Exposing The Cancer Genome Atlas (TCGA) as a SPARQL endpoint

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 facilities across the USA

CHORUS Deliverable 2.1: State of the Art on Multimedia Search Engines

Based on the information provided by European projects and national initiatives related to multimedia search as well as domains experts that participated in the CHORUS Think-thanks and workshops, this document reports on the state of the art related to multimedia content search from, a technical, and socio-economic perspective. The technical perspective includes an up to date view on content based indexing and retrieval technologies, multimedia search in the context of mobile devices and peer-to-peer networks, and an overview of current evaluation and benchmark inititiatives to measure the performance of multimedia search engines. From a socio-economic perspective we inventorize the impact and legal consequences of these technical advances and point out future directions of research

Quality Assessment of Linked Datasets using Probabilistic Approximation

With the increasing application of Linked Open Data, assessing the quality of datasets by computing quality metrics becomes an issue of crucial importance. For large and evolving datasets, an exact, deterministic computation of the quality metrics is too time consuming or expensive. We employ probabilistic techniques such as Reservoir Sampling, Bloom Filters and Clustering Coefficient estimation for implementing a broad set of data quality metrics in an approximate but sufficiently accurate way. Our implementation is integrated in the comprehensive data quality assessment framework Luzzu. We evaluated its performance and accuracy on Linked Open Datasets of broad relevance.Comment: 15 pages, 2 figures, To appear in ESWC 2015 proceeding

Trusty URIs: Verifiable, Immutable, and Permanent Digital Artifacts for Linked Data

To make digital resources on the web verifiable, immutable, and permanent, we propose a technique to include cryptographic hash values in URIs. We call them trusty URIs and we show how they can be used for approaches like nanopublications to make not only specific resources but their entire reference trees verifiable. Digital artifacts can be identified not only on the byte level but on more abstract levels such as RDF graphs, which means that resources keep their hash values even when presented in a different format. Our approach sticks to the core principles of the web, namely openness and decentralized architecture, is fully compatible with existing standards and protocols, and can therefore be used right away. Evaluation of our reference implementations shows that these desired properties are indeed accomplished by our approach, and that it remains practical even for very large files.Comment: Small error corrected in the text (table data was correct) on page 13: "All average values are below 0.8s (0.03s for batch mode). Using Java in batch mode even requires only 1ms per file.

Making Digital Artifacts on the Web Verifiable and Reliable

The current Web has no general mechanisms to make digital artifacts --- such as datasets, code, texts, and images --- verifiable and permanent. For digital artifacts that are supposed to be immutable, there is moreover no commonly accepted method to enforce this immutability. These shortcomings have a serious negative impact on the ability to reproduce the results of processes that rely on Web resources, which in turn heavily impacts areas such as science where reproducibility is important. To solve this problem, we propose trusty URIs containing cryptographic hash values. We show how trusty URIs can be used for the verification of digital artifacts, in a manner that is independent of the serialization format in the case of structured data files such as nanopublications. We demonstrate how the contents of these files become immutable, including dependencies to external digital artifacts and thereby extending the range of verifiability to the entire reference tree. Our approach sticks to the core principles of the Web, namely openness and decentralized architecture, and is fully compatible with existing standards and protocols. Evaluation of our reference implementations shows that these design goals are indeed accomplished by our approach, and that it remains practical even for very large files.Comment: Extended version of conference paper: arXiv:1401.577