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

Ray Fergerson ray.fergerson at stanford.edu
Fri May 15 15:24:11 PDT 2015


Rachel,



I’ve deleted all submissions on this except for the last one for this
ontology. The last one still doesn’t load but we think that this is a
problem with your 3rd party export software. I’ve left the last broken
submission in the system as a reminder. Alternatively we could delete this
last submission or even the entire ontology and wait for a software update
from your vendor.



Ray



From: Rachel Drysdale [mailto:rdrysdale at plos.org]
Sent: Wednesday, April 15, 2015 3:54 AM
To: Ray Fergerson; support at bioontology.org
Subject: RE: [bioontology-support] [BioPortal] Feedback from
Rachel.Drysdale



Hi Ray



I see that your or my efforts have resulted in a SKOS upload at

http://bioportal.bioontology.org/ontologies/PLOSTHES

but it is showing the “(Uploaded, Error Rdf)” error message thing.

Although I’m grateful for your efforts to help me with this, do you think
we should call time on this attempt?

Access Innovations have their hands full right now with moving towards
their annual MAIstro software upgrade.  I shouldn’t think they’ll be able
to commit to reviewing the exports until that is completely finished.



Best regards,

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: 09 April 2015 11:29
To: Ray Fergerson; support at bioontology.org
Cc: Rachel Drysdale
Subject: RE: [bioontology-support] [BioPortal] Feedback from
Rachel.Drysdale



Hi Ray



Apologies for delay

I have just attempted to upload plosthes.2014-5.skos.xml

I was not able to run it through your validator at

 <http://bioportal.bioontology.org/validate_ontology_file>
http://bioportal.bioontology.org/validate_ontology_file

because the upload dialog box seems to have dropped off
.



And as far as I can see uploading the file doesn’t seem to be be
proceeding either, so here it is as an attachment.



How’s that?  J



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: 04 April 2015 01:04
To: Rachel Drysdale; support at bioontology.org
Subject: RE: [bioontology-support] [BioPortal] Feedback from
Rachel.Drysdale



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



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