Re: [Obo-anatomy] Uberon parsing failing

[Ray F. <ray...@st...>]

Great. Thanks.

Want to make sure that I have the right download address. Currently we
download from:

http://purl.obolibrary.org/obo/uberon.obo

What we should use instead is:

http://purl.obolibrary.org/obo/uberon/ext.owl

Correct?

Ray

-----Original Message-----
From: Chris Mungall [mailto:cjm...@lb...] 
Sent: Friday, April 4, 2014 3:32 PM
To: Ray Fergerson
Cc: obo...@li...
Subject: Re: Uberon parsing failing

Hi Ray,

Will be fixed in the next release. Btw, I would advise loading from the
OWL, as specified in the obo library registry

Cheers
Chris

On 4 Apr 2014, at 14:29, Ray Fergerson wrote:

> Chris and OBO anatomy group,
>
>
>
> The latest versions of Uberon are not parsing. The error message is 
> given below.
>
>
>
> Ray
>
>
>
> The official OBO parser fails with the following message:
>
>
>
> {code}
>
> Parser: OBOFormatOWLAPIParser
>
> LINENO: 154674 - expected newline or end of line but found: bones\\"
> because they support the mother's pouch ('marsupium' is Latin for
> 'pouch'), but their presence on other groups of mammals indicates that
> this was not their original function, which some researchers think was 
> to
> assist locomotion by supporting some of the muscles that flex the 
> thigh.
> The epipubic bones were first described in 1698 but their functions 
> have
> remained unresolved. It has been suggested that they form part of a
> kinetic linkage stretching from the femur on one side to the ribs on 
> the
> opposite side. This linkage is formed by a series of muscles: each
> epipubic bone is connected to the femur by the pectineus muscle, and 
> to
> the ribs and vertebrae by the pyramidalis, rectus abdominis, and 
> external
> and internal obliques. According to this hypothesis, the epipubic 
> bones
> act as levers to stiffen the trunk during
> locomotion[Wikipedia:Epipubic_bone]." xsd:string
>
>
>
>
>
> LINE: property_value: external_definition "Epipubic bones are a pair 
> of
> bones projecting forward from the pelvic bones of modern marsupials 
> and of
> some fossil mammals: multituberculates, monotremes, and even basal
> eutherians (the ancestors of placental mammals). In modern marsupials 
> the
> epipubic bones are often called \\"marsupial bones\\" because they 
> support
> the mother's pouch ('marsupium' is Latin for 'pouch'), but their 
> presence
> on other groups of mammals indicates that this was not their original
> function, which some researchers think was to assist locomotion by
> supporting some of the muscles that flex the thigh. The epipubic bones
> were first described in 1698 but their functions have remained 
> unresolved.
> It has been suggested that they form part of a kinetic linkage 
> stretching
> from the femur on one side to the ribs on the opposite side. This 
> linkage
> is formed by a series of muscles: each epipubic bone is connected to 
> the
> femur by the pectineus muscle, and to the ribs and vertebrae by the
> pyramidalis, rectus abdominis, and external and internal obliques.
> According to this hypothesis, the epipubic bones act as levers to 
> stiffen
> the trunk during locomotion[Wikipedia:Epipubic_bone]." xsd:string
>
> {code}