Re: [cellml-discussion] Graphing metadata
David Nickerson wrote: Therefore, you have to be aware of the relationship between RDF/XML and the RDF data model, and make sure you put your rdf:ID in the right place (as with any other attribute in RDF). ok - I think something just dropped into place. So in this case what I would do is define my simulation like cs:simulation rdf:Description rdf:ID=simulation-ID cs:simulationNamecool_name/cs:simulationName ... /rdf:Description /cs:simulation and then I can use that ID to reference the simulation. Is that making sense now? Probably a good thing that this discussion is starting to make me work out how RDF actually works :-) Yes, that will do what you want (I am assuming, of course, that cs:simulation is a propertyElt of some sort). BTW the specification is supposed to describe what the RDF graph will look like, and not constrain the RDF/XML that you can use. The RDF/XML is merely provided to give a non-normative example of RDF/XML which results in a valid RDF graph. Perhaps this needs to be made clearer in the specification? Possibly it could be clearer, but that is certainly the way I understand it. I'm just using the RDF/XML as a way that I almost understand to illustrate the RDF... And I agree that it would be good to be able to define a graph externally for any simulation, so maybe we need something to say that while the blank node approach is valid it is more useful not to use them? Or do we actually want to define this as part of the specification? I don't think we should be constraining the RDF/XML that can be used to encode the RDF, because this is supposed to be an RDF level specification. Because anonymous nodes are convenience feature of RDF/XML, rather than part of RDF proper, it wouldn't really make sense to put a normative constraint at this level (after all, people could be using languages other than RDF/XML to represent the data anyway). Simply putting the document through a parse / serialise cycle on any of the existing RDF software would remove anonymous nodes anyway, since most parsers assign the nodes a URL, and the serialisers just spit this out again. agreed. I wouldn't be opposed, however, to adding a style guideline recommending that graph nodes be given an explicit URL (we actually say that they would normally be an anonymous node at the moment), so they can be referenced. The only disadvantages of this is that the resulting RDF/XML is longer and more deeply nested, and that people could be tempted to perform open-world extensions to existing simulations, rather than making a copy at a new URL. do you really mean graph nodes, or do you mean cs:simulation nodes? If Sorry, it should be simulation nodes at least (although perhaps commenting on graphs would also be useful, for example, graph http://www.cellml.org/models/myModel/download#mygraph demonstrates that (reified statement node) could be useful metadata for knowledge management systems, as could access to almost any node in the RDF graph). Suggesting that anonymous nodes not be used could be one approach, although it would result in harder to read metadata in the hand-coded case (the model repository will mess up nicely hand-optimised RDF/XML anyway, though). you do mean graph nodes then I'm even more confused than I thought... To me it makes sense that simulation(s) are defined within a model, and in some cases it makes sense to also define graphs within a model. However, there are also many cases where you want to plot graphs using data from multiple models. So this means either having graph metadata external to the models and simulations or creating a single super model that imports all the models of interest and using that. I can see cases where both of these approaches will useful. Thanks, David ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] Graphing metadata
Hi all, I have just been looking through the graphing metadata specification (http://www.cellml.org/specifications/metadata/graphs) and have a couple of questions (pretty much due to my continuing RDF ignorance). This specification seems to have dropped behind the simulation specification a bit, so I'm using the simulation spec rather than the example given in the graphing spec. In the fragment cg:x-variable rdf:parseType=Resource cg:simulation rdf:nodeID=mainsim/ cg:variablerdf:Description rdf:about=#time//cg:variable /cg:x-variable (and similar for the y-variable and the text states the use of cg:simulation but the example contains cs:simulation) I can see how the use of the rdf:nodeID on the cg:simulation works when the simulation and the graph metadata are contained in the same graph. But what I want to do is have my graph metadata independent of the simulation (and model) metadata. For example, I want to specify a graph which plots variables from different models each specified in a different model at different URIs. So my question is whether the following RDF is the equivalent of the above fragment for the case where the graph metadata is in a different RDF graph to the simulation: cg:x-variable rdf:parseType=Resource cg:simulation rdf:resource=file:///example/models/swing.xml#mainsim/ cg:variablerdf:Description rdf:about=#time//cg:variable /cg:x-variable given the cs:simulation is defined cs:simulation rdf:ID=mainsim rdf:parseType=Resource ... /cs:simulation in the file at the URI file:///example/models/swing.xml ?? And if this is the case, is it then valid to also define a rdf:nodeID on the same simulation node for use in graphs within simulation's graph? or in such a case is it better to just always use the rdf:ID? Thanks, David. -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty of Engineering National University of Singapore Email: [EMAIL PROTECTED] ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Graphing metadata
David Nickerson wrote: Hi all, I have just been looking through the graphing metadata specification (http://www.cellml.org/specifications/metadata/graphs) and have a couple of questions (pretty much due to my continuing RDF ignorance). This specification seems to have dropped behind the simulation specification a bit, so I'm using the simulation spec rather than the example given in the graphing spec. In the fragment cg:x-variable rdf:parseType=Resource cg:simulation rdf:nodeID=mainsim/ cg:variablerdf:Description rdf:about=#time//cg:variable /cg:x-variable (and similar for the y-variable and the text states the use of cg:simulation but the example contains cs:simulation) I can see how the use of the rdf:nodeID on the cg:simulation works when the simulation and the graph metadata are contained in the same graph. But what I want to do is have my graph metadata independent of the simulation (and model) metadata. For example, I want to specify a graph which plots variables from different models each specified in a different model at different URIs. So my question is whether the following RDF is the equivalent of the above fragment for the case where the graph metadata is in a different RDF graph to the simulation: cg:x-variable rdf:parseType=Resource cg:simulation rdf:resource=file:///example/models/swing.xml#mainsim/ cg:variablerdf:Description rdf:about=#time//cg:variable /cg:x-variable given the cs:simulation is defined cs:simulation rdf:ID=mainsim rdf:parseType=Resource ... /cs:simulation The fragment you have given reifies the anonymous node generated by parseTypeResourcePropertyElement, as per . http://www.w3.org/TR/2004/REC-rdf-syntax-grammar-20040210/#parseTypeLiteralPropertyElt i.e. what you have is equivalent to (I am assuming that the above fragment is in rdf:Description rdf:about=#mymodel ), and writing out very long hand, unoptimised RDF: rdf:Description rdf:about=#mymodel cg:simulation rdf:Description rdf:about=http://www.example.org/generated-anonymous-node-URL#0; / /cg:simulation /rdf:Description rdf:Description rdf:about=#mainsim rdf:subjectrdf:Description rdf:about=#mymodel//rdf:subject rdf:predicaterdf:Description rdf:about=http://www.cellml.org/metadata/graphs/1.0#simulation//rdf:predicate rdf:objectrdf:Description rdf:about=http://www.example.org/generated-anonymous-node-URL#0//rdf:object rdf:typerdf:Description rdf:about=|http://www.w3.org/1999/02/22-rdf-syntax-ns#Statement|//rdf:type /rdf:Description This is clearly not what you want. You can't use rdf:parseType=Resource to get this, because that always generates an anonymous node. Instead, you need to explictly add an rdf:Description like this: rdf:Description rdf:about=#mymodel cg:simulation rdf:Description rdf:ID=mainsim ... /rdf:Description /cg:simulation /rdf:Description in the file at the URI file:///example/models/swing.xml ?? And if this is the case, is it then valid to also define a rdf:nodeID on the same simulation node for use in graphs within simulation's graph? or in such a case is it better to just always use the rdf:ID? Nodes can only have one URL. If it is an anonymous node, the RDF parser will generate a URL for it (unless it has an rdf:nodeID which matches an existing rdf:nodeID, in which case it will use the existing URL instead). Since you don't know what URL is generated, you cannot refer to an anonymous node outside of the document. If you use an rdf:ID, you explicitly set the URL to xml:base # rdf:ID. In summary: * You can have rdf:nodeID, or rdf:ID, but not both. * Use anonymous nodes if it would never make sense to access the node from outside the document. * Assign an explicit URL with rdf:ID or rdf:about if it would make sense to access the node from outside the document. Of course, it could be argued that it should be possible to define a graph externally for any simulation, and that would suggest that we should never use anonymous nodes to describe simulations. BTW if you are unsure what RDF graph gets generated from RDF/XML, the W3C RDF validator has a feature to visualise this. See http://www.w3.org/RDF/Validator/ Best regards, Andrew ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Graphing metadata
Andrew Miller wrote: David Nickerson wrote: Thanks Andrew, cleared a few things up. So now for some more ideas/questions... When defining a graph outside the scope of a single model or when combining results from multiple model's, does it still make sense to use the about=modelid ? I have been looking at how to define my graph externally and came up with this: rdf:RDF xmlns:rdf=http://www.w3.org/1999/02/22-rdf-syntax-ns#; xmlns:cs=http://www.cellml.org/metadata/simulation/1.0#; xmlns:cg=http://www.cellml.org/metadata/graphs/1.0#; rdf:Description cg:graph rdf:parseType=Resource cg:traces rdf:parseType=Collection rdf:Description cg:type rdf:resource=http://www.cellml.org/metadata/graphs/1.0#line/ cg:colour#ff/cg:colour cg:x-variable xml:base=parabola.xml rdf:parseType=Resource cg:simulation rdf:resource=#parabola_simulation/ cg:variable rdf:resource=#time/ /cg:x-variable cg:y-variable xml:base=parabola.xml rdf:parseType=Resource cg:simulation rdf:resource=#parabola_simulation/ cg:variable rdf:resource=#y/ /cg:y-variable /rdf:Description rdf:Description cg:type rdf:resource=http://www.cellml.org/metadata/graphs/1.0#scatter/ cg:colour#ff/cg:colour cg:glyph rdf:resource=http://www.cellml.org/metadata/graphs/1.0#circles/ cg:x-variable xml:base=parabola.xml rdf:parseType=Resource cg:simulation rdf:resource=#parabola_simulation_large_maxDT/ cg:variable rdf:resource=#time/ /cg:x-variable cg:y-variable xml:base=parabola.xml rdf:parseType=Resource cg:simulation rdf:resource=#parabola_simulation_large_maxDT/ cg:variable rdf:resource=#y/ /cg:y-variable /rdf:Description /cg:traces /cg:graph /rdf:Description /rdf:RDF In this example, all the xml-base attributes are the same so I could just specify it once on the top element, but potentially they could all be different. I presume you are aware that absolute URLs are allowed in rdf:about as well as relative ones? If you are going to use xml:base, you need to give a suitable absolute URL, as only one base URL is used to resolve relative URLs (i.e. it will not resolve against each base URL until it gets an absolute URL). Refer to section 5.2 of rfc2396.txt: Note that only the scheme component is required to be present in the base URI; the other components may be empty or undefined. So you need at least an http: or file: on your base URI (and obviously, a path as well if you are not going to give it in your relative URIs). hmmm...my example above seems to resolve the URIs as I expect when I put it through the RDF validator, and I can change the parabola.xml to something else for some of them and it'll resolve the relative URLs ok as well - but maybe that is processor dependent and may not always work? Are you just suggesting that it would be better to simply have rdf:resource=parabola.xml#parabola_simulation rather than use the xml:base attribute? Not sure why I didn't do that originally, makes more sense. The rdf:resource's for the cg:variable reference cmeta:id's defined on the variable's from the simulation's model (as defined in the spec) but the cg:simulation references the cs:simulation via the rdf:ID on the cs:simulation, eg, cs:simulation rdf:ID=parabola_simulation_large_maxDT rdf:parseType=Resource cs:simulationNameparabola_large_maxDT/cs:simulationName ... /cs:simulation I have used the validator tool Andrew mentioned, and the graph I get out looks like what I want for this graph metadata, and if I mangle simulation metadata into the RDF I paste into the validator everything seems to point to the right placesbut given Andrew's description below I'm guessing I shouldn't be using rdf:ID's in this way? You can use rdf:ID, but you have to be careful where you put it, because not all elements are treated equally in RDF/XML. In terms of the parser rules specified in the RDF/XML specification: Section 7.2.11 (for nodeElt) says: If there is an attribute /a/ with /a/.URI http://www.w3.org/TR/2004/REC-rdf-syntax-grammar-20040210/#eventterm-attribute-URI == |rdf:ID|, then /e/.subject http://www.w3.org/TR/2004/REC-rdf-syntax-grammar-20040210/#eventterm-element-subject := uri(identifier http://www.w3.org/TR/2004/REC-rdf-syntax-grammar-20040210/#eventterm-identifier-identifier := resolve(/e/, concat(#, /a/.string-value http://www.w3.org/TR/2004/REC-rdf-syntax-grammar-20040210/#eventterm-attribute-string-value))). So if you are putting the rdf:ID on a nodeElt, you are setting the subject of the node element, which is what you want. However, if you put the rdf:ID on a resourcePropertyElt,
