Keynote: We-Key, or Professional Wikis? (ISMB Bio-Ont SIG 2009)

Barend Mons

Showed the graph from from 2007 about Web X.0. What is Web 4.0? wwww? Why Would We Wiki? The “egosystem”. The key to successful wikis is that we are prepared to share our knowledge and prepared to get attribution for it. How can we make wikis for professional use? Not like wikipedia, but with community annotation and review. The very important thing is that we recognize authority. This is why they started the Concept Web Alliance.

The problem (also with wikis) is that no-one wants structured data entry – at least to write it: they want instead to just write free text. However, even if they don’t want structured data entry, they do want structured data! In the concept/token/object triangle: a concept should have a unique idea (e.g. malaria, transmission, mosquito).

Solving ambiguity with synonyms generally works nicely: use massive communities that we have in life sciences to do translation/addition of synonyms. It is therefore theoretically achievable to have a unique identifier for each concept. A triple to him is Concept1->Concept3-> Concept2, where Concept3 is the “relation”, e.g. (1: Barend Mons) (3: published) (2: this article).

Harmonizing data: they suggest doing this by going from data sources (in a daily feed) -> single MRS -> (via concept mapping) -> Peregrine, where the harmonized data will be. From Peregrine, you can link to a system that allows community annotation. The resulting triples are constructed in an unsupervised fashion. This will result in a massive triple store that is open for everyone to use however they like (e.g. as RDF or OWL or OBO etc).

There are different types of triples, such as curated tripes, observational triples and hypothetical triples. (Allyson: not sure if these are actually stored any differently, or just an explanation of the types of triples you can get.) Donate hypothetical triples to the database, even if you’re not sure. Later, if someone has evidence, you may get a nano-credit. These triples aren’t ontologies – they’re a rough source for ontologies. Then he provided an example using ErasmusMC.

Then there was a nice screenshot of the prototype of Wiki Professional. (url might be Also it seems it can show a regular page like PubMed and overlay the things it knows about the text on the page.

So, how is CWA different from SW (semantic web)? It has strictly non-semantic unique identifiers for concepts; a strict triple format; a layered structure (curated observational hypothetical); triple provenance; strict separation of authority and community; see the triple as a nano-publication with nano-credits – see how innovative you are rather than how many papers you’ve written.

FriendFeed discussion:

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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