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Nicky,<br>
Thanks, I'm looking forward to checking it out! But no animals. :-(<br>
Steve<br>
<br>
Nicky Nicolson wrote:
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<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);">Hello
Steve,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);">Thanks
for triggering an interesting thread.
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);">Just
waving the IPNI flag for a minute:<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);"><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: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);">At
ipni.org we support our own HTTP proxy for LSIDs:<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);"><a
moz-do-not-send="true"
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: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);">…
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: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);">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: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);">IPNI
only serves data about names, no taxa here.
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);">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 moz-do-not-send="true"
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"><span
style="font-size: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);">The
HTTP proxy above returns RDF metadata for the specified record.</span><br>
<br>
<span
style="font-size: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);">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: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);">The
service is outlined here:
</span><span
style="font-size: 11pt; font-family: "Calibri",sans-serif; color: windowtext;"><a
moz-do-not-send="true" href="http://data1.kew.org/reconciliation/">http://data1.kew.org/reconciliation/</a>
</span><span
style="font-size: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);">and
details of the IPNI service in particular are here:
<a moz-do-not-send="true"
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: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);">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: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);">cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);">Nicky<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri",sans-serif; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<div>
<div
style="border-style: solid none none; border-color: rgb(225, 225, 225) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<p class="MsoNormal"><b><span
style="font-size: 11pt; font-family: "Calibri",sans-serif; color: windowtext;"
lang="EN-US">From:</span></b><span
style="font-size: 11pt; font-family: "Calibri",sans-serif; color: windowtext;"
lang="EN-US"> <a class="moz-txt-link-abbreviated" href="mailto:tdwg-content-bounces@lists.tdwg.org">tdwg-content-bounces@lists.tdwg.org</a>
[<a class="moz-txt-link-freetext" href="mailto:tdwg-content-bounces@lists.tdwg.org">mailto:tdwg-content-bounces@lists.tdwg.org</a>] <b>On Behalf Of </b>Steve
Baskauf<br>
<b>Sent:</b> 16 October 2015 14:09<br>
<b>To:</b> Dmitry Mozzherin <a class="moz-txt-link-rfc2396E" href="mailto:dmozzherin@gmail.com"><dmozzherin@gmail.com></a><br>
<b>Cc:</b> Chuck Miller (Contact) <a class="moz-txt-link-rfc2396E" href="mailto:chuck.miller@mobot.org"><chuck.miller@mobot.org></a>;
<a class="moz-txt-link-abbreviated" href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a>; Jonathan A Rees <a class="moz-txt-link-rfc2396E" href="mailto:rees@mumble.net"><rees@mumble.net></a>;
Shorthouse, David <a class="moz-txt-link-rfc2396E" href="mailto:david.shorthouse@umontreal.ca"><david.shorthouse@umontreal.ca></a><br>
<b>Subject:</b> Re: [tdwg-content] status of uBio<o:p></o:p></span></p>
</div>
</div>
<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 moz-do-not-send="true"
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: 5pt; margin-bottom: 5pt;">
<div>
<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>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</blockquote>
<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 moz-do-not-send="true" href="http://bioimages.vanderbilt.edu">http://bioimages.vanderbilt.edu</a><o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="http://vanderbilt.edu/trees">http://vanderbilt.edu/trees</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
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.
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu">http://bioimages.vanderbilt.edu</a>
<a class="moz-txt-link-freetext" href="http://vanderbilt.edu/trees">http://vanderbilt.edu/trees</a>
</pre>
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