WikiProteins Brings Scientific Collaboration to the WikiSphere


      Bookmark and Share

BEST PRACTICES SERIES

Article ImageMany of the most significant scientific discoveries in human history have been the result of partnerships—the Curies and their work on radiation; Watson, Crick, and Franklin and the structure of DNA; and countless others. Without the teamwork that existed within those brain trusts, it’s easy to imagine that many important discoveries might have eluded solitary, isolated scientists for years. But the particular style of collaboration that has been practiced by scientists for centuries is starting to look old-fashioned. Scenes of white-coated researchers huddled furtively over a single microscope are a thing of the past. Collaboration in science, as in business, is going online, and a new project called WikiProteins, the first so-called WikiProfessional, is trying to find out how far technology can go to facilitate scientific discovery.

WikiProteins, which went live in early spring, has adapted the ubiquitous Wikipedia model in an effort to aggregate biomedical information from a collection of databases and resources into a single portal. The project is being spearheaded by Barend Mons, a bioinformatician at the Erasmus Medical Center in Rotterdam, the Netherlands. The goal of the project is to improve upon the existing information repositories relevant to the biomedical community by inviting the community to maintain its own collective resource. The initial data for WikiProteins comes from sources including Medline, UniProtKB/Swiss-Prot, GeneOntology, IntAct, and the Unified Medical Language System.

The wiki contains information on more than a million biomedical concepts, and allows scientists to add their own knowledge about concepts in their area of expertise. The hope is that this capability will allow scientists whose research might not otherwise intersect to learn from and collaborate with each other. In WikiProteins, data can be added both in free text and in a structured way, enabling community management of the underlying relational databases.

WikiProteins is just the first of what are being dubbed WikiProfessionals, an endeavor that officially launched in late March. In Barend Mons’s vision, a WikiProfessional is an online workspace that enables real-time knowledge exchange and exploration. The workspace functions as a "Semantic Wiki," connecting relational MediaWiki software with computational text analysis technology, called "Knowlets." According to the WikiProfessional website, "Knowlets summarize information about a concept and are composed of factual data from databases, co-occurrence with other concepts in sentences, and indirect associations with other concepts."

WikiProteins is a consortium initiative and is technically supported by Stichting Open Progress and the company Knewco, Inc. According to the biographical profile on WikiProteins, Knewco was born out of a chance meeting between Mons and Wikipedia founder Jimmy Wales at a scientific conference in Latin America. Mons shared his idea for Knowlets with Wales, and Wales directed Mons toward a wiki-based project called OmegaWiki that aimed to produce a free, multilingual resource for lexicological information (referred to as the "Ultimate Wiktionary").

WikiProfessional evolved out of the Knewco/OmegaWiki partnership, with the analytical power of the Knowlet technology being applied to the stores of biomedical information included in WikiProteins.

WikiProfessional is working to develop other wikis for aggregating information to serve professionals in various industries. In the works already are WikiAuthors, WikiChemicals, and WikiClinical. But the organization has extended an open invitation to develop a WikiProfessional for any topic of interest that could stand to benefit from wiki technology.