[tdwg-content] status of uBio
Steve Baskauf
steve.baskauf at vanderbilt.edu
Fri Oct 16 16:51:00 CEST 2015
Nicky,
Thanks, I'm looking forward to checking it out! But no animals. :-(
Steve
Nicky Nicolson wrote:
>
> Hello Steve,
>
> Thanks for triggering an interesting thread.
>
> Just waving the IPNI flag for a minute:
>
>
>
> 1. They have managed to stick around for a long time and are stable in
> their format (as LSIDs and HTTP proxied LSIDs).
>
> At ipni.org we support our own HTTP proxy for LSIDs:
>
> http://ipni.org/urn:lsid:ipni.org:names:12345-1
>
> … and it’s been an age since I tried to resolve an LSID using the
> formal LSID spec but a quick run-through today shows that all the
> steps appear to be in working order.
>
>
> 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.
>
>
>
> IPNI is comprehensive for vascular plants (at species level). We’ll be
> addressing the data gaps at infra-specific level – but it’s very
> useful for us to be armed with reasons (from users like yourself) as
> to why we should spend time doing this.
>
>
> 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).
>
> IPNI only serves data about names, no taxa here.
>
> We are pushing IPNI IDs into our taxonomic resources so that a user
> can flexibly match a name and get an IPNI identifier (the
> nomenclatural part), and then as a later step query a taxonomic
> resource for their current view as to the taxonomic status of that
> name. We are aiming for a clean separation of names matching from the
> (multiple, potentially different) uses of those names to form taxonomies.
>
>
> 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.
>
>
>
> The HTTP proxy above returns RDF metadata for the specified record.
>
> New developments (most of the functionality outlined above is 8-10
> years old), I’ve been working on exposing IPNI data through standard
> match services – namely the Open Refine reconciliation API, which
> permits much more flexible names look-ups using a lot of heuristics
> gathered from matching data port exercises carried out at Kew over the
> past few years. Currently the main hitch with this service is that it
> includes duplicate records. This is something we’re working on
> resolving right now.
>
> The service is outlined here: http://data1.kew.org/reconciliation/ and
> details of the IPNI service in particular are here:
> http://data1.kew.org/reconciliation/about/IpniName
>
>
>
> If you’re interested in using IPNI, I’d be happy to hear any comments
> on the functionality above and / or any requests as to how we can make
> it more useful for you.
>
>
>
> cheers,
>
> Nicky
>
>
>
>
>
> *From:* tdwg-content-bounces at lists.tdwg.org
> [mailto:tdwg-content-bounces at lists.tdwg.org] *On Behalf Of *Steve Baskauf
> *Sent:* 16 October 2015 14:09
> *To:* Dmitry Mozzherin <dmozzherin at gmail.com>
> *Cc:* Chuck Miller (Contact) <chuck.miller at mobot.org>;
> tdwg-content at lists.tdwg.org; Jonathan A Rees <rees at mumble.net>;
> Shorthouse, David <david.shorthouse at umontreal.ca>
> *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
>
--
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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