Dr. Knowledge Or: I Stopped Worrying and Love the Semantic Web
Relaxed keynote for the bioinformatics research group COEUS lab meeting.
Semantic Web intro + COEUS
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
WAVe: Web Analysis of the Variome
WAVe has been finally published on Human Mutation (IF: 6.887) Lopes, P., Dalgleish, R. and Oliveira, J. L. (2011), WAVe: web analysis of the variome. Human Mutation, 32. doi: 10.1002/humu.21499
Taverna & EU-ADR
Presentation shown to Taverna development team to kick-off the discussion on how to improve and enhance Taverna usage in the EU-ADR Web Platform. Open publication – Free publishing – More adr
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
WAVe & Semantic Web @ GEN2PHEN GAM6
GEN2PHEN GAM 6 September 27th, 2010, Montpellier WAVe Open publication – Free publishing – More bioinformatics Open publication – Free publishing – More semantic web
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…