Tools for automatic or semi-automatic extraction of ontology concepts from GEO meta-data to RDF.
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7.1 years ago
William ★ 4.9k

Are there any (opensource) tools that can help with automatic or semi-automatic mapping of  keys and values in GEO metadata to concepts in an (medical) ontology?

All the metadata in GEO is based on free-text keys and values and I would like to convert this to something more machine readable based on concepts in a (medical) ontology.

Metadata like gender, organism and tissue are often presents for different studies but also often named differently. For instance gender can be called gender or sex and the values might be M/F or Male/Female, While this all means the same.

Google and Wikipedia bring me to this page:

http://en.wikipedia.org/wiki/Knowledge_extraction

And to this demo for free text

https://dandelion.eu/products/datatxt/nex/demo/?exec=true#results

The metadata I get from GEO is not free text but already in a table. Are there tools aimed at biology research that can convert a table with free text column keys and values to something more machine readable based on extracted concepts?

Lets say for example this table: 

age sex Treatment Responder

individual1 10 M Aspirin Responder

individual2 22 M Aspirin Responder

individual3 45 F Ibuprofen nonresponder
GEO metadata ontology rdf • 2.1k views
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