Re: Can RDFa be used on XML: pharma information
This may also be an interesting way of intersecting microarray (mageml) and semantic web (rdfa) ... -Kei Ivan Herman wrote: I am sorry if I come into this thread very late. Additionally to what Ralph just said, the RDFa distiller running on the W3C site: http://www.w3.org/2007/08/pyRdfa/ should actually work with an arbitrary XML file, although only SVG is 'announced' there (which is probably my mistake). If there is a problem then, well... it is my bug:-( Ivan Ralph R. Swick wrote: At 10:48 PM 6/23/2009 +1000, Rick Jelliffe wrote: I see that the 2008 draft http://www.w3.org/2006/07/SWD/RDFa/rdfa-overview says RDFa itself is intended to be a technique that allows for adding metadata to any (XML) markup document, including SMIL, RSS, SVG, MathML, etc. Note, however, that in the current state, RDFa is being defined only for the (X)HTML family of languages. The RDFa specification was designed with the intent that other languages than XHTML could take advantage of RDFa markup. (The terminology host language was used in some drafts to signal this direction.) The charter under which the group was operating was specific to XHTML, thus the wording in the W3C Recommendation. So I think I will go ahead and add some RDFa markup to the XML, By all means, reuse the RDFa vocabulary if it seems appropriate for your application.
RE: Can RDFa be used on XML: pharma information
hi kei, there is already something better than RDFa tags in MAGE-ML, the OntologyEntry tags. Their purpose is exactly to provide the information to link to the semantic web. The examples you provided from NIH are well annotated with those tags. cheers, michael Michael Miller Lead Software Developer Rosetta Biosoftware Business Unit www.rosettabio.com -Original Message- From: public-semweb-lifesci-requ...@w3.org [mailto:public-semweb-lifesci-requ...@w3.org] On Behalf Of Kei Cheung Sent: Friday, July 24, 2009 10:56 AM To: Ivan Herman Cc: Ralph R. Swick; Rick Jelliffe; public-semweb-lifesci@w3.org Subject: Re: Can RDFa be used on XML: pharma information This may also be an interesting way of intersecting microarray (mageml) and semantic web (rdfa) ... -Kei Ivan Herman wrote: I am sorry if I come into this thread very late. Additionally to what Ralph just said, the RDFa distiller running on the W3C site: http://www.w3.org/2007/08/pyRdfa/ should actually work with an arbitrary XML file, although only SVG is 'announced' there (which is probably my mistake). If there is a problem then, well... it is my bug:-( Ivan Ralph R. Swick wrote: At 10:48 PM 6/23/2009 +1000, Rick Jelliffe wrote: I see that the 2008 draft http://www.w3.org/2006/07/SWD/RDFa/rdfa-overview says RDFa itself is intended to be a technique that allows for adding metadata to any (XML) markup document, including SMIL, RSS, SVG, MathML, etc. Note, however, that in the current state, RDFa is being defined only for the (X)HTML family of languages. The RDFa specification was designed with the intent that other languages than XHTML could take advantage of RDFa markup. (The terminology host language was used in some drafts to signal this direction.) The charter under which the group was operating was specific to XHTML, thus the wording in the W3C Recommendation. So I think I will go ahead and add some RDFa markup to the XML, By all means, reuse the RDFa vocabulary if it seems appropriate for your application.
Re: Can RDFa be used on XML: pharma information
This is probably technically possible - but you'd need to process a lot of complex mage-ml to get out some quite simple information - there's a node-edge sample processing graph, plus all the external data files in there - mage-ml is mostly tags and the files are large. We've moved internally to MAGE-TAB format, we have a MAGE-TAB parser that's being used by a couple of groups. We will be developing a standalone parser/backend database which will allow users to build a standalone atlas. There may be more mileage in developing that parser further to support RDF than to persue MAGE-ML. thanks Helen Kei Cheung wrote: This may also be an interesting way of intersecting microarray (mageml) and semantic web (rdfa) ... -Kei Ivan Herman wrote: I am sorry if I come into this thread very late. Additionally to what Ralph just said, the RDFa distiller running on the W3C site: http://www.w3.org/2007/08/pyRdfa/ should actually work with an arbitrary XML file, although only SVG is 'announced' there (which is probably my mistake). If there is a problem then, well... it is my bug:-( Ivan Ralph R. Swick wrote: At 10:48 PM 6/23/2009 +1000, Rick Jelliffe wrote: I see that the 2008 draft http://www.w3.org/2006/07/SWD/RDFa/rdfa-overview says RDFa itself is intended to be a technique that allows for adding metadata to any (XML) markup document, including SMIL, RSS, SVG, MathML, etc. Note, however, that in the current state, RDFa is being defined only for the (X)HTML family of languages. The RDFa specification was designed with the intent that other languages than XHTML could take advantage of RDFa markup. (The terminology host language was used in some drafts to signal this direction.) The charter under which the group was operating was specific to XHTML, thus the wording in the W3C Recommendation. So I think I will go ahead and add some RDFa markup to the XML, By all means, reuse the RDFa vocabulary if it seems appropriate for your application.
Re: Can RDFa be used on XML: pharma information
I am sorry if I come into this thread very late. Additionally to what Ralph just said, the RDFa distiller running on the W3C site: http://www.w3.org/2007/08/pyRdfa/ should actually work with an arbitrary XML file, although only SVG is 'announced' there (which is probably my mistake). If there is a problem then, well... it is my bug:-( Ivan Ralph R. Swick wrote: At 10:48 PM 6/23/2009 +1000, Rick Jelliffe wrote: I see that the 2008 draft http://www.w3.org/2006/07/SWD/RDFa/rdfa-overview says RDFa itself is intended to be a technique that allows for adding metadata to any (XML) markup document, including SMIL, RSS, SVG, MathML, etc. Note, however, that in the current state, RDFa is being defined only for the (X)HTML family of languages. The RDFa specification was designed with the intent that other languages than XHTML could take advantage of RDFa markup. (The terminology host language was used in some drafts to signal this direction.) The charter under which the group was operating was specific to XHTML, thus the wording in the W3C Recommendation. So I think I will go ahead and add some RDFa markup to the XML, By all means, reuse the RDFa vocabulary if it seems appropriate for your application. -- Ivan Herman, W3C Semantic Web Activity Lead Home: http://www.w3.org/People/Ivan/ mobile: +31-641044153 PGP Key: http://www.ivan-herman.net/pgpkey.html FOAF: http://www.ivan-herman.net/foaf.rdf smime.p7s Description: S/MIME Cryptographic Signature
rdfs:sameAs ( was Re: Can RDFa be used on XML: pharma information)
Thanks for everyone for their useful help yesterday. I am deferring the RDFa parts, and instead will concentrate on making page-level RDF descriptions that may be useful for data links for the outside world. (The HTML pages are now full of ids, hproduct microformats class, HTML rel, and dublin Core, which may be some use.) So new plan is concentrate on simple RDF indexes on topical lines first. That seems rather less pioneering. Here is an example. For the medicines, I am first making abstract LSIDs for all the WHO ATC codes in our system (no representation retrievable). Then there will be a atc.rdf document with items like the following: rdf:Description rdf:about=urn:lsid:www.pbs.gov.au:atc-code:P01 rdfs:labelP01/rdfs:label foaf:isPrimaryTopicOf rdf:resource=http://www.pbs.gov.au/html/consumer/search/results?atc-code=A01A#pbs-search-results/ foaf:page rdf:resource=http://www.whocc.no/atcddd/indexdatabase/index.php?query=A01A/ rdfs:seeAlso rdf:resource=http://dbpedia.openlinksw.com:8890/page/ATC_code_A01A/ /rdf:Description Now the foaf:isPrimaryTopicOf is fine. And the rdfs:seeAlso is fine there. But the foaf:page has me feckless and fretting. It is the closest I can get for a semantic WHO URI. I really want to say What that page is about is what this page is about, ie that topic belonging to the LSID I am using is an alias for the topic in that page. I am tempted to use rdfs:sameAs but that seems to be used when the two pages are identical rather than two topics being the same. (Actually, rdfs:sameAs gets used sometimes semantically and sometimes for pages.) What is best practice here please? I suppose I could also use foaf:isPrimaryTopicOf too: is it ettiquette to say that some external page is actually about a local identifier? Cheers Rick Jelliffe
Re: Can RDFa be used on XML: pharma information
On Tue, Jun 23, 2009 at 11:20 AM, Rick Jellifferjelli...@allette.com.au wrote: I am working on improving the semweb markup on an Australian government Department of Health and Aging website, which has HTML and XML versions of the medicines allowed for prescription and the amount the government pays. It has various links to interesting documents, and we want to make it more semweb friendly. Here are two example pages to give you the idea (they have different selections of data): http://www.pbs.gov.au/html/consumer/search/results?term=Zyprexa%20Zydispublication=GE http://www.pbs.gov.au/xml/consumer/search/results?term=Zyprexa%20Zydispublication=GE We are doing some general things like improving the microformats (DC and hproduct) in the HTML. But the plan was to decorate the XML (which has extra information) with the appropriate RDFa, which seems perfect. But now I see that the RDFa spec says that RDFa is designed for use on XHTML. We do no want to use it that way, we want to augment the XML. So I was wondering if anyone here had any advice? I see the choices Instead of the XML end point, I would express all that content as RDF (possibly in the XML format). If you need the XML for the metadata info on the request, you could consider putting a RDF element somewhere in your custom XML. Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/
Re: Can RDFa be used on XML: pharma information
Hi Rick, I think adding parts of RDFa into your XML without turning the whole XML into some kind of XHTML document will not help much. If you want to use RDFa and make your data part of the Semantic Web, why don't you add more RDFa to your current HTML pages? I see that they do not contain all of the data in your XML file, but still there is some valuable information in the tables that is still without semantic markup. In case that the HTML and XML are generated from the same databases (and this seems to be the case), you could also make the information that is currently only available in the XML version available in the HTML version. If you want to hide the details from the reader, but make it available to the machines, then you can use 'hidden' RDFa. Just some ideas. Cheers, Matthias Samwald DERI Galway, Ireland http://deri.ie/ Konrad Lorenz Institute for Evolution Cognition Research, Austria http://kli.ac.at/ -- From: Rick Jelliffe rjelli...@allette.com.au Sent: Tuesday, June 23, 2009 11:20 AM To: public-semweb-lifesci@w3.org Subject: Can RDFa be used on XML: pharma information I am working on improving the semweb markup on an Australian government Department of Health and Aging website, which has HTML and XML versions of the medicines allowed for prescription and the amount the government pays. It has various links to interesting documents, and we want to make it more semweb friendly. Here are two example pages to give you the idea (they have different selections of data): http://www.pbs.gov.au/html/consumer/search/results?term=Zyprexa%20Zydispublication=GE http://www.pbs.gov.au/xml/consumer/search/results?term=Zyprexa%20Zydispublication=GE We are doing some general things like improving the microformats (DC and hproduct) in the HTML. But the plan was to decorate the XML (which has extra information) with the appropriate RDFa, which seems perfect. But now I see that the RDFa spec says that RDFa is designed for use on XHTML. We do no want to use it that way, we want to augment the XML. So I was wondering if anyone here had any advice? I see the choices 1) Convert to old RDF or some other format and making this available too: but we really don't want to do this (an extra thing to maintain, more bandwidth, etc) 2) Just ploughing ahead and using RDFa on XML even if nothing can use it. (Would that be the case?) 3) Err, Something clever from people on this list. Any ideas about what people do with RDF? Cheers Rick Jelliffe
Re: Can RDFa be used on XML: pharma information
So there is still no convenient way to mark up existing XML as RDF? It was a showstopper 10 years ago but I kind of expected there would have been some progresssigh (Like I said, it has different info from the HTML so adding RDFa to the HTML won't work; also the XML has existing customers so we don't want to alter that, though the idea of duplicating the XML data as RDF seems workable but a terrible hack; and we want to avoid having a new datafeed.) Cheers Rick Jelliffe
Re: Can RDFa be used on XML: pharma information
On Tue, Jun 23, 2009 at 11:49 AM, Rick Jellifferjelli...@allette.com.au wrote: So there is still no convenient way to mark up existing XML as RDF? It was a showstopper 10 years ago but I kind of expected there would have been some progresssigh Define 'markup'... you can just embed your RDF in your XML, using RDF/XML... the namespacing is the indication what is RDF and what is not... no other 'markup' needed... Can you elaborate on the inconveniences you talk about a bit more? That makes providing solutions easier... Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/
Re: Can RDFa be used on XML: pharma information
On 23/6/09 11:49, Rick Jelliffe wrote: So there is still no convenient way to mark up existing XML as RDF? It was a showstopper 10 years ago but I kind of expected there would have been some progresssigh Well, since you didn't seem keen on converting all the XML to RDF I didn't point you at http://www.w3.org/TR/2007/REC-grddl-20070911/ ... but that's certainly one of the answers to how to map XML into RDF that we didn't have in 1999. Since you're an XSLT genius, maybe it wouldn't be horribly painful just to write a convertor XSLT and link that from the namespace doc of your XML files? cheers, Dan
Re: Can RDFa be used on XML: pharma information
Dan Brickley wrote: On 23/6/09 11:49, Rick Jelliffe wrote: So there is still no convenient way to mark up existing XML as RDF? It was a showstopper 10 years ago but I kind of expected there would have been some progresssigh Well, since you didn't seem keen on converting all the XML to RDF I didn't point you at http://www.w3.org/TR/2007/REC-grddl-20070911/ ... but that's certainly one of the answers to how to map XML into RDF that we didn't have in 1999. Since you're an XSLT genius, maybe it wouldn't be horribly painful just to write a convertor XSLT and link that from the namespace doc of your XML files? I quite like the idea of GRDDL actually. I'm looking at it tonight too. Thanks! Rick
Re: Can RDFa be used on XML: pharma information
Egon Willighagen wrote: On Tue, Jun 23, 2009 at 11:49 AM, Rick Jellifferjelli...@allette.com.au wrote: So there is still no convenient way to mark up existing XML as RDF? It was a showstopper 10 years ago but I kind of expected there would have been some progresssigh Define 'markup'... Markup = annotation. Taking existing data and adding stuff to make it more useful, without disrupting existing uses of that data (and without creating the size/maintenance issues you get from duplication.) One of the rationales for this project is to make more effective use of bandwidth, which makes me lean against duplication somewhat, but it may indeed be the appropriate way. Cheers, and thanks, Rick Jelliffe
Re: Can RDFa be used on XML: pharma information
On Tue, Jun 23, 2009 at 12:15 PM, Rick Jellifferjelli...@allette.com.au wrote: Markup = annotation. Taking existing data and adding stuff to make it more useful, without disrupting existing uses of that data (and without creating the size/maintenance issues you get from duplication.) One of the rationales for this project is to make more effective use of bandwidth, which makes me lean against duplication somewhat, but it may indeed be the appropriate way. OK, so the requirement is to: 1. stick with the current XML, 2. provide RDF/XML. I think XSLT route proposed by others is the way to go then, making a third end point, which would take the current XML as input, convert it with XSLT to RDF/XML. Using RDF/XML has the advantage here that you can validate your XSLT stylesheet for the output content too, increasing your changes of detecting typos etc. Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/
Re: Can RDFa be used on XML: pharma information
Hi Rick, So there is still no convenient way to mark up existing XML as RDF? It was a showstopper 10 years ago but I kind of expected there would have been some progress I rather think that using XML as the default representation for RDF was the showstopper back then. RDF/XML is not a good serialisation for RDF, Turtle and N-Triples would have been a much better choice in comparison. I guess the choice for RDF/XML was made for diplomatic reasons (not basing any kind of new data standard on XML was unthinkable at that time), rather than practicality. (Like I said, it has different info from the HTML so adding RDFa to the HTML won't work; also the XML has existing customers so we don't want to alter that, though the idea of duplicating the XML data as RDF seems workable but a terrible hack; and we want to avoid having a new datafeed.) So you do not want to alter the XML in a substantial way, and neither want to create a RDF representation out of the XML via some kind of transformation? I am afraid that solving you problem is not possible under these constraints. Cheers, Matthias Samwald DERI Galway, Ireland http://deri.ie/ Konrad Lorenz Institute for Evolution Cognition Research, Austria http://kli.ac.at/
Re: Can RDFa be used on XML: pharma information
I see that the 2008 draft http://www.w3.org/2006/07/SWD/RDFa/rdfa-overview says RDFa itself is intended to be a technique that allows for adding metadata to any (XML) markup document, including SMIL, RSS, SVG, MathML, etc. Note, however, that in the current state, RDFa is being defined only for the (X)HTML family of languages. So I think I will go ahead and add some RDFa markup to the XML, so that there is some data on the web which might stimulate developers or inform them, and tell the client that we may need to change tack. Cheers Rick Jelliffe
Re: Can RDFa be used on XML: pharma information
On Tue, Jun 23, 2009 at 2:48 PM, Rick Jellifferjelli...@allette.com.au wrote: I see that the 2008 draft http://www.w3.org/2006/07/SWD/RDFa/rdfa-overview says RDFa itself is intended to be a technique that allows for adding metadata to any (XML) markup document, including SMIL, RSS, SVG, MathML, etc. Note, however, that in the current state, RDFa is being defined only for the (X)HTML family of languages. So I think I will go ahead and add some RDFa markup to the XML, so that there is some data on the web which might stimulate developers or inform them, and tell the client that we may need to change tack. The problem here is to define what attributes your XML will use to define the RDFa hooks... what attributes will define a new subject, the predicate, and how you define the object... Because the XML is using a local namespace, it will be unrecognizable for any client... however, given you define those attributes (or via new elements), you should be able to embed this RDFa in the HTML more easily too... Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/
Re: Can RDFa be used on XML: pharma information
Egon Willighagen wrote: The problem here is to define what attributes your XML will use to define the RDFa hooks... what attributes will define a new subject, the predicate, and how you define the object... Yes, we lose the html:base element and html:link, but why would we lose the predicates? @rel and @rev would presumably be available on any element: couldn't it be used so that instead of div about=http://dbpedia.org/resource/Albert_Einstein; span property=foaf:nameAlbert Einstein/span span property=dbp:dateOfBirth datatype=xsd:date1879-03-14/span div rel=dbp:birthPlace resource=http://dbpedia.org/resource/Germany; span property=dbp:conventionalLongNameFederal Republic of Germany/span /div /div I can have person about=http://dbpedia.org/resource/Albert_Einstein; name property=foaf:nameAlbert Einstein/name dob property=dbp:dateOfBirth datatype=xsd:date1879-03-14/dob nation rel=dbp:birthPlace resource=http://dbpedia.org/resource/Germany; name property=dbp:conventionalLongNameFederal Republic of Germany/name /nation /person It seems to me that where-ever RDFa does not rely on HTML semantics, it should be free (there is no conceptual impediment) to use on XML: it can certainly determine whether an XML element has a legit XMLliteral or mixed or element content. Because the XML is using a local namespace, it will be unrecognizable for any client... however, given you define those attributes (or via new elements), you should be able to embed this RDFa in the HTML more easily too... What is the necessary difference, for an RDFa engine, between span about=urn:ISBN:0091808189 typeof=biblio:book property=dc:title Canteen Cuisine /span and my:book about=urn:ISBN:0091808189 typeof=biblio:book property=dc:title Canteen Cuisine /my:book Cheers Rick Jelliffe
Re: Can RDFa be used on XML: pharma information
Hello, A nice example of the traps of data linking. The data seems to say that Einstein was born in the Federal Republic of Germany. In fact, he was born before the FRG was founded. Take care Oliver On Tue, Jun 23, 2009 at 9:22 AM, Rick Jellifferjelli...@allette.com.au wrote: Egon Willighagen wrote: The problem here is to define what attributes your XML will use to define the RDFa hooks... what attributes will define a new subject, the predicate, and how you define the object... Yes, we lose the html:base element and html:link, but why would we lose the predicates? @rel and @rev would presumably be available on any element: couldn't it be used so that instead of div about=http://dbpedia.org/resource/Albert_Einstein; span property=foaf:nameAlbert Einstein/span span property=dbp:dateOfBirth datatype=xsd:date1879-03-14/span div rel=dbp:birthPlace resource=http://dbpedia.org/resource/Germany; span property=dbp:conventionalLongNameFederal Republic of Germany/span /div /div I can have person about=http://dbpedia.org/resource/Albert_Einstein; name property=foaf:nameAlbert Einstein/name dob property=dbp:dateOfBirth datatype=xsd:date1879-03-14/dob nation rel=dbp:birthPlace resource=http://dbpedia.org/resource/Germany; name property=dbp:conventionalLongNameFederal Republic of Germany/name /nation /person It seems to me that where-ever RDFa does not rely on HTML semantics, it should be free (there is no conceptual impediment) to use on XML: it can certainly determine whether an XML element has a legit XMLliteral or mixed or element content. Because the XML is using a local namespace, it will be unrecognizable for any client... however, given you define those attributes (or via new elements), you should be able to embed this RDFa in the HTML more easily too... What is the necessary difference, for an RDFa engine, between span about=urn:ISBN:0091808189 typeof=biblio:book property=dc:title Canteen Cuisine /span and my:book about=urn:ISBN:0091808189 typeof=biblio:book property=dc:title Canteen Cuisine /my:book Cheers Rick Jelliffe -- Oliver Ruebenacker, Computational Cell Biologist BioPAX Integration at Virtual Cell (http://vcell.org/biopax) Center for Cell Analysis and Modeling http://www.oliver.curiousworld.org
Re: Can RDFa be used on XML: pharma information
Egon Willighagen wrote: Namespace... to solve this, you could do instead: my:book xhtml:about=urn:ISBN:0091808189 xhtml:typeof=biblio:book xhtml:property=dc:title Canteen Cuisine /my:book where the prefix xhtml would be bound to the namespace belonging to XHTML+RDFa... Waaa? In XML namespaces, an attribute with no qualifier is in no namespace. Does the RDF community work things so that you can detach any attribute with non namespace and re-use it with its element's namespace/prefix? Are you saying that a generic RDFa processor would actually be looking for xhtml:*/@property and would not understand */@property? Or are you saying that a generic RDFa processor would also accept */@xshtml:property Cheers Rick Jelliffe
Re: Can RDFa be used on XML: pharma information
At 10:48 PM 6/23/2009 +1000, Rick Jelliffe wrote: I see that the 2008 draft http://www.w3.org/2006/07/SWD/RDFa/rdfa-overview says RDFa itself is intended to be a technique that allows for adding metadata to any (XML) markup document, including SMIL, RSS, SVG, MathML, etc. Note, however, that in the current state, RDFa is being defined only for the (X)HTML family of languages. The RDFa specification was designed with the intent that other languages than XHTML could take advantage of RDFa markup. (The terminology host language was used in some drafts to signal this direction.) The charter under which the group was operating was specific to XHTML, thus the wording in the W3C Recommendation. So I think I will go ahead and add some RDFa markup to the XML, By all means, reuse the RDFa vocabulary if it seems appropriate for your application.
