From: Richard C. <rc...@eb...> - 2006-11-21 11:34:52
|
Hello all I just want to raise a discussion point about two ontologies currently = in the OBO foundry: attribute_and_value.obo and quality.obo. I had a = cursory look at the files and I'm wondering if what I'm seeing is what is = actually intended and if so, does it break ontology best practices? The questions I have are: - can one term be in more than one namespace? (for example, PATO:0000001 = is in namespace attribute and also in quality) What's the significance of = this? If you look at GO, which has 3 namespaces, I believe that one term is = only assigned to one namespace (though I'm not 100% sure about this).=20 - if a term is defined with a relationship in one file, should it not = have the same relationships in the other? See PATO:0000004 in the text below. Though I can see the arguments that term X might logically and = semantically have different relations in namesapce Y vs namespace Z, in practice, it = just makes everything confusing and hard to handle on a day-to-day basis as = most applications that use the ontology will not keep track of the namespace = (or to be honest, even care about it) - should one term id should have a constant name, or can it be variable according to namespace? Case and point, look at PATO:0000002 in the file exerpts below. Is this just a simple oversight, or is this voluntary? If = so, doesn't that open a big old can of worms for the reasons I've mentioned above re: namespace usage in real life? ------------------------ /obo/ontology/phenotype/attribute_and_value.obo [Term] id: PATO:0000000 name: pato namespace: attribute [Term] id: PATO:0000001 name: attribute namespace: attribute is_a: PATO:0000000 ! pato [Term] id: PATO:0000002 name: value namespace: attribute is_a: PATO:0000456 ! abstract [Term] id: PATO:0000003 name: assay namespace: attribute is_obsolete: true [Term] id: PATO:0000004 name: mobility namespace: attribute def: "The quality of moving freely." [XX:<new dbxref>] is_a: PATO:0000001 ! attribute ------------------------ /obo/ontology/phenotype/quality.obo format-version: 1.0 date: 19:11:2006 13:54 saved-by: George Gkoutos auto-generated-by: OBO-Edit 1.002 default-namespace: quality [Term] id: PATO:0000000 name: pato is_obsolete: true [Term] id: PATO:0000001 name: quality def: "A dependent entity that\ninheres in a bearer by virtue of how the bearer is related to other entities." [PATO :GVG] [Term] id: PATO:0000002 name: value is_obsolete: true [Term] id: PATO:0000003 name: assay is_obsolete: true [Term] id: PATO:0000004 name: mobility def: "A quality of moving freely." [PATO :GVG] is_a: PATO:0001237 ! monadic quality of continuant Cheers, Rc -- Richard Cote Software Engineer - PRIDE Project Team (Sequence Database Group) =20 European Bioinformatics Institute =20 Wellcome Trust Genome Campus RC...@eb... =20 Hinxton =20 Cambridge CB10 1SD Phone: (+44) 1223 492610 =20 United Kingdom Fax : (+44) 1223 494468=20 |
From: Richard C. <rc...@eb...> - 2006-11-21 11:43:49
|
I made a mistake in my previous email. > - should one term id should have a constant name, or can it be variable > according to namespace? Case and point, look at PATO:0000002 in the file > exerpts below. Is this just a simple oversight, or is this voluntary? If so, > doesn't that open a big old can of worms for the reasons I've mentioned > above re: namespace usage in real life? PATO:0000001 has a different name in both files, not PATO:0000002. > ------------------------ > /obo/ontology/phenotype/attribute_and_value.obo > > [Term] > id: PATO:0000001 > name: attribute > namespace: attribute > is_a: PATO:0000000 ! pato > > ------------------------ /obo/ontology/phenotype/quality.obo > > [Term] > id: PATO:0000001 > name: quality > def: "A dependent entity that\ninheres in a bearer by virtue > of how the bearer is related to other entities." [PATO :GVG] The question is still valid though :) Cheers, Rc -- Richard Cote Software Engineer - PRIDE Project Team (Sequence Database Group) European Bioinformatics Institute Wellcome Trust Genome Campus RC...@eb... Hinxton Cambridge CB10 1SD Phone: (+44) 1223 492610 United Kingdom Fax : (+44) 1223 494468 |
From: John Day-R. <joh...@ay...> - 2006-11-21 18:35:57
|
I can answer this question from an OBO format point of view - I can't speak to an ontology standards point of view, though... Richard Cote wrote: > - can one term be in more than one namespace? (for example, PATO:0000001 is > in namespace attribute and also in quality) What's the significance of this? > If you look at GO, which has 3 namespaces, I believe that one term is only > assigned to one namespace (though I'm not 100% sure about this). > No. OBO format requires that term belong to a single namespace. Note that OBO namespaces are not like XML namespaces. An XML namespace impacts the meaning of term ids by create a distinct id space. In OBO format, the idspace tag is used for this purpose (and few OBO parsers correctly implement this tag at the moment). In OBO, the namespace is really used to identify which ontology a term belongs to. Since terms from the same ontology may be stored in separate files, or terms from multiple ontologies stored in one file, this tag is used as a means of grouping terms into ontologies independent of how the terms are stored. > - if a term is defined with a relationship in one file, should it not have > the same relationships in the other? See PATO:0000004 in the text below. > Though I can see the arguments that term X might logically and semantically > have different relations in namesapce Y vs namespace Z, in practice, it just > makes everything confusing and hard to handle on a day-to-day basis as most > applications that use the ontology will not keep track of the namespace (or > to be honest, even care about it) > It's okay for one OBO file to define a term, and for another file to specify additional relationships for that term, but a special syntax is used. In the second file, only the id and the additional relationships are specified. Note that in this model one file doesn't REspecify the term relationships; it specified additional relationships. This means of providing additional term relationships exists so that relationships that are not of general interest can be stored in a separate file from the main ontology. For example, if someone created a bunch of cross-links between the GO and the Fruitfly Anatomy Ontology, those links could be stored in a third file to avoid irritating users of the Fly Anatomy and GO who aren't interested in those special-purpose links. It is an error to load two OBO files that define a unary property (like name, definition, comment, etc) in different ways. The file snippet you've attached would generate an error if the two ontologies are loaded simultaneously, because the unary name property is defined for some terms in both files. > - should one term id should have a constant name, or can it be variable > according to namespace? Case and point, look at PATO:0000002 in the file > exerpts below. Is this just a simple oversight, or is this voluntary? If so, > doesn't that open a big old can of worms for the reasons I've mentioned > above re: namespace usage in real life? > See above. -John |
From: Chris M. <cj...@fr...> - 2006-11-21 21:29:39
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On Nov 21, 2006, at 3:30 AM, Richard Cote wrote: > Hello all > > I just want to raise a discussion point about two ontologies > currently in > the OBO foundry: attribute_and_value.obo and quality.obo. I had a > cursory > look at the files and I'm wondering if what I'm seeing is what is > actually > intended and if so, does it break ontology best practices? Hi Richard I think the problems stems from you using attribute_and_value.obo, which is deprecated - you'll see the obo metadata and front page refers to quality.obo > The questions I have are: > > - can one term be in more than one namespace? (for example, PATO: > 0000001 is > in namespace attribute and also in quality) What's the significance > of this? > If you look at GO, which has 3 namespaces, I believe that one term > is only > assigned to one namespace (though I'm not 100% sure about this). Yes, each term belongs to a single namespace (ontology) in GO > - if a term is defined with a relationship in one file, should it > not have > the same relationships in the other? See PATO:0000004 in the text > below. > Though I can see the arguments that term X might logically and > semantically > have different relations in namesapce Y vs namespace Z, in > practice, it just > makes everything confusing and hard to handle on a day-to-day basis > as most > applications that use the ontology will not keep track of the > namespace (or > to be honest, even care about it) Again, I think you have a copy of an old file In actual fact, an obo file can augment another obo file with additional relationships (but it cannot retract them). This goes for owl too. However, it is good practice for an ontology maintainer to make available the entire ontology in a single file. Good practice has been followed in this case, it's just you have an old copy of a file > - should one term id should have a constant name, or can it be > variable > according to namespace? Case and point, look at PATO:0000002 in the > file > exerpts below. Is this just a simple oversight, or is this > voluntary? If so, > doesn't that open a big old can of worms for the reasons I've > mentioned > above re: namespace usage in real life? [snip] again, ditch attribute_and_value.obo and you should have no problems. Note the cvs directory may have old files littered around (we'll try and get round to removing them). But this shouldn't matter if you use the existing metadata file or the main web page. The existing metadata file does have limitations - we haven't indicated that attribute_and_value has been superseded by quality.obo. In a few months we'll have a new system in place that should make some of this clearer. Cheers Chris > Cheers, > Rc > > -- > Richard Cote > Software Engineer - PRIDE Project Team (Sequence Database Group) > > European Bioinformatics Institute > Wellcome Trust Genome Campus RC...@eb... > Hinxton > Cambridge CB10 1SD Phone: (+44) 1223 492610 > United Kingdom Fax : (+44) 1223 494468 > > > ---------------------------------------------------------------------- > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to > share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php? > page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Obo-discuss mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-discuss > |
From: Georgios V. G. (Genetics) <gg...@ge...> - 2006-11-21 11:42:13
|
Hi Richard, the attribute_and_value.obo is the old format of PATO now superseded by the quality.obo which is the current version. The link for PATO from the OBO site is pointing to the quality.obo. Best wishes, George ------------------------------------------------------ On Tue, 21 Nov 2006, Richard Cote wrote: > Hello all > > I just want to raise a discussion point about two ontologies currently in > the OBO foundry: attribute_and_value.obo and quality.obo. I had a cursory > look at the files and I'm wondering if what I'm seeing is what is actually > intended and if so, does it break ontology best practices? > > The questions I have are: > > - can one term be in more than one namespace? (for example, PATO:0000001 is > in namespace attribute and also in quality) What's the significance of this? > If you look at GO, which has 3 namespaces, I believe that one term is only > assigned to one namespace (though I'm not 100% sure about this). > > - if a term is defined with a relationship in one file, should it not have > the same relationships in the other? See PATO:0000004 in the text below. > Though I can see the arguments that term X might logically and semantically > have different relations in namesapce Y vs namespace Z, in practice, it just > makes everything confusing and hard to handle on a day-to-day basis as most > applications that use the ontology will not keep track of the namespace (or > to be honest, even care about it) > > - should one term id should have a constant name, or can it be variable > according to namespace? Case and point, look at PATO:0000002 in the file > exerpts below. Is this just a simple oversight, or is this voluntary? If so, > doesn't that open a big old can of worms for the reasons I've mentioned > above re: namespace usage in real life? > > ------------------------ /obo/ontology/phenotype/attribute_and_value.obo > > [Term] > id: PATO:0000000 > name: pato > namespace: attribute > > [Term] > id: PATO:0000001 > name: attribute > namespace: attribute > is_a: PATO:0000000 ! pato > > [Term] > id: PATO:0000002 > name: value > namespace: attribute > is_a: PATO:0000456 ! abstract > > [Term] > id: PATO:0000003 > name: assay > namespace: attribute > is_obsolete: true > > [Term] > id: PATO:0000004 > name: mobility > namespace: attribute > def: "The quality of moving freely." [XX:<new dbxref>] > is_a: PATO:0000001 ! attribute > > ------------------------ /obo/ontology/phenotype/quality.obo > > format-version: 1.0 > date: 19:11:2006 13:54 > saved-by: George Gkoutos > auto-generated-by: OBO-Edit 1.002 > default-namespace: quality > > [Term] > id: PATO:0000000 > name: pato > is_obsolete: true > > [Term] > id: PATO:0000001 > name: quality > def: "A dependent entity that\ninheres in a bearer by virtue of how the > bearer is related to other entities." [PATO :GVG] > > [Term] > id: PATO:0000002 > name: value > is_obsolete: true > > [Term] > id: PATO:0000003 > name: assay > is_obsolete: true > > [Term] > id: PATO:0000004 > name: mobility > def: "A quality of moving freely." [PATO :GVG] > is_a: PATO:0001237 ! monadic quality of continuant > > Cheers, > Rc > > -- > Richard Cote > Software Engineer - PRIDE Project Team (Sequence Database Group) > > European Bioinformatics Institute > Wellcome Trust Genome Campus RC...@eb... > Hinxton > Cambridge CB10 1SD Phone: (+44) 1223 492610 > United Kingdom Fax : (+44) 1223 494468 > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Obo-discuss mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-discuss > |