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From: Christian K. <Chr...@un...> - 2011-01-17 11:26:37
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On 13.01.2011 14:23, Nick Juty wrote: > I thought it would be worth opening up the discussion about BioModels.net qualifiers, in order to start moving forward more earnestly. > The premise is that we wish to have qualifiers that follow the "SUBJECT has PREDICATE whose value is OBJECT" statement, and thereby need to convert or > add additional qualifiers as nouns, rather than the existing situation where they are verbs. > What is the reason for this wish? I'm totally fine with verbs as qualifiers. In my view there are predicates and facts should be: "SUBJECT PREDICATE OBJECT" This is the RDF way and I always thought that the qualifiers are to be used in this sense. Christian. -- Christian Knuepfer Friedrich-Schiller-Universitaet Jena Institut fuer Informatik Ernst-Abbe-Platz 1-4 D-07743 Jena, Germany Office: Ernst-Abbe-Platz 2, Room 3237 Phone: Intl.+49/3641/9-46353 Fax: Intl.+49/3641/9-46302 e-mail: mailto:tr...@in... WWW: http://www.minet.uni-jena.de/~tral PGP Key-ID: 0xC3329342 PGP Public Key: http://www.minet.uni-jena.de/~tral/data/christian_knuepfer_pub.asc Fingerprint: 5656 7F57 8E58 FC7B AC58 6714 3DA4 3181 C332 9342 -- <javascript:void(0);> |
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From: Neil S. <nei...@ma...> - 2011-01-15 09:36:55
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Hi all, While we're at it, what are people's thoughts on adding new qualifiers? For example, I and others would like concepts like formula, charge, SMILES, etc. and apply them to metabolites. "Modification" is another that occasionally arises for proteins. Thoughts? Cheers, Neil. On 14 Jan 2011, at 23:00, Nicolas Le novère <le...@eb...> wrote: > On 14/01/11 14:25, Neil Swainston wrote: > >> I think the goal is to recommend that the core annotations and "new" >> Annot annotations are used mutually exclusively. So, the core will use >> the old qualifiers and the Annot the new ones. In both cases, the >> qualifiers will be perennial. > > Neil is correct. There won't be two schemes but only one scheme. > "bqbiol:hasPart" and "bqbiol:part" are not two qualifiers. They are two > forms of the same qualifier. The definition on biomodels.net will just be > amended as follow: > > hasPart, part > > The biological entity represented by the model component includes the > subject of the referenced resource, either physically or logically. This > relation might be used to link a complex to the description of its components. > > >> I'm looking at the Annot specification now (sorry for the delay...) and >> in this I think that it would make sense to include a mapping from the >> core qualifiers to the new Annot ones (essentially, the finalised list >> that was produced by Nick J recently). >> >> Cheers, >> >> Neil. >> >> Neil Swainston Experimental Officer >> >> Manchester Centre for Integrative Systems Biology Manchester >> Interdisciplinary Biocentre University of Manchester Manchester M1 7DN >> United Kingdom >> >> On 14 Jan 2011, at 00:26, Mike Hucka wrote: >> >>> Maybe I missed it in the discussions so far, but is some versioning >>> going to be added, so that when reading a given model, a consumer can >>> figure out which qualifier scheme is being used? Or do you think it >>> won't be required, because the new terms will map one-to-one to the >>> old ones, and all a consumer would need to know is both terms for a >>> given relationship? >>> >>> MH >>> >>> ------------------------------------------------------------------------------ >>> >>> > Protect Your Site and Customers from Malware Attacks >>> Learn about various malware tactics and how to avoid them. Understand >>> malware threats, the impact they can have on your business, and how >>> you can protect your company and customers by using code signing. >>> http://p.sf.net/sfu/oracle-sfdevnl >>> _______________________________________________ Sbml-annot mailing >>> list Sbm...@li... >>> https://lists.sourceforge.net/lists/listinfo/sbml-annot >> >> ------------------------------------------------------------------------------ >> >> > Protect Your Site and Customers from Malware Attacks >> Learn about various malware tactics and how to avoid them. Understand >> malware threats, the impact they can have on your business, and how you >> can protect your company and customers by using code signing. >> http://p.sf.net/sfu/oracle-sfdevnl >> _______________________________________________ Sbml-annot mailing list >> Sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbml-annot > > > -- > Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC, > Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468, > Skype:n.lenovere, AIM:nlenovere, twitter:@lenovere > http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ > > > ------------------------------------------------------------------------------ > Protect Your Site and Customers from Malware Attacks > Learn about various malware tactics and how to avoid them. Understand > malware threats, the impact they can have on your business, and how you > can protect your company and customers by using code signing. > http://p.sf.net/sfu/oracle-sfdevnl > _______________________________________________ > Sbml-annot mailing list > Sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-annot |
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From: Nicolas Le n. <le...@eb...> - 2011-01-14 23:00:36
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On 14/01/11 14:25, Neil Swainston wrote: > I think the goal is to recommend that the core annotations and "new" > Annot annotations are used mutually exclusively. So, the core will use > the old qualifiers and the Annot the new ones. In both cases, the > qualifiers will be perennial. Neil is correct. There won't be two schemes but only one scheme. "bqbiol:hasPart" and "bqbiol:part" are not two qualifiers. They are two forms of the same qualifier. The definition on biomodels.net will just be amended as follow: hasPart, part The biological entity represented by the model component includes the subject of the referenced resource, either physically or logically. This relation might be used to link a complex to the description of its components. > I'm looking at the Annot specification now (sorry for the delay...) and > in this I think that it would make sense to include a mapping from the > core qualifiers to the new Annot ones (essentially, the finalised list > that was produced by Nick J recently). > > Cheers, > > Neil. > > Neil Swainston Experimental Officer > > Manchester Centre for Integrative Systems Biology Manchester > Interdisciplinary Biocentre University of Manchester Manchester M1 7DN > United Kingdom > > On 14 Jan 2011, at 00:26, Mike Hucka wrote: > >> Maybe I missed it in the discussions so far, but is some versioning >> going to be added, so that when reading a given model, a consumer can >> figure out which qualifier scheme is being used? Or do you think it >> won't be required, because the new terms will map one-to-one to the >> old ones, and all a consumer would need to know is both terms for a >> given relationship? >> >> MH >> >> ------------------------------------------------------------------------------ >> >> Protect Your Site and Customers from Malware Attacks >> Learn about various malware tactics and how to avoid them. Understand >> malware threats, the impact they can have on your business, and how >> you can protect your company and customers by using code signing. >> http://p.sf.net/sfu/oracle-sfdevnl >> _______________________________________________ Sbml-annot mailing >> list Sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbml-annot > > ------------------------------------------------------------------------------ > > Protect Your Site and Customers from Malware Attacks > Learn about various malware tactics and how to avoid them. Understand > malware threats, the impact they can have on your business, and how you > can protect your company and customers by using code signing. > http://p.sf.net/sfu/oracle-sfdevnl > _______________________________________________ Sbml-annot mailing list > Sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-annot -- Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468, Skype:n.lenovere, AIM:nlenovere, twitter:@lenovere http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ |
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From: Dagmar W. <dag...@un...> - 2011-01-14 19:25:19
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Hello, maybe I understood it completely the wrong way, but I thought that sbml-annot suggests the use of bio/model qualifiers from biomodels.net (which is in principle a different project, not bound to SBML)... and biomodels.net changes the qualifier it offers? I am a bit reluctant about using two qualifier schemes... this sounds like it will result in a big mess. Already tricky to handle the "old" and "new" annotations. Let's not continue this on qualifier-level!? Dagmar On 01/14/2011 03:25 PM, Neil Swainston wrote: > Hi Mike, > > I think the goal is to recommend that the core annotations and "new" Annot annotations are used mutually exclusively. So, the core will use the old qualifiers and the Annot the new ones. In both cases, the qualifiers will be perennial. > > I'm looking at the Annot specification now (sorry for the delay...) and in this I think that it would make sense to include a mapping from the core qualifiers to the new Annot ones (essentially, the finalised list that was produced by Nick J recently). > > Cheers, > > Neil. > > Neil Swainston > Experimental Officer > > Manchester Centre for Integrative Systems Biology > Manchester Interdisciplinary Biocentre > University of Manchester > Manchester M1 7DN > United Kingdom > > On 14 Jan 2011, at 00:26, Mike Hucka wrote: > >> Maybe I missed it in the discussions so far, but is some versioning going to be added, so that when reading a given model, a consumer can figure out which qualifier scheme is being used? Or do you think it won't be required, because the new terms will map one-to-one to the old ones, and all a consumer would need to know is both terms for a given relationship? >> >> MH >> >> ------------------------------------------------------------------------------ >> Protect Your Site and Customers from Malware Attacks >> Learn about various malware tactics and how to avoid them. Understand >> malware threats, the impact they can have on your business, and how you >> can protect your company and customers by using code signing. >> http://p.sf.net/sfu/oracle-sfdevnl >> _______________________________________________ >> Sbml-annot mailing list >> Sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbml-annot > ------------------------------------------------------------------------------ > Protect Your Site and Customers from Malware Attacks > Learn about various malware tactics and how to avoid them. Understand > malware threats, the impact they can have on your business, and how you > can protect your company and customers by using code signing. > http://p.sf.net/sfu/oracle-sfdevnl > _______________________________________________ > Sbml-annot mailing list > Sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-annot |
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From: Neil S. <nei...@ma...> - 2011-01-14 14:25:10
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Hi Mike, I think the goal is to recommend that the core annotations and "new" Annot annotations are used mutually exclusively. So, the core will use the old qualifiers and the Annot the new ones. In both cases, the qualifiers will be perennial. I'm looking at the Annot specification now (sorry for the delay...) and in this I think that it would make sense to include a mapping from the core qualifiers to the new Annot ones (essentially, the finalised list that was produced by Nick J recently). Cheers, Neil. Neil Swainston Experimental Officer Manchester Centre for Integrative Systems Biology Manchester Interdisciplinary Biocentre University of Manchester Manchester M1 7DN United Kingdom On 14 Jan 2011, at 00:26, Mike Hucka wrote: > Maybe I missed it in the discussions so far, but is some versioning going to be added, so that when reading a given model, a consumer can figure out which qualifier scheme is being used? Or do you think it won't be required, because the new terms will map one-to-one to the old ones, and all a consumer would need to know is both terms for a given relationship? > > MH > > ------------------------------------------------------------------------------ > Protect Your Site and Customers from Malware Attacks > Learn about various malware tactics and how to avoid them. Understand > malware threats, the impact they can have on your business, and how you > can protect your company and customers by using code signing. > http://p.sf.net/sfu/oracle-sfdevnl > _______________________________________________ > Sbml-annot mailing list > Sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-annot |
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From: Mike H. <mh...@ca...> - 2011-01-14 00:27:07
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Maybe I missed it in the discussions so far, but is some versioning going to be added, so that when reading a given model, a consumer can figure out which qualifier scheme is being used? Or do you think it won't be required, because the new terms will map one-to-one to the old ones, and all a consumer would need to know is both terms for a given relationship? MH |
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From: Nicolas Le n. <le...@eb...> - 2011-01-13 13:52:57
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On 13/01/11 13:41, Ron Henkel wrote: > Hi, > > How strict is the requirement that a qualifier needs to be a noun (or > better exactly one noun)? > > For example the 'isEncodedBy' qualifier: if we used "encoder" here it > might be confused, for example, with the person who is the encoder. > > So I was thinking if it is possible to use something as "encodingDNA". > It might ease the finding of proper qualifier terms. Would this still be > a valid predicate since it is not exactly a noun? I think this kind of thing would in principle be fine even if not elegant. Note that in that case, it would not work because this is not restricted to DNA. In general I would ban all biological meaning from the qualifiers. But I believe you found another candidate: encoding > Cheers, > Ron > > On 13.01.2011 14:23, Nick Juty wrote: >> Dear annotation package people, >> >> I thought it would be worth opening up the discussion about BioModels.net qualifiers, in order to start moving forward more earnestly. >> The premise is that we wish to have qualifiers that follow the "SUBJECT has PREDICATE whose value is OBJECT" statement, and thereby need to convert or >> add additional qualifiers as nouns, rather than the existing situation where they are verbs. >> >> Below is a list of potential candidate equivalents to existing qualifiers found here: http://biomodels.net/qualifiers/ >> >> In some cases, the noun translation is quite apparent, and in others, not so much ;p I think if we iterate round a little, we can reach a moderate >> consensus. >> >> >> model-qualifiers >> ================ >> is => 'identity' >> isDescribedBy => 'description' >> >> >> biology-qualifier >> ================ >> hasPart => 'part' >> hasProperty => 'property' >> hasVersion => 'version', (relates class to instance; animal is a hypernym of cat) >> is => 'identity' >> isDescribedBy => 'description' >> isHomologTo => 'homolog(ue)' >> >> >> The next few are more difficult, and I have collected together candidate 'equivalents'. >> >> model-qualifiers: >> ================ >> 'isDerivedFrom' - needs to reflect modifications to an original model. >> Candidates: progenitor, antecedent, ancestor, basis, base, foundation, origin >> >> biology-qualifiers: >> ================ >> 'isEncodedBy' - e.g. protein is encoded by DNA >> Candidates: encoder >> >> 'encodes' - e.g. DNA encodes protein >> Candidates: encodement >> >> 'isPartOf' - e.g. subunit A is part of complex B >> Candidates: encompassment, assembly, partship, parthood, whole, meronym (relates part to whole; finger is a meronym of hand) >> >> 'isPropertyOf' - e.g. enzyme activity A is property of entity B >> Candidates: bearer, carrier, >> >> 'isVersionOf' - needs to convey the sense of belonging to some class >> Candidates: consociate, cohort, superclass, hyponym (relates instance to class to; cat is a hyponym of animal) >> >> 'occursIn' - may be sensible to split it into 'physical containment' and 'taxonomic instantiation' types. >> We could use 'encompassment' or 'containment' ('container'), for the physical type, and 'instantiation' for occurrence in a species. >> >> I'd appreciate your thoughts on these, and also on other qualifiers you guys have in mind. >> >> cheers, >> >> Nick >> >> >> >> ------------------------------------------------------------------------------ >> Protect Your Site and Customers from Malware Attacks >> Learn about various malware tactics and how to avoid them. Understand >> malware threats, the impact they can have on your business, and how you >> can protect your company and customers by using code signing. >> http://p.sf.net/sfu/oracle-sfdevnl >> _______________________________________________ >> Sbml-annot mailing list >> Sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbml-annot > -- Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468, Skype:n.lenovere, AIM:nlenovere, twitter:@lenovere http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ |
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From: Ron H. <ron...@un...> - 2011-01-13 13:41:29
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Hi, How strict is the requirement that a qualifier needs to be a noun (or better exactly one noun)? For example the 'isEncodedBy' qualifier: if we used "encoder" here it might be confused, for example, with the person who is the encoder. So I was thinking if it is possible to use something as "encodingDNA". It might ease the finding of proper qualifier terms. Would this still be a valid predicate since it is not exactly a noun? Cheers, Ron On 13.01.2011 14:23, Nick Juty wrote: > Dear annotation package people, > > I thought it would be worth opening up the discussion about BioModels.net qualifiers, in order to start moving forward more earnestly. > The premise is that we wish to have qualifiers that follow the "SUBJECT has PREDICATE whose value is OBJECT" statement, and thereby need to convert or > add additional qualifiers as nouns, rather than the existing situation where they are verbs. > > Below is a list of potential candidate equivalents to existing qualifiers found here: http://biomodels.net/qualifiers/ > > In some cases, the noun translation is quite apparent, and in others, not so much ;p I think if we iterate round a little, we can reach a moderate > consensus. > > > model-qualifiers > ================ > is => 'identity' > isDescribedBy => 'description' > > > biology-qualifier > ================ > hasPart => 'part' > hasProperty => 'property' > hasVersion => 'version', (relates class to instance; animal is a hypernym of cat) > is => 'identity' > isDescribedBy => 'description' > isHomologTo => 'homolog(ue)' > > > The next few are more difficult, and I have collected together candidate 'equivalents'. > > model-qualifiers: > ================ > 'isDerivedFrom' - needs to reflect modifications to an original model. > Candidates: progenitor, antecedent, ancestor, basis, base, foundation, origin > > biology-qualifiers: > ================ > 'isEncodedBy' - e.g. protein is encoded by DNA > Candidates: encoder > > 'encodes' - e.g. DNA encodes protein > Candidates: encodement > > 'isPartOf' - e.g. subunit A is part of complex B > Candidates: encompassment, assembly, partship, parthood, whole, meronym (relates part to whole; finger is a meronym of hand) > > 'isPropertyOf' - e.g. enzyme activity A is property of entity B > Candidates: bearer, carrier, > > 'isVersionOf' - needs to convey the sense of belonging to some class > Candidates: consociate, cohort, superclass, hyponym (relates instance to class to; cat is a hyponym of animal) > > 'occursIn' - may be sensible to split it into 'physical containment' and 'taxonomic instantiation' types. > We could use 'encompassment' or 'containment' ('container'), for the physical type, and 'instantiation' for occurrence in a species. > > I'd appreciate your thoughts on these, and also on other qualifiers you guys have in mind. > > cheers, > > Nick > > > > ------------------------------------------------------------------------------ > Protect Your Site and Customers from Malware Attacks > Learn about various malware tactics and how to avoid them. Understand > malware threats, the impact they can have on your business, and how you > can protect your company and customers by using code signing. > http://p.sf.net/sfu/oracle-sfdevnl > _______________________________________________ > Sbml-annot mailing list > Sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-annot -- Dipl.-Inf. Ron Henkel Research Training Group dIEM oSiRiS Lehrstuhl Datenbank- und Informationssysteme Institut für Informatik Universität Rostock 18051 Rostock Tel: +49 381 498 7440 E-Mail: ron...@un... Link: http://wwwmosi.informatik.uni-rostock.de/diemosiris/Members/rhenkel |
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From: Nick J. <ju...@eb...> - 2011-01-13 13:23:11
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Dear annotation package people, I thought it would be worth opening up the discussion about BioModels.net qualifiers, in order to start moving forward more earnestly. The premise is that we wish to have qualifiers that follow the "SUBJECT has PREDICATE whose value is OBJECT" statement, and thereby need to convert or add additional qualifiers as nouns, rather than the existing situation where they are verbs. Below is a list of potential candidate equivalents to existing qualifiers found here: http://biomodels.net/qualifiers/ In some cases, the noun translation is quite apparent, and in others, not so much ;p I think if we iterate round a little, we can reach a moderate consensus. model-qualifiers ================ is => 'identity' isDescribedBy => 'description' biology-qualifier ================ hasPart => 'part' hasProperty => 'property' hasVersion => 'version', (relates class to instance; animal is a hypernym of cat) is => 'identity' isDescribedBy => 'description' isHomologTo => 'homolog(ue)' The next few are more difficult, and I have collected together candidate 'equivalents'. model-qualifiers: ================ 'isDerivedFrom' - needs to reflect modifications to an original model. Candidates: progenitor, antecedent, ancestor, basis, base, foundation, origin biology-qualifiers: ================ 'isEncodedBy' - e.g. protein is encoded by DNA Candidates: encoder 'encodes' - e.g. DNA encodes protein Candidates: encodement 'isPartOf' - e.g. subunit A is part of complex B Candidates: encompassment, assembly, partship, parthood, whole, meronym (relates part to whole; finger is a meronym of hand) 'isPropertyOf' - e.g. enzyme activity A is property of entity B Candidates: bearer, carrier, 'isVersionOf' - needs to convey the sense of belonging to some class Candidates: consociate, cohort, superclass, hyponym (relates instance to class to; cat is a hyponym of animal) 'occursIn' - may be sensible to split it into 'physical containment' and 'taxonomic instantiation' types. We could use 'encompassment' or 'containment' ('container'), for the physical type, and 'instantiation' for occurrence in a species. I'd appreciate your thoughts on these, and also on other qualifiers you guys have in mind. cheers, Nick |
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From: Stefan H. <sh...@vb...> - 2010-11-19 10:24:10
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Hello All, On 11/17/2010 8:15 PM, Mike Hucka wrote: >> Considering how often in the past we struggled to remove features >> added "in case" (e.g. charge, outside, species/comparmentType ...) we >> could argue the other way ;-) > True, but many of those were very about specific attributes, not whole > external schemes like RDF. I'm thinking in particular of all the > restrictions on XHTML syntax in the earlier specs, which were relaxed > later. > I am with Mike and Neil. There is not reason to single out rdf:seq from the four possible containers. We are not adding any 'property' to the package we just remove a syntax limitation by allowing it. This is definitely different than charge and outside etc. Thanks, Stefan -- Stefan Hoops, Ph.D. Senior Project Associate Virginia Bioinformatics Institute - 0477 Virginia Tech Bioinformatics Facility II Blacksburg, Va 24061, USA Phone: (540) 231-1799 Fax: (540) 231-2606 Email: sh...@vb... |
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From: Dagmar W. <dag...@un...> - 2010-11-19 06:35:00
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Thanks to everybody for your opinions. The almost over-all agreement seems to be to leave rdf:Seq in the proposal. If someone comes up with a meaningful example for the use of it - I am still interested to learn :-) Best, Dagmar ________________________________________ From: Mike Hucka [mh...@ca...] Sent: 19 November 2010 04:31 To: sbm...@li... Subject: [sbml-annot] Fwd: Re: rdf:Seq I think Stefan meant to send this to the whole list, not to me specifically: ----- Begin forwarded message ----- From: Stefan Hoops <sh...@vb...> Subject: Re: [sbml-annot] rdf:Seq Date: Thu, 18 Nov 2010 16:00:41 +0100 To: Mike Hucka <mh...@ca...> Hello All, On 11/17/2010 8:15 PM, Mike Hucka wrote: >> Considering how often in the past we struggled to remove features >> added "in case" (e.g. charge, outside, species/comparmentType ...) we >> could argue the other way ;-) > True, but many of those were very about specific attributes, not whole > external schemes like RDF. I'm thinking in particular of all the > restrictions on XHTML syntax in the earlier specs, which were relaxed later. > I am with Mike and Neil. There is not reason to single out rdf:seq from the four possible containers. We are not adding any 'property' to the package we just remove a syntax limitation by allowing it. This is definitely different than charge and outside etc. Thanks, Stefan -- Stefan Hoops, Ph.D. Senior Project Associate Virginia Bioinformatics Institute - 0477 Virginia Tech Bioinformatics Facility II Blacksburg, Va 24061, USA Phone: (540) 231-1799 Fax: (540) 231-2606 Email: sh...@vb... ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev _______________________________________________ Sbml-annot mailing list Sbm...@li... https://lists.sourceforge.net/lists/listinfo/sbml-annot |
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From: Mike H. <mh...@ca...> - 2010-11-19 03:31:44
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I think Stefan meant to send this to the whole list, not to me specifically: ----- Begin forwarded message ----- From: Stefan Hoops <sh...@vb...> Subject: Re: [sbml-annot] rdf:Seq Date: Thu, 18 Nov 2010 16:00:41 +0100 To: Mike Hucka <mh...@ca...> Hello All, On 11/17/2010 8:15 PM, Mike Hucka wrote: >> Considering how often in the past we struggled to remove features >> added "in case" (e.g. charge, outside, species/comparmentType ...) we >> could argue the other way ;-) > True, but many of those were very about specific attributes, not whole > external schemes like RDF. I'm thinking in particular of all the > restrictions on XHTML syntax in the earlier specs, which were relaxed later. > I am with Mike and Neil. There is not reason to single out rdf:seq from the four possible containers. We are not adding any 'property' to the package we just remove a syntax limitation by allowing it. This is definitely different than charge and outside etc. Thanks, Stefan -- Stefan Hoops, Ph.D. Senior Project Associate Virginia Bioinformatics Institute - 0477 Virginia Tech Bioinformatics Facility II Blacksburg, Va 24061, USA Phone: (540) 231-1799 Fax: (540) 231-2606 Email: sh...@vb... |
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From: Mike H. <mh...@ca...> - 2010-11-17 19:15:39
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> Considering how often in the past we struggled to remove features > added "in case" (e.g. charge, outside, species/comparmentType ...) we > could argue the other way ;-) True, but many of those were very about specific attributes, not whole external schemes like RDF. I'm thinking in particular of all the restrictions on XHTML syntax in the earlier specs, which were relaxed later. MH |
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From: Dagmar W. <dag...@un...> - 2010-11-17 12:55:08
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Hej Mike, hej Neil, Significance seems to be something pretty tough to annotate (I think we had this discussion before about "this Go annotation is better than that ChEBI annotation"). If we then in addition have notions of space and time - would that mean the meaning of the sequence depends on the element that has been annotated? And how would we determine the semantics of a particular annotation in a specific context automatically? Is this not getting too complicated then? In general, I would like to see rdf:Seq being supported together with the other three container types... it is just a bit unsatisfying not to have an example for the use of it. Also, it seems to me we should have a clear semantics for use of the sequence container in Annot. Otherwise we will not be able to conclude anything from the annotations. Maybe a way to go is to support it in the first draft, see what use people make of it and then define the semantics :-) Not very elegant though. Dagmar On 11/16/2010 11:19 AM, Neil Swainston wrote: > Hi all, > > My thoughts on this is that, although they may be undesirable, and although we can't (yet) think of decent use cases, we should *probably* support them, just in case anyone comes up with a useful use case in future. > > I don't know why we would support three of the four collection types. Might as well support the lot and see what happens. > > Cheers, > > Neil. > > Neil Swainston > Experimental Officer > > Manchester Centre for Integrative Systems Biology > Manchester Interdisciplinary Biocentre > University of Manchester > Manchester M1 7DN > United Kingdom > > On 15 Nov 2010, at 12:51, Nicolas Le novère wrote: > > >> I generally hate ordering. But would that be a way to encode relationships >> between triples? Like using qualifiers like bqmodel:disjointFrom within an >> li, that would say it is disjoint from the next? >> >> On 15/11/10 12:09, Dagmar Waltemath wrote: >> >>> Hello, >>> >>> we are proposing to use all RDF container types in the new SBML >>> annotations. >>> >>> While I can see the use of rdf:List, rdf:Bag and rdf:Alt, >>> I was just wondering if we ever thought about the semantics behind >>> <rdf:Seq> blocks? >>> RDF just suggests to use the container for lists where the order of >>> elements is important. >>> >>> The question I came up with was: What does the order of the occurring >>> annotations inside such a block tell us? >>> >>> Does anyone have a good example where order will really matter? >>> Dagmar >>> >>> ------------------------------------------------------------------------------ >>> Centralized Desktop Delivery: Dell and VMware Reference Architecture >>> Simplifying enterprise desktop deployment and management using >>> Dell EqualLogic storage and VMware View: A highly scalable, end-to-end >>> client virtualization framework. Read more! >>> http://p.sf.net/sfu/dell-eql-dev2dev >>> _______________________________________________ >>> Sbml-annot mailing list >>> Sbm...@li... >>> https://lists.sourceforge.net/lists/listinfo/sbml-annot >>> >> >> -- >> Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC, >> Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468, >> Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho...(NOT email) >> http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/, @lenovere >> >> >> ------------------------------------------------------------------------------ >> Centralized Desktop Delivery: Dell and VMware Reference Architecture >> Simplifying enterprise desktop deployment and management using >> Dell EqualLogic storage and VMware View: A highly scalable, end-to-end >> client virtualization framework. Read more! >> http://p.sf.net/sfu/dell-eql-dev2dev >> _______________________________________________ >> Sbml-annot mailing list >> Sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbml-annot >> > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2& L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today > http://p.sf.net/sfu/msIE9-sfdev2dev > _______________________________________________ > Sbml-annot mailing list > Sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-annot > |
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From: Nicolas Le n. <le...@eb...> - 2010-11-17 08:12:35
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Considering how often in the past we struggled to remove features added "in case" (e.g. charge, outside, species/comparmentType ...) we could argue the other way ;-) On 17/11/10 03:06, Mike Hucka wrote: > Considering how explicit limitations in the past have come back to haunt > SBML, maybe this is not a bad idea :-). > > MH > > On Tue, 16 Nov 2010 10:19:41 +0000, Neil Swainston wrote: >> Hi all, >> >> My thoughts on this is that, although they may be undesirable, and >> although we can't (yet) think of decent use cases, we should >> *probably* support them, just in case anyone comes up with a useful >> use case in future. >> >> I don't know why we would support three of the four collection types. >> Might as well support the lot and see what happens. >> >> Cheers, >> >> Neil. >> >> Neil Swainston Experimental Officer >> >> Manchester Centre for Integrative Systems Biology Manchester >> Interdisciplinary Biocentre University of Manchester Manchester M1 >> 7DN United Kingdom >> >> On 15 Nov 2010, at 12:51, Nicolas Le novère wrote: >> >>> I generally hate ordering. But would that be a way to encode >>> relationships between triples? Like using qualifiers like >>> bqmodel:disjointFrom within an li, that would say it is disjoint >>> from the next? >>> >>> On 15/11/10 12:09, Dagmar Waltemath wrote: >>>> Hello, >>>> >>>> we are proposing to use all RDF container types in the new SBML >>>> annotations. >>>> >>>> While I can see the use of rdf:List, rdf:Bag and rdf:Alt, I was >>>> just wondering if we ever thought about the semantics behind >>>> <rdf:Seq> blocks? RDF just suggests to use the container for >>>> lists where the order of elements is important. >>>> >>>> The question I came up with was: What does the order of the >>>> occurring annotations inside such a block tell us? >>>> >>>> Does anyone have a good example where order will really matter? >>>> Dagmar >>>> >>>> ------------------------------------------------------------------------------ >>>> >>>> Centralized Desktop Delivery: Dell and VMware Reference Architecture >>>> Simplifying enterprise desktop deployment and management using >>>> Dell EqualLogic storage and VMware View: A highly scalable, >>>> end-to-end client virtualization framework. Read more! >>>> http://p.sf.net/sfu/dell-eql-dev2dev >>>> _______________________________________________ Sbml-annot mailing >>>> list Sbm...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sbml-annot >>> >>> >>> -- Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, >>> WTGC, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 >>> Fax:468, Skype:n.lenovere, AIM:nlenovere, >>> MSN:nle...@ho...(NOT email) http://www.ebi.ac.uk/~lenov/, >>> http://www.ebi.ac.uk/compneur/, @lenovere >>> >>> >>> ------------------------------------------------------------------------------ >>> >>> Centralized Desktop Delivery: Dell and VMware Reference Architecture >>> Simplifying enterprise desktop deployment and management using Dell >>> EqualLogic storage and VMware View: A highly scalable, end-to-end >>> client virtualization framework. Read more! >>> http://p.sf.net/sfu/dell-eql-dev2dev >>> _______________________________________________ Sbml-annot mailing >>> list Sbm...@li... >>> https://lists.sourceforge.net/lists/listinfo/sbml-annot >> >> ------------------------------------------------------------------------------ >> >> Beautiful is writing same markup. Internet Explorer 9 supports >> standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2& L3. >> Spend less time writing and rewriting code and more time creating >> great experiences on the web. Be a part of the beta today >> http://p.sf.net/sfu/msIE9-sfdev2dev >> _______________________________________________ Sbml-annot mailing >> list Sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbml-annot -- Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho...(NOT email) http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/, @lenovere |
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From: Mike H. <mh...@ca...> - 2010-11-17 03:06:35
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Considering how explicit limitations in the past have come back to haunt SBML, maybe this is not a bad idea :-). MH On Tue, 16 Nov 2010 10:19:41 +0000, Neil Swainston wrote: > Hi all, > > My thoughts on this is that, although they may be undesirable, and > although we can't (yet) think of decent use cases, we should > *probably* support them, just in case anyone comes up with a useful > use case in future. > > I don't know why we would support three of the four collection types. > Might as well support the lot and see what happens. > > Cheers, > > Neil. > > Neil Swainston > Experimental Officer > > Manchester Centre for Integrative Systems Biology > Manchester Interdisciplinary Biocentre > University of Manchester > Manchester M1 7DN > United Kingdom > > On 15 Nov 2010, at 12:51, Nicolas Le novère wrote: > >> I generally hate ordering. But would that be a way to encode relationships >> between triples? Like using qualifiers like bqmodel:disjointFrom within an >> li, that would say it is disjoint from the next? >> >> On 15/11/10 12:09, Dagmar Waltemath wrote: >>> Hello, >>> >>> we are proposing to use all RDF container types in the new SBML >>> annotations. >>> >>> While I can see the use of rdf:List, rdf:Bag and rdf:Alt, >>> I was just wondering if we ever thought about the semantics behind >>> <rdf:Seq> blocks? >>> RDF just suggests to use the container for lists where the order of >>> elements is important. >>> >>> The question I came up with was: What does the order of the occurring >>> annotations inside such a block tell us? >>> >>> Does anyone have a good example where order will really matter? >>> Dagmar >>> >>> ------------------------------------------------------------------------------ >>> Centralized Desktop Delivery: Dell and VMware Reference Architecture >>> Simplifying enterprise desktop deployment and management using >>> Dell EqualLogic storage and VMware View: A highly scalable, end-to-end >>> client virtualization framework. Read more! >>> http://p.sf.net/sfu/dell-eql-dev2dev >>> _______________________________________________ >>> Sbml-annot mailing list >>> Sbm...@li... >>> https://lists.sourceforge.net/lists/listinfo/sbml-annot >> >> >> -- >> Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC, >> Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468, >> Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho...(NOT email) >> http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/, @lenovere >> >> >> ------------------------------------------------------------------------------ >> Centralized Desktop Delivery: Dell and VMware Reference Architecture >> Simplifying enterprise desktop deployment and management using >> Dell EqualLogic storage and VMware View: A highly scalable, end-to-end >> client virtualization framework. Read more! >> http://p.sf.net/sfu/dell-eql-dev2dev >> _______________________________________________ >> Sbml-annot mailing list >> Sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbml-annot > > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today > http://p.sf.net/sfu/msIE9-sfdev2dev > _______________________________________________ > Sbml-annot mailing list > Sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-annot |
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From: Neil S. <nei...@ma...> - 2010-11-16 10:19:50
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Hi all, My thoughts on this is that, although they may be undesirable, and although we can't (yet) think of decent use cases, we should *probably* support them, just in case anyone comes up with a useful use case in future. I don't know why we would support three of the four collection types. Might as well support the lot and see what happens. Cheers, Neil. Neil Swainston Experimental Officer Manchester Centre for Integrative Systems Biology Manchester Interdisciplinary Biocentre University of Manchester Manchester M1 7DN United Kingdom On 15 Nov 2010, at 12:51, Nicolas Le novère wrote: > I generally hate ordering. But would that be a way to encode relationships > between triples? Like using qualifiers like bqmodel:disjointFrom within an > li, that would say it is disjoint from the next? > > On 15/11/10 12:09, Dagmar Waltemath wrote: >> Hello, >> >> we are proposing to use all RDF container types in the new SBML >> annotations. >> >> While I can see the use of rdf:List, rdf:Bag and rdf:Alt, >> I was just wondering if we ever thought about the semantics behind >> <rdf:Seq> blocks? >> RDF just suggests to use the container for lists where the order of >> elements is important. >> >> The question I came up with was: What does the order of the occurring >> annotations inside such a block tell us? >> >> Does anyone have a good example where order will really matter? >> Dagmar >> >> ------------------------------------------------------------------------------ >> Centralized Desktop Delivery: Dell and VMware Reference Architecture >> Simplifying enterprise desktop deployment and management using >> Dell EqualLogic storage and VMware View: A highly scalable, end-to-end >> client virtualization framework. Read more! >> http://p.sf.net/sfu/dell-eql-dev2dev >> _______________________________________________ >> Sbml-annot mailing list >> Sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbml-annot > > > -- > Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC, > Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468, > Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho...(NOT email) > http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/, @lenovere > > > ------------------------------------------------------------------------------ > Centralized Desktop Delivery: Dell and VMware Reference Architecture > Simplifying enterprise desktop deployment and management using > Dell EqualLogic storage and VMware View: A highly scalable, end-to-end > client virtualization framework. Read more! > http://p.sf.net/sfu/dell-eql-dev2dev > _______________________________________________ > Sbml-annot mailing list > Sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-annot |
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From: Mike H. <mh...@ca...> - 2010-11-15 21:12:08
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Hi,
My $0.02 worth:
I think the natural uses of ordering are for
- time ("this occurred before/after that")
- space ("this is located before/after that")
- significance ("this is the preferred/best/highest ranked")
Somehow it would seem risky to use it for doing things like encoding tuples [a,b,c]. It would seem like a misuse of the ordering: an element's place in the order would actually signify a specific property (like "the second element is the relation") and not a general list-like relationship ("1 before 2, 2 before 3, 3 before 4, ...").
MH
On Mon, 15 Nov 2010 13:09:15 +0100, Dagmar Waltemath wrote:
> Hello,
>
> we are proposing to use all RDF container types in the new SBML
> annotations.
>
> While I can see the use of rdf:List, rdf:Bag and rdf:Alt,
> I was just wondering if we ever thought about the semantics behind
> <rdf:Seq> blocks?
> RDF just suggests to use the container for lists where the order of
> elements is important.
>
> The question I came up with was: What does the order of the occurring
> annotations inside such a block tell us?
>
> Does anyone have a good example where order will really matter?
> Dagmar
>
> ------------------------------------------------------------------------------
> Centralized Desktop Delivery: Dell and VMware Reference Architecture
> Simplifying enterprise desktop deployment and management using
> Dell EqualLogic storage and VMware View: A highly scalable, end-to-end
> client virtualization framework. Read more!
> http://p.sf.net/sfu/dell-eql-dev2dev
> _______________________________________________
> Sbml-annot mailing list
> Sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbml-annot
|
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From: Nicolas Le n. <le...@eb...> - 2010-11-15 12:51:48
|
I generally hate ordering. But would that be a way to encode relationships between triples? Like using qualifiers like bqmodel:disjointFrom within an li, that would say it is disjoint from the next? On 15/11/10 12:09, Dagmar Waltemath wrote: > Hello, > > we are proposing to use all RDF container types in the new SBML > annotations. > > While I can see the use of rdf:List, rdf:Bag and rdf:Alt, > I was just wondering if we ever thought about the semantics behind > <rdf:Seq> blocks? > RDF just suggests to use the container for lists where the order of > elements is important. > > The question I came up with was: What does the order of the occurring > annotations inside such a block tell us? > > Does anyone have a good example where order will really matter? > Dagmar > > ------------------------------------------------------------------------------ > Centralized Desktop Delivery: Dell and VMware Reference Architecture > Simplifying enterprise desktop deployment and management using > Dell EqualLogic storage and VMware View: A highly scalable, end-to-end > client virtualization framework. Read more! > http://p.sf.net/sfu/dell-eql-dev2dev > _______________________________________________ > Sbml-annot mailing list > Sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-annot -- Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho...(NOT email) http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/, @lenovere |
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From: Dagmar W. <dag...@un...> - 2010-11-15 12:22:36
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Hello, we are proposing to use all RDF container types in the new SBML annotations. While I can see the use of rdf:List, rdf:Bag and rdf:Alt, I was just wondering if we ever thought about the semantics behind <rdf:Seq> blocks? RDF just suggests to use the container for lists where the order of elements is important. The question I came up with was: What does the order of the occurring annotations inside such a block tell us? Does anyone have a good example where order will really matter? Dagmar |
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From: Nicolas Le n. <le...@eb...> - 2010-10-17 16:50:22
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[I turn that to the list. Why people never use mailing-lists more than once is a mistery to me] Neil, I believe you convinced us. And turning the biomodels qualifiers to nouns is on our to-do list. We'll do that momentarily. On 17/10/10 17:25, Neil Swainston wrote: > Hi all, > > OK, that's one issue down. > > The final one, as far as I can see, is: do we need new predicates? > > I've long banged on about the fact that predicates should represent > properties of the subject (therefore nouns, not verbs) but as no-one > else seems to care less about this, then I'm fine with ignoring it. > > However, I would like some way of specifying modifications on proteins. > Could you at least indulge me that? > > Cheers, > > Neil. > > Neil Swainston > Experimental Officer, (Acting) Project Manager > > Manchester Centre for Integrative Systems Biology > Manchester Interdisciplinary Biocentre > University of Manchester > Manchester M1 7DN > England > > On 15 Oct 2010, at 21:53, Nicolas Le novère wrote: > >> I agree. Let's keep negation out of the loop. The package already >> extends a lot the current capabilities of the core annotations. >> >> On 15/10/10 21:44, Neil Swainston wrote: >>> Hi Dagmar et al., >>> >>> Yep, I guess that Proposal 4 does have this problem. It's certainly >>> not *the* solution. >>> >>> I'm almost tempted to write up everything as a first draft, version >>> 1, but *without* negation. This would provide a benchmark which can >>> be updated if/when a solution is found, or we decide to use OWL, or >>> our contracts expire. Whichever comes soonest. >>> >>> Thoughts? >>> >>> Cheers, >>> >>> Neil. >>> >>> Neil Swainston >>> Experimental Officer >>> >>> Manchester Centre for Integrative Systems Biology >>> Manchester Interdisciplinary Biocentre >>> University of Manchester >>> Manchester M1 7DN >>> England >>> >>> On 15 Oct 2010, at 20:52, Dagmar >>> Waltemath<dag...@un... >>> <mailto:dag...@un...>> wrote: >>> >>>> May I ask my question again: >>>> Ron, Wolf will that lead to trouble with the similarity measure >>>> tools which build on extracting existing annotations? >>>> Or will those troubles occur on way or the other? >>>> >>>> Dagmar >>>> >>>> On 10/15/2010 09:46 PM, Neil Swainston wrote: >>>>> Hi all (again), >>>>> >>>>> I'm inclined to agree with Ron on this. That's one of the reason's >>>>> that I'd advocate Proposal 4 - it reduces the need to generate too >>>>> many new predicates. >>>>> >>>>> Cheers, >>>>> >>>>> Neil. >>>>> >>>>> Neil Swainston >>>>> Experimental Officer >>>>> >>>>> Manchester Centre for Integrative Systems Biology >>>>> Manchester Interdisciplinary Biocentre >>>>> University of Manchester >>>>> Manchester M1 7DN >>>>> England >>>>> >>>>> On 14 Oct 2010, at 09:30, Ron Henkel<ron...@un... >>>>> <mailto:ron...@un...>> wrote: >>>>> >>>>> >>>>>>>> So, given there is opt 1 and 4 to chose from, I'd probably go >>>>>>>> for opt 1. >>>>>>>> One disadvantage with that option however is that we might be a bit >>>>>>>> reluctant to introduce, officially, negative qualifiers if we >>>>>>>> know it >>>>>>>> will probably only be a temporal solution (thinking about how to >>>>>>>> get rid >>>>>>>> of them afterwards). But maybe even that is not an issue... Nicolas? >>>>>>>> >>>>>>> We would not get rid of them. Whatever we choose afterward, they >>>>>>> would >>>>>>> still be valid qualifiers. But as I said before, we do not need a >>>>>>> lot of >>>>>>> them. Negating "part" and "version" will go a long way. >>>>>>> >>>>>> If we find a solution that is able to express negations without >>>>>> touching qualifier we should not have pairs of qualifier/negated >>>>>> qualifier (isPart / isNotPart) as a leftover from a previous >>>>>> version. I personally think we should avoid possible negation of >>>>>> negated qualifier at all cost. >>>>>> >>>>>> -- >>>>>> Dipl.-Inf. Ron Henkel >>>>>> Research Training Group dIEM oSiRiS >>>>>> >>>>>> Lehrstuhl Datenbank- und Informationssysteme >>>>>> Institut für Informatik >>>>>> Universität Rostock >>>>>> 18051 Rostock >>>>>> >>>>>> Tel: +49 381 498 7440 >>>>>> E-Mail: ron...@un... <mailto:ron...@un...> >>>>>> >>>> >> >> >> -- >> Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust >> Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 >> Fax:468,Skype:n.lenovere,AIM:nlenovere,MSN:nle...@ho...(NOT >> email) >> http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/, @lenovere >> >> > -- Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,Skype:n.lenovere,AIM:nlenovere,MSN:nle...@ho...(NOT email) http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/, @lenovere |
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From: Nicolas Le N. <le...@eb...> - 2010-08-03 06:53:29
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I do not thinks we will need negative versions of all qualifiers. AbsentPart makes sense, because an entity has a defined number of parts. Same for NotVersion. However negations of Homolog, Description etc. are not useful because unbounded. Aside note on negation: The qualifiers are not part of the SBML annot. package. But the general negation is. -- Nicolas LE NOVERE, EMBL-EBI, Mob:+447833147074, Tel:+441223494521, Skype:n.lenovere, http://www.ebi.ac.uk/~lenov/ -----Original Message----- From: Dagmar Waltemath <dag...@un...> Date: Tue, 03 Aug 2010 07:39:23 To: <sbm...@li...> Subject: Re: [sbml-annot] Fwd: Re: [Obo-discuss] Ontological Realism and OBO Foundry Criteria Hej Neil, that should be the same approach as the one we discussed already during the meeting, introducing negative versions of the qualifiers we have defined, is that right? (Or is there a difference that I do not see?) I remember from the discussions that some of us thought this was just leading to a great number of qualifiers and was not a very clean solution... which then led to the idea of having a negation element (the NOT). Just to recap the meeting... I am still in favor of a general negation operator, I have to say. But I do not have a proper solution how to implement that :-) Dagmar On 08/02/2010 11:55 AM, Neil Swainston wrote: > Hi Nicolas et al, > > It seems that the OBO people are suggesting using "negative" predicates. So effectively, to follow this, we'd be saying X has NO_MODIFICATION of type PHOSPHORYLATION, for example. This seems reasonably reasonable...? > > Cheers, > > Neil. > > Neil Swainston > Experimental Officer > > Manchester Centre for Integrative Systems Biology > Manchester Interdisciplinary Biocentre > University of Manchester > Manchester M1 7DN > England > > On 27 Jul 2010, at 18:25, Nicolas Le novère wrote: > > >> See post below, about the "lack" relationships. Not without resonance with >> our own predicament. >> >> -------- Original Message -------- >> Subject: Re: [Obo-discuss] Ontological Realism and OBO Foundry Criteria >> Date: Tue, 27 Jul 2010 13:07:04 -0400 >> From: Barry Smith<phi...@bu...> >> Reply-To: obo...@li... >> To: obo...@li..., obo...@li... >> >> At 12:53 PM 7/27/2010, Adam M. Goldstein wrote: >> >> >>> On Jul 27, 2010, at 9:04 AM, Barry Smith wrote: >>> >>> >>>> At 12:14 PM 7/26/2010, Phillip Lord wrote: >>>> >>>>> Barry Smith<phi...@bu...> writes: >>>>> >>>>>> At 07:35 AM 7/18/2010, Robert Stevens wrote: >>>>>> >>>>>>> we can find lots of evidence for instances. We have lots of evidence, >>>>>>> for example, for individual glucose molecules. What evidence do we >>>>>>> have for the other entity -- the glucose universal? >>>>>>> >>>>>> The fact that scientists describe multiple instances thus. >>>>>> Repeatedly. Effectively. Usefully. (Also, of course, revisably -- >>>>>> scientist might teach us better.) >>>>>> >>>>>> In addition, of course, there is the chemist's conception of the >>>>>> corresponding category. >>>>>> >>>>>> So scientists are able to describe those repeated instances >>>>>> effectively because they are somehow able to match their conception >>>>>> to something in those instances, something repeatedly observed. This >>>>>> cannot BE the scientists' conception, because it was there before the >>>>>> scientists came along. >>>>>> >>>>> >>>>> Which kind of sums up my confusion over realism and the bendability of >>>>> your notion of reality. Scientists have found absent hand repeatable >>>>> effective and useful, yet according to you it is not reality. >>>>> >>>> See, again, Ceusters W, Elkin P, Smith B. Negative Findings in >>>> Electronic Health Records and Biomedical Ontologies: A Realist >>>> Approach. International Journal of Medical Informatics 2007;2007:326-333. >>>> >>>> >>> http://www.referent-tracking.com/RTU/sendfile/?file=IJMI-MIE2006-Ceusters3-1.pdf >>> >>>> >>> >>> As a general point about list postings, I want to point out that >>> referring someone to an article is not as useful as it might seem. >>> What part of this article do you think is most important? What in >>> the article is going to answer the question of the original poster? >>> Surely this can be summed up in a few sentences, or slightly more, >>> even, or at least, some indication of the general strategy for >>> >> You might read the RESULTS and CONCLUSION parts of the Abstract: >> >> RESULTS: We introduced a new family of 'lacks' relations into the OBO >> Relation Ontology. The relation lacks_part, for example, defined in >> terms of the positive relation part_of, holds between a particular p >> and a universal u when p has no instance of u as part. Since p and u >> both exist, assertions involving 'lacks_part' and its cognates meet >> the requirements of positivity. CONCLUSION: By expanding the OBO >> Relation Ontology, we were able to accommodate nearly all occurrences >> of negative findings in the sample studied. >> >> >>> >>>>> They have >>>>> found absolute space useful but non-existent, yet it is reality. Numbers >>>>> are the cornerstone of mathematics and, therefore, more science; you >>>>> still haven't told me whether these are real yet. Ingvar did at least >>>>> tell me his position (only "1" exists). >>>>> >>>> The strategy, in order to keep BFO as small as possible, is to focus >>>> only on what is non-abstract, emphasizing always that it is subject >>>> to the open world assumption, and thus that things might change. SUMO >>>> includes many abstracta, and is accordingly huge. >>>> >>>> >>> >>> The bit about space always has seemed curious to me. Why should >>> absolute space be built into the BFO, when it's known that there >>> isn't any such thing? If there is anything that's settled science, >>> it's probably that one thing. >>> >>> Regarding the size of an ontology, if there are lots of things in >>> the world, shouldn't there be, accordingly, lots of terms in the >>> ontology that describes them? There are useful taxonomies of all >>> species ever known to have existed, with tens of millions of >>> categories. No person can keep it all in mind, but even before >>> digital representations of it, taxonomists could easily work with >>> the tree of life. Similarly for neuroanatomy, for instance. >>> >> BFO is designed as a very small discipline-neutral ontology. It does >> not contain any terms pertaining to specific scientific domains. We >> are addressing the issue of how spatial regions are to be dealt with >> in the context of the planned release of BFO 2.0. >> >> >> >>> ------------------ >>> Adam M. Goldstein PhD, MSLIS >>> -- >>> z_c...@sh... >>> http://www.shiftingbalance.org >>> http://www.twitter.com/shiftingbalance >>> -- >>> http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180621 >>> -- >>> Associate Editor >>> Reviews Editor >>> Evolution: Education& Outreach >>> http://www.springer.com/life+sci/journal/12052 >>> -- >>> (914) 637-2717 (msg) >>> -- >>> Dept of Philosophy >>> Iona College >>> 715 North Avenue >>> New Rochelle NY 10801 >>> >>> ------------------------------------------------------------------------------ >>> The Palm PDK Hot Apps Program offers developers who use the >>> Plug-In Development Kit to bring their C/C++ apps to Palm for a share >>> of $1 Million in cash or HP Products. Visit us here for more details: >>> http://ad.doubleclick.net/clk;226879339;13503038;l? >>> http://clk.atdmt.com/CRS/go/247765532/direct/01/ >>> _______________________________________________ >>> Obo-discuss mailing list >>> Obo...@li... >>> https://lists.sourceforge.net/lists/listinfo/obo-discuss >>> >> >> >> ------------------------------------------------------------------------------ >> The Palm PDK Hot Apps Program offers developers who use the >> Plug-In Development Kit to bring their C/C++ apps to Palm for a share >> of $1 Million in cash or HP Products. Visit us here for more details: >> http://ad.doubleclick.net/clk;226879339;13503038;l? >> http://clk.atdmt.com/CRS/go/247765532/direct/01/ >> _______________________________________________ >> Obo-discuss mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-discuss >> >> ------------------------------------------------------------------------------ >> The Palm PDK Hot Apps Program offers developers who use the >> Plug-In Development Kit to bring their C/C++ apps to Palm for a share >> of $1 Million in cash or HP Products. Visit us here for more details: >> http://ad.doubleclick.net/clk;226879339;13503038;l? >> http://clk.atdmt.com/CRS/go/247765532/direct/01/ >> _______________________________________________ >> Sbml-annot mailing list >> Sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbml-annot >> > ------------------------------------------------------------------------------ > The Palm PDK Hot Apps Program offers developers who use the > Plug-In Development Kit to bring their C/C++ apps to Palm for a share > of $1 Million in cash or HP Products. Visit us here for more details: > http://p.sf.net/sfu/dev2dev-palm > _______________________________________________ > Sbml-annot mailing list > Sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-annot > ------------------------------------------------------------------------------ The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm _______________________________________________ Sbml-annot mailing list Sbm...@li... https://lists.sourceforge.net/lists/listinfo/sbml-annot |
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From: Dagmar W. <dag...@un...> - 2010-08-03 06:05:53
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Hej Neil, that should be the same approach as the one we discussed already during the meeting, introducing negative versions of the qualifiers we have defined, is that right? (Or is there a difference that I do not see?) I remember from the discussions that some of us thought this was just leading to a great number of qualifiers and was not a very clean solution... which then led to the idea of having a negation element (the NOT). Just to recap the meeting... I am still in favor of a general negation operator, I have to say. But I do not have a proper solution how to implement that :-) Dagmar On 08/02/2010 11:55 AM, Neil Swainston wrote: > Hi Nicolas et al, > > It seems that the OBO people are suggesting using "negative" predicates. So effectively, to follow this, we'd be saying X has NO_MODIFICATION of type PHOSPHORYLATION, for example. This seems reasonably reasonable...? > > Cheers, > > Neil. > > Neil Swainston > Experimental Officer > > Manchester Centre for Integrative Systems Biology > Manchester Interdisciplinary Biocentre > University of Manchester > Manchester M1 7DN > England > > On 27 Jul 2010, at 18:25, Nicolas Le novère wrote: > > >> See post below, about the "lack" relationships. Not without resonance with >> our own predicament. >> >> -------- Original Message -------- >> Subject: Re: [Obo-discuss] Ontological Realism and OBO Foundry Criteria >> Date: Tue, 27 Jul 2010 13:07:04 -0400 >> From: Barry Smith<phi...@bu...> >> Reply-To: obo...@li... >> To: obo...@li..., obo...@li... >> >> At 12:53 PM 7/27/2010, Adam M. Goldstein wrote: >> >> >>> On Jul 27, 2010, at 9:04 AM, Barry Smith wrote: >>> >>> >>>> At 12:14 PM 7/26/2010, Phillip Lord wrote: >>>> >>>>> Barry Smith<phi...@bu...> writes: >>>>> >>>>>> At 07:35 AM 7/18/2010, Robert Stevens wrote: >>>>>> >>>>>>> we can find lots of evidence for instances. We have lots of evidence, >>>>>>> for example, for individual glucose molecules. What evidence do we >>>>>>> have for the other entity -- the glucose universal? >>>>>>> >>>>>> The fact that scientists describe multiple instances thus. >>>>>> Repeatedly. Effectively. Usefully. (Also, of course, revisably -- >>>>>> scientist might teach us better.) >>>>>> >>>>>> In addition, of course, there is the chemist's conception of the >>>>>> corresponding category. >>>>>> >>>>>> So scientists are able to describe those repeated instances >>>>>> effectively because they are somehow able to match their conception >>>>>> to something in those instances, something repeatedly observed. This >>>>>> cannot BE the scientists' conception, because it was there before the >>>>>> scientists came along. >>>>>> >>>>> >>>>> Which kind of sums up my confusion over realism and the bendability of >>>>> your notion of reality. Scientists have found absent hand repeatable >>>>> effective and useful, yet according to you it is not reality. >>>>> >>>> See, again, Ceusters W, Elkin P, Smith B. Negative Findings in >>>> Electronic Health Records and Biomedical Ontologies: A Realist >>>> Approach. International Journal of Medical Informatics 2007;2007:326-333. >>>> >>>> >>> http://www.referent-tracking.com/RTU/sendfile/?file=IJMI-MIE2006-Ceusters3-1.pdf >>> >>>> >>> >>> As a general point about list postings, I want to point out that >>> referring someone to an article is not as useful as it might seem. >>> What part of this article do you think is most important? What in >>> the article is going to answer the question of the original poster? >>> Surely this can be summed up in a few sentences, or slightly more, >>> even, or at least, some indication of the general strategy for >>> >> You might read the RESULTS and CONCLUSION parts of the Abstract: >> >> RESULTS: We introduced a new family of 'lacks' relations into the OBO >> Relation Ontology. The relation lacks_part, for example, defined in >> terms of the positive relation part_of, holds between a particular p >> and a universal u when p has no instance of u as part. Since p and u >> both exist, assertions involving 'lacks_part' and its cognates meet >> the requirements of positivity. CONCLUSION: By expanding the OBO >> Relation Ontology, we were able to accommodate nearly all occurrences >> of negative findings in the sample studied. >> >> >>> >>>>> They have >>>>> found absolute space useful but non-existent, yet it is reality. Numbers >>>>> are the cornerstone of mathematics and, therefore, more science; you >>>>> still haven't told me whether these are real yet. Ingvar did at least >>>>> tell me his position (only "1" exists). >>>>> >>>> The strategy, in order to keep BFO as small as possible, is to focus >>>> only on what is non-abstract, emphasizing always that it is subject >>>> to the open world assumption, and thus that things might change. SUMO >>>> includes many abstracta, and is accordingly huge. >>>> >>>> >>> >>> The bit about space always has seemed curious to me. Why should >>> absolute space be built into the BFO, when it's known that there >>> isn't any such thing? If there is anything that's settled science, >>> it's probably that one thing. >>> >>> Regarding the size of an ontology, if there are lots of things in >>> the world, shouldn't there be, accordingly, lots of terms in the >>> ontology that describes them? There are useful taxonomies of all >>> species ever known to have existed, with tens of millions of >>> categories. No person can keep it all in mind, but even before >>> digital representations of it, taxonomists could easily work with >>> the tree of life. Similarly for neuroanatomy, for instance. >>> >> BFO is designed as a very small discipline-neutral ontology. It does >> not contain any terms pertaining to specific scientific domains. We >> are addressing the issue of how spatial regions are to be dealt with >> in the context of the planned release of BFO 2.0. >> >> >> >>> ------------------ >>> Adam M. Goldstein PhD, MSLIS >>> -- >>> z_c...@sh... >>> http://www.shiftingbalance.org >>> http://www.twitter.com/shiftingbalance >>> -- >>> http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180621 >>> -- >>> Associate Editor >>> Reviews Editor >>> Evolution: Education& Outreach >>> http://www.springer.com/life+sci/journal/12052 >>> -- >>> (914) 637-2717 (msg) >>> -- >>> Dept of Philosophy >>> Iona College >>> 715 North Avenue >>> New Rochelle NY 10801 >>> >>> ------------------------------------------------------------------------------ >>> The Palm PDK Hot Apps Program offers developers who use the >>> Plug-In Development Kit to bring their C/C++ apps to Palm for a share >>> of $1 Million in cash or HP Products. Visit us here for more details: >>> http://ad.doubleclick.net/clk;226879339;13503038;l? >>> http://clk.atdmt.com/CRS/go/247765532/direct/01/ >>> _______________________________________________ >>> Obo-discuss mailing list >>> Obo...@li... >>> https://lists.sourceforge.net/lists/listinfo/obo-discuss >>> >> >> >> ------------------------------------------------------------------------------ >> The Palm PDK Hot Apps Program offers developers who use the >> Plug-In Development Kit to bring their C/C++ apps to Palm for a share >> of $1 Million in cash or HP Products. Visit us here for more details: >> http://ad.doubleclick.net/clk;226879339;13503038;l? >> http://clk.atdmt.com/CRS/go/247765532/direct/01/ >> _______________________________________________ >> Obo-discuss mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-discuss >> >> ------------------------------------------------------------------------------ >> The Palm PDK Hot Apps Program offers developers who use the >> Plug-In Development Kit to bring their C/C++ apps to Palm for a share >> of $1 Million in cash or HP Products. Visit us here for more details: >> http://ad.doubleclick.net/clk;226879339;13503038;l? >> http://clk.atdmt.com/CRS/go/247765532/direct/01/ >> _______________________________________________ >> Sbml-annot mailing list >> Sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbml-annot >> > ------------------------------------------------------------------------------ > The Palm PDK Hot Apps Program offers developers who use the > Plug-In Development Kit to bring their C/C++ apps to Palm for a share > of $1 Million in cash or HP Products. Visit us here for more details: > http://p.sf.net/sfu/dev2dev-palm > _______________________________________________ > Sbml-annot mailing list > Sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-annot > |
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From: Neil S. <nei...@ma...> - 2010-08-02 10:23:30
|
Hi Nicolas et al, It seems that the OBO people are suggesting using "negative" predicates. So effectively, to follow this, we'd be saying X has NO_MODIFICATION of type PHOSPHORYLATION, for example. This seems reasonably reasonable...? Cheers, Neil. Neil Swainston Experimental Officer Manchester Centre for Integrative Systems Biology Manchester Interdisciplinary Biocentre University of Manchester Manchester M1 7DN England On 27 Jul 2010, at 18:25, Nicolas Le novère wrote: > See post below, about the "lack" relationships. Not without resonance with > our own predicament. > > -------- Original Message -------- > Subject: Re: [Obo-discuss] Ontological Realism and OBO Foundry Criteria > Date: Tue, 27 Jul 2010 13:07:04 -0400 > From: Barry Smith <phi...@bu...> > Reply-To: obo...@li... > To: obo...@li..., obo...@li... > > At 12:53 PM 7/27/2010, Adam M. Goldstein wrote: > >> On Jul 27, 2010, at 9:04 AM, Barry Smith wrote: >> >>> At 12:14 PM 7/26/2010, Phillip Lord wrote: >>>> Barry Smith <phi...@bu...> writes: >>>>> At 07:35 AM 7/18/2010, Robert Stevens wrote: >>>>>> we can find lots of evidence for instances. We have lots of evidence, >>>>>> for example, for individual glucose molecules. What evidence do we >>>>>> have for the other entity -- the glucose universal? >>>>> >>>>> The fact that scientists describe multiple instances thus. >>>>> Repeatedly. Effectively. Usefully. (Also, of course, revisably -- >>>>> scientist might teach us better.) >>>>> >>>>> In addition, of course, there is the chemist's conception of the >>>>> corresponding category. >>>>> >>>>> So scientists are able to describe those repeated instances >>>>> effectively because they are somehow able to match their conception >>>>> to something in those instances, something repeatedly observed. This >>>>> cannot BE the scientists' conception, because it was there before the >>>>> scientists came along. >>>> >>>> >>>> Which kind of sums up my confusion over realism and the bendability of >>>> your notion of reality. Scientists have found absent hand repeatable >>>> effective and useful, yet according to you it is not reality. >>> >>> See, again, Ceusters W, Elkin P, Smith B. Negative Findings in >>> Electronic Health Records and Biomedical Ontologies: A Realist >>> Approach. International Journal of Medical Informatics 2007;2007:326-333. >>> >> http://www.referent-tracking.com/RTU/sendfile/?file=IJMI-MIE2006-Ceusters3-1.pdf >>> >> >> >> As a general point about list postings, I want to point out that >> referring someone to an article is not as useful as it might seem. >> What part of this article do you think is most important? What in >> the article is going to answer the question of the original poster? >> Surely this can be summed up in a few sentences, or slightly more, >> even, or at least, some indication of the general strategy for > > You might read the RESULTS and CONCLUSION parts of the Abstract: > > RESULTS: We introduced a new family of 'lacks' relations into the OBO > Relation Ontology. The relation lacks_part, for example, defined in > terms of the positive relation part_of, holds between a particular p > and a universal u when p has no instance of u as part. Since p and u > both exist, assertions involving 'lacks_part' and its cognates meet > the requirements of positivity. CONCLUSION: By expanding the OBO > Relation Ontology, we were able to accommodate nearly all occurrences > of negative findings in the sample studied. > >> >>>> They have >>>> found absolute space useful but non-existent, yet it is reality. Numbers >>>> are the cornerstone of mathematics and, therefore, more science; you >>>> still haven't told me whether these are real yet. Ingvar did at least >>>> tell me his position (only "1" exists). >>> >>> The strategy, in order to keep BFO as small as possible, is to focus >>> only on what is non-abstract, emphasizing always that it is subject >>> to the open world assumption, and thus that things might change. SUMO >>> includes many abstracta, and is accordingly huge. >>> >> >> >> The bit about space always has seemed curious to me. Why should >> absolute space be built into the BFO, when it's known that there >> isn't any such thing? If there is anything that's settled science, >> it's probably that one thing. >> >> Regarding the size of an ontology, if there are lots of things in >> the world, shouldn't there be, accordingly, lots of terms in the >> ontology that describes them? There are useful taxonomies of all >> species ever known to have existed, with tens of millions of >> categories. No person can keep it all in mind, but even before >> digital representations of it, taxonomists could easily work with >> the tree of life. Similarly for neuroanatomy, for instance. > > BFO is designed as a very small discipline-neutral ontology. It does > not contain any terms pertaining to specific scientific domains. We > are addressing the issue of how spatial regions are to be dealt with > in the context of the planned release of BFO 2.0. > > >> ------------------ >> Adam M. Goldstein PhD, MSLIS >> -- >> z_c...@sh... >> http://www.shiftingbalance.org >> http://www.twitter.com/shiftingbalance >> -- >> http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180621 >> -- >> Associate Editor >> Reviews Editor >> Evolution: Education & Outreach >> http://www.springer.com/life+sci/journal/12052 >> -- >> (914) 637-2717 (msg) >> -- >> Dept of Philosophy >> Iona College >> 715 North Avenue >> New Rochelle NY 10801 >> >> ------------------------------------------------------------------------------ >> The Palm PDK Hot Apps Program offers developers who use the >> Plug-In Development Kit to bring their C/C++ apps to Palm for a share >> of $1 Million in cash or HP Products. Visit us here for more details: >> http://ad.doubleclick.net/clk;226879339;13503038;l? >> http://clk.atdmt.com/CRS/go/247765532/direct/01/ >> _______________________________________________ >> Obo-discuss mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-discuss > > > > ------------------------------------------------------------------------------ > The Palm PDK Hot Apps Program offers developers who use the > Plug-In Development Kit to bring their C/C++ apps to Palm for a share > of $1 Million in cash or HP Products. Visit us here for more details: > http://ad.doubleclick.net/clk;226879339;13503038;l? > http://clk.atdmt.com/CRS/go/247765532/direct/01/ > _______________________________________________ > Obo-discuss mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-discuss > > ------------------------------------------------------------------------------ > The Palm PDK Hot Apps Program offers developers who use the > Plug-In Development Kit to bring their C/C++ apps to Palm for a share > of $1 Million in cash or HP Products. Visit us here for more details: > http://ad.doubleclick.net/clk;226879339;13503038;l? > http://clk.atdmt.com/CRS/go/247765532/direct/01/ > _______________________________________________ > Sbml-annot mailing list > Sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-annot |
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From: Nicolas Le n. <le...@eb...> - 2010-07-27 17:25:30
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See post below, about the "lack" relationships. Not without resonance with our own predicament. -------- Original Message -------- Subject: Re: [Obo-discuss] Ontological Realism and OBO Foundry Criteria Date: Tue, 27 Jul 2010 13:07:04 -0400 From: Barry Smith <phi...@bu...> Reply-To: obo...@li... To: obo...@li..., obo...@li... At 12:53 PM 7/27/2010, Adam M. Goldstein wrote: >On Jul 27, 2010, at 9:04 AM, Barry Smith wrote: > > > At 12:14 PM 7/26/2010, Phillip Lord wrote: > >> Barry Smith <phi...@bu...> writes: > >>> At 07:35 AM 7/18/2010, Robert Stevens wrote: > >>>> we can find lots of evidence for instances. We have lots of evidence, > >>>> for example, for individual glucose molecules. What evidence do we > >>>> have for the other entity -- the glucose universal? > >>> > >>> The fact that scientists describe multiple instances thus. > >>> Repeatedly. Effectively. Usefully. (Also, of course, revisably -- > >>> scientist might teach us better.) > >>> > >>> In addition, of course, there is the chemist's conception of the > >>> corresponding category. > >>> > >>> So scientists are able to describe those repeated instances > >>> effectively because they are somehow able to match their conception > >>> to something in those instances, something repeatedly observed. This > >>> cannot BE the scientists' conception, because it was there before the > >>> scientists came along. > >> > >> > >> Which kind of sums up my confusion over realism and the bendability of > >> your notion of reality. Scientists have found absent hand repeatable > >> effective and useful, yet according to you it is not reality. > > > > See, again, Ceusters W, Elkin P, Smith B. Negative Findings in > > Electronic Health Records and Biomedical Ontologies: A Realist > > Approach. International Journal of Medical Informatics 2007;2007:326-333. > > > http://www.referent-tracking.com/RTU/sendfile/?file=IJMI-MIE2006-Ceusters3-1.pdf > > > > >As a general point about list postings, I want to point out that >referring someone to an article is not as useful as it might seem. >What part of this article do you think is most important? What in >the article is going to answer the question of the original poster? >Surely this can be summed up in a few sentences, or slightly more, >even, or at least, some indication of the general strategy for You might read the RESULTS and CONCLUSION parts of the Abstract: RESULTS: We introduced a new family of 'lacks' relations into the OBO Relation Ontology. The relation lacks_part, for example, defined in terms of the positive relation part_of, holds between a particular p and a universal u when p has no instance of u as part. Since p and u both exist, assertions involving 'lacks_part' and its cognates meet the requirements of positivity. CONCLUSION: By expanding the OBO Relation Ontology, we were able to accommodate nearly all occurrences of negative findings in the sample studied. > > >> They have > >> found absolute space useful but non-existent, yet it is reality. Numbers > >> are the cornerstone of mathematics and, therefore, more science; you > >> still haven't told me whether these are real yet. Ingvar did at least > >> tell me his position (only "1" exists). > > > > The strategy, in order to keep BFO as small as possible, is to focus > > only on what is non-abstract, emphasizing always that it is subject > > to the open world assumption, and thus that things might change. SUMO > > includes many abstracta, and is accordingly huge. > > > > >The bit about space always has seemed curious to me. Why should >absolute space be built into the BFO, when it's known that there >isn't any such thing? If there is anything that's settled science, >it's probably that one thing. > >Regarding the size of an ontology, if there are lots of things in >the world, shouldn't there be, accordingly, lots of terms in the >ontology that describes them? There are useful taxonomies of all >species ever known to have existed, with tens of millions of >categories. No person can keep it all in mind, but even before >digital representations of it, taxonomists could easily work with >the tree of life. Similarly for neuroanatomy, for instance. BFO is designed as a very small discipline-neutral ontology. It does not contain any terms pertaining to specific scientific domains. We are addressing the issue of how spatial regions are to be dealt with in the context of the planned release of BFO 2.0. >------------------ >Adam M. Goldstein PhD, MSLIS >-- >z_c...@sh... >http://www.shiftingbalance.org >http://www.twitter.com/shiftingbalance >-- >http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=180621 >-- >Associate Editor >Reviews Editor >Evolution: Education & Outreach >http://www.springer.com/life+sci/journal/12052 >-- >(914) 637-2717 (msg) >-- >Dept of Philosophy >Iona College >715 North Avenue >New Rochelle NY 10801 > >------------------------------------------------------------------------------ >The Palm PDK Hot Apps Program offers developers who use the >Plug-In Development Kit to bring their C/C++ apps to Palm for a share >of $1 Million in cash or HP Products. Visit us here for more details: >http://ad.doubleclick.net/clk;226879339;13503038;l? >http://clk.atdmt.com/CRS/go/247765532/direct/01/ >_______________________________________________ >Obo-discuss mailing list >Obo...@li... >https://lists.sourceforge.net/lists/listinfo/obo-discuss ------------------------------------------------------------------------------ The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://ad.doubleclick.net/clk;226879339;13503038;l? http://clk.atdmt.com/CRS/go/247765532/direct/01/ _______________________________________________ Obo-discuss mailing list Obo...@li... https://lists.sourceforge.net/lists/listinfo/obo-discuss |
