<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Steve - Sorry for the delay. Comments inline<div><br><div><div>On 7 May 2011, at 22:12, Steve Baskauf wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
<div bgcolor="#ffffff" text="#000000">
David,<br>
I have had a bit of time to read the document that you linked below and
to play around with what you suggested below. I had a couple
clarifying questions. But before I ask them, I'd like to give just a
bit of feedback on the GBIF Darwin Core page
(<a class="moz-txt-link-freetext" href="http://www.gbif.org/informatics/standards-and-tools/publishing-data/data-standards/darwin-core-archives/">http://www.gbif.org/informatics/standards-and-tools/publishing-data/data-standards/darwin-core-archives/</a>).
The font and color of the hyperlinks on that page are so similar to the
default text font that I had difficulty knowing they were there. I
guess they are blue and the base font is black, but to my (admittedly
aging) eyes, they were barely distinguishable. I had to mouse over the
text and watch the cursor to find the links. This was the same on all
five of the major web browsers. Also, you might put a link on that
page to the XML Descriptor file document you linked in the message
below. I don't think I would have found it if I hadn't emailed you.<br>
<br>
OK, so here's my first question. I understood the explanation of how
to make a field be generated by using a variable in a static mapping.
So when the actual text datafile is created, do you just leave the
statically mapped column empty? E.g. if I have something like:<br>
<br>
<tt> <field index="11"
term=<a class="moz-txt-link-rfc2396E" href="http://purl.org/dc/terms/source">"http://purl.org/dc/terms/source"</a>/><br>
<field index="12"
default=<a class="moz-txt-link-rfc2396E" href="http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:{11}">"http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:{11}"</a>
term=<a class="moz-txt-link-rfc2396E" href="http://rs.tdwg.org/dwc/terms/scientificNameID">"http://rs.tdwg.org/dwc/terms/scientificNameID"</a>/><br>
<br>
</tt>would I just populate column 11 with uBio's locally unique ID
number and leave column 12 blank (i.e. have two consecutive delimiters
with no characters between)?<br></div></blockquote><div><br></div><div>The example I gave is slightly different. First, if you had just the uBio integer identifier in the scientificNameID field</div><div><br></div><div><field index="11" term="<a href="http://rs.tdwg.org/dwc/terms/scientificNameID">http://rs.tdwg.org/dwc/terms/scientificNameID</a>"/></div><div><br></div><div>You could assign it to the dc:source term as a global value. Note that by making this a global value it doesn't get a index number as it doesn't map to a column in your data file. It is as if you are creating a new column to store this new concatenated value.</div><div><br></div><div><div><field index="11" term="<a href="http://rs.tdwg.org/dwc/terms/scientificNameID">http://rs.tdwg.org/dwc/terms/scientificNameID</a>"/></div><div><field term="<a href="http://purl.org/dc/terms/source">http://purl.org/dc/terms/source</a>" default="<a href="http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:{11}">http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:{11}</a>" /></div></div><div><br></div><div>I realise now that this won't work for you in what you asked. It works once but it doesn't work for all the </div><div><br></div><br><blockquote type="cite"><div bgcolor="#ffffff" text="#000000">
<br>
The second question is a little trickier. The main purpose that I
would want to use this for is to enable the use of GUIDs. Using GUIDs
rather than local IDs seems to be considered a better practice (or at
least an allowed practice) in both the DwC term descriptions (e.g.
<a class="moz-txt-link-freetext" href="http://rs.tdwg.org/dwc/terms/index.htm#taxonID">http://rs.tdwg.org/dwc/terms/index.htm#taxonID</a>) and in the GBIF Darwin
Core Archives web page I complained about above. However, it is
difficult for me to see how one would accomplish this with the Darwin
Core Archives format, at least if one wishes to cut down on file size
(and transmission time) using the "variable in a static mapping"
shortcut. The problem is what to use for the field names for the
locally unique identifiers. </div></blockquote><blockquote type="cite"><div bgcolor="#ffffff" text="#000000"> In your example below, you suggested
dc:source. That's actually not an option listed in the Darwin Core
Archives Assistant. </div></blockquote><div><br></div><div>dc:source is the "source" element in both the Taxon and Occurrence Core definitions in the DWC-A Asst.</div><br><blockquote type="cite"><div bgcolor="#ffffff" text="#000000"> Is any allowable Dublin Core term valid as a DWC-A
field if one just jury-rigs the XML file after generating it with the
Assistant? In the metafile documentation dcterms:identifier is also
used and not listed in DWC-A Assistant. <br></div></blockquote><div><br></div><div>dc:identifier is not used in the core definitions but is used in the Alternative Identifiers extension.</div><br><blockquote type="cite"><div bgcolor="#ffffff" text="#000000">
<br>
This becomes tricker still if one wants to use GUIDs for several fields
in the datafile. For example, I want to have dwc:taxonID,
dwc:scientificNameID, and dwc:nameAccordingToID be fields in my taxon
file. I can't use dcterms:source for all three of the locally unique
identifiers that I'd like to use as variables in the static mappings
for the xxxID terms. </div></blockquote><div><br></div><div>I realise now that the example I gave won't work for this. As I read it now you would like to use local integer identifiers in your database but expand them in the output file using a "template" that would conform to the template I used in my globals example.</div><div>In this case, we don't want to refer to a different element we want the current element to substitute the local identifier it contains with the more inflated template. In other words if your data file says that taxonID=100 has a parent taxon with an ID = 99 you want to conflate the integer with the more complete GUID following the template. This currently isn't something we have discussed supporting but I think we could by allowing for value substitution via a template placed in the default value. We could for example, support it using the example below. Note in this case the substitute variable IS the value itself.</div><div><br></div><div><div><id index="0"/ default="urn:lsid:ubio.org:namebank:{0} "> # we dont need to assign a term here. It is implied. See next comment below.</div><div><field index="1" default="urn:lsid:ubio.org:namebank:{1} " term="<a href="http://rs.tdwg.org/dwc/terms/parentNameUsageID">http://rs.tdwg.org/dwc/terms/parentNameUsageID</a>"/></div><div><br></div><div><br></div></div><blockquote type="cite"><div bgcolor="#ffffff" text="#000000">Also, I'm not sure about this, but from the
examples, it looks like the ID field in the core Taxon file is assumed
to be dwc:taxonID. </div></blockquote><div><br></div><div>That is correct. It is implied that the core ID is dwc:taxonID for Taxon and dwc:occurrenceID for Occurrence.</div><br><blockquote type="cite"><div bgcolor="#ffffff" text="#000000"> At least taxonID doesn't show up on the DWC-A
assistant list and the ID field is labeled as "taxonID" in the
examples. But I'm going to run into problems if I actually want
dwc:taxonID to be a GUID rather than my locally unique identifier. I
can't have the base ID and another column containing a static mapping
having the base ID as a variable both be identified as dwc:taxonID.<br>
<br>
It seems like in the interest of facilitating GUIDs, it would be
beneficial to allow the DWC-A to include fields that are identified
simply as local variables to be used in static mappings without
requiring that each field to map to DwC or Dublin Core. I haven't
actually picked my way through the XML schema or tried doing this and
then validating the XML file to see if I could get away with it,
however.<br></div></blockquote><div><br></div><div>I think you have made the case and I think we could accommodate it by simple interpreting the default in the way I specified. Otherwise I could imagine we would have to add a "template" attribute to the field element. However, I don't think this is needed. I guess I'd like feedback from Tim, John W or Markus on this.</div><div><br></div><div><br></div><br><blockquote type="cite"><div bgcolor="#ffffff" text="#000000">
<br>
Steve<br>
<br>
David Remsen (GBIF) wrote:
<blockquote cite="mid:2100EDA7-2A1A-429E-A9E0-D2104F7AEA08@gbif.org" type="cite">Hi Steve,
<div><br>
</div>
<div>There is a way to do what you ask but not exactly the way you
specified.</div>
<div><br>
</div>
<div>The way to do is via a template that refers to a particular
column. </div>
<div>So if you put the ubio integer ID into dwc:scientificName you
could could put the following into, for example, dc:source</div>
<div><br>
</div>
<div><a moz-do-not-send="true" href="http://www.ubio.org/authority">http://www.ubio.org/authority</a>/metadata.php?lsid=urn:lsid:ubio.org:namebank:<scientificName></div>
<div><br>
</div>
<div>as the default and set the column to a global.</div>
<div><br>
</div>
<div>
<div style="margin: 0px; font-family: 'Trebuchet MS'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;">You
can see more in this document on the XML Descriptor file.</div>
<div style="margin: 0px; font-family: 'Trebuchet MS'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"><br>
</div>
<div style="margin: 0px; font-family: 'Trebuchet MS'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 12px; line-height: normal; font-size-adjust: none; font-stretch: normal;"><a moz-do-not-send="true" href="http://links.gbif.org/gbif_dwc-a_metafile_en_v1/">http://links.gbif.org/gbif_dwc-a_metafile_en_v1/</a></div>
</div>
<div><br>
</div>
<div>The vocabularies option was, as far as I know, intended to
provide a URI for a vocabulary so that we might be able to validate
values against the vocabulary items.</div>
<div><br>
</div>
<div>Best,</div>
<div>David</div>
<div><br>
<div><span class="Apple-style-span" style="font-size: 12px; ">
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<div>
<div>----------------------------------------------------------------------------</div>
<div>David Remsen, Senior Programme Officer</div>
<div>Electronic Catalog of Names of Known Organisms</div>
<div>Global Biodiversity Information Facility Secretariat</div>
<div>Universitetsparken 15, DK-2100 Copenhagen, Denmark</div>
<div>Tel: +45-35321472 Fax: +45-35321480</div>
<div>Mobile +45 28751472</div>
<div>Skype: dremsen</div>
<div>----------------------------------------------------------------------------</div>
<div><br>
</div>
</div>
</span></span></span></div>
</span></div><span class="Apple-style-span" style="font-size: 12px; ">
</span><br class="Apple-interchange-newline">
<br class="Apple-interchange-newline">
</div>
<br>
<div>
<div>On 29 Apr 2011, at 22:21, Steve Baskauf wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div>I am playing around with Darwin Core Arcives, in particular
the DwC-A <br>
Assistant (<a moz-do-not-send="true" href="http://tools.gbif.org/dwca-assistant/">http://tools.gbif.org/dwca-assistant/</a>).
One thing that I am <br>
not exactly clear about is how to use the "Vocabulary" column in the <br>
assistant. The description that comes up when you mouse over the
column <br>
heading says that it should ideally be a URI that identifies the <br>
vocabulary and resolves to some machine readable form like RDF. So
what <br>
I'm wondering is whether I can put what effectively amounts to as a <br>
namespace in that spot. <br>
<br>
For example, a URI for the name "Acer rubrum L." that actually resolves
<br>
to RDF is:<br>
<a moz-do-not-send="true" href="http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:456216">http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:456216</a><br>
I think that would qualify as a valid HTTP URI guid because it's the <br>
proxied form of an LSID. So I would like to use it as a value for the <br>
dwc:scientificNameID column in a DwC-A taxon record. However, the only
<br>
part of the identifier that makes the string unique within uBio's
domain <br>
is the last number - if I'm always using a uBio guid, the first <br>
approximately 75 characters will be the same for all of the guids. So <br>
can I just put <br>
<a class="moz-txt-link-rfc2396E" href="http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:">"http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:"</a>
<br>
in the Vocabulary column and then just put the locally unique numbers <br>
(e.g. "456216") in the column for dwc:scientificNameID? Should an <br>
application using a DwC-A file be smart enough to append the <br>
"vocabulary" string on the front of the actual value in the text file? <br>
Or is that not how the "Vocabulary" column is intended to be used?<br>
<br>
Steve<br>
<br>
-- <br>
Steven J. Baskauf, Ph.D., Senior Lecturer<br>
Vanderbilt University Dept. of Biological Sciences<br>
<br>
postal mail address:<br>
VU Station B 351634<br>
Nashville, TN 37235-1634, U.S.A.<br>
<br>
delivery address:<br>
2125 Stevenson Center<br>
1161 21st Ave., S.<br>
Nashville, TN 37235<br>
<br>
office: 2128 Stevenson Center<br>
phone: (615) 343-4582, fax: (615) 343-6707<br>
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu/">http://bioimages.vanderbilt.edu</a><br>
<br>
_______________________________________________<br>
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<br>
</div>
</blockquote>
</div>
<br>
</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:
VU Station B 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) 343-6707
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu/">http://bioimages.vanderbilt.edu</a>
</pre>
</div>
</blockquote></div><br></div></body></html>