Semantic Wiki Links article published

A while back, I posted an entry here called "Stepping towards a Semantic Wikipedia" that quickly became the most-visited post on this blog.  Today, after several months of waiting, I discovered by accident that the official peer-reviewed article on the same subject is now available (the editors never bothered to tell us that it came out).  The article elaborates on a pattern that allows Wikipedia users to write content directly into the semantic Web.  The article is called "Building a biomedical semantic network in Wikipedia with Semantic Wiki Links" and is now available at DATABASE: The Journal of Biological Databases and Curation.  Here is the abstract:

"Wikipedia is increasingly used as a platform for collaborative data curation, but its current technical implementation has significant limitations that hinder its use in biocuration applications. Specifically, while editors can easily link between two articles in Wikipedia to indicate a relationship, there is no way to indicate the nature of that relationship in a way that is computationally accessible to the system or to external developers. For example, in addition to noting a relationship between a gene and a disease, it would be useful to differentiate the cases where genetic mutation or altered expression causes the disease. Here, we introduce a straightforward method that allows Wikipedia editors to embed computable semantic relations directly in the context of current Wikipedia articles. In addition, we demonstrate two novel applications enabled by the presence of these new relationships. The first is a dynamically generated information box that can be rendered on all semantically enhanced Wikipedia articles. The second is a prototype gene annotation system that draws its content from the gene-centric articles on Wikipedia and exposes the new semantic relationships to enable previously impossible, user-defined queries."

I will also be presenting a poster about this and related work at the upcoming Biocuration meeting in Washington DC.  Stop by for a chat!

Stepping towards a Semantic Wikipedia

(Update, check out our publication in Database for a full-length, peer-reviewed version of this article.)

It is now possible to specify the nature of the relationships between things described by Wikipedia articles directly in the context of the article.  The image below is a screenshot taken a few moments ago of the Phospholamban article on Wikipedia (with excited arrows added).  The infobox at the top right is dynamically generated from semantic markup in the article using a Wikipedia user script written by my colleague Sal and accessible from his user page. 

Semantic markup now live in Wikipedia

How it works

Wikilinks in the article have been annotated with the kind of relationship that they indicate using the Semantic Wiki Link (SWL) template. The template allows any Wikipedia editor (including you!) to specify the type of connection that exists between the article where the link is being placed and the target of the link. This information is encoded following the microformat pattern. Essentially, we encode the meaning of the links in class attributes that wrap the link.

This works as follows:

1. Editor inserts a SWL into a Wikipedia article with this syntax:
• {{SWL | target=protein kinase S | label=PKA | type =substrate_for}}
• This means "the concept where you see this link is related to protein kinase A (labeled PKA) with the relationship type "substrate for". So, in the example above, it says: "Phospholamban is a substrate for PKA".
• The {{}} denotes a Wikipedia template. Templates can take parameters (here parameters are separated by |'s) and use them to produce new WikiText dynamically which, in turn, is rendered as HTML when a page is loaded.
2. When the page is rendered, the template generates the following semi-semantic HTML markup (with some formatting omitted for clarity):

• 
  
3. Programs, like the script that generated that infobox and added the green highlighting, can look for the SWL class attribute can then extract the meaning of the SWL links based on the class of its first child element - here "substrate_for".
4. In addition, when the template is processed it adds a category to the article it is placed on that corresponds to the relationship type. (See for example, the category for substrate.) This category provides a logical grouping (e.g. all things that serve as a biochemical substrate) but, perhaps more importantly, it provides a place to record the meaning of the relationship. This meaning can be defined as text, but can also be defined through reference to external sources such as ontologies on the semantic web.

Why its awesome

This pattern makes it possible for the vast number of Wikipedia users to simply and easily contribute machine readable content to the Web. This enormous user community collaboratively created the world's largest encyclopedia and one of the most valuable websites on the planet. Who better to help build the semantic Web? While, technically, the microformat-like implementation leaves much to be desired in terms of its robustness and its precision, it is a solution that can work. This is demonstrated by the success of projects like Google's recent recipe search that are based entirely on simple microformats.

How you can help

This is a new idea that not everyone in Wikipedia will be thrilled to see. They will claim that the SWLs will clutter the markup and will not provide enough value to make it worth it because Wikipedia itself does not support semantic links. You can help by:

• Using the template to enhance articles.
• Writing code that makes use of the added meaning such as user scripts, aggregators, or scripts that import the relationships into other structured repositories like FreeBase or DBpedia.
• Helping define the nature of the semantic links (at their associated category pages) and mapping them to properties defined in ontologies.
• Discussing (and voting for) the idea on the various 'talk pages' on Wikipedia.

Why its awesome again

Did I mention that this pattern makes it possible for the vast number of Wikipedia users to simply and easily contribute machine readable content to the Web? Thats pretty cool if you think about it...

Update: To make the user script work for you so you can see the infobox, do this:

• Create a Wikipedia user account if you don't have one already
• Go to/create your user page. (e.g. my user name there is i9606 and my user page is located at http://en.wikipedia.org/wiki/User:I9606 )
• Edit your user page add this to it - 

[[/common.js]]

• Visit your new common.js add this to it - 

importScript('User:Sal9000/SWLinfobox.js');

• When that is saved, you should be all set. Now go visit an enhanced page like Phospholamban and look for the green box at the upper right corner.

The script will run whenever you access a Wikipedia page while you are logged in to your account. Its a lot like GreaseMonkey, (which I've had some fun with in the past) but its not tied to your browser and will only work on Wikipedia. If enough people like a user script, it can be added to the default set of Wikipedia user preferences.. which would be pretty cool ;). The best part? You (or a programmer friend of yours) can write your own script and make it do whatever you want with the data!