I've recently gone to the hearth of Mediterranean, Athens, for the annual meeting of the DC-THERA network, an FP6 project. A number of people and organisations collaborate in the context of this project, under the hat of dendritic cells research (DC). Even me, the amateurish biologist, can guess the importance of this kind of cells for the Immune system, and their consequent importance for the development of a number of vaccines and therapies. In fact, the DC are the all-around players of the Immune system, able to sense different types of pathogenic stimuli, and to play the role of bridge agents between the front-line Innate Immune Response, and the specialised, evolving and memory-capable Adaptive Response.
The DC-THERA network tries to put together multiple competencies on DCs, as well as on Bioinformatics, with the main aim of developing DC-based vaccines and therapies.
A day with Biology and Medicine
I could only grasp some general understanding on the first day, being it focused on the “Bio” side of the issue. Nonetheless, one thing it seemed clear was the difficulty of transferring this kind of research from the bench to the patients, for effective and safe healing. The bench-to-bed route is complex and requires long time. One of the reasons, for instance, (fortunately) is the set of regulatory issues to take into consideration before making available a vaccine to the general public. Despite that, some interesting results were presented during the meeting, for instance the approaches used for the development of DC-based vaccines, presented by Dr Chris Schmidt.
Proposing Computer Science to the Life Science guys
I was more at my ease on the second day, when the Bioinformatics session took place. Here, pathways and computational methods for pathway-based biological discovery were topics which had a certain focus. In particular, Prof. Duccio Cavalieri highlighted how pathway-based queries can be more effective (than gene-by-gene queries) in crawling repositories of high-throughput data, such as microarray repositories, one of which is being developed by the DC-THERA network as well. This is also shown in the work presented by Prof. Sorin Draghici, where several aspects about the role that molecular entities play in biological systems are exploited to analyse microarray data (see also here).
Pathway means, for the Bioinformatician, information with semantic structure, conceptualisation, ontologies. The presentation by Andrea Splendiani sees the pathways from this point of view. He gave an overview of RDFScape software. Being developed as an extension of Cytoscape, it allows, in a general and flexible way, to exploit the power of bio-ontologies for doing integrated analysis of numbers (e.g.: gene expression, protein-protein interactions) and semantic annotations (e.g.: BioPAX, Gene Ontology).
There are key aspects in the developments of Bioinformatics of the next future. For instance: a) managing biological knowledge by providing an effective and machine-readable representation of the meaning of things b) connecting biological knowledge and knowledge related to it (e.g.: regulatory information, results related to data sets and outlined by analysing them). This was also mentioned by Prof. Cavalieri (who pointed us to this comment). Me, Andrea, Ciro Scognamiglio and Michaela Güendel are involved in DCTHERA with the project for the development of a “DCTHERA directory”. As Michaela presented, this is similar, in its conception, to the Italian Biodirectory, another similar solution of ours, but with a reasonable compromise, which takes into account several aspects: need to be flexible in the representation of heterogeneous information (e.g.: protocols and SOPs, data set summary descriptions, bio-materials summary descriptions), need to connect semantically related information (even by means of automatic inference), need to balance complexity and time/budget restrictions. In addition, semantics, ontologies and web technologies (i.e.: Semantic Web) will play a valuable role in the kind of information we have to deal with. So that it will be also similar, at least in its approach, to the SWED project.
Yet another topic was the setting up of a microarray resource for the network. This is particularly interesting to me because it could be a starting point for integrating a traditional data repository with the Bioinformatics tools developed by some of the DC-THERA participants. I presented my PhD work as a possible approach to perform a part of such an integration, the one which concerns with storing results from gene expression analysis, together with data the analysis is based on.