This page points to external listings as well as providing a place to describe different approaches for converting existing tabular data (spreadsheets and CSV files, mostly) to RDF.For starters, OpenRefine and
References gleaned from the public-semweb-lifesci@w3.org list:
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Rafael Richards: Healthcare data published by the CDC unfortunately comes as nearly 200 separate spreadsheets:
Lee Feigenbaum: As you say, Anzo (in particular Anzo for Excel) is designed for enterprises to curate large numbers of spreadsheets, map them to ontologies & to existing RDF instance data, and maintain them as changes are made to the spreadsheets or to the data in the spreadsheets. It can be used for CSV-style "tabular" spreadsheets and also for arbitrarily "human-oriented" spreadsheets. It can be used both in interactive modes (where people are opening up and interacting with spreadsheets) and also in automated batch modes.
Anzo stores the RDF data from spreadsheets in an RDF database. Anzo includes both authenticated and unauthenticated SPARQL endpoints for this data; Anzo can also directly publish the data as Linked Data. Finally, Anzo gives you several ways to export RDF data from the database.
Anzo is available in several editions:
- Anzo Express Starter -- includes Anzo for Excel as above for limited #s of users; freely available
- Anzo Express -- includes Anzo for Excel and Anzo on the Web, a user-friendly browser-based dashboard tool for visualization, searching, and analyzing RDF data
- Anzo Enterprise -- includes the above in addition to tools to connect to data in relational databases, to integrate unstructured data from documents, web pages, etc., to run rules and reasoning and work flow processes, various server-side and client-side APIs, etc.
We also make Anzo available for free for academic use.
If you're interested in learning more about Anzo or trying it out for some of these CDC spreadsheets or the HL7/CIMI work or for any other purpose, please drop me a note and I'll be happy to help you out.
OpenRefine and its predecessor Google Refine are worth learning, and Eliza from Weill Cornell wrote and has
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documented a Google Refine plugin for VIVO.
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Tim Lebo from RPI maintains a Alternative Tabular to RDF Converters page on Github.
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Peter Ansell: Michel Dumontier's php-lib library is what Bio2RDF has been using for converting TSV, CSV files (and other file formats) to RDF [1]. It contains some aspects that are Bio2RDF specific, namely its support for prefixed URIs, but any Pull Requests on GitHub would be appreciated to generalise that. OSX has PHP installed by default as far as I know so you can use it on the command line without any other dependencies.
You can find examples of scripts using php-lib in the bio2rdf-scripts repository on GitHub [2]. A fairly simple example would be the HGNC converter, which is Tab separated, but quite similar [3].
[1] https://github.com/micheldumontier/php-lib
[2] https://github.com/bio2rdf/bio2rdf-scripts
[3] https://github.com/bio2rdf/bio2rdf-scripts/blob/master/hgnc/hgnc.php#L129
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Katy Wolstencroft: Our tool, RightField (http://www.rightfield.org.uk), allows you to embed ontology term selection into spreadsheets, and to extract these selections as RDF. It is designed more for assisting in the data collection process (i.e. when users fill in a spreadsheet that has been marked-up using RightField, they are automatically collecting semantically enriched data).
Our paper from last year's eScience conference describes the RDF extraction in more detail:
Wolstencroft, Katherine; Owen, Stuart; Goble, Carole; Nguyen, Quyen; Krebs, Olga; Muller, Wolfgang; , "RightField: Semantic enrichment of Systems Biology data using spreadsheets," E-Science (e-Science), 2012 IEEE 8th International Conference on , vol., no., pp.1-8, 8-12 Oct. 2012
doi: 10.1109/eScience.2012.6404412
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