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

Ray Fergerson rayferg at
Wed Aug 26 15:03:41 PDT 2015


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:

As you can see, this file indicates that the latest version of MAMO is downloadable at:

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 Perhaps for you this link is out of date for some reason.

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.


-----Original Message-----

From: Nicolas Le Novere [mailto:n.lenovere at] 
Sent: Wednesday, August 26, 2015 2:48 PM
To: Ray Fergerson; support at; 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] *On Behalf Of 
> *support at
> *Sent:* Wednesday, August 26, 2015 2:28 AM
> *To:* support at; n.lenovere at
> *Subject:* [bioontology-support] [BioPortal] Feedback from Nicolas Le 
> Novere
> Name: Nicolas Le Novere
> Email: n.lenovere at <mailto:n.lenovere at>
> Location:
> *Feedback:*
> There is a problem with the parsing of the Mathematical Modelling 
> Ontology (MAMO) 
> 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,,

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