Semantic wikis, wikis enhanced with Semantic Web technologies, are appropriate systems for community-authored knowledge models. They are particularly suitable for scientific collaboration. This paper details the design principles of WikiBridge, a semantic wiki.
1 Introduction
Collaborative environments for scientific knowledge are essential for scientists
to formalize their ideas and to develop theories collaboratively. Large
numerous corpuses created in a collaborative effort have emerged in recent years.
For example the encyclopedia Wikipedia contains human-readable articles with
texts, images which are grouped into categories and access with a full text
search engine. Despite the power of wiki, it is difficult to answer a specific
query because of the purely textual information stored. As a result, automated
tools cannot understand knowledge and thus exploit it. Semantic wikis offer
an open environment which allows to aggregate knowledge produced by
different teams involved in different research fields. It also allows interoperability
among corpuses in case of annotations defined using ontologies. Nevertheless,
representing and managing life sciences data and related knowledge require
a deep understanding of life sciences concepts. Chen and Carlis in [
Our main objective is to build a platform that allows: 1) to capture both free and controlled data; 2) to verify that annotations have meaning in relation to domain knowledge; 3) and to ensure a reasonable cost of developing and maintaining.
The rest of the paper is organized as follow: section 2 describes the state of art of semantic wikis in Life Sciences, section 3 presents the design principles of WikiBridge. Finally, section 4 concludes the paper.
Wikis are simple to use, flexible and do not impose a predefined workflow, but with growing amount of content in wikis, it becomes increasingly difficult to find relevant information. In traditional wiki, semantics is not explicit, but is implicitly described by links between articles and by the context of the link (surrounding text): wiki engine does not interpret the knowledge contained in links graphs. A Semantic Wiki is a wiki enhanced with Semantic Web technologies that made it an appropriate system for community-authored knowledge models by adding machine readable semantics. Moreover, a semantic wiki supports incremental formalization of knowledge and offers enhanced navigation and query capabilities. We get insight below into semantic wikis for life sciences.
A wiki page of wikipedia1 maintains a list of bioinformatics wikis and
several semantic wikis projects dedicated to Life Sciences. In Makna [
WikiBridge is developed as a prototype tool to support knowledge engineers
in collaboratively formalizing knowledge. In this purpose we have extended
MediaWiki with some structural DBMS capabilities and semantic tools (see
figure 1). WikiBridge’s design principles are influenced by requirements given by
Uren et al. [
WikiBridge offers an interactive WYSIWYG editor using AJAX technology to communicate with the server backend in addition to the traditional structured text editor (offered by MediaWiki) that supports interactive typing of links and resources. The structured data can be managed by Semantic Forms extension2 for MediaWiki. Documents can be in different formats such as word files, graphic files, excel sheets, XML formats, OBO flat file. 1 http://en.wikipedia.org/wiki/Portal:Gene_Wiki/Other_Wikis 2 http://www.mediawiki.org/wiki/Extension:Semantic_Forms Document Management System
Data
Source Documents
Annotation Support
produce Annotation
Storage Query Engine
Knowledge Engineering
produce
Knowledge engineer Scientists
In a knowledge engineering process, it is common that non-technical domain experts work together with experienced knowledge engineers. This means that certain advanced functionalities can be hidden for novice users but are available to experienced users. Thus we use Access Control List (ACL) to describe privilege control depending on user identity and group affiliation.
WikiBridge supports annotation functionalities within the same interface as the primary data to avoid unnecessary context and application switches. In the meantime, these annotations must be maintained on clearly separated layers to keep integrity and traceability of the primary data. Different types of annotations have been identified: 1) simple annotation allows to tag a subject by describing some of its properties by a set of attribute value couples; 2) nary relation allows to map a subject with two or more values and references to other elements (subjects). In this case, some values properties reference another subject; 3) recursive annotation allows to explain or clarify an attribute by a sub-annotation. To be able to exchange data with other applications (e.g. ontology editors, Web Services, other wikis), WikiBridge is purely based on existing Semantic Web standards such as the Web Ontology Language OWL for describing ontologies and W3C’s RDF for annotations. Annotations are stored by RAP as RDF triples, separately from the original document. We explicitly store in a database the conceptual model defining the structure of the domain ontology; ontology is loaded from Protégé by a specific program. Information access has been designed with taking into account some features about users. We have thus identified an usage typology in accordance to 1) kind of usage: reader, investigation, clarification; 2) knowledge degree of the domain: domain specialists like biologist researchers and non specialists. Queries are expressed in SPARQL. We consider reasoning as one of the most important functionalities as it allows : 1) to emerge knowledge that is not explicit in the data; 2) to check annotations, and 3) to enhance navigation and search. First order logic constraints are checked with a Java component that interacts with Pellet and Jena. WikiBridge extension connects to the constraint checker by the means of a web service. 4
Conclusion In this article, we have presented WikiBridge, a feature-rich semantic wiki. The first experiment of the use of WikiBridge3 shows many interesting possibilities for scientific community, mainly the possibility to scientists share and collaboratively build annotated knowledge. We have demonstrated that flexibility and data quality required by scientific applications can be achieved by using wiki with semantic web technologies.