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Invalid character in bao_complete.owl #47

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stevevestal opened this issue Nov 22, 2020 · 4 comments
Closed

Invalid character in bao_complete.owl #47

stevevestal opened this issue Nov 22, 2020 · 4 comments

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@stevevestal
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When I fetched subject ontology from http://www.bioassayontology.org/bao/bao_complete.owl and tried loading it using Apache Jena, I got a RiotException that the file had an invalid format:

[line: 248, col: 10] {E202} Expecting XML start or end element(s). String data "\" not allowed. Maybe a striping error.

At line 248, there is a stray "\" in the file. Deleting this allowed the file to load.

@whinis
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whinis commented Nov 22, 2020

Thank you for this, will be updated soon

@stevevestal
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I also get a RiotException for bao_vocabulary_role.owl and bao_clo_import.owl that characters are not in UTF-8 unicode format. Loading a local copy and forcing a save in the Eclipse XML editor to write in standard UTF-8 will work for bao_vocabulary_role but not for bao_clo_import. Apache Jena still finds a number of characters it does not like in that one.

@whinis
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whinis commented Nov 26, 2020

Thank you, I typically load this in Protege and never seen any reports of issues. I will load in Jena and see what it tells me.

@whinis
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whinis commented Dec 15, 2020

I have uploaded a new version and it seems to validate with Jena that I downloaded as much as it can (did not test imports as I don't entirely control the ontologies). Can you confirm ?

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