Re: [Chebi-ontology] Syntax errors in chebi.obo

[Chris M. <cjm...@lb...>]

Thanks Janna!

On Feb 2, 2011, at 9:25 AM, Janna Hastings wrote:

> Hi Chris,
> 
> now fixed and will go live in the next release (which happens to be next
> week)
> 
> Thanks, Janna
> 
> 
>> -----Original Message-----
>> From: jan...@gm... [mailto:jan...@gm...] On
>> Behalf Of Janna Hastings
>> Sent: 28 January 2011 09:23
>> To: cjm...@lb...
>> Cc: che...@li...; Chebi Developers;
>> pet...@ch...
>> Subject: Re: [Chebi-ontology] Syntax errors in chebi.obo
>> 
>> Hi Chris,
>> 
>> OK -- thanks!  We will fix these asap and let you know.
>> 
>> Cheers, Janna
>> 
>> 
>> 
>>> -----Original Message-----
>>> From: Chris Mungall [mailto:cjm...@lb...]
>>> Sent: 28 January 2011 00:59
>>> To: chebi-ontology Ontology
>>> Cc: Peter Robinson
>>> Subject: [Chebi-ontology] Syntax errors in chebi.obo
>>> 
>>> Hi Chebi folks
>>> 
>>> There's a problem with the existing obo file. double quotes appearing
>>> inside quoted text should be escaped.
>>> 
>>> You have this at the moment:
>>> 
>>> [Term]
>>> id: CHEBI:59040
>>> name: lymecycline
>>> def: "Lymecycline is a tetracycline-based broad-spectrum antibiotic.
>> It
>>> is approximately 5000 times more soluble than tetracycline base and
>> is
>>> unique amongst tetracyclines in that it is absorbed by the "active
>>> transport" process across the intestinal wall." []
>>> 
>>> The def line should be changed to:
>>> 
>>> def: "Lymecycline is a tetracycline-based broad-spectrum antibiotic.
>> It
>>> is approximately 5000 times more soluble than tetracycline base and
>> is
>>> unique amongst tetracyclines in that it is absorbed by the \"active
>>> transport\" process across the intestinal wall." []
>>> 
>>> I recommend validating the ontology prior to release. You can use
>> this:
>>> 
>>> 	http://code.google.com/p/oboformat/
>>> 
>>> At the moment you have to check this out from svn, but we can make a
>>> release if it's easier for you.
>>> 
>>> After checking out, run this:
>>> 
>>> 	bin/obolib-obo2owl file:chebi.obo -o file://`pwd`/chebi.owl
>>> 
>>> Note that we'll be switching to using this converter for generating
>> the
>>> official obo foundry owl, and it's much stricter with the old one
>> with
>>> syntax errors.
>>> 
>>> The parser is still quite lenient with some of the other syntax
>> errors
>>> in the chebi obo file, such as the incorrectly formatted xrefs. It
>>> would be good to fix these though.
>>> 
>>> Also, one more request. Can you add this line to the header of the
>>> ontology
>>> 
>>> ontology: chebi
>>> 
>>> (all lowercase)
>>> 
>>> This ensures the OntologyIRI for the generated OWL is correct.
>>> 
>>> Thanks,
>>> Chris
>>> 
>>> 
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>