URIs as annotation values not showing up #13

Open
cmungall opened this Issue May 16, 2014 · 4 comments

Comments

Projects
None yet
3 participants
@cmungall

Example:
http://purl.obolibrary.org/obo/UBERON_0001882

The database_cross_references field shows all values of this property that are literals.

but not IRIs. Underlying OWL:

   <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001882">
...
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleus accumbens</rdfs:label>
         <oboInOwl:hasDbXref rdf:resource="http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=277"/>
        <oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/Nucleus_accumbens"/>
        <oboInOwl:hasDbXref rdf:resource="http://ncicb.nci.nih.gov/xml/owl/EVS/Accumbens_Nucleus"/>
        <oboInOwl:hasDbXref rdf:resource="http://uri.neuinfo.org/nif/nifstd/birnlex_727"/>
@ontoden

This comment has been minimized.

Show comment
Hide comment
@ontoden

ontoden May 16, 2014

Contributor

I see. We will try to fix this soon.

Interestingly, the page of the example also includes figure image reference:

<foaf:depicted_by rdf:resource="http://upload.wikimedia.org/wikipedia/commons/9/93/Circuit_du_syst%C3%A8me_de_recompense.jpg"/>

Probably we can try to use this example to show the image.

Thanks,

Oliver


From: Chris Mungall [notifications@github.com]
Sent: Thursday, May 15, 2014 9:19 PM
To: ontoden/ontobee
Subject: [ontobee] URIs as annotation values not showing up (#13)

Example:
http://purl.obolibrary.org/obo/UBERON_0001882

The database_cross_references field shows all values of this property that are literals.

but not IRIs. Underlying OWL:

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001882">
...
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleus accumbens/rdfs:label
<oboInOwl:hasDbXref rdf:resource="http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=277"/>
<oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/Nucleus_accumbens"/>
<oboInOwl:hasDbXref rdf:resource="http://ncicb.nci.nih.gov/xml/owl/EVS/Accumbens_Nucleus"/>
<oboInOwl:hasDbXref rdf:resource="http://uri.neuinfo.org/nif/nifstd/birnlex_727"/>


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/13.


Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

Contributor

ontoden commented May 16, 2014

I see. We will try to fix this soon.

Interestingly, the page of the example also includes figure image reference:

<foaf:depicted_by rdf:resource="http://upload.wikimedia.org/wikipedia/commons/9/93/Circuit_du_syst%C3%A8me_de_recompense.jpg"/>

Probably we can try to use this example to show the image.

Thanks,

Oliver


From: Chris Mungall [notifications@github.com]
Sent: Thursday, May 15, 2014 9:19 PM
To: ontoden/ontobee
Subject: [ontobee] URIs as annotation values not showing up (#13)

Example:
http://purl.obolibrary.org/obo/UBERON_0001882

The database_cross_references field shows all values of this property that are literals.

but not IRIs. Underlying OWL:

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001882">
...
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleus accumbens/rdfs:label
<oboInOwl:hasDbXref rdf:resource="http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=277"/>
<oboInOwl:hasDbXref rdf:resource="http://en.wikipedia.org/wiki/Nucleus_accumbens"/>
<oboInOwl:hasDbXref rdf:resource="http://ncicb.nci.nih.gov/xml/owl/EVS/Accumbens_Nucleus"/>
<oboInOwl:hasDbXref rdf:resource="http://uri.neuinfo.org/nif/nifstd/birnlex_727"/>


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/13.


Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

@cmungall

This comment has been minimized.

Show comment
Hide comment
@cmungall

cmungall May 16, 2014

Images would be great

There's something odd to do with the character escaping in this example

  • try cerebellum for an image that works

On 15 May 2014, at 18:37, ontoden wrote:

I see. We will try to fix this soon.

Interestingly, the page of the example also includes figure image
reference:

<foaf:depicted_by
rdf:resource="http://upload.wikimedia.org/wikipedia/commons/9/93/Circuit_du_syst%C3%A8me_de_recompense.jpg"/>

Probably we can try to use this example to show the image.

Thanks,

Oliver


From: Chris Mungall [notifications@github.com]
Sent: Thursday, May 15, 2014 9:19 PM
To: ontoden/ontobee
Subject: [ontobee] URIs as annotation values not showing up (#13)

Example:
http://purl.obolibrary.org/obo/UBERON_0001882

The database_cross_references field shows all values of this property
that are literals.

but not IRIs. Underlying OWL:

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001882">
...
<rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleus
accumbens/rdfs:label
<oboInOwl:hasDbXref
rdf:resource="http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=277"/>
<oboInOwl:hasDbXref
rdf:resource="http://en.wikipedia.org/wiki/Nucleus_accumbens"/>
<oboInOwl:hasDbXref
rdf:resource="http://ncicb.nci.nih.gov/xml/owl/EVS/Accumbens_Nucleus"/>
<oboInOwl:hasDbXref
rdf:resource="http://uri.neuinfo.org/nif/nifstd/birnlex_727"/>


Reply to this email directly or view it on
GitHubhttps://github.com/ontoden/ontobee/issues/13.


Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues


Reply to this email directly or view it on GitHub:
#13 (comment)

Images would be great

There's something odd to do with the character escaping in this example

  • try cerebellum for an image that works

On 15 May 2014, at 18:37, ontoden wrote:

I see. We will try to fix this soon.

Interestingly, the page of the example also includes figure image
reference:

<foaf:depicted_by
rdf:resource="http://upload.wikimedia.org/wikipedia/commons/9/93/Circuit_du_syst%C3%A8me_de_recompense.jpg"/>

Probably we can try to use this example to show the image.

Thanks,

Oliver


From: Chris Mungall [notifications@github.com]
Sent: Thursday, May 15, 2014 9:19 PM
To: ontoden/ontobee
Subject: [ontobee] URIs as annotation values not showing up (#13)

Example:
http://purl.obolibrary.org/obo/UBERON_0001882

The database_cross_references field shows all values of this property
that are literals.

but not IRIs. Underlying OWL:

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001882">
...
<rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleus
accumbens/rdfs:label
<oboInOwl:hasDbXref
rdf:resource="http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=277"/>
<oboInOwl:hasDbXref
rdf:resource="http://en.wikipedia.org/wiki/Nucleus_accumbens"/>
<oboInOwl:hasDbXref
rdf:resource="http://ncicb.nci.nih.gov/xml/owl/EVS/Accumbens_Nucleus"/>
<oboInOwl:hasDbXref
rdf:resource="http://uri.neuinfo.org/nif/nifstd/birnlex_727"/>


Reply to this email directly or view it on
GitHubhttps://github.com/ontoden/ontobee/issues/13.


Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues


Reply to this email directly or view it on GitHub:
#13 (comment)

@ontoden

This comment has been minimized.

Show comment
Hide comment
@ontoden

ontoden May 19, 2014

Contributor

Hi Chris,

Bin in my lab has made it happen: now we can see the images in Ontobee:

http://www.ontobee.org/browser/rdf.php?o=UBERON&iri=http://purl.obolibrary.org/obo/UBERON_0001882
more examples:
http://purl.obolibrary.org/obo/UBERON_0001874
http://purl.obolibrary.org/obo/UBERON_0001875
http://purl.obolibrary.org/obo/UBERON_0002741

The other issue about the database_cross_references has also seen solved.

Please check out.

Best,

Oliver

From: Chris Mungall [mailto:notifications@github.com]
Sent: Friday, May 16, 2014 12:18 AM
To: ontoden/ontobee
Cc: ontoden
Subject: Re: [ontobee] URIs as annotation values not showing up (#13)

Images would be great

There's something odd to do with the character escaping in this example

  • try cerebellum for an image that works

On 15 May 2014, at 18:37, ontoden wrote:

I see. We will try to fix this soon.

Interestingly, the page of the example also includes figure image
reference:

<foaf:depicted_by
rdf:resource="http://upload.wikimedia.org/wikipedia/commons/9/93/Circuit_du_syst%C3%A8me_de_recompense.jpg"/>

Probably we can try to use this example to show the image.

Thanks,

Oliver


From: Chris Mungall [notifications@github.com]
Sent: Thursday, May 15, 2014 9:19 PM
To: ontoden/ontobee
Subject: [ontobee] URIs as annotation values not showing up (#13)

Example:
http://purl.obolibrary.org/obo/UBERON_0001882

The database_cross_references field shows all values of this property
that are literals.

but not IRIs. Underlying OWL:

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001882">
...
<rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleus
accumbens/rdfs:label
<oboInOwl:hasDbXref
rdf:resource="http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=277"/>
<oboInOwl:hasDbXref
rdf:resource="http://en.wikipedia.org/wiki/Nucleus_accumbens"/>
<oboInOwl:hasDbXref
rdf:resource="http://ncicb.nci.nih.gov/xml/owl/EVS/Accumbens_Nucleus"/>
<oboInOwl:hasDbXref
rdf:resource="http://uri.neuinfo.org/nif/nifstd/birnlex_727"/>


Reply to this email directly or view it on
GitHubhttps://github.com/ontoden/ontobee/issues/13.


Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues


Reply to this email directly or view it on GitHub:
#13 (comment)


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/13#issuecomment-43295305.


Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

Contributor

ontoden commented May 19, 2014

Hi Chris,

Bin in my lab has made it happen: now we can see the images in Ontobee:

http://www.ontobee.org/browser/rdf.php?o=UBERON&iri=http://purl.obolibrary.org/obo/UBERON_0001882
more examples:
http://purl.obolibrary.org/obo/UBERON_0001874
http://purl.obolibrary.org/obo/UBERON_0001875
http://purl.obolibrary.org/obo/UBERON_0002741

The other issue about the database_cross_references has also seen solved.

Please check out.

Best,

Oliver

From: Chris Mungall [mailto:notifications@github.com]
Sent: Friday, May 16, 2014 12:18 AM
To: ontoden/ontobee
Cc: ontoden
Subject: Re: [ontobee] URIs as annotation values not showing up (#13)

Images would be great

There's something odd to do with the character escaping in this example

  • try cerebellum for an image that works

On 15 May 2014, at 18:37, ontoden wrote:

I see. We will try to fix this soon.

Interestingly, the page of the example also includes figure image
reference:

<foaf:depicted_by
rdf:resource="http://upload.wikimedia.org/wikipedia/commons/9/93/Circuit_du_syst%C3%A8me_de_recompense.jpg"/>

Probably we can try to use this example to show the image.

Thanks,

Oliver


From: Chris Mungall [notifications@github.com]
Sent: Thursday, May 15, 2014 9:19 PM
To: ontoden/ontobee
Subject: [ontobee] URIs as annotation values not showing up (#13)

Example:
http://purl.obolibrary.org/obo/UBERON_0001882

The database_cross_references field shows all values of this property
that are literals.

but not IRIs. Underlying OWL:

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001882">
...
<rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleus
accumbens/rdfs:label
<oboInOwl:hasDbXref
rdf:resource="http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=277"/>
<oboInOwl:hasDbXref
rdf:resource="http://en.wikipedia.org/wiki/Nucleus_accumbens"/>
<oboInOwl:hasDbXref
rdf:resource="http://ncicb.nci.nih.gov/xml/owl/EVS/Accumbens_Nucleus"/>
<oboInOwl:hasDbXref
rdf:resource="http://uri.neuinfo.org/nif/nifstd/birnlex_727"/>


Reply to this email directly or view it on
GitHubhttps://github.com/ontoden/ontobee/issues/13.


Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues


Reply to this email directly or view it on GitHub:
#13 (comment)


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/13#issuecomment-43295305.


Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

@ontoden

This comment has been minimized.

Show comment
Hide comment
@ontoden

ontoden May 19, 2014

Contributor

Great work Bin! Very nice!

I see there are duplicates but this is a problem on my end, will fix.

On 19 May 2014, at 12:28, He, Yongqun wrote:

Hi Chris,

Bin in my lab has made it happen: now we can see the images in
Ontobee:

http://www.ontobee.org/browser/rdf.php?o=UBERON&iri=http://purl.obolibrary.org/obo/UBERON_0001882
more examples:
http://purl.obolibrary.org/obo/UBERON_0001874
http://purl.obolibrary.org/obo/UBERON_0001875
http://purl.obolibrary.org/obo/UBERON_0002741

The other issue about the database_cross_references has also seen
solved.

Please check out.

Best,

Oliver

From: Chris Mungall [mailto:notifications@github.com]
Sent: Friday, May 16, 2014 12:18 AM
To: ontoden/ontobee
Cc: ontoden
Subject: Re: [ontobee] URIs as annotation values not showing up (#13)

Images would be great

There's something odd to do with the character escaping in this
example

  • try cerebellum for an image that works

On 15 May 2014, at 18:37, ontoden wrote:

I see. We will try to fix this soon.

Interestingly, the page of the example also includes figure image
reference:

<foaf:depicted_by
rdf:resource="http://upload.wikimedia.org/wikipedia/commons/9/93/Circuit_du_syst%C3%A8me_de_recompense.jpg"/>

Probably we can try to use this example to show the image.

Thanks,

Oliver


From: Chris Mungall [notifications@github.com]
Sent: Thursday, May 15, 2014 9:19 PM
To: ontoden/ontobee
Subject: [ontobee] URIs as annotation values not showing up (#13)

Example:
http://purl.obolibrary.org/obo/UBERON_0001882

The database_cross_references field shows all values of this property
that are literals.

but not IRIs. Underlying OWL:

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001882">
...
<rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleus
accumbens/rdfs:label
<oboInOwl:hasDbXref
rdf:resource="http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=277"/>
<oboInOwl:hasDbXref
rdf:resource="http://en.wikipedia.org/wiki/Nucleus_accumbens"/>
<oboInOwl:hasDbXref
rdf:resource="http://ncicb.nci.nih.gov/xml/owl/EVS/Accumbens_Nucleus"/>
<oboInOwl:hasDbXref
rdf:resource="http://uri.neuinfo.org/nif/nifstd/birnlex_727"/>


Reply to this email directly or view it on
GitHubhttps://github.com/ontoden/ontobee/issues/13.


Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues


Reply to this email directly or view it on GitHub:
#13 (comment)


Reply to this email directly or view it on
GitHubhttps://github.com/ontoden/ontobee/issues/13#issuecomment-43295305.


Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues

You received this message because you are subscribed to the Google
Groups "Ontobee-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send
an email to ontobee-discuss+unsubscribe@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

Contributor

ontoden commented May 19, 2014

Great work Bin! Very nice!

I see there are duplicates but this is a problem on my end, will fix.

On 19 May 2014, at 12:28, He, Yongqun wrote:

Hi Chris,

Bin in my lab has made it happen: now we can see the images in
Ontobee:

http://www.ontobee.org/browser/rdf.php?o=UBERON&iri=http://purl.obolibrary.org/obo/UBERON_0001882
more examples:
http://purl.obolibrary.org/obo/UBERON_0001874
http://purl.obolibrary.org/obo/UBERON_0001875
http://purl.obolibrary.org/obo/UBERON_0002741

The other issue about the database_cross_references has also seen
solved.

Please check out.

Best,

Oliver

From: Chris Mungall [mailto:notifications@github.com]
Sent: Friday, May 16, 2014 12:18 AM
To: ontoden/ontobee
Cc: ontoden
Subject: Re: [ontobee] URIs as annotation values not showing up (#13)

Images would be great

There's something odd to do with the character escaping in this
example

  • try cerebellum for an image that works

On 15 May 2014, at 18:37, ontoden wrote:

I see. We will try to fix this soon.

Interestingly, the page of the example also includes figure image
reference:

<foaf:depicted_by
rdf:resource="http://upload.wikimedia.org/wikipedia/commons/9/93/Circuit_du_syst%C3%A8me_de_recompense.jpg"/>

Probably we can try to use this example to show the image.

Thanks,

Oliver


From: Chris Mungall [notifications@github.com]
Sent: Thursday, May 15, 2014 9:19 PM
To: ontoden/ontobee
Subject: [ontobee] URIs as annotation values not showing up (#13)

Example:
http://purl.obolibrary.org/obo/UBERON_0001882

The database_cross_references field shows all values of this property
that are literals.

but not IRIs. Underlying OWL:

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0001882">
...
<rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">nucleus
accumbens/rdfs:label
<oboInOwl:hasDbXref
rdf:resource="http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=277"/>
<oboInOwl:hasDbXref
rdf:resource="http://en.wikipedia.org/wiki/Nucleus_accumbens"/>
<oboInOwl:hasDbXref
rdf:resource="http://ncicb.nci.nih.gov/xml/owl/EVS/Accumbens_Nucleus"/>
<oboInOwl:hasDbXref
rdf:resource="http://uri.neuinfo.org/nif/nifstd/birnlex_727"/>


Reply to this email directly or view it on
GitHubhttps://github.com/ontoden/ontobee/issues/13.


Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues


Reply to this email directly or view it on GitHub:
#13 (comment)


Reply to this email directly or view it on
GitHubhttps://github.com/ontoden/ontobee/issues/13#issuecomment-43295305.


Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues

You received this message because you are subscribed to the Google
Groups "Ontobee-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send
an email to ontobee-discuss+unsubscribe@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment