Simple, ontology-based representation of biomedical statements (ISMB Bio-Ont SIG 2009)

…through fine-granular entity tagging and new web standards

Matthias Samwald et al.

He’s trying to make sense of a very large number of complicated interactions and connections between molecular phenomena. He’s part of the SW’s HCLSIG as part of W3C. Example: huge queries in the neurocommons knowledgebase, where they span multiple data sources. But there are still very few tools suitable for end users. He came up with <a>Tag, or associative tags. Here, you tag statements, not documents. You tag with entities, and not strings. It’s implemented with a bookmarklet. There is more to the bookmarklet than meets the eye: it is RDFa + SIOC + domain ontologies / terminologies. RDFa – allow you to imbed OWL and RDF snippets within HTML. Doing things this way means we don’t need to build everything from scratch, as can use existing HTML tools, e.g. move to a wordpress blog. aTags can also be generated by NLP web services.

Linked-data paradigm: entities have URIs that can be resolved to yield further information. Developers need understandable and predictable data structures across distributed data sources. They also don’t want to reinvent the wheel, and develop GUIs simply. Balance semantics and pragmatics.

FriendFeed discussion: http://ff.im/4xj6c

Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!

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