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[bioontology-support] [BioPortal] Feedback from Nicolas Le Novere

Nicolas Rodriguez rodrigue at ebi.ac.uk
Thu Sep 3 16:30:27 PDT 2015


Still the same problem, the purl does resolve to the same page as you 
but then I am getting the error.

Nico


Le 04/09/2015 00:15, Ray Fergerson a écrit :
>
> This is quite strange. Are you sure that this link:
>
> http://purl.bioontology.org/ontology/MAMO
>
> Does not work for you. For me it resolves to
>
> http://bioportal.bioontology.org/ontologies/MAMO?p=classes&conceptid=root
>
> which displays fine. Can you clear your cache?
>
> Ray
>
> *From:*Nicolas Rodriguez [mailto:rodrigue at ebi.ac.uk]
> *Sent:* Thursday, September 3, 2015 4:09 PM
> *To:* Ray Fergerson; support at bioontology.org; Nicolas Rodriguez
> *Subject:* Re: [bioontology-support] [BioPortal] Feedback from Nicolas 
> Le Novere
>
> Le 03/09/2015 23:55, Ray Fergerson a écrit :
>
>     I am not seeing any error with the classes view or with the purl. Is this still happening for you?
>
> yes, I am getting an error message:
>
>
>   We're sorry but something has gone wrong. We have been notified of
>   this error.
>
>
>
>
>   
> Ray
>   
> -----Original Message-----
> From: Nicolas Rodriguez [mailto:rodriguezn at babraham.ac.uk]
> Sent: Thursday, September 3, 2015 3:07 AM
> To: Ray Fergerson;support at bioontology.org  <mailto:support at bioontology.org>; Nicolas Rodriguez
> Subject: Re: [bioontology-support] [BioPortal] Feedback from Nicolas Le Novere
>   
> On 01/09/15 21:48, Ray Fergerson wrote:
>
>     Hummm. It appears that my change got lost somehow. Either that or I just bungled it. I have changed it again. I'll check that it gets updated tonight.
>
>   
> The summary page seems to be good now, I can see the new submission and the owl seems to be the right one.
>   
> Although, now there is an error when I try to go to the classes view.
> That might be du to the fact that we are getting an error when trying to access the PURL athttp://purl.bioontology.org/ontology/MAMO.
>   
> Speaking about PURL, we updatedhttp://purl.obolibrary.org/obo/mamo.owl
> and it now point to the latest svn version so should always be valid.
>   
> Thanks,
> Nico
>   
>
>       
>
>       
>
>     -----Original Message-----
>
>     From: Nicolas Rodriguez [mailto:rodriguezn at babraham.ac.uk]
>
>     Sent: Tuesday, September 1, 2015 3:50 AM
>
>     To: Ray Fergerson;support at bioontology.org  <mailto:support at bioontology.org>; Nicolas Rodriguez
>
>     Subject: Re: [bioontology-support] [BioPortal] Feedback from Nicolas
>
>     Le Novere
>
>       
>
>     On 28/08/15 21:25, Ray Fergerson wrote:
>
>         OK, I switched the link. With luck the latest version should show up in a few hours.
>
>     It seems that there are still no changes on bioportal.
>
>     If I load
>
>     https://svn.code.sf.net/p/mamo-ontology/code/tags/latest/mamo-xml.owl  on Protege, I have 98 classes with 4 top level 'branch'.
>
>       
>
>     At the moment,
>
>     http://bioportal.bioontology.org/ontologies/MAMO/?p=summary  show only 19 classes.
>
>     And it does not show any new submissions, it is still the one from august 20.
>
>       
>
>         As you discovered, the ontologies.txt file is maintained by another group. They are in the process of switching away from ontologies.txt to another file but it won't hurt to exist there as well. Ideally you would get yourselves installed in both files.
>
>     ontologies.txt is read only now so no chances to update our information there. I am in contact with them to update the github based information.
>
>         Let me know if this doesn't show up by Monday.
>
>           
>
>         Ray
>
>           
>
>         -----Original Message-----
>
>         From: Nicolas Rodriguez [mailto:rodriguezn at babraham.ac.uk]
>
>         Sent: Friday, August 28, 2015 3:53 AM
>
>         To: Ray Fergerson;support at bioontology.org  <mailto:support at bioontology.org>; Nicolas Rodriguez
>
>         Subject: Re: [bioontology-support] [BioPortal] Feedback from Nicolas
>
>         Le Novere
>
>           
>
>         On 28/08/15 10:40, Nicolas Rodriguez wrote:
>
>             On 28/08/15 09:56, Nicolas Rodriguez wrote:
>
>                 Hi Ray,
>
>                   
>
>                 On 26/08/15 23:03, Ray Fergerson wrote:
>
>                     Nicolas,
>
>                       
>
>                     OK, I think that I know what went wrong. We have been updating all
>
>                     ontology sources to use the download link from the latest OBO
>
>                     Foundry "ontologies.txt" files. This file is available at:
>
>                       
>
>                     http://obo-registry.googlecode.com/svn/trunk/metadata/ontologies.t
>
>                     x
>
>                     t
>
>                       
>
>                     As you can see, this file indicates that the latest version of
>
>                     MAMO is downloadable at:
>
>                       
>
>                     http://sourceforge.net/p/mamo-ontology/code/13/tree/trunk/mamo-xml.
>
>                     o
>
>                     wl
>
>                       
>
>                     In most cases for OBO ontologies, updating to the ontologies.txt
>
>                     download link is the right thing to do and gets the correct file.
>
>                     Perhaps for you this link is out of date for some reason.
>
>                 Here is the correct link that should be used to always get the
>
>                 latest release of mamo:
>
>                   
>
>                 http://sourceforge.net/p/mamo-ontology/code/tags/latest/mamo-xml.ow
>
>                 l
>
>                   
>
>         Sorry I made a mistake, the direct link to the file is:
>
>           
>
>         https://svn.code.sf.net/p/mamo-ontology/code/tags/latest/mamo-xml.owl
>
>           
>
>                 Could you replace the current version with this one ?
>
>                   
>
>                 Is it enough to write it here to have the link updated in
>
>                 http://obo-registry.googlecode.com/svn/trunk/metadata/ontologies.tx
>
>                 t or do I have to write to an other email address.
>
>                   
>
>             I had a look at the OBO Foundry web site and sent a link to the
>
>             obo-discuss mailing list to ask to have an update of the link.
>
>               
>
>             I guess very soon you will have to use one of the registry file in
>
>             https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/regis
>
>             t r y as the google code project is read only and cannot be updated
>
>             any more.
>
>               
>
>               
>
>                 Thanks,
>
>                 Nico
>
>                   
>
>                     Best would be if you could provide us by email a URL where we
>
>                     could always get the latest version of MAMO. It would be wise to
>
>                     have the ontologies.txt file updated as well. This would require
>
>                     contacting the OBO team that manages this file. This later would
>
>                     prevent any additional confusion.
>
>                       
>
>                     If there is no URL for the latest version then we can shift you
>
>                     over to "manual" update and you can upload the file whenever you would like.
>
>                       
>
>                     Ray
>
>                       
>
>                     -----Original Message-----
>
>                       
>
>                     From: Nicolas Le Novere [mailto:n.lenovere at gmail.com]
>
>                     Sent: Wednesday, August 26, 2015 2:48 PM
>
>                     To: Ray Fergerson;support at bioontology.org  <mailto:support at bioontology.org>; Nicolas Rodriguez
>
>                     Subject: Re: [bioontology-support] [BioPortal] Feedback from
>
>                     Nicolas Le Novere
>
>                       
>
>                     Dear Ray,
>
>                       
>
>                     It seems the OWL file has been chopped severely. You can see it by
>
>                     comparing the current one with the previous version. I am also a
>
>                     bit puzzled by the dates. Two submissions are dated "2015-04-18".
>
>                     But their upload dates are different. While one is indeed from
>
>                     04/18/2015, the other is from 08/20/2015.
>
>                       
>
>                     I attach the latest version that should have been the one uploaded
>
>                     on 08/20/2015.
>
>                     (Nico, this is the one from the directory "tags/latest/mamo-xml.owl"
>
>                     Is this correct?)
>
>                       
>
>                     Best regards
>
>                       
>
>                     On 26/08/15 22:37, Ray Fergerson wrote:
>
>                         After a small amount of poking around, I cannot see any problem.
>
>                         Can you point me to what is missing? Are there classes in the OWL
>
>                         file that are not being displayed? If so, can you name a couple?
>
>                           
>
>                         Thanks.
>
>                           
>
>                         Ray
>
>                           
>
>                         *From:*bioontology-support
>
>                         [mailto:bioontology-support-bounces at lists.stanford.edu] *On
>
>                         Behalf Of*support at bioontology.org  <mailto:*support at bioontology.org>
>
>                         *Sent:* Wednesday, August 26, 2015 2:28 AM
>
>                         *To:*support at bioontology.org  <mailto:support at bioontology.org>;n.lenovere at gmail.com  <mailto:n.lenovere at gmail.com>
>
>                         *Subject:* [bioontology-support] [BioPortal] Feedback from
>
>                         Nicolas Le Novere
>
>                           
>
>                         Name: Nicolas Le Novere
>
>                           
>
>                         Email:n.lenovere at gmail.com  <mailto:n.lenovere at gmail.com>  <mailto:n.lenovere at gmail.com>  <mailto:n.lenovere at gmail.com>
>
>                           
>
>                         Location:
>
>                         http://bioportal.bioontology.org/ontologies/MAMO?p=classes
>
>                           
>
>                           
>
>                         *Feedback:*
>
>                           
>
>                         There is a problem with the parsing of the Mathematical Modelling
>
>                         Ontology (MAMO)
>
>                         http://bioportal.bioontology.org/ontologies/MAMO?p=classes
>
>                           
>
>                         Only some branches appear.
>
>                           
>

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