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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hello Steve,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Thanks for triggering an interesting thread.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Just waving the IPNI flag for a minute:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal">1. They have managed to stick around for a long time and are stable in their format (as LSIDs and HTTP proxied LSIDs).<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">At ipni.org we support our own HTTP proxy for LSIDs:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><a href="http://ipni.org/urn:lsid:ipni.org:names:12345-1">http://ipni.org/urn:lsid:ipni.org:names:12345-1</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">… 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.<o:p></o:p></span></p>
<p class="MsoNormal"><br>
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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">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.<o:p></o:p></span></p>
<p class="MsoNormal"><br>
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).
<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">IPNI only serves data about names, no taxa here.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">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.<o:p></o:p></span></p>
<p class="MsoNormal"><br>
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 (<a href="http://rdf.library.vanderbilt.edu">http://rdf.library.vanderbilt.edu</a>) when I discovered that
the server was down. The RDF is somewhat ad hoc, but hey, it's there.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">The HTTP proxy above returns RDF metadata for the specified record.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">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.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">The service is outlined here:
</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext;mso-fareast-language:EN-US"><a href="http://data1.kew.org/reconciliation/">http://data1.kew.org/reconciliation/</a>
</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">and details of the IPNI service in particular are here:
<a href="http://data1.kew.org/reconciliation/about/IpniName">http://data1.kew.org/reconciliation/about/IpniName</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Nicky<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext"> tdwg-content-bounces@lists.tdwg.org
[mailto:tdwg-content-bounces@lists.tdwg.org] <b>On Behalf Of </b>Steve Baskauf<br>
<b>Sent:</b> 16 October 2015 14:09<br>
<b>To:</b> Dmitry Mozzherin <dmozzherin@gmail.com><br>
<b>Cc:</b> Chuck Miller (Contact) <chuck.miller@mobot.org>; tdwg-content@lists.tdwg.org; Jonathan A Rees <rees@mumble.net>; Shorthouse, David <david.shorthouse@umontreal.ca><br>
<b>Subject:</b> Re: [tdwg-content] status of uBio<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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.<br>
<br>
I have been interested in using the uBio identifiers for several reasons:<br>
1. They have managed to stick around for a long time and are stable in their format (as LSIDs and HTTP proxied LSIDs).<br>
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.<br>
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).
<br>
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 (<a href="http://rdf.library.vanderbilt.edu">http://rdf.library.vanderbilt.edu</a>) when I discovered that
the server was down. The RDF is somewhat ad hoc, but hey, it's there.<br>
<br>
There isn't really any other source that has all of these characteristics. So please keep uBio going indefinitely, if at all possible.
<br>
Steve<br>
<br>
Dmitry Mozzherin wrote: <o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<p class="MsoNormal">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.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>Steven J. Baskauf, Ph.D., Senior Lecturer<o:p></o:p></pre>
<pre>Vanderbilt University Dept. of Biological Sciences<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>postal mail address:<o:p></o:p></pre>
<pre>PMB 351634<o:p></o:p></pre>
<pre>Nashville, TN 37235-1634, U.S.A.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>delivery address:<o:p></o:p></pre>
<pre>2125 Stevenson Center<o:p></o:p></pre>
<pre>1161 21st Ave., S.<o:p></o:p></pre>
<pre>Nashville, TN 37235<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>office: 2128 Stevenson Center<o:p></o:p></pre>
<pre>phone: (615) 343-4582, fax: (615) 322-4942<o:p></o:p></pre>
<pre>If you fax, please phone or email so that I will know to look for it.<o:p></o:p></pre>
<pre><a href="http://bioimages.vanderbilt.edu">http://bioimages.vanderbilt.edu</a><o:p></o:p></pre>
<pre><a href="http://vanderbilt.edu/trees">http://vanderbilt.edu/trees</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
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