- From: M. Scott Marshall <marshall@science.uva.nl>
- Date: Mon, 20 Feb 2006 16:55:57 +0100
- To: kc28 <kei.cheung@yale.edu>
- CC: public-semweb-lifesci@w3.org
> YeastHub (http://yeasthub.gersteinlab.org) provides an interactive web > interface to allow the user to register and map a web-accessible tabular > dataset into RDF/XML. If needed, we can turn this interactive interface > into a programmatic one to allow broader use. As part of a semantic web for data integration experiment(submitted for publishing), I adapted/hacked the Mapper program[1] to convert tabular data from a web source (ENCODE at UCSC, in csv format) to (our) RDF format ala YeastHub. Mapper can read from several common formats and database connections and write to the same, with possible transformations. The reason that we chose to start with the Mapper code, aside from the fact that it already worked on small examples, is that the mappings are disclosed in an XML file - as opposed to being coded directly into the program. Ideally, the mapping commands would be expressed in a standardized "mapping language" (which one? suggestions?), preferably expressible in RDF for the sake of uniformity and provenance. It is probably worth noting that what we generally find to be missing is information about the _semantic type_ of the data columns (yes, no surprise here!). In the best situation, when you've found information about the syntactic datatypes, you must still guess the semantic type and its relations to other types from the name in the header. Maybe someday, data exports will include not only options to export data and datatype to RDF but also the relevant semantic data types. best, scott [1]http://www.javaworld.com/javaworld/jw-04-2002/jw-0426-mapper.html -- M. Scott Marshall tel. +31 (0) 20 525 7765 http://staff.science.uva.nl/~marshall http://ibu.micro-array.nl/ Integrative Bioinformatics Unit, University of Amsterdam
Received on Monday, 20 February 2006 15:56:18 UTC