[Obo-anatomy] Uberon parsing failing
Ray Fergerson
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}
Chris Mungall
Will be fixed in the next release. Btw, I would advise loading from the
OWL, as specified in the obo library registry
Cheers
Chris
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Ray Fergerson
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