WikiPathways: building research communities on biological pathways.

Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology annotations, the ability to mark pathways as private for a limited time and the availability of stable hyperlinks to pathways and the elements therein. WikiPathways content is freely available in a variety of formats such as the BioPAX standard, and the content is increasingly adopted by external databases and tools, including Wikipedia. A recent development is the use of WikiPathways as a staging ground for centrally curated databases such as Reactome. WikiPathways is seeing steady growth in the number of users, page views and edits for each pathway. To assess whether the community curation experiment can be considered successful, here we analyze the relation between use and contribution, which gives results in line with other wiki projects. The novel use of pathway pages as supplementary material to publications, as well as the addition of tailored content for research domains, is expected to stimulate growth further

Where are your Manners? Sharing Best Community Practices in the Web 2.0

The Web 2.0 fosters the creation of communities by offering users a wide array of social software tools. While the success of these tools is based on their ability to support different interaction patterns among users by imposing as few limitations as possible, the communities they support are not free of rules (just think about the posting rules in a community forum or the editing rules in a thematic wiki). In this paper we propose a framework for the sharing of best community practices in the form of a (potentially rule-based) annotation layer that can be integrated with existing Web 2.0 community tools (with specific focus on wikis). This solution is characterized by minimal intrusiveness and plays nicely within the open spirit of the Web 2.0 by providing users with behavioral hints rather than by enforcing the strict adherence to a set of rules.Comment: ACM symposium on Applied Computing, Honolulu : \'Etats-Unis d'Am\'erique (2009

Simple identification tools in FishBase

Simple identification tools for fish species were included in the FishBase information system from its inception. Early tools made use of the relational model and characters like fin ray meristics. Soon pictures and drawings were added as a further help, similar to a field guide. Later came the computerization of existing dichotomous keys, again in combination with pictures and other information, and the ability to restrict possible species by country, area, or taxonomic group. Today, www.FishBase.org offers four different ways to identify species. This paper describes these tools with their advantages and disadvantages, and suggests various options for further development. It explores the possibility of a holistic and integrated computeraided strategy

The Conference Review Process

This presentation is for students on the 3rd year ECS Multimedia course where students run their own conference, and submit and review papers. In this presentation we explain the academic review process, look at the structure of a review, and give some examples of positive and negative reviews

Towards OpenMath Content Dictionaries as Linked Data

"The term 'Linked Data' refers to a set of best practices for publishing and connecting structured data on the web". Linked Data make the Semantic Web work practically, which means that information can be retrieved without complicated lookup mechanisms, that a lightweight semantics enables scalable reasoning, and that the decentral nature of the Web is respected. OpenMath Content Dictionaries (CDs) have the same characteristics - in principle, but not yet in practice. The Linking Open Data movement has made a considerable practical impact: Governments, broadcasting stations, scientific publishers, and many more actors are already contributing to the "Web of Data". Queries can be answered in a distributed way, and services aggregating data from different sources are replacing hard-coded mashups. However, these services are currently entirely lacking mathematical functionality. I will discuss real-world scenarios, where today's RDF-based Linked Data do not quite get their job done, but where an integration of OpenMath would help - were it not for certain conceptual and practical restrictions. I will point out conceptual shortcomings in the OpenMath 2 specification and common bad practices in publishing CDs and then propose concrete steps to overcome them and to contribute OpenMath CDs to the Web of Data.Comment: Presented at the OpenMath Workshop 2010, http://cicm2010.cnam.fr/om