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[bioontology-support] [BioPortal] Feedback from Rachel.Drysdale

Rachel Drysdale rdrysdale at plos.org
Mon Mar 16 10:52:34 PDT 2015


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: 0000-0003-3037-0216<http://orcid.org/0000-0003-3037-0216>
Carlyle House, Carlyle Road, Cambridge CB4 3DN | United Kingdom
rdrysdale at plos.org<mailto:rdrysdale at plos.org> I Main +44 (0) 1223-442810
plos.org<http://www.plos.org/> I Facebook<http://www.facebook.com/PLoS.org> I Twitter<http://twitter.com/PLOS> I Blog<http://blogs.plos.org/>



From: Ray Fergerson [mailto:ray.fergerson at stanford.edu]
Sent: 13 March 2015 23:59
To: Rachel Drysdale; 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]
Sent: Thursday, March 12, 2015 7:06 AM
To: Ray Fergerson; support at bioontology.org<mailto: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 (www.accessinn.com/<http://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: 0000-0003-3037-0216<http://orcid.org/0000-0003-3037-0216>
Carlyle House, Carlyle Road, Cambridge CB4 3DN | United Kingdom
rdrysdale at plos.org<mailto:rdrysdale at plos.org> I Main +44 (0) 1223-442810
plos.org<http://www.plos.org/> I Facebook<http://www.facebook.com/PLoS.org> I Twitter<http://twitter.com/PLOS> I Blog<http://blogs.plos.org/>



From: Ray Fergerson [mailto:ray.fergerson at stanford.edu]
Sent: 11 March 2015 21:08
To: Rachel Drysdale; support at bioontology.org<mailto: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]
Sent: 11 March 2015 21:11
To: Rachel Drysdale; support at bioontology.org<mailto: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]
Sent: Wednesday, March 11, 2015 9:42 AM
To: Ray Fergerson; support at bioontology.org<mailto: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: 0000-0003-3037-0216<http://orcid.org/0000-0003-3037-0216>
Carlyle House, Carlyle Road, Cambridge CB4 3DN | United Kingdom
rdrysdale at plos.org<mailto:rdrysdale at plos.org> I Main +44 (0) 1223-442810
plos.org<http://www.plos.org/> I Facebook<http://www.facebook.com/PLoS.org> I Twitter<http://twitter.com/PLOS> I Blog<http://blogs.plos.org/>



From: Rachel Drysdale
Sent: 11 March 2015 15:02
To: Ray Fergerson; support at bioontology.org<mailto: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<mailto: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]
Sent: 10 March 2015 21:43
To: Rachel Drysdale; support at bioontology.org<mailto: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/ 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



This device should allow you to detect other errors in your ontology

before you submit it.



Ray


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