- From: Roderic Page <r.page@bio.gla.ac.uk>
- Date: Mon, 12 Jan 2009 17:23:58 +0000
- To: public-lod@w3.org
- Cc: Daniel O'Connor <daniel.oconnor@gmail.com>
- Message-Id: <38356F0C-8F06-45E0-8590-A5086C039DDC@bio.gla.ac.uk>
Dear Daniel, Regarding publications (and your off-list inquiry about bioGUID) I've tweaked bioGUID to serve some simple RDF, given a publication identifier such as a DOI or a PubMed id. I like simplicity, so I use Dublin Core and PRISM as vocabularies to describe a journal article. Example URIs are: http://bioguid.info/pmid:9628005 http://bioguid.info/doi:10.1097/MPH.0b013e318186533f In a web browser these display HTML, but in a tool like http://dataviewer.zitgist.com/ you get RDF. Under the hood bioGUID is an OpenURL resolver that wraps CrossRef and PubMed, but also has access to JSTOR, and a database of other literature that I'm building (mainly taxonomic -- I developed this as part of a project on biological taxonomy). To do a search for an article you can do an OpenURL query (and you can ask for JSON or RDF to be returned), e.g. http://bioguid.info/openurl?genre=article&title=Molecular Phylogenetics and Evolution&volume=42&spage=157&display=rdf This is all a bit crude (I hacked the RDF stuff together this afternoon), but it may be of use. Regards Rod On 10 Jan 2009, at 10:14, Daniel O'Connor wrote: > Hey all, > I'm Daniel O'Connor, a software engineer from Australia. > > At the moment I'm trying to get a lot of food nutrition data > together from a whole bunch of different sources and create a bit of > an ontology; publish it as RDF; and make sure its chock full of > linked data goodness; and I could use your help, advice, pointers > and encouragement. > > Use cases include things like shopping, diet / fitness applications, > cooking, and much more. > what did you eat today? -> hey, that's only 75% of your recommended > daily energy intake > what is the approximate food energy in this recipe? > tell me the fattiest food I'm eating and replace it with one with > more protein (but the same energy content) > > The data sources I've got on my list so far are: > USDA's SR21 food nutrients data (public domain) > Australia's NUTTAB 06 data (not so public domain) > Canadia's CNF data (haven't delved into it in depth) > The typical format provided is CSV, so I'm going through and mapping > those CSV exports back into a RDBMS (php + mysql / pgsql / etc), > then providing tools to generate RDF out, and publishing the static > results. > > > You can see (and get) the code from: > http://freebase-owl.googlecode.com/svn/trunk/nutrition/ > > and read a bit more about installing from: > http://clockwerx.blogspot.com/2009/01/generating-nutritional-data-rdf-from.html > > > and view samples of the output: > USDA: > http://lauken.com/doconnor/nutrition/usda/1006.rdf > > NUTTAB: > http://lauken.com/doconnor/nutrition/nuttab/01A10027.rdf > > Ontology (draft!): > http://www.lauken.com/doconnor/nutrition/0.1/schema.rdf > > > > There's a lot of work for me here, and if anyone here has knowledge > or a helping hand, I'd love to hear from you, especially regarding > the ones in bold. > Resolve licensing agreements with Aust. government for rights to > reproduce data (in progress) > Model Canadian data > Find or create a suitable ontology for Nutrition data (I would have > expected some common terms from the bio-rdf community, but I don't > have the background to know what I'm looking for) > Model the USDA, NUTTAB and Canadian extensions as appropriate > Find or create (ick hope not) an ontology for measurements in > relation to typical nutrition measurements (again, there's no > semantic web concepts for milligrams, kilocalories, etc - not even > in dbpedia. timbl did some very high level concepts of what a Gram / > etc is; but its not quite the same) > Find or create a list of terms used in nutrition data (shorthand/ > abbreivations) - ie CBODF = "Carbohydrate by difference", but I > can't seem to find a good list of these outside of the USDA data > itself. > Find or create a journal publications ontology (dublincore might do > it though; or some other bibliographic ontology) - suggestions? > Find or create science terms ontology (Paper, Subject, Experiment, > Samples, etc) - anyone? > Create owl:sameAs links to DBPedia topics in some automated fashion > - this is tricky, because a lot of the data is written as "Cheese, > blue" and is much more granular than wikipedia articles about Cheese. > Create owl:sameAs links to Freebase topics in some automated fashion > - ditto > Interlink Canadian, NUTTAB, USDA data in some automated fashion - > similar - different naming schemes make using dc:title as a IFP a > bit annoying. > Render full sets of RDF for each > Publish these somewhere - http://lauken.com/doconnor/ is not > suitable for anything more than a sandbox > Provide human interfaces as appropriate - if anyone wanted to create > shiny XSLT -> XHTML perhaps; or PHP glue... > Setup a SPARQL endpoint (I have a hell of a time doing this in my > development environment, so this might not happen) - HELP! > Provide unit test coverage for all generator tools > Refactor lots > > > --------------------------------------------------------- Roderic Page Professor of Taxonomy DEEB, FBLS Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK Email: r.page@bio.gla.ac.uk Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rodpage1962@aim.com Facebook: http://www.facebook.com/profile.php?id=1112517192 Twitter: http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
Received on Monday, 12 January 2009 17:24:35 UTC