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Hi Steve,
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<div class="">if it’s animals you are after and the following characteristics (shared with IPNI):</div>
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<div class="">1) comprehensive</div>
<div class="">2) names not taxa</div>
<div class="">3) LSIDs that deference to RDF using consistent vocabulary (TDWG LSID)</div>
<div class="">4) closed, or at least non-open</div>
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<div class="">then ION (<a href="http://www.organismnames.com" class="">http://www.organismnames.com</a> ) is for you. Each name has an LSID that actually works and returns a name plus (often) a bibliographic citation as a string.</div>
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<div class="">My frustration with Ion being closed, and only serving bibliographic strings instead of DOIs, Handles, BHL BioStor etc. was what led me to *cough* copy ION and augment it to create BioNames
<a href="http://bionames.org" class="">http://bionames.org</a> </div>
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<div class="">For example, ION has urn:lsid:organismnames.com:name:5109777 and BioNames has <a href="http://bionames.org/names/cluster/5109777" class="">http://bionames.org/names/cluster/5109777</a> (plus the original description with DOI <a href="http://dx.doi.org/10.11646/zootaxa.3616.4.3" class="">http://dx.doi.org/10.11646/zootaxa.3616.4.3</a>,
see <a href="http://bionames.org/references/384cdd42133009235d59af9b41c55290" class="">http://bionames.org/references/384cdd42133009235d59af9b41c55290</a></div>
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<div class="">I’m working on a similar mapping of references to DOIs, etc. for IPNI...</div>
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<div class="">ION exposes RDF, BioNames doesn’t (which won’t surprise you I guess, it has a JSON API). If it was of use I could add RDF to BioNames, probably JSON-LD.</div>
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<div class="">Regards</div>
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<div class="">Rod</div>
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---------------------------------------------------------<br class="">
Roderic Page<br class="">
Professor of Taxonomy<br class="">
Institute of Biodiversity, Animal Health and Comparative Medicine<br class="">
College of Medical, Veterinary and Life Sciences<br class="">
Graham Kerr Building<br class="">
University of Glasgow<br class="">
Glasgow G12 8QQ, UK<br class="">
<br class="">
Email: <span class="Apple-tab-span" style="white-space: pre;"> </span><a href="mailto:Roderic.Page@glasgow.ac.uk" class="">Roderic.Page@glasgow.ac.uk</a><br class="">
Tel: <span class="Apple-tab-span" style="white-space: pre;"> </span>+44 141 330 4778<br class="">
Skype: <span class="Apple-tab-span" style="white-space: pre;"> </span>rdmpage<br class="">
Facebook: <span class="Apple-tab-span" style="white-space: pre;"> </span>http://www.facebook.com/rdmpage<br class="">
LinkedIn: <span class="Apple-tab-span" style="white-space: pre;"> </span>http://uk.linkedin.com/in/rdmpage<br class="">
Twitter: <span class="Apple-tab-span" style="white-space: pre;"> </span>http://twitter.com/rdmpage<br class="">
Blog: <span class="Apple-tab-span" style="white-space: pre;"> </span>http://iphylo.blogspot.com<br class="">
ORCID: <span class="Apple-tab-span" style="white-space: pre;"> </span>http://orcid.org/0000-0002-7101-9767</div>
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Citations: <span class="Apple-tab-span" style="white-space: pre;"> </span><a href="http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ" class="">http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ</a></div>
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ResearchGate<span class="Apple-tab-span" style="white-space: pre;"> </span><a href="https://www.researchgate.net/profile/Roderic_Page" class="">https://www.researchgate.net/profile/Roderic_Page</a><br class="">
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<div class="">On 16 Oct 2015, at 15:51, Steve Baskauf <<a href="mailto:steve.baskauf@vanderbilt.edu" class="">steve.baskauf@vanderbilt.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class="">Nicky,</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class="">Thanks,
I'm looking forward to checking it out! But no animals. :-(</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class="">Steve</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">
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<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class="">Nicky
Nicolson wrote:</span>
<blockquote cite="mid:DBXPR07MB3189E8B54EBC1A95AC399C7823D0@DBXPR07MB318.eurprd07.prod.outlook.com" type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255);" class="">
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Hello Steve,<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Thanks for triggering an interesting thread.<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Just waving the IPNI flag for a minute:<o:p class=""></o:p></span></div>
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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 class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">At<span class="Apple-converted-space"> </span><a href="http://ipni.org/" style="color: purple; text-decoration: underline;" class="">ipni.org</a><span class="Apple-converted-space"> </span>we
support our own HTTP proxy for LSIDs:<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><a moz-do-not-send="true" href="http://ipni.org/urn:lsid:ipni.org:names:12345-1" style="color: purple; text-decoration: underline;" class="">http://ipni.org/urn:lsid:ipni.org:names:12345-1</a><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">… 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 class=""></o:p></span></div>
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<br class="">
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 class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">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 class=""></o:p></span></div>
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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 class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">IPNI only serves data about names, no taxa here.<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">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 class=""></o:p></span></div>
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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/" style="color: purple; text-decoration: underline;" class="">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 class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">The HTTP proxy above returns RDF metadata for the specified record.</span><br class="">
<br class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">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 class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">The service is outlined here:<span class="Apple-converted-space"> </span></span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: windowtext;" class=""><a moz-do-not-send="true" href="http://data1.kew.org/reconciliation/" style="color: purple; text-decoration: underline;" class="">http://data1.kew.org/reconciliation/</a><span class="Apple-converted-space"> </span></span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">and
details of the IPNI service in particular are here:<span class="Apple-converted-space"> </span><a moz-do-not-send="true" href="http://data1.kew.org/reconciliation/about/IpniName" style="color: purple; text-decoration: underline;" class="">http://data1.kew.org/reconciliation/about/IpniName</a><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">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 class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">cheers,<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Nicky<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div>
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<b class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: windowtext;" class="">From:</span></b><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: windowtext;" class=""><span class="Apple-converted-space"> </span><a class="moz-txt-link-abbreviated" href="mailto:tdwg-content-bounces@lists.tdwg.org" style="color: purple; text-decoration: underline;">tdwg-content-bounces@lists.tdwg.org</a><span class="Apple-converted-space"> </span>[<a class="moz-txt-link-freetext" href="mailto:tdwg-content-bounces@lists.tdwg.org" style="color: purple; text-decoration: underline;">mailto:tdwg-content-bounces@lists.tdwg.org</a>]<span class="Apple-converted-space"> </span><b class="">On
Behalf Of<span class="Apple-converted-space"> </span></b>Steve Baskauf<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>16 October 2015 14:09<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Dmitry Mozzherin<span class="Apple-converted-space"> </span><a class="moz-txt-link-rfc2396E" href="mailto:dmozzherin@gmail.com" style="color: purple; text-decoration: underline;"><dmozzherin@gmail.com></a><br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span>Chuck Miller (Contact)<span class="Apple-converted-space"> </span><a class="moz-txt-link-rfc2396E" href="mailto:chuck.miller@mobot.org" style="color: purple; text-decoration: underline;"><chuck.miller@mobot.org></a>;<span class="Apple-converted-space"> </span><a class="moz-txt-link-abbreviated" href="mailto:tdwg-content@lists.tdwg.org" style="color: purple; text-decoration: underline;">tdwg-content@lists.tdwg.org</a>;
Jonathan A Rees<span class="Apple-converted-space"> </span><a class="moz-txt-link-rfc2396E" href="mailto:rees@mumble.net" style="color: purple; text-decoration: underline;"><rees@mumble.net></a>; Shorthouse, David<span class="Apple-converted-space"> </span><a class="moz-txt-link-rfc2396E" href="mailto:david.shorthouse@umontreal.ca" style="color: purple; text-decoration: underline;"><david.shorthouse@umontreal.ca></a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [tdwg-content] status of uBio<o:p class=""></o:p></span></div>
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<o:p class=""> </o:p></div>
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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 class="">
<br class="">
I have been interested in using the uBio identifiers for several reasons:<br class="">
1. They have managed to stick around for a long time and are stable in their format (as LSIDs and HTTP proxied LSIDs).<br class="">
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 class="">
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). <span class="Apple-converted-space"> </span><br class="">
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/" style="color: purple; text-decoration: underline;" class="">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 class="">
<br class="">
There isn't really any other source that has all of these characteristics. So please keep uBio going indefinitely, if at all possible. <span class="Apple-converted-space"> </span><br class="">
Steve<br class="">
<br class="">
Dmitry Mozzherin wrote:<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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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 class=""></o:p></div>
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<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New';" class="">-- <o:p class=""></o:p></pre>
<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New';" class="">Steven J. Baskauf, Ph.D., Senior Lecturer<o:p class=""></o:p></pre>
<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New';" class="">Vanderbilt University Dept. of Biological Sciences<o:p class=""></o:p></pre>
<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New';" class=""><o:p class=""> </o:p></pre>
<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New';" class="">postal mail address:<o:p class=""></o:p></pre>
<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New';" class="">PMB 351634<o:p class=""></o:p></pre>
<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New';" class="">Nashville, TN 37235-1634, U.S.A.<o:p class=""></o:p></pre>
<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New';" class=""><o:p class=""> </o:p></pre>
<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New';" class="">delivery address:<o:p class=""></o:p></pre>
<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New';" class="">2125 Stevenson Center<o:p class=""></o:p></pre>
<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New';" class="">1161 21st Ave., S.<o:p class=""></o:p></pre>
<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New';" class="">Nashville, TN 37235<o:p class=""></o:p></pre>
<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New';" class=""><o:p class=""> </o:p></pre>
<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New';" class="">office: 2128 Stevenson Center<o:p class=""></o:p></pre>
<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New';" class="">phone: (615) 343-4582, fax: (615) 322-4942<o:p class=""></o:p></pre>
<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New';" class="">If you fax, please phone or email so that I will know to look for it.<o:p class=""></o:p></pre>
<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New';" class=""><a moz-do-not-send="true" href="http://bioimages.vanderbilt.edu/" style="color: purple; text-decoration: underline;" class="">http://bioimages.vanderbilt.edu</a><o:p class=""></o:p></pre>
<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New';" class=""><a moz-do-not-send="true" href="http://vanderbilt.edu/trees" style="color: purple; text-decoration: underline;" class="">http://vanderbilt.edu/trees</a><o:p class=""></o:p></pre>
<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New';" class=""><o:p class=""> </o:p></pre>
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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/" style="color: purple; text-decoration: underline;">http://bioimages.vanderbilt.edu</a>
<a class="moz-txt-link-freetext" href="http://vanderbilt.edu/trees" style="color: purple; text-decoration: underline;">http://vanderbilt.edu/trees</a>
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