[tdwg-content] status of uBio

[Dmitry Mozzherin]

All name strings from uBio are in GNI and they do have UUIDs v5 generated
from them as it is described in this blog post -
http://globalnames.org/news/2015/05/31/gn-uuid-0-5-0. And we do have uBio
IDs associated with these UUIDs via GNI.



On Fri, Oct 16, 2015 at 3:25 PM, Richard Pyle <deepreef at bishopmuseum.org>
wrote:

> > 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).
>
>
>
> :-)
>
>
>
> Actually, saying that uBio identifiers refer to “names” is a bit like
> saying uBio identifiers refer to “stuff” (which is only slightly more
> ambiguous than “names”).  I think what you mean (a bit more explicitly) is
> that uBio identifiers refer to “name-strings”, wherein each unique literal
> UTF-8-encoded string of characters purported to represent a scientific name
> receives an integer as an identifier.
>
>
>
> GNI also assigns unique identifiers to such name-strings, but the
> difference is that the GNI identifier is a hash of the string itself.
> Thus, given a string, you can algorithmically derive the GNI identifier for
> it.  There is no way to algorithmically convert the uBio name-strings into
> their corresponding integer uBio identifiers.
>
>
>
> I have a question, and a suggestion.
>
>
>
> Question: Are new uBio integer identifiers ever going to be minted?  Or do
> we just want to maintain them for legacy purposes?
>
>
>
> Suggestion: Regardless of the answer to the question, I suggest that Dima
> generate an index for uBio integer identifiers and the corresponding hash
> uuid used by GNI.  I will import these into BioGUID.org, so going forward
> we will always have an index to translate the uBio integers into the GN
> hashed UUIDs.  From there, it would be a simple step to allow GN services
> to process uBio identifiers natively, and do all the cool things that Steve
> (and others) would like uBio/GN to do.
>
>
>
> Aloha,
>
> Rich
>
>
>
>
>
> *From:* tdwg-content-bounces at lists.tdwg.org [mailto:
> tdwg-content-bounces at lists.tdwg.org] *On Behalf Of *Steve Baskauf
> *Sent:* Friday, October 16, 2015 3:09 AM
> *To:* Dmitry Mozzherin
> *Cc:* Chuck Miller; tdwg-content at lists.tdwg.org; Jonathan A Rees;
> Shorthouse, David
> *Subject:* Re: [tdwg-content] status of uBio
>
>
>
> 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
> possible.
> Steve
>
> 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.
>
> http://bioimages.vanderbilt.edu
>
> http://vanderbilt.edu/trees
>
>
>
>
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