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OBOFoundry / purl.obolibrary.org

A system for managing OBO PURLs
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http://purl.obolibrary.org/obo/pato# does not redirect #236

Closed mobb closed 8 years ago

mobb commented 8 years ago

Hello - We are importing pato into another ontology, along with several other OBO ontologies. The other imports' namespaces resolve to http://www.berkeleybop.org/. the PATO namespace points to a 404 (https://github.com/pato-phenotype/pato#). We do see a dir http://www.berkeleybop.org/ontologies/pato/ -- perhaps pato is supposed to redirect there, too? thanks.

cmungall commented 8 years ago

These are the PURLs you should use for the ontology

http://purl.obolibrary.org/obo/pato.obo http://purl.obolibrary.org/obo/pato.owl

Don't hardcode any berkeleybop URLs, always use the PURLs

We should have it such that http://purl.obolibrary.org/obo/pato redirects to the homepage. Just curious is this a technical issue for you?

On 29 Aug 2016, at 15:51, mobb wrote:

Hello - We are importing pato into another ontology, along with several other OBO ontologies. The other imports' namespaces resolve to http://www.berkeleybop.org/. the PATO namespace points to a 404 (https://github.com/pato-phenotype/pato#). We do see a dir http://www.berkeleybop.org/ontologies/pato/ -- perhaps pato is supposed to redirect there, too? thanks.

You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/OBOFoundry/purl.obolibrary.org/issues/236

mobb commented 8 years ago

This link does not redirect:

We should have it such that http://purl.obolibrary.org/obo/pato redirects to the homepage. Just curious is this a technical issue for you?
cmungall commented 8 years ago

I don't know exactly what you mean by:

We're having problems with Protege importing a file that uses the namespace: http://purl.obolibrary.org/obo/pato#

note that namespace declarations are local to each document. As far as any software is concerned, everything is expanded to a full URI.

I'm not really following what you are trying to do with your imports. It looks as if you have extracted modules from ontologies like PATO, UO. However, they don't appear to resolve:

$ curl http://purl.dataone.org/PATO_import.owl
<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
<html><head>
<title>302 Found</title>
</head><body>
<h1>Found</h1>
<p>The document has moved <a href="https://purl.dataone.org/PATO_import.owl">here</a>.</p>
<hr>
<address>Apache/2.4.7 (Ubuntu) Server at purl.dataone.org Port 80</address>
</body></html>

This is nothing to do with PATO though.

Are you saying that the namespace for pato should not follow the pattern we used for uo and envo?

I don't follow. PATO, UO and all the OBO Library ontologies should behave in the same way. You can either import the complete ontology using the official OBO purl. Or you can use your favorite module extraction tools (ROBOT, OntoFox, etc) to create a submodule which you would give a purl that you take charge of resolving. But this has nothing to do with namespaces.

You can also email obo-discuss for further help (about to leave to a meeting...)

mobb commented 8 years ago

Sorry - too many examples. I have removed them from the git comment. This is the problem:

You say:

We should have it such that http://purl.obolibrary.org/obo/patoredirects to the homepage. Just curious is this a technical issue for you? http://purl.obolibrary.org/obo/pato does not redirect.

Margaret O'Brien Information Management Marine Science Institute, UCSB Santa Barbara, CA 93106 805-893-2071 (voice) http://sbc.lternet.edu

On 8/29/16 4:21 PM, Chris Mungall wrote:

I don't know exactly what you mean by:

We're having problems with Protege importing a file that uses the
namespace: http://purl.obolibrary.org/obo/pato#

note that namespace declarations are local to each document. As far as any software is concerned, everything is expanded to a full URI.

I'm not really following what you are trying to do with your imports. It looks as if you have extracted modules from ontologies like PATO, UO. However, they don't appear to resolve:

|$ curl http://purl.dataone.org/PATO_import.owl <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN"> 302 Found

Found

The document has moved <a href="https://purl.dataone.org/PATO_import.owl">here.

Apache/2.4.7 (Ubuntu) Server at purl.dataone.org Port 80
| This is nothing to do with PATO though. ``` Are you saying that the namespace for pato should not follow the pattern we used for uo and envo? ``` I don't follow. PATO, UO and all the OBO Library ontologies should behave in the same way. You can either import the complete ontology using the official OBO purl. Or you can use your favorite module extraction tools (ROBOT, OntoFox, etc) to create a submodule which you would give a purl that you take charge of resolving. But this has nothing to do with namespaces. You can also email obo-discuss for further help (about to leave to a meeting...) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/purl.obolibrary.org/issues/236#issuecomment-243287324, or mute the thread https://github.com/notifications/unsubscribe-auth/AEtBifkXfZWJ7q_cshDLZXOM4a2oEhLZks5qk2mWgaJpZM4Jv-n7.
cmungall commented 8 years ago

OK, we will have this resolve to the home page. Is this in line with your expectations?

On 29 Aug 2016, at 16:23, mobb wrote:

Sorry - too many examples. I have removed them from the git comment.  This is the problem:

You say:

We should have it such that   http://purl.obolibrary.org/obo/patoredirects to the homepage. Just  curious is this a technical issue for you? http://purl.obolibrary.org/obo/pato does not redirect.

mobb commented 8 years ago

yes.

Margaret O'Brien Information Management Marine Science Institute, UCSB Santa Barbara, CA 93106 805-893-2071 (voice) http://sbc.lternet.edu

On 8/29/16 4:29 PM, Chris Mungall wrote:

OK, we will have this resolve to the home page. Is this in line with your expectations?

On 29 Aug 2016, at 16:23, mobb wrote:

Sorry - too many examples. I have removed them from the git comment. This is the problem:

You say:

We should have it such that

http://purl.obolibrary.org/obo/patoredirects to

the homepage. Just curious is this a technical issue for you?

http://purl.obolibrary.org/obo/pato does

not redirect.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/purl.obolibrary.org/issues/236#issuecomment-243288765, or mute the thread https://github.com/notifications/unsubscribe-auth/AEtBibjYRZKYT7l-xEdIM8Dfh0wrdmfSks5qk2tmgaJpZM4Jv-n7.

saralafia commented 8 years ago

The PATO namespace http://purl.obolibrary.org/obo/pato# redirects to https://github.com/pato-phenotype/pato# which is broken. Is it supposed to point to http://www.berkeleybop.org/ontologies/pato/ ? Thanks!

cmungall commented 8 years ago

There should be no hashes in any PATO PURL. Where did you come across this URL?