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| Eric Prud'hommeaux; Helena Deus; M. Scott Marshall. |
| Query federation is a way to make use of distributed data sources on the Web, including many SPARQL endpoints as well as relational databases. SWObjects makes use of mapping rules represented as SPARQL Constructs to dynamically rewrite the terms and predicates of a SPARQL query into corresponding terms in another vocabulary and connect the resulting query with the appropriate service for answering the query. SWObjects can also rewrite SPARQL queries in SQL, effectively including relational databases alongside SPARQL endpoints in a linked data federation. The author of SWObjects, Eric Prud'hommeaux, is the W3C staff contact for the W3C Health Care and Life Sciences Interest Group (HCLS IG) and will give the tutorial via a teleconference connection,... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5538/version/1 |
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| Jonas Almeida; Helena Deus; Wolfgang Maass. |
| Use of semantic web abstractions, in particular of domain neural Knowledge Organization Systems (KOS), to manage distributed, cloud based, integrative bioinformatics infrastructure. This presentation derives from recent publication:

Almeida JS, Deus HF, Maass W. (2010) S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. BMC Bioinformatics. 2010 Jul 20;11(1):387. [PMID 20646315].

These PowerPoint slides were presented at Semantic Web Applications and Tools for Life Sciences December 10th, 2010, Berlin, Germany (http://www.swat4ls.org/2010/progr.php), keynote 9-10 am. |
| Tipo: Presentation |
Palavras-chave: Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5537/version/1 |
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| Helena Deus. |
| Cancer is still one of the leading causes of death in the developed world. To address this problem, the US National Institutes of Health (NIH) has launched The Cancer Genome Atlas (TCGA), a large scale systematic approach to characterize tumor samples from 20 cancer types and approximately 10,000 donor patients by using multiple high-throughput approaches. 

Multidisciplinary projects such as TCGA and related projects across Europe aim at identifying cancer “driver” mutations to be used as therapeutic targets or diagnostic tests. Extracting and aggregating the knowledge necessary to identify such mutations remains a challenge primarily due to the need to reliably integrate the experimental datasets... |
| Tipo: Poster |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6169/version/1 |
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| Andra Waagmeester; Helena Deus; Chris T. Evelo. |
| Biology has become a data intensive science. Discovery of new biological facts increasingly relies on the ability to find and match appropriate biological data. For instance for functional annotation of genes of interest or for identification of pathways affected by over-expressed genes. Functional and pathway information about genes and proteins is typically distributed over a variety of databases and the literature.

Pathways are a convenient, easy to interpret way to describe known biological interactions. WikiPathways provides community curated pathways. WikiPathways users integrate their knowledge with facts from the literature and biological databases. The curated pathway is then reviewed and possibly corrected or... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6679/version/1 |
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| Helena Deus. |
| Automated discovery of candidate biomarkers from multiple databases has been the central challenge in the Life Sciences in general and in the study of systemic processes such as those documented by The Cancer Genome Atlas (TCGA) in particular. 

The maturation of Semantic Web technologies offers solutions to those problems by allowing the query to be defined by navigating a normally represented domains of discourse instantiated by the data. 

We address the systems challenge of The Cancer 
Genome Atlas initiative (http://cancergenome.nih.gov/), which generates a large scale repository of high throughput molecular biology data generated and processed at 5 academic... |
| Tipo: Poster |
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics; Data Standards. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6303/version/1 |
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