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Re: Nutrition / Linked data

From: Roderic Page <r.page@bio.gla.ac.uk>
Date: Mon, 12 Jan 2009 17:23:58 +0000
Cc: Daniel O'Connor <daniel.oconnor@gmail.com>
Message-Id: <38356F0C-8F06-45E0-8590-A5086C039DDC@bio.gla.ac.uk>
To: public-lod@w3.org
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

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