[tdwg-content] status of uBio

Steve Baskauf steve.baskauf at vanderbilt.edu
Fri Oct 16 15:08:35 CEST 2015

Thanks all for the information and comments about the status of uBio.  
I'm glad to hear that the server will probably come back up.  If not, 
then I hope the data will be made available to those who said they would 
be willing to host it.

I have been interested in using the uBio identifiers for several reasons:
1. They have managed to stick around for a long time and are stable in 
their format (as LSIDs and HTTP proxied LSIDs).
2. The coverage of names is really good for plants, animals, different 
geographic locations, etc.  I also use ITIS identifiers but it's fairly 
common for me to not be able to find one for the name I need, which 
almost never happens with uBio.
3. It's somewhat clear what uBio identifiers refer to: names vs. 
something more nebulous involving taxa or ... something.  (Not trying to 
push your button, Rich Pyle). 
4. You can actually get RDF associated with the LSID version of the uBio 
identifiers.  I was wanting to download some to play with in our new 
triplestore (http://rdf.library.vanderbilt.edu) when I discovered that 
the server was down.  The RDF is somewhat ad hoc, but hey, it's there.

There isn't really any other source that has all of these 
characteristics.  So please keep uBio going indefinitely, if at all 

Dmitry Mozzherin wrote:
> I had been administering uBio for the last year, but now I am moving 
> from MBL. uBio machine is in a bad shape, and it crashes after a few 
> hours of work. My plan is to create Docker containers for database, 
> code and data, which should make whole system much more stable, and 
> much more manageable. Good news I will definitely try my best to do 
> it, the bad news I am spread thinner than usual with move, 
> transferring hardware and grant, GN things, EOL things, and figuring 
> out what to do with the house etc. uBio 'code' part is about 35 Gb, 
> which makes the task more complicated, but I am quite optimistic that 
> I will be able to make containers and put them either on an  MBL 
> machine, run it from University of Illinois, or give it to Naturalis 
> -- depending on what will make more sense for Dave Remsen, MBL and all 
> interested in the project.

Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences

postal mail address:
PMB 351634
Nashville, TN  37235-1634,  U.S.A.

delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235

office: 2128 Stevenson Center
phone: (615) 343-4582,  fax: (615) 322-4942
If you fax, please phone or email so that I will know to look for it.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.tdwg.org/pipermail/tdwg-content/attachments/20151016/df8eb63c/attachment.html 

More information about the tdwg-content mailing list