linking OBI IDs to website entry

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linking OBI IDs to website entry

Bjoern Peters
Hi all,

As we are starting to use OBI IDs in our production system, we would like to link directly from an OBI ID to a corresponding website with definition, metadata, synonyms etc. I know Alan had previously prototyped such a page; is their an estimate when this would be available? Otherwise I assume we would be using bioportal.

Best,

Bjoern


--
Bjoern Peters
Assistant Member
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters

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Re: linking OBI IDs to website entry

He, Oliver
It's now available for VO IDs. For example, if you click on the VO class 'DNA vaccine':
it will directly link to:
In addition, if you look for the source of the web page, it's owl format and contains all information about this term. So we have managed to separate the web display and source OWL file output.
 
This feature has partially been expanded to all other ontologies in OntoBee:
 
It contains OBI:
for example, OBI term 'injection':
Again, the source code of this page is an OWL file displaying the information about this term.
We don't have a direct link to the above page from a click on the URL yet: http://purl.obolibrary.org/obo/OBI_0000426 
Some work needs to be done first from http://purl.obolibrary.org/obo/ to make this occur.
 
Chris Mungall has proposed to use OntoBee for all OBO foundry ontology term visualization. OntoBee is using the ontology updates from Neurocommons RDF triple store. Now my team is working with Chris and Alan to get more features available.
 
Best,
Oliver
  

>>> Bjoern Peters <[hidden email]> 8/26/2010 6:24 PM >>>
Hi all,

As we are starting to use OBI IDs in our production system, we would like to link directly from an OBI ID to a corresponding website with definition, metadata, synonyms etc. I know Alan had previously prototyped such a page; is their an estimate when this would be available? Otherwise I assume we would be using bioportal.

Best,

Bjoern


--
Bjoern Peters
Assistant Member
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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Re: linking OBI IDs to website entry

Bjoern Peters
Oliver: That looks really nice, excellent!
Chris:  We would like to start using the purl links from the start when that part of our production system goes online in about 2 months. Is it reasonable to assume that they would be working by then (i.e. http://purl.obolibrary.org/obo/OBI_0000426  would redirect to the corresponding ontobee page)?

All: I assume/hope that all are okay with  using this system for OBI. As the purls can be redirected in the future, I don't think there is any risk at all in going ahead with this, as clearly it is much better than having no resolvable link at all.

Best,

Bjoern


It's now available for VO IDs. For example, if you click on the VO class 'DNA vaccine':
it will directly link to:
In addition, if you look for the source of the web page, it's owl format and contains all information about this term. So we have managed to separate the web display and source OWL file output.
 
This feature has partially been expanded to all other ontologies in OntoBee:
 
It contains OBI:
for example, OBI term 'injection':
Again, the source code of this page is an OWL file displaying the information about this term.
We don't have a direct link to the above page from a click on the URL yet: http://purl.obolibrary.org/obo/OBI_0000426 
Some work needs to be done first from http://purl.obolibrary.org/obo/ to make this occur.
 
Chris Mungall has proposed to use OntoBee for all OBO foundry ontology term visualization. OntoBee is using the ontology updates from Neurocommons RDF triple store. Now my team is working with Chris and Alan to get more features available.
 
Best,
Oliver
  

>>> Bjoern Peters <[hidden email]> 8/26/2010 6:24 PM >>>
Hi all,

As we are starting to use OBI IDs in our production system, we would like to link directly from an OBI ID to a corresponding website with definition, metadata, synonyms etc. I know Alan had previously prototyped such a page; is their an estimate when this would be available? Otherwise I assume we would be using bioportal.

Best,

Bjoern


--
Bjoern Peters
Assistant Member
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues



--
Bjoern Peters
Assistant Member
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters

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Be part of this innovative community and reach millions of netbook users
worldwide. Take advantage of special opportunities to increase revenue and
speed time-to-market. Join now, and jumpstart your future.
http://p.sf.net/sfu/intel-atom-d2d
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Re: linking OBI IDs to website entry

He, Oliver
Sounds great to me! Thanks!
Oliver

>>> Bjoern Peters <[hidden email]> 8/26/2010 10:39 PM >>>
Oliver: That looks really nice, excellent!
Chris:  We would like to start using the purl links from the start when that part of our production system goes online in about 2 months. Is it reasonable to assume that they would be working by then (i.e. http://purl.obolibrary.org/obo/OBI_0000426  would redirect to the corresponding ontobee page)?

All: I assume/hope that all are okay with  using this system for OBI. As the purls can be redirected in the future, I don't think there is any risk at all in going ahead with this, as clearly it is much better than having no resolvable link at all.

Best,

Bjoern


It's now available for VO IDs. For example, if you click on the VO class 'DNA vaccine':
it will directly link to:
In addition, if you look for the source of the web page, it's owl format and contains all information about this term. So we have managed to separate the web display and source OWL file output.
 
This feature has partially been expanded to all other ontologies in OntoBee:
 
It contains OBI:
for example, OBI term 'injection':
Again, the source code of this page is an OWL file displaying the information about this term.
We don't have a direct link to the above page from a click on the URL yet: http://purl.obolibrary.org/obo/OBI_0000426 
Some work needs to be done first from http://purl.obolibrary.org/obo/ to make this occur.
 
Chris Mungall has proposed to use OntoBee for all OBO foundry ontology term visualization. OntoBee is using the ontology updates from Neurocommons RDF triple store. Now my team is working with Chris and Alan to get more features available.
 
Best,
Oliver
  

>>> Bjoern Peters <[hidden email]> 8/26/2010 6:24 PM >>>
Hi all,

As we are starting to use OBI IDs in our production system, we would like to link directly from an OBI ID to a corresponding website with definition, metadata, synonyms etc. I know Alan had previously prototyped such a page; is their an estimate when this would be available? Otherwise I assume we would be using bioportal.

Best,

Bjoern


--
Bjoern Peters
Assistant Member
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues



--
Bjoern Peters
Assistant Member
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

------------------------------------------------------------------------------
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Be part of this innovative community and reach millions of netbook users
worldwide. Take advantage of special opportunities to increase revenue and
speed time-to-market. Join now, and jumpstart your future.
http://p.sf.net/sfu/intel-atom-d2d
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Re: linking OBI IDs to website entry

Bjoern Peters
In reply to this post by Bjoern Peters
If possible, I would like to see this in action immediately. If that is unrealistic, how about within the next 2 weeks?

Thanks,

Bjoern


Yes, just let me or Alan know when you want this to go into action.


On Aug 27, 2010, at 1:24 PM, Yongqun He wrote:

> Sounds great to me! Thanks!
> Oliver
>
> >>> Bjoern Peters <[hidden email]> 8/26/2010 10:39 PM >>>
> Oliver: That looks really nice, excellent!
> Chris:  We would like to start using the purl links from the start  
> when that part of our production system goes online in about 2  
> months. Is it reasonable to assume that they would be working by  
> then (i.e. http://purl.obolibrary.org/obo/OBI_0000426  would  
> redirect to the corresponding ontobee page)?
>
> All: I assume/hope that all are okay with  using this system for  
> OBI. As the purls can be redirected in the future, I don't think  
> there is any risk at all in going ahead with this, as clearly it is  
> much better than having no resolvable link at all.
>
> Best,
>
> Bjoern
>
> It's now available for VO IDs. For example, if you click on the VO  
> class 'DNA vaccine':
> http://purl.obolibrary.org/obo/VO_0000032
> it will directly link to:
> http://www.violinet.org/vaccineontology/vobrowser/rdf.php?iri=http://purl.obolibrary.org/obo/VO_0000032
> In addition, if you look for the source of the web page, it's owl  
> format and contains all information about this term. So we have  
> managed to separate the web display and source OWL file output.
>
> This feature has partially been expanded to all other ontologies in  
> OntoBee:
> http://www.ontobee.org/
>
> It contains OBI:
> http://www.ontobee.org/browser/index.php?o=OBI
> for example, OBI term 'injection':
> http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.org/obo/OBI_0000426
> Again, the source code of this page is an OWL file displaying the  
> information about this term.
> We don't have a direct link to the above page from a click on the  
> URL yet: http://purl.obolibrary.org/obo/OBI_0000426
> Some work needs to be done first from http://purl.obolibrary.org/
> obo/ to make this occur.
>
> Chris Mungall has proposed to use OntoBee for all OBO foundry  
> ontology term visualization. OntoBee is using the ontology updates  
> from Neurocommons RDF triple store. Now my team is working with  
> Chris and Alan to get more features available.
>
> Best,
> Oliver
>
>
> >>> Bjoern Peters <[hidden email]> 8/26/2010 6:24 PM >>>
> Hi all,
>
> As we are starting to use OBI IDs in our production system, we would  
> like to link directly from an OBI ID to a corresponding website with  
> definition, metadata, synonyms etc. I know Alan had previously  
> prototyped such a page; is their an estimate when this would be  
> available? Otherwise I assume we would be using bioportal.
>
> Best,
>
> Bjoern
>
>
> --
> Bjoern Peters
> Assistant Member
> La Jolla Institute for Allergy and Immunology
> 9420 Athena Circle
> La Jolla, CA 92037, USA
> Tel: 858/752-6914
> Fax: 858/752-6987
> http://www.liai.org/pages/faculty-peters
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should  
> not be used for urgent or sensitive issues
>
>
>
> --
> Bjoern Peters
> Assistant Member
> La Jolla Institute for Allergy and Immunology
> 9420 Athena Circle
> La Jolla, CA 92037, USA
> Tel: 858/752-6914
> Fax: 858/752-6987
> http://www.liai.org/pages/faculty-peters
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should  
> not be used for urgent or sensitive issues




--
Bjoern Peters
Assistant Member
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters

------------------------------------------------------------------------------
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Be part of this innovative community and reach millions of netbook users
worldwide. Take advantage of special opportunities to increase revenue and
speed time-to-market. Join now, and jumpstart your future.
http://p.sf.net/sfu/intel-atom-d2d
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Re: linking OBI IDs to website entry

NCBO
Administrator
Hi Bjoern,

BioPortal is able to return both HTML and RDF for ontologies. To have the OBI PURLs return this information, I believe all that is needed is to set-up the re-directs on the PURL server for the OBI IDs.  The RDF that is returned is described here: http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Term_Service .

Trish


On Fri, Aug 27, 2010 at 6:56 PM, Bjoern Peters <[hidden email]> wrote:
If possible, I would like to see this in action immediately. If that is unrealistic, how about within the next 2 weeks?

Thanks,

Bjoern


Yes, just let me or Alan know when you want this to go into action.



On Aug 27, 2010, at 1:24 PM, Yongqun He wrote:

> Sounds great to me! Thanks!
> Oliver
>
> >>> Bjoern Peters <[hidden email]> 8/26/2010 10:39 PM >>>
> Oliver: That looks really nice, excellent!
> Chris:  We would like to start using the purl links from the start  
> when that part of our production system goes online in about 2  
> months. Is it reasonable to assume that they would be working by  
> then (i.e. http://purl.obolibrary.org/obo/OBI_0000426  would  
> redirect to the corresponding ontobee page)?
>
> All: I assume/hope that all are okay with  using this system for  
> OBI. As the purls can be redirected in the future, I don't think  
> there is any risk at all in going ahead with this, as clearly it is  
> much better than having no resolvable link at all.
>
> Best,
>
> Bjoern
>
> It's now available for VO IDs. For example, if you click on the VO  
> class 'DNA vaccine':
> http://purl.obolibrary.org/obo/VO_0000032
> it will directly link to:
> http://www.violinet.org/vaccineontology/vobrowser/rdf.php?iri=http://purl.obolibrary.org/obo/VO_0000032
> In addition, if you look for the source of the web page, it's owl  
> format and contains all information about this term. So we have  
> managed to separate the web display and source OWL file output.
>
> This feature has partially been expanded to all other ontologies in  
> OntoBee:
> http://www.ontobee.org/
>
> It contains OBI:
> http://www.ontobee.org/browser/index.php?o=OBI
> for example, OBI term 'injection':
> http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.org/obo/OBI_0000426
> Again, the source code of this page is an OWL file displaying the  
> information about this term.
> We don't have a direct link to the above page from a click on the  
> URL yet: http://purl.obolibrary.org/obo/OBI_0000426
> Some work needs to be done first from http://purl.obolibrary.org/
> obo/ to make this occur.
>
> Chris Mungall has proposed to use OntoBee for all OBO foundry  
> ontology term visualization. OntoBee is using the ontology updates  
> from Neurocommons RDF triple store. Now my team is working with  
> Chris and Alan to get more features available.
>
> Best,
> Oliver
>
>
> >>> Bjoern Peters <[hidden email]> 8/26/2010 6:24 PM >>>
> Hi all,
>
> As we are starting to use OBI IDs in our production system, we would  
> like to link directly from an OBI ID to a corresponding website with  
> definition, metadata, synonyms etc. I know Alan had previously  
> prototyped such a page; is their an estimate when this would be  
> available? Otherwise I assume we would be using bioportal.

>
> Best,
>
> Bjoern
>
>
> --
> Bjoern Peters
> Assistant Member
> La Jolla Institute for Allergy and Immunology
> 9420 Athena Circle
> La Jolla, CA 92037, USA
> Tel: 858/752-6914
> Fax: 858/752-6987
> http://www.liai.org/pages/faculty-peters
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should  
> not be used for urgent or sensitive issues
>
>
>
> --
> Bjoern Peters
> Assistant Member
> La Jolla Institute for Allergy and Immunology
> 9420 Athena Circle
> La Jolla, CA 92037, USA
> Tel: 858/752-6914
> Fax: 858/752-6987
> http://www.liai.org/pages/faculty-peters
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should  
> not be used for urgent or sensitive issues




--
Bjoern Peters
Assistant Member
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters

------------------------------------------------------------------------------
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Be part of this innovative community and reach millions of netbook users
worldwide. Take advantage of special opportunities to increase revenue and
speed time-to-market. Join now, and jumpstart your future.
http://p.sf.net/sfu/intel-atom-d2d
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