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From: Hilmar L. <hl...@ne...> - 2011-11-21 19:55:20
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The ontology tag is duplicated in the 1.4 format documentation, both 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 -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Chris M. <cjm...@lb...> - 2011-11-21 22:50:26
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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. On Nov 21, 2011, at 11:54 AM, Hilmar Lapp wrote: > The ontology tag is duplicated in the 1.4 format documentation, both > 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 > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure > contains a definitive record of customers, application performance, > security threats, fraudulent activity, and more. Splunk takes this > data and makes sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > Obo-format mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-format |
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From: Hilmar L. <hl...@ne...> - 2011-11-21 22:57:17
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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. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Chris M. <cjm...@lb...> - 2011-11-21 23:04:17
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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 > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > |
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