“Philosophically we wanted to hand off the responsibility for the quality of the content of the system to the community and then provide generic technology that can be used to grow the knowledgebase on a daily basis,”
Given high-throughput data and the increasing number of papers describing them, “comprehensive and timely annotation of the literature for facts by any central team of experts [is] an unachievable goal. Computer assistance in the annotation process is, therefore urgently needed,” the scientists wrote in a paper published in the current issue of Genome Biology.
WikiProteins was created over the last two years and announced on May 28, by a team of scientists from the Swiss Institute of Bioinformatics, the GO consortium and the IntAct database at the European Molecular Biology Laboratory-European Bioinformatics Institute, Erasmus Medical Centre, Leiden University Medical Centre, both in the Netherlands, the Brazilian Stela Institute, the WikiMedia Foundation, and Knewco.
The project is an interactive and semantically supported workspace based on Wiki pages and contains a knowledgebase, a navigation tool, and a section on the people in its annotating community. Beneath that layer is a relational Wiki based on WikiData software, an indexer, and software that creates components called Knowlets, which stores the relationships between all the mined concepts.
The WikiProteins terminology has been mapped to concept identifiers in the Wiki-based terminology system called OmegaWiki. WikiProteins and OmegaWiki are driven by a relational database that is linked to the Knowlets by on-the-fly indexing of all Wiki pages. An indexer called Peregrine is designed to recognize concepts by the Wiki, and the indexer is coupled to a terminology system derived from OmegaWiki.
Each biomedical concept has its own page that includes up-to-date annotations. Registered users can become annotators and edit records. WikiProteins shows the new record alongside the original one that was mined from the authoritative databases. Professional annotators at their respective databases can choose to incorporate some of new community-entered information into their database.
Do you want to know more?