A semantic web application framework for health systems interoperability

Pedro Lopes & José Luís Oliveira DOI: 10.1145/2064747.2064768 Presentation Open publication – Free publishing – More bioinformatics Abstract Relevant biomedical advances happen daily, and the medical profession relies on this evolution to deliver an improved patient care. In addition, the growing magnitude of data generated by biomedical software and hardware since the initial discovery of the human genome is remarkable in size and variety. Hence, best-of-breed software solutions are at best a couple years behind clinical practice demands. In this paper we detail an innovative Semantic Web interoperability framework, which provides developers with a complete software stack for semantic application deployment. Interoperability is the defining feature of this framework. On the one hand, new instances are…

Towards Knowledge Federation for Biomedical Applications

Towards Knowledge Federation for Biomedical Applications Pedro Lopes & José Luís Oliveira DOI: 10.1145/2063518.2063530 I-Semantics 2011, 7th International Conference on Semantic Systems; September 2011 – Graz, Austria Open publication – Free publishing – More semantic Abstract: Knowledge federation is a particular matter of concern in the life sciences domain. The magnitude of data generated by biomedical software and hardware since the initial discovery of the human genome is tremendous in quantity and diversity. Consequently, state-of-the-art software solutions have always lagged behind researchers’ demands, even more so with recent developments in high-throughput sequencing technology and open access to digital disease records. The maturity of Semantic Web technologies brought with it new strategies to tackle life sciences challenges….

ISCB SCS 2011

A knowledge federation strategy for integrating genotype-to-phenotype data July 15 – Vienna, Austria

Internship Labmeeting

WAVe, Semantic Web and The Meaning of Life Talk given and Brookeslab Lab Meeting. It covers mostly WAVe and Semantic Web stuff, the topics I’ve worked with during my internship. Open publication – Free publishing – More wave

BioABC

Biological Augmented Browsing Connector Explore the ideas of augmented browsing in life sciences-related applications. Key topics: REST based web service accepts LSRN identifiers HTML output according to provided identifier type JavaScript to trigger service execution JS library + CSS Adaptable to any application

Intelligent Data Gathering for Bioinformatics

Update: merged with ConceptBrowser from Sérgio Matos. New application that will search results for user submitted queries in various search engines (Google, Yahoo, Bing…). A map is built from the results, showing relations between pages, what the pages contain, what the pages refers to… and then, show information about the pages in an outstanding workspace. For instance, searching for BRCA2 in Google provides an immense amount of information that cannot be ignored: wiki pages, uniprot, genome.gov… If we could organize this information in a coherent manner, it could mean something in bioinformatics. Moreover, we can predefine a set of “known links” and offer more information about these links. If a link points to uniprot, we…

Semantic Web in GEN2PHEN

GEN2PHEN

Semantic Web developments are gaining momentum in the scientific research community: the usage of semantics is finally being considered as a valuable solution to integrate resources and compose services.

WAVe database model

First stable version of the database model is complete. Upcoming issues: how to crawl the databases to get the variants where is GEN2PHEN lsdb listing how to get variation metadata like publications and so on, will a specific parser for each database be required? develop the final app in C# or Java? C# would be faster… Java stripes?

WAVe 1 – 0 Coeus

WAVe has beaten Coeus in a closed match yesterday afternoon… A top-2-bottom perspective should be followed and development in WAVe should kick off ASAP There is no information available on how will coeus and its semantic web developments recover from such a defeat…

Redmine update + Coeus

Redmine update status: running 0.8.7 @ bioserver.ieeta.pt:8000 The problem is in the ruby service (loops between on and off). I don’t know if it’s a versioning problem or a mongrel one… I’ll wait for the next redmine release and try to fix it. Coeus will be the name of the semantic concept management platform I’ll be developing for my PhD. He was one the 12 greek titans, the god of wisdom/knowledge/intelligence. Future post in Plog will explain everything. I am also responsible for the Semantic Web section in GEN2PHEN KC, must prepare an opening post.