An algebra and conceptual model for semantic tagging of collaborative digital libraries

Cost-effective semantic description and annotation of shared knowledge resources has always been of great importance for digital libraries and large scale information systems in general. With the emergence of the Social Web and Web 2.0 technologies, a more effective semantic description and annotation, e.g., folksonomies, of digital library contents is envisioned to take place in collaborative and personalised environments. However, there is a lack of foundation and mathematical rigour for coping with contextualised management and retrieval of semantic annotations throughout their evolution as well as diversity in users and user communities. In this paper, we propose an ontological foundation for semantic annotations of digital libraries in terms of flexonomies. The proposed theoretical model relies on a high dimensional space with algebraic operators for contextualised access of semantic tags and annotations. The set of the proposed algebraic operators, however, is an adaptation of the set theoretic operators selection, projection, difference, intersection, union in database theory. To this extent, the proposed model is meant to lay the ontological foundation for a Digital Library 2.0 project in terms of geometric spaces rather than logic (description) based formalisms as a more efficient and scalable solution to the semantic annotation problem in large scale.

RT-Bst: an integrated approach for reverse transcription and enrichment of cDNA from viral RNA

The synthesis of cDNA from RNA is challenging due to the inefficiency of reverse transcription (RT). In order to address this, a method was developed known as RT-Bst for sequential RT of RNA and Bst DNA polymerase amplification for enrichment of cDNA in a single tube reaction. Using genomic RNA from bacteriophage MS2, the yield of cDNA produced by RT alone and RT-Bst were compared by analysis of PCR-amplified products. Using random primers a superior performance was observed when amplifying MS2 RNA following RT-Bst compared to RT alone, indicating that greater quantities of cDNA were present after RT-Bst. RT-Bst was also compared with RT alone for their relative ability to produce sufficient cDNA to amplify 8 target regions spanning the respiratory syncytial virus (RSV) genome. Six out of 8 targets were amplified consistently by PCR subsequent to RT-Bst amplification whereas only 3 out of 8 targets could be amplified after RT alone. RSV sequences were selectively amplified using RSV specific primers from a mixed template containing an excess of MS2 RNA in a RT-Bst reaction without amplifying MS2 sequences. This suggests that RT-Bst can be used to amplify RNA sequences non-specifically using random primers and specifically using sequence specific primers and enhances the yield of cDNA when compared to RT alone.