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Re: [sbml-annot] annotation spec
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From: Nicolas Le n. <le...@eb...> - 2011-01-22 19:26:26
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My 2-cents: Merging of SBML files is none of SBML business. There is a package on model composition. We have to cope with this situation, not the merging. Annotations are contained in their elements. With model composition, there is no ambiguity. But this is a good reason why model composition should always be done using complete SBML elements, and not random pieces of XML as it has been suggested. On 22/01/11 19:12, Dagmar Waltemath wrote: > Hi, > > > On 01/21/2011 04:44 PM, Neil Swainston wrote: >> Hi Nick, >> >> You make a good point here regarding annotation of attributes. >> >> Everyone else: if we are merging two files, is the use of XPath as we now suggest OK? >> >> For example... >> >> //species[id='y']/@initialConcentration >> >> If a species id="y" is in both files, how do we know which one we're refering to? > > Am I right assuming that we have a problem anyways if merging two SBML > files with identical species names, e.g. which species[id='y'] are we > referring to from a reaction in the speciesference? Is that valid > SBML/XML actually? > > But, again, I wasn't sure why we said to prefer the short paths to the > complete ones? Can anyone help me? > >> Another way would be to use... >> >> ancestor-or-self::species[1]/@initialConcentration >> >> Which, when used in an annotation tag, would find the first parent "species" element above the annotation. i.e. the annotation would refer to the species in which it is enclosed. > > Did we not exclude this because species orders might get mixed up, e.g. > when loading SBML files in and out of software tools? (SBML doesn't > force any order on its elements?) > > Dagmar > > > >> This may be a non-issue. But if anyone responds I'd be happy to discuss further. >> >> Cheers, >> >> Neil. >> >> Neil Swainston >> Experimental Officer >> >> Manchester Centre for Integrative Systems Biology >> Manchester Interdisciplinary Biocentre >> University of Manchester >> Manchester M1 7DN >> United Kingdom >> >> On 21 Jan 2011, at 15:29, Nick Juty wrote: >> >>> Cheers for getting back to me ;p >>> >>> For the XPath thing, I was thinking if you merged 2 models, each with an element with id=y (say), the new model would have 2 different y ids, would that cause issues? Not being familiar with validation of SBML, at what point does the new model become invalid? eg I imagined someone hacking together 2 submodels without computational assistance (just to be complicated).... >>> >>> For the anno: prefix, you're right - it could be giraffe - which strangely sounds good! >>> >>> cheers! >>> >>> Nick >>> >>> Neil Swainston wrote: >>>> Cheers, Nick, >>>> I've merged in your changes with some that Dagmar suggested: >>>> http://dl.dropbox.com/u/8980329/Annot.doc >>>> Hope the link now works. >>>> Regarding using ids in XPath statements, SBML requires that ids are unique within a model. So the situation that you mention shoudn't arise, I guess? (Or are you considering some modular extension of Level 3 that I'm not fully familiar with?) >>>> With the annot:annotation thing, I guess it is a little confusing, but these should only ever be read by software anyways. The annot prefix is only really shorthand for the full namespace... >>>> http://www.sbml.org/sbml/level3/version1/annot/version1 >>>> ..so in principle one could change this to "giraffe" of whatever and the RDF would still be valid. Do you have any suggestions, though? It's certainly not too late to raise any issues. >>>> Cheers, >>>> Neil. >>>> Neil Swainston >>>> Experimental Officer >>>> Manchester Centre for Integrative Systems Biology >>>> Manchester Interdisciplinary Biocentre >>>> University of Manchester >>>> Manchester M1 7DN >>>> United Kingdom >>>> On 21 Jan 2011, at 14:07, Nick Juty wrote: >>>>> Hi Neil, >>>>> >>>>> Just going through the proposal. >>>>> I have a couple of questions/comments. Pretty much all of this is optional though - feel free to ignore as much of it as you wish. In fact you could conceivably just trash the email completely ;p >>>>> >>>>> Have a good weekend! >>>>> >>>>> cheers >>>>> >>>>> Nick >>>>> >>>>> Ps Well actually the 1st point I would change for accuracy ... >>>>> >>>>> ========================= >>>>> Page 5 - "To uniquely identify a controlled vocabulary term or object, the MIRIAM Resources scheme is used." >>>>> I would change that to the scheme described in the MIRIAM Standard. >>>>> >>>>> Page 6 - "FURTHER RDF:LI ELEMENT" >>>>> Would it be possible to expand the example to actually show 2 URIs (say Ex1, Ex2), then modify the sentence below to something like: >>>>> ...RDF provides three additional concepts to encode the relations between the statements, Ex1 and Ex2 above, other than the one (rdf:bag) to which the core spec is currently limited. >>>>> The examples below do detail it well though - so thats optional! >>>>> >>>>> Page 7 - "Furthermore, no clear definition of the different or similar meanings between the following two examples is provided:" >>>>> Furthermore, there is no clear definition that states the semantic difference between the 2 alternative encodings of the same information below: >>>>> >>>>> Page 9 - "Adding the XML attribute annot:required to the<sbml> element and setting its value to false indicates this:" >>>>> would reword that to something like: This can be defined by adding the XML attribute annot:required to the<sbml> element, and setting its value to false: >>>>> >>>>> Page 9 - XPath question. //x['y'] selects the x nodes, with id=y. What happens when you have 2 models stitched together and there is more than 1 'y'? >>>>> >>>>> Page 12 comment - annot:annotation looks messy to me. If I was not familiar with the spec/core/extenstions, and used SBML for the first time, I would think my parser/writer had stuttered or something. I guess its too late to propose something else? >> ------------------------------------------------------------------------------ >> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! >> Finally, a world-class log management solution at an even better price-free! >> Download using promo code Free_Logger_4_Dev2Dev. Offer expires >> February 28th, so secure your free ArcSight Logger TODAY! >> http://p.sf.net/sfu/arcsight-sfd2d >> _______________________________________________ >> Sbml-annot mailing list >> Sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbml-annot > > > ------------------------------------------------------------------------------ > Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! > Finally, a world-class log management solution at an even better price-free! > Download using promo code Free_Logger_4_Dev2Dev. Offer expires > February 28th, so secure your free ArcSight Logger TODAY! > http://p.sf.net/sfu/arcsight-sfd2d > _______________________________________________ > 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/ |
