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

Ray Fergerson rayferg at stanford.edu
Tue Sep 1 13:48:36 PDT 2015


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.

Ray

-----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; 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; 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.tx
>>>> 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.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/regist
>> 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; 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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