"issue" property equivalence

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Alf Eaton

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Jan 9, 2013, 11:31:28 AM1/9/13
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Is BIBO's "issue" property equivalent to PRISM's "issue" property?

If so, perhaps this could be added to the BIBO OWL file:

<owl:DatatypeProperty rdf:about="&prism;issue">
<owl:equivalentProperty rdf:resource="issue"/>
</owl:DatatypeProperty>

Bruce D'Arcus

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Jan 9, 2013, 11:36:45 AM1/9/13
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This raises an issue (no pun intended):

How are we going to deal with maintenance going forward?

Ideally, I'd like to be able to commit a change like this to a repository, and to do nothing else. But I don't believe that's possible ATM.

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Christopher Gutteridge

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Jan 9, 2013, 11:43:14 AM1/9/13
to bibliographic-ontolog...@googlegroups.com, Bruce D'Arcus
I know of two practical options (there may be more):

Make the definitive version a Turtle file an put it in git (and github?). Turtle works more elegantly with line-based version control than RDF+XML does.

The other reasonable approach we've been looking at is "neologism", which is a heavily customised Drupal site which lets you create, and maintain, vocabularies in a user friendly way.
eg. http://neologism.ecs.soton.ac.uk/

I'd have thought the simple version control route would make more sense to bibo as it already has an established documentation site.
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Bruce D'Arcus

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Jan 9, 2013, 12:10:06 PM1/9/13
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That a) github provides serving of human-readable files, and b) I can imagine some simple workflow to exploit that here.

On Jan 9, 2013 7:04 AM, "Christopher Gutteridge" <c...@ecs.soton.ac.uk> wrote:
I don't follow.
On 09/01/13 16:44, Bruce D'Arcus wrote:

Keep in mind, too, there's github pages.

Frederick Giasson

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Jan 13, 2013, 7:54:18 PM1/13/13
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Hi Bruce,

> This raises an issue (no pun intended):
>
> How are we going to deal with maintenance going forward?
>
> Ideally, I'd like to be able to commit a change like this to a
> repository, and to do nothing else. But I don't believe that's
> possible ATM.
>

I will create a GitHub repository for BIBO early this week, then I will
migrate what we got from google SVN to GitHub. That way, it will be much
easier to manage the update of the ontology with several contributors by
creating pull requests, etc.

Will send the details tomorrow or on Tuesday

Thanks,

Fred

Frederick Giasson

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Jan 15, 2013, 12:29:16 PM1/15/13
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Hi Everybody,

I migrated everything to GitHub. You can access/fork that repository from here:

    https://github.com/structureddynamics/Bibliographic-Ontology-BIBO

So, basically, you can fork this repository, work on BIBO, and do a push request such that we merge the changes into the main repo.

Changes that are discussed and agreed on that list will be automatically merged, changed that are push requested that hasn't been discussed will need to be discussed on this list, or on the push request's page (in the comment section).


Hope it helps improving bibo in short, middle and long term :)

Take care,

Fred

Jan Polowinski

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Jan 15, 2013, 1:15:46 PM1/15/13
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Hello,

I'm now receiving an error when trying to load BIBO (with the OWL-API), which I imported in my ontology:
Errormessage: SpaceRequiredBetweenPublicAndSystem
From http://markmail.org/message/6ntweyjiclzeokbu I understand that this happens when something's wrong with the DOCTYPE settings. Are you sure the new bibo ontology document is correct with respect to these settings? Yesterday everything worked fine.

Remark: We are using BIBO to create quotations and link ontology terms to documents (in the domain of visualization, e.g.: http://purl.org/viso/graphic/ ). As a workaround I temporarily removed the import now. I'd like to take the chance and thank you for you work on BIBO!

Best regards
Jan
--
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PhD student

Technische Universität Dresden
Department of Computer Science
Software- and Multimedia-Technology
01062 Dresden

Phone: +49 351 463 38311
Mobile: +49 176 80158257
E-Mail: jan.pol...@tu-dresden.de

Jan Polowinski

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Jan 15, 2013, 1:25:32 PM1/15/13
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Additional note:

It seems that working directly with https://raw.github.com/structureddynamics/Bibliographic-Ontology-BIBO/1.3/bibo.xml.owl

works fine, only http://purl.org/ontology/bibo/ which forwards to

https://raw.github.com/structureddynamics/Bibliographic-Ontology-BIBO/1.3/bibo.xml.owl#

(with the trailing hash), causes the problem.

Jan

Frederick Giasson

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Jan 15, 2013, 1:32:31 PM1/15/13
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Hi!

> It seems that working directly with https://raw.github.com/structureddynamics/Bibliographic-Ontology-BIBO/1.3/bibo.xml.owl
>
> works fine, only http://purl.org/ontology/bibo/ which forwards to
>
> https://raw.github.com/structureddynamics/Bibliographic-Ontology-BIBO/1.3/bibo.xml.owl#
>
> (with the trailing hash), causes the problem.
>


Sorry about that, an issue in the purl.org configuration.

Try it again and tell me if it works now.

Take care,

Fred

Jan Polowinski

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Jan 15, 2013, 1:49:39 PM1/15/13
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Hi,

thanks for fixing that quickly. However, there still seems to be some difference between using the BIBO-URI vs using the Document URL that causes our application to fail:

We are using the lode tool (links below are using the original). The first variant works, the second returns the same error as on our lode installation (White spaces are required between publicId and systemId):

http://www.essepuntato.it/lode/owlapi/closure/https://raw.github.com/structureddynamics/Bibliographic-Ontology-BIBO/1.3/bibo.xml.owl
http://www.essepuntato.it/lode/owlapi/closure/http://purl.org/ontology/bibo/

Jan

Frederick Giasson

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Jan 15, 2013, 2:03:00 PM1/15/13
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Hi,

> thanks for fixing that quickly. However, there still seems to be some difference between using the BIBO-URI vs using the Document URL that causes our application to fail:
>
> We are using the lode tool (links below are using the original). The first variant works, the second returns the same error as on our lode installation (White spaces are required between publicId and systemId):
>
> http://www.essepuntato.it/lode/owlapi/closure/https://raw.github.com/structureddynamics/Bibliographic-Ontology-BIBO/1.3/bibo.xml.owl
> http://www.essepuntato.it/lode/owlapi/closure/http://purl.org/ontology/bibo/


Not sure why OWLAPI chokes with this purl, would required some more
investigation. Was it working in the past?

Thanks,

Fred

Jan Polowinski

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Jan 15, 2013, 2:12:42 PM1/15/13
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It worked until this afternoon, as far as I remember. At least yesterday it was no problem. I can't remember having changed something that could have caused the change, but I will test a bit more.
I noticed it stopped working just after I received the mail concerning the Git-Hub update, so I thought it may be due to these changes.

Jan

Frederick Giasson

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Jan 15, 2013, 2:23:57 PM1/15/13
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Yes necessarily.

Not sure if the problem is that GitHub returns the document as "text/plain"

There was a way to change that with Google SVN, but it appears that it
is not the case with GitHub.

Is there a way to debug the OWLAPI to know how it tries to get that
document and why it chokes?

Thanks,

Fred

Jan Polowinski

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Jan 15, 2013, 4:46:25 PM1/15/13
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I searched the OWL-API for mime types and only found this in AbtractOWLParser.java:

protected String getRequestTypes() {
return "application/rdf+xml, application/xml; q=0.5, text/xml; q=0.3, */*; q=0.2";
}


it is used by

/**
* A convenience method that obtains an input stream from a URI.
* This method sets up the correct request type and wraps the input
* stream within a buffered input stream
* @param documentIRI The URI from which the input stream should be returned
* @return The input stream obtained from the URI
* @throws IOException if there was an <code>IOException</code> in obtaining the input stream from the URI.
*/
protected InputStream getInputStream(IRI documentIRI) throws IOException { ...


I conclude that "text/plain" is not one of the requested types. (Maybe I'm wrong, since actually Turtle should also be handled by the OWL-API which is not XML?!).

Still I think it would be best if the server would be able to respond to "application/rdf+xml" requests. This is also recommended in recipes for Linked Data. Maybe this could be achieved by an intermediate server doing some content negotiation? I recently set up a server to deliver "application/rdf+xml" for tools and "text/html" for browsers following http://www.w3.org/2001/sw/BestPractices/VM/http-examples/2005-11-18/#recipe9. However, I'm new to this - there may be better/easier/newer ways to achieve the same.

Frederick Giasson

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Jan 15, 2013, 5:27:06 PM1/15/13
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Hi Jan

> I searched the OWL-API for mime types and only found this in AbtractOWLParser.java:
>
> protected String getRequestTypes() {
> return "application/rdf+xml, application/xml; q=0.5, text/xml; q=0.3, */*; q=0.2";
> }
>
>
> it is used by
>
> /**
> * A convenience method that obtains an input stream from a URI.
> * This method sets up the correct request type and wraps the input
> * stream within a buffered input stream
> * @param documentIRI The URI from which the input stream should be returned
> * @return The input stream obtained from the URI
> * @throws IOException if there was an <code>IOException</code> in obtaining the input stream from the URI.
> */
> protected InputStream getInputStream(IRI documentIRI) throws IOException { ...
>
>
> I conclude that "text/plain" is not one of the requested types. (Maybe I'm wrong, since actually Turtle should also be handled by the OWL-API which is not XML?!).
>
> Still I think it would be best if the server would be able to respond to "application/rdf+xml" requests. This is also recommended in recipes for Linked Data. Maybe this could be achieved by an intermediate server doing some content negotiation? I recently set up a server to deliver "application/rdf+xml" for tools and "text/html" for browsers following http://www.w3.org/2001/sw/BestPractices/VM/http-examples/2005-11-18/#recipe9. However, I'm new to this - there may be better/easier/newer ways to achieve the same.

Yes, I think we won't have choice to do this since as far as I know
there is no way to do that in GitHub.

I can do that, but not sure I can do that this week. If someone is
interested in setting this up (a server that does the conneg, and that
take the content from github and feed it to the requester), then I can
point purl.org to it.

Thought?

Thanks,

Fred

Christopher Gutteridge

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Jan 16, 2013, 4:10:38 AM1/16/13
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It should be as simple as running "git pull" once per hour on a
webserver-- any chance it can run on http://bibliontology.com/ ?

Although it could be as simple as this php script:
-----
<?php
header( "Content-type: application/rdf+xml" );
readfile(
"https://raw.github.com/structureddynamics/Bibliographic-Ontology-BIBO/1.3/bibo.xml.owl"
);
-----
Or if you want the quickest and dirtiest solution:
http://graphite.ecs.soton.ac.uk/stuff2rdf/?in=rdf&uri=https%3A%2F%2Fraw.github.com%2Fstructureddynamics%2FBibliographic-Ontology-BIBO%2F1.3%2Fbibo.xml.owl&out=rdf%2Fxml

Failing that I could host it at our university, although I'd suggest
using a subdomain for it so it appeared on, say, vocab.bibliontology.com
rather than bibo.ecs.soton.ac.uk as it's not our ontology.
--
Christopher Gutteridge -- http://users.ecs.soton.ac.uk/cjg

University of Southampton Open Data Service: http://data.southampton.ac.uk/
You should read the ECS Web Team blog: http://blogs.ecs.soton.ac.uk/webteam/

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Alf Eaton

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Jan 16, 2013, 12:36:55 PM1/16/13
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Frederick Giasson

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Jan 16, 2013, 5:02:07 PM1/16/13
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Hi Christopher!

Yes, will try to do this by the end of this week. We will host this on
bibliontology.com

Thanks,

Fred

Frederick Giasson

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Jan 21, 2013, 9:23:44 AM1/21/13
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Hi Everybody,

All these conneg issues should now be fixed. Please confirm in works on
all your systems.

Thanks,

Fred
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