[Obo-format] ontology tag duplicated in 1.4 documentation
Hilmar Lapp
occurrences are under "Optional tags":
1st occurrence: "The ID space of this ontology. This should correspond
to to the ID prefix of the terms that belong to that ontology,
translated to lowercase. For GO, the value of this field will be "go".
For the cell ontology (i.e. the ontology that contains CL:0000001),
the value will be "cl". If the obo document contains some alternative
cut or extension of the ontology (for example, a GO slim, or an
ontology merged with another), then the ontology should be of form "X/
Y", where X is the basic ontology name, and Y identifies the cut. For
example go/gosubset_prok. A URI is also permitted in here. In the
translation to OWL, the usual default prefix rules will apply, with
the ".owl" suffix. E.g. "go" will be treated as "http://purl.obo-library.org/obo/go.owl
"
2nd occurrence: "The URI that uniquely identifies this ontology. If a
full URI is not specified, this will be prefixed with http://purl.obolibrary.org/obo/
"
"ID space of the ontology" and "URI that uniquely identifies this
ontology" don't strike me as the same things, so these two are in
conflict.
Which one is correct, and could this be fixed, please?
-hilmar
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Chris Mungall
I removed the second instance from the guide.
Hilmar, I'd recommend you use the formal specification rather than the guide
Specification:
http://purl.obolibrary.org/obo/oboformat/spec.html
Guide:
http://www.geneontology.org/GO.format.obo-1_4.shtml
All documents and reference parser and translator implementation collected here:
http://purl.obolibrary.org/obo/oboformat
The guide is something of a historic artefact, we produced it for obof1.0 and 1.2, and it was thus easy to produce it for 1.4. It's intended as an (informative) companion to the formal (normative) spec. I have attempted to clarify this in the new introductory paragraph for the guide.
The guide will gradually become obsolete as we gather better user documentation to support the specification.
Hilmar Lapp
On Nov 21, 2011, at 5:50 PM, Chris Mungall wrote:
> I'd recommend you use the formal specification rather than the guide
>
> Specification:
> http://purl.obolibrary.org/obo/oboformat/spec.html
>
> Guide:
> http://www.geneontology.org/GO.format.obo-1_4.shtml
>
FYI, I found the latter by searching Google for "obo format 1.4". It's
the top hit. If you don't want people to use it, I'd replace it with a
redirect, or put a big red fat warning at the top.
Chris Mungall
On Nov 21, 2011, at 2:57 PM, Hilmar Lapp wrote:
>
> On Nov 21, 2011, at 5:50 PM, Chris Mungall wrote:
>
>> I'd recommend you use the formal specification rather than the guide
>>
>> Specification:
>> http://purl.obolibrary.org/obo/oboformat/spec.html
>>
>> Guide:
>> http://www.geneontology.org/GO.format.obo-1_4.shtml
>>
>
> FYI, I found the latter by searching Google for "obo format 1.4". It's the top hit. If you don't want people to use it, I'd replace it with a redirect, or put a big red fat warning at the top.
At this time we still support the guide, so we don't want to redirect. We'll try and draw attention to the introductory paragraph. It would be good to increase the prominence of the spec over the guide in searches though