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[bioontology-support] Bioportal

Trish Whetzel whetzel at
Tue Dec 30 16:49:51 PST 2008

I went back to check on your questions, however the BioPortal site is down.
I've sent a note to report this, however Stanford is closed for Winter break
so responses are slow during this time. 




From: Trish Whetzel [mailto:whetzel at] 
Sent: Tuesday, December 23, 2008 10:49 AM
To: Eamonn Maguire
Cc: Philippe; Susanna Sansone
Subject: Re: Bioportal


Hi Eamonn


I'll look into this more a little later today - on vacation and have a few
errands to run first. As for the first item, there is a problem with the
latest loading of OBI so if you go back about 3 versions that loading is ok.
Do the REST calls work with that version?




On Dec 23, 2008, at 5:03 AM, "Eamonn Maguire" <maguire at> wrote:

Hi Trish,


I've been working on bioportal integration on and off for a few weeks now
but there appears to be a few problems. I'll list the ones i've encountered
and you can hopefully tell me that i'm doing something stupid :o) 


1) When i query for microscope for example in OBI (Ontology ID 39082) for
microscope as a 'concept' or as an appearance in the metadata ('meta') i get
no results, even though it is clearly in OBI. This probably has something to
do with OBI being down or something since this URL
( displays "There is no
data to support this query at this time. If you have questions, please
contact us at admin at"  If i do a query for a label within my
code, i get an IO error since the server returns a 500 response code when i
make the following query
39082. If it would be possible to get this back up and running or suggest a
way in which we could resort to differing ontology versions when one is
down, that would be extremely useful. I imagine that this error is a simple
one to fix though and not so much an error on the side of the software, but
an error caused by the ontology not being loaded?? (I'm just guessing since
i don't know! :o) )


2) If i do a search on the meta data, e.g.
2, I get an error saying the URL doesn't exist. Replacing meta with
properties throws the same error as in 1). 


If you could provide answers/suggestions/comments on these points, I'd be
very grateful! In the meantime, I wish you a great holiday and happy new
year :o)

Eamonn Maguire

maguire at
eamonnmag at

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