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

Nicolas Rodriguez rodriguezn at babraham.ac.uk
Fri Aug 28 03:53:03 PDT 2015


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.txt
>>>
>>> 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.owl
>>>
>>> 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 Perhaps for you this link is out of date for some reason.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.owl
>>

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.txt
>> 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/registry
> 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; 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
>>>> *Sent:* Wednesday, August 26, 2015 2:28 AM
>>>> *To:* support at bioontology.org; 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>
>>>>
>>>> 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.
>>>>
>>>
>>> --
>>> Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge,
>>> CB22 3AT
>>> Tel: +441223496433, Mob:+447833147074, twitter:@lenovere,
>>> Skype:n.lenovere n.lenovere at gmail.com,
>>> http://orcid.org/0000-0002-6309-7327
>>> http://lenoverelab.org/, http://lenoverelab.org/perso/lenov/
>>
>

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