Search Mailing List Archives
[bioontology-support] [BioPortal] Feedback from Rachel.Drysdale
Ray Fergerson
ray.fergerson at stanford.edu
Fri Apr 3 17:03:30 PDT 2015
Rachel,
There may be one more thing to try. If you can export as SKOS then you
might be able to load this. Otherwise I will create a tracker item to
delete your ontology.
Ray
From: Rachel Drysdale [mailto:rdrysdale at plos.org]
Sent: Tuesday, March 31, 2015 4:58 AM
To: Ray Fergerson; support at bioontology.org
Cc: Rachel Drysdale
Subject: RE: [bioontology-support] [BioPortal] Feedback from
Rachel.Drysdale
Hi Ray
I’ve looked into this a little and the structure is indeed very different
from owl format of successfully posted ontologies such as
http://bioportal.bioontology.org/ontologies/EDAM
Differences abound – lack of classes, business of representing URLs
That was educational, but it is beyond me to do anything about it, and it
is not high on the list for our vendors (who are already working on a
couple of things for us) though I’ve sent on my findings.
I expect the vendor will rectify the export, but I am doubtful that it
will be in a timescale of days/weeks.
In the meantime – I think we should take the PLOS thesaurus down as it
does not look good from anyone’s perspective. Is that going to be
possible? Apologies for inconvenience – I realise this is not ideal. The
only export formats on offer that match your specs were the two owl ones
(neither obo nor UMLS available as an export option), so there is no
alternative to try
.or I would
All best,
Rachel
PLOS I OPEN FOR DISCOVERY
Rachel Drysdale Ph.D. I Taxonomy Manager
ORCID: <http://orcid.org/0000-0003-3037-0216> 0000-0003-3037-0216
Carlyle House, Carlyle Road, Cambridge CB4 3DN | United Kingdom
<mailto:rdrysdale at plos.org> rdrysdale at plos.org I Main +44 (0) 1223-442810
<http://www.plos.org/> plos.org I <http://www.facebook.com/PLoS.org>
Facebook I <http://twitter.com/PLOS> Twitter I <http://blogs.plos.org/>
Blog
From: Ray Fergerson [mailto:ray.fergerson at stanford.edu]
Sent: 18 March 2015 21:53
To: Rachel Drysdale; support at bioontology.org
Subject: RE: [bioontology-support] [BioPortal] Feedback from
Rachel.Drysdale
Rachel,
The content in the various download formats matches the content that is in
the UI. Just browsing through the OWL file that you have uploaded, it does
not appear to contain things identified as OWL classes (other than the
four metaclasses). This is almost certainly an export problem.
I agree that, as is, the ontology as loaded into BioPortal does not
provide much value. With luck you get some help from you export experts.
We can let it hang around for a while though to give you a chance to sort
this out.
Ray
From: Rachel Drysdale [ <mailto:rdrysdale at plos.org>
mailto:rdrysdale at plos.org]
Sent: Wednesday, March 18, 2015 2:48 AM
To: Ray Fergerson; <mailto:support at bioontology.org>
support at bioontology.org
Cc: Rachel Drysdale
Subject: RE: [bioontology-support] [BioPortal] Feedback from
Rachel.Drysdale
Hi Ray,
I’ve been in touch with the vendor about the export I uploaded and they
will look into it. It may be that it is relatively untested and something
is bockety in it. Shall we leave it up until they’ve had a chance to get
back?
The downloads on your web page don’t download for me in a way that has
content, not even the csv one, but at least the link to github provides
access to xml and xlsx formats.
If I can’t sort this out in a timescale of days/weeks maybe we should just
take the page down – doesn’t look very good for either of us the way it is
now does it.
All best
Rachel
PLOS I OPEN FOR DISCOVERY
Rachel Drysdale Ph.D. I Taxonomy Manager
ORCID: <http://orcid.org/0000-0003-3037-0216> 0000-0003-3037-0216
Carlyle House, Carlyle Road, Cambridge CB4 3DN | United Kingdom
<mailto:rdrysdale at plos.org> rdrysdale at plos.org I Main +44 (0) 1223-442810
<http://www.plos.org/> plos.org I <http://www.facebook.com/PLoS.org>
Facebook I <http://twitter.com/PLOS> Twitter I <http://blogs.plos.org/>
Blog
From: Ray Fergerson [ <mailto:ray.fergerson at stanford.edu>
mailto:ray.fergerson at stanford.edu]
Sent: 17 March 2015 22:50
To: Rachel Drysdale; <mailto:support at bioontology.org>
support at bioontology.org
Subject: RE: [bioontology-support] [BioPortal] Feedback from
Rachel.Drysdale
Have a look at how it appears in BioPortal. My guess from the names is
that the things displayed as classes are actually some sort of metaclass.
Ray
From: Rachel Drysdale [ <mailto:rdrysdale at plos.org>
mailto:rdrysdale at plos.org]
Sent: Monday, March 16, 2015 10:53 AM
To: Ray Fergerson; <mailto:support at bioontology.org>
support at bioontology.org
Cc: Rachel Drysdale
Subject: RE: [bioontology-support] [BioPortal] Feedback from
Rachel.Drysdale
Hi Ray
Yes those stats look odd.
PLOSTHES is actually 10 tiers deep, with 11 top tier terms.
It has 10961 ‘preferred’ (valid) terms.
Not sure what ‘Classes’ are in this context.
Hmmm
Will have to do some homework
And see if the vendor has anything illuminating to say about the export.
Rachel
PLOS I OPEN FOR DISCOVERY
Rachel Drysdale Ph.D. I Taxonomy Manager
ORCID: <http://orcid.org/0000-0003-3037-0216> 0000-0003-3037-0216
Carlyle House, Carlyle Road, Cambridge CB4 3DN | United Kingdom
<mailto:rdrysdale at plos.org> rdrysdale at plos.org I Main +44 (0) 1223-442810
<http://www.plos.org/> plos.org I <http://www.facebook.com/PLoS.org>
Facebook I <http://twitter.com/PLOS> Twitter I <http://blogs.plos.org/>
Blog
From: Ray Fergerson [ <mailto:ray.fergerson at stanford.edu>
mailto:ray.fergerson at stanford.edu]
Sent: 13 March 2015 23:59
To: Rachel Drysdale; <mailto:support at bioontology.org>
support at bioontology.org
Subject: RE: [bioontology-support] [BioPortal] Feedback from
Rachel.Drysdale
Fixed.
Your ontology had a single error (an un-escaped less-than sign). We
corrected this and submitted it and it now works properly. In the future
though, when you resubmit a new version, you need to address the error.
The line is 36,514 and the fix was to replace:
usually <2 mm diameter
with
usually <2 mm diameter
Also note that your ontology has only 4 classes and 14785 individuals. Is
this really what you want? My guess is that your exporter may be failing
to produce OWL classes.
Ray
From: Rachel Drysdale [ <mailto:rdrysdale at plos.org>
mailto:rdrysdale at plos.org]
Sent: Thursday, March 12, 2015 7:06 AM
To: Ray Fergerson; <mailto:support at bioontology.org>
support at bioontology.org
Cc: Rachel Drysdale
Subject: RE: [bioontology-support] [BioPortal] Feedback from
Rachel.Drysdale
Thanks very much for further help – OWL 2 export with .owl suffix seems to
do the trick.
There was some experimentation with export formats and suffixes to get to
this stage, and I get the impression that running same file through
validator twice can produce a ‘success’ result followed by a ‘fail’.
I can’t figure out how to remove the ‘Erro Rdf’ rows – is there a way to
do that?
Would be tidier, but at least the status is clear if that is impossible.
To answer your other question,
>I am not familiar with this dialog box. From what application is it?
It is MAIstro which we license from Access Innovations (
<http://www.accessinn.com/> www.accessinn.com/), our vendors for this
work. MAIstro includes the taxonomy management sw plus rulebase for
Machine Aided Indexing that we use to annotate content.
All best,
Rachel
PLOS I OPEN FOR DISCOVERY
Rachel Drysdale Ph.D. I Taxonomy Manager
ORCID: <http://orcid.org/0000-0003-3037-0216> 0000-0003-3037-0216
Carlyle House, Carlyle Road, Cambridge CB4 3DN | United Kingdom
<mailto:rdrysdale at plos.org> rdrysdale at plos.org I Main +44 (0) 1223-442810
<http://www.plos.org/> plos.org I <http://www.facebook.com/PLoS.org>
Facebook I <http://twitter.com/PLOS> Twitter I <http://blogs.plos.org/>
Blog
From: Ray Fergerson [ <mailto:ray.fergerson at stanford.edu>
mailto:ray.fergerson at stanford.edu]
Sent: 11 March 2015 21:08
To: Rachel Drysdale; <mailto:support at bioontology.org>
support at bioontology.org
Subject: RE: [bioontology-support] [BioPortal] Feedback from
Rachel.Drysdale
I would suggest OWL2. The extension for such a file (OWL/RDF) should be
“.owl” though and not “.txt”. I am not familiar with this dialog box. From
what application is it? It doesn’t look like Protégé to me. If your native
format is “.obo” then we can read that directly.
Ray
From: Ray Fergerson [ <mailto:ray.fergerson at stanford.edu>
mailto:ray.fergerson at stanford.edu]
Sent: 11 March 2015 21:11
To: Rachel Drysdale; <mailto:support at bioontology.org>
support at bioontology.org
Subject: RE: [bioontology-support] [BioPortal] Feedback from
Rachel.Drysdale
This is the same error (see RDF/XML below). The way the validator works is
that it first tries to identify the file format from the extension. If
this fails then it runs all possible parsers over the input. That is why
you see the results from multiple parsers.
The best way forward if the native format is OBO is just to submit the OBO
file (with extension .obo). If the native format is something else then
export as OWL 2, ensure that the extension is “.owl” and then validate
this file.
Ray
From: Rachel Drysdale [ <mailto:rdrysdale at plos.org>
mailto:rdrysdale at plos.org]
Sent: Wednesday, March 11, 2015 9:42 AM
To: Ray Fergerson; <mailto:support at bioontology.org>
support at bioontology.org
Subject: RE: [bioontology-support] [BioPortal] Feedback from
Rachel.Drysdale
PS I tried the OWL 2 export (came out as a .txt file) and uploaded that
but still get “Error Rdf” statement and here is what validate_ontology
produced
cid:image001.jpg at 01D05CCC.CCB0FFA0
Any ideas?
Rachel
PLOS I OPEN FOR DISCOVERY
Rachel Drysdale Ph.D. I Taxonomy Manager
ORCID: <http://orcid.org/0000-0003-3037-0216> 0000-0003-3037-0216
Carlyle House, Carlyle Road, Cambridge CB4 3DN | United Kingdom
<mailto:rdrysdale at plos.org> rdrysdale at plos.org I Main +44 (0) 1223-442810
<http://www.plos.org/> plos.org I <http://www.facebook.com/PLoS.org>
Facebook I <http://twitter.com/PLOS> Twitter I <http://blogs.plos.org/>
Blog
From: Rachel Drysdale
Sent: 11 March 2015 15:02
To: Ray Fergerson; <mailto:support at bioontology.org>
support at bioontology.org
Cc: Rachel Drysdale
Subject: RE: [bioontology-support] [BioPortal] Feedback from
Rachel.Drysdale
Hi Ray,
>Essentially you have created a URL that contains 2 "#" characters. I
don't think that this is allowed.
This appears to be a feature of all 'Related Term' fields in the OWL
export of our thesaurus.
So there are 1142 such cases.
So I could go to our vendor to query this feature of the OWL export
option, or (possibly most expedient way out) I could ask you if any of the
other export formats on offer would do instead. Here is the full range:
cid:image002.png at 01D05CCC.CCB0FFA0
What do you think?
Thanks for further help
Rachel
PLOS I OPEN FOR DISCOVERY
Rachel Drysdale Ph.D. I Taxonomy Manager
ORCID: 0000-0003-3037-0216
Carlyle House, Carlyle Road, Cambridge CB4 3DN | United Kingdom
rdrysdale at plos.org I Main +44 (0) 1223-442810
plos.org I Facebook I Twitter I Blog
-----Original Message-----
From: Ray Fergerson [ <mailto:ray.fergerson at stanford.edu>
mailto:ray.fergerson at stanford.edu]
Sent: 10 March 2015 21:43
To: Rachel Drysdale; <mailto:support at bioontology.org>
support at bioontology.org
Subject: RE: [bioontology-support] [BioPortal] Feedback from
Rachel.Drysdale
Sorry for the long delay. We finally have this figured out.
The error in the file, that prevents parsing is:
----------
org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException:
[line=121:column=41] IRI '#T#T8798' cannot be resolved against current
base IRI <http://localhost/owlfiles/plosthes.2014-5/>
http://localhost/owlfiles/plosthes.2014-5/ reason is: Illegal
character in fragment at index 2: #T#T8798
Validator has been updated to pick this up now. Passing to Ray Fergerson
for user contact.
----------------
Essentially you have created a URL that contains 2 "#" characters. I don't
think that this is allowed.
We have also fixed the problem with our validator. It is accessible at:
<http://bioportal.bioontology.org/validate_ontology_file>
http://bioportal.bioontology.org/validate_ontology_file
This device should allow you to detect other errors in your ontology
before you submit it.
Ray
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20150403/9f9949c2/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.jpg
Type: image/jpeg
Size: 30070 bytes
Desc: not available
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20150403/9f9949c2/attachment-0001.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image002.png
Type: image/png
Size: 36783 bytes
Desc: not available
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20150403/9f9949c2/attachment-0001.png>
More information about the bioontology-support
mailing list