<div><div>Dear Trish and Paul,</div><div>sorry for my late reply, but now everything works, both i2b2-ncbo tool and the view information editing page :) </div><div><br></div><div>Just want to inform you better about what happened with the i2b2-ncbo tool. </div>
<div>First i've modified the tool in order to extract virtual ontology, and it worked well with all the other </div><div>view (eg neoplasm_hamartoma --> ID 2085)</div><div>Before you've parsed the subtree i didn't get a specific error but the file i get was empty, that never happened with other virtual ontology i used in the past. As i could understand the problem was due to the SNOMED-CT version i've used. </div>
<div><br></div><div>Thanks very much for your precious help.</div><div>Best</div><div>Arianna</div></div><div><div><br></div><div><br><br><div class="gmail_quote">2012/5/14 Trish Whetzel <span dir="ltr"><<a href="mailto:whetzel@stanford.edu" target="_blank">whetzel@stanford.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word"><div>Also, the latest version of the Body Structure subtree from SNOMED-CT [1] is now parsed and I have confirmed it can be accessed via the NCBO Web services. I believe it should also be ready for use with the i2b2-ncbo extraction tool.</div>
<div><br></div><div>Trish </div><div><br></div><div>[1] <a href="http://bioportal.bioontology.org/ontologies/48006?p=terms" target="_blank">http://bioportal.bioontology.org/ontologies/48006?p=terms</a></div><div><div>
<div><br></div><br><div><div>On May 14, 2012, at 11:35 AM, Paul R Alexander wrote:</div><br><blockquote type="cite">
<div bgcolor="#FFFFFF" text="#000000">
Editing the view information should now work properly. Sorry for the
inconvenience.<br>
<br>
Paul R Alexander<br>
Senior Software Engineer<br>
NCBO BioPortal<br>
Stanford Center for Biomedical Informatics Research<br>
<br>
<br>
<div>On 5/14/12 9:51 AM, Trish Whetzel
wrote:<br>
</div>
<blockquote type="cite">
<div>Hi Arianna,</div>
<div><br>
</div>
<div>You are listed as the admin for the new version so I'm not
sure why selecting the Admin tab option "Edit View Information"
is re-directing you to the "Home" page. Paul, do you know why
this is happening?</div>
<div><br>
</div>
<div>What error message is the i2b2-ncbo extraction tool
returning? Are you using the ontology version id "48004" with
the tool? The latest version, 48006, did not complete parsing
and we will look into this. </div>
<div><br>
</div>
<div>Trish </div>
<div><br>
</div>
<br>
<div>
<div>On May 14, 2012, at 8:15 AM, arianna dagliati wrote:</div>
<br>
<blockquote type="cite">Dear Trish,
<div>you can find the screenshot attached. </div>
<div>I'm using the NCBO Extraction tool package that you find
at this link <a href="https://community.i2b2.org/wiki/display/NCBO/NCBO+Ontology+Tools" target="_blank">https://community.i2b2.org/wiki/display/NCBO/NCBO+Ontology+Tools</a></div>
<div><br>
</div>
<div>Arianna<br>
<br>
<div class="gmail_quote">2012/5/14 Trish Whetzel <span dir="ltr"><<a href="mailto:whetzel@stanford.edu" target="_blank">whetzel@stanford.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div>BioPortal is designed to support multiple
versions of ontologies, therefore I'm not sure that
is the issue. Can you send a screenshot of the page
with the Administer link, is it the page: <a href="http://bioportal.bioontology.org/ontologies/2105?p=terms" target="_blank">http://bioportal.bioontology.org/ontologies/2105?p=terms</a>
?</div>
<div><br>
</div>
<div>Also, is this the link for the i2b2 ncbo tool you
refer to: <a href="http://i2b2.bioontology.org/" target="_blank">http://i2b2.bioontology.org/</a></div>
<span><font color="#888888">
<div>
<br>
</div>
<div>Trish </div>
</font></span>
<div>
<div>
<div><br>
</div>
<br>
<div>
<div>On May 14, 2012, at 3:21 AM, arianna
dagliati wrote:</div>
<br>
<blockquote type="cite">Dear Trish,
<div>i'm sorry to disturb you again, but i
still can't use the i2b2 ncbo tool through
ncbo rest service, i think it's due to the
duplication of the view (mine, wrong, in
owl/xml and the one you've uploaded in the
correct rdf/owl format). </div>
<div>is it possible for you to delete the
wrong one? </div>
<div>i think there could be a bug because when
i click on administer --> edit version
i'm redirected to the bioportal homepage.</div>
<div><br>
</div>
<div>Thanks!</div>
<div><br>
</div>
<div>Best</div>
<div>Arianna<br>
<br>
<div class="gmail_quote">2012/5/7 arianna
dagliati <span dir="ltr"><<a href="mailto:aridag@gmail.com" target="_blank">aridag@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Trish,
<div>thank you very much for your help!</div>
<div><br>
</div>
<div>Best</div>
<div><span><font color="#888888">Arianna</font></span>
<div>
<div><br>
<div><br>
<div class="gmail_quote">2012/5/4
Trish Whetzel <span dir="ltr"><<a href="mailto:whetzel@stanford.edu" target="_blank">whetzel@stanford.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div>Hi Arianna, </div>
<div><br>
</div>
<div>The file was saved as
OWL/XML, but needs to be
saved as RDF/XML for
loading into BioPortal.
I've re-loaded the the
RDF/XML formatted file.</div>
<span><font color="#888888">
<div><br>
</div>
<div>Trish </div>
</font></span>
<div>
<div>
<div><br>
</div>
<br>
<div>
<div>On May 3, 2012,
at 11:23 AM, Trish
Whetzel wrote:</div>
<br>
<blockquote type="cite">
<div style="word-wrap:break-word">
<div>We'll take
a look at
this.</div>
<div><br>
</div>
<div>Trish </div>
<div><br>
</div>
<br>
<div>
<div>On May 3,
2012, at 2:45
AM, <a href="mailto:support@bioontology.org" target="_blank">support@bioontology.org</a>
wrote:</div>
<br>
<blockquote type="cite">
<div><br>
Name: aridag<br>
<br>
Email: <a href="mailto:aridag@gmail.com" target="_blank">aridag@gmail.com</a><br>
<br>
Location: <a href="http://bioportal.bioontology.org/" target="_blank">http://bioportal.bioontology.org/</a><br>
<br>
Comment:<br>
Dear NCBO
support,<br>
i've submitted
a SNOMED view
ontology last
week.<br>
=======================<br>
Description:
The Body
Structure
subtree in
SNOMED-CT<br>
Ontology ID:
2105<br>
=======================<br>
but i got an
error back
accessing it (<a href="http://bioportal.bioontology.org/ontologies/2105?p=terms" target="_blank">http://bioportal.bioontology.org/ontologies/2105?p=terms</a>)
and i can't
use the
extraction
rest service
(for i2b2 NCBO
tool).<br>
<br>
Could you
please advice
me if there's
anything wrong
with the owl
file i've
uploaded? or
it's just a
matter of time
you need to
process the
view?<br>
<br>
Thank you.<br>
Best <br>
Arianna - <a href="mailto:aridag@gmail.com" target="_blank">aridag@gmail.com</a><br>
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