Semantic Web repositories for genomics data using the eXframe platform

Background: With the advent of inexpensive assay technologies, there has been an unprecedented growth in genomics data as well as the number of databases in which it is stored. In these databases, sample annotation using ontologies and controlled vocabularies is becoming more common. However, the annotation is rarely available as Linked Data, in a machine-readable format, or for standardized queries using SPARQL. This makes large-scale reuse, or integration with other knowledge bases very difficult. Methods: To address this challenge, we have developed the second generation of our eXframe platform, a reusable framework for creating online repositories of genomics experiments. This second generation model now publishes Semantic Web data. To accomplish this, we created an experiment model that covers provenance, citations, external links, assays, biomaterials used in the experiment, and the data collected during the process. The elements of our model are mapped to classes and properties from various established biomedical ontologies. Resource Description Framework (RDF) data is automatically produced using these mappings and indexed in an RDF store with a built-in Sparql Protocol and RDF Query Language (SPARQL) endpoint. Conclusions: Using the open-source eXframe software, institutions and laboratories can create Semantic Web repositories of their experiments, integrate it with heterogeneous resources and make it interoperable with the vast Semantic Web of biomedical knowledge

Pain Research Forum: application of scientific social media frameworks in neuroscience

Background: Social media has the potential to accelerate the pace of biomedical research through online collaboration, discussions, and faster sharing of information. Focused web-based scientific social collaboratories such as the Alzheimer Research Forum have been successful in engaging scientists in open discussions of the latest research and identifying gaps in knowledge. However, until recently, tools to rapidly create such communities and provide high-bandwidth information exchange between collaboratories in related fields did not exist. Methods: We have addressed this need by constructing a reusable framework to build online biomedical communities, based on Drupal, an open-source content management system. The framework incorporates elements of Semantic Web technology combined with social media. Here we present, as an exemplar of a web community built on our framework, the Pain Research Forum (PRF) (http://painresearchforum.org). PRF is a community of chronic pain researchers, established with the goal of fostering collaboration and communication among pain researchers. Results: Launched in 2011, PRF has over 1300 registered members with permission to submit content. It currently hosts over 150 topical news articles on research; more than 30 active or archived forum discussions and journal club features; a webinar series; an editor-curated weekly updated listing of relevant papers; and several other resources for the pain research community. All content is licensed for reuse under a Creative Commons license; the software is freely available. The framework was reused to develop other sites, notably the Multiple Sclerosis Discovery Forum (http://msdiscovery.org) and StemBook (http://stembook.org). Discussion: Web-based collaboratories are a crucial integrative tool supporting rapid information transmission and translation in several important research areas. In this article, we discuss the success factors, lessons learned, and ongoing challenges in using PRF as a driving force to develop tools for online collaboration in neuroscience. We also indicate ways these tools can be applied to other areas and uses

Neologism: Easy Vocabulary Publishing

Abstract. Creating, documenting, publishing and maintaining an RDF Schema vocabulary is a complex, time-consuming task. This makes vocabulary maintainers reluctant to evolve their creations quickly in response to user feedback; it prevents use of RDF for casual, ad-hoc data publication about niche topics; it leads to poorly documented vocabularies, and contributes to poor compliance of vocabularies with bestpractice recommendations. Neologism is a web-based vocabulary editor and publishing system that dramatically reduces the time required to create, publish and modify vocabularies. By removing a lot of pain from this process, Neologism will contribute to a generally more interesting, relevant and standards-compliant Semantic Web.

RDF and XML: Towards a unified query layer

lopes2010aInternational audienceOne of the requirements of current Semantic Web applications is to deal with heterogeneous data. The Resource Description Framework (RDF) is the W3C recommended standard for data representation, yet data represented and stored using the Extensible Markup Language (XML) is almost ubiquitous and remains the standard for data exchange. While RDF has a standard XML representation, XML Query languages are of limited use for transformations between natively stored RDF data and XML. Being able to work with both XML and RDF data using a common framework would be a great advantage and eliminate unnecessary intermediate steps that are currently used when handling both formats