and advance to next character while editing the same field
- in-progress Save (Cmd-S)
- simultaneous save of main document and taxon list files
- lock layout of interface panels (look in the Settings menu - Nicole Washington added this, it’s really handy)
No Comments » | Curation Tools, Informatics, Phenote | Tagged: Curator resources, Releases | Permalink
Posted by Jim
