Publications & alike

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ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level

Summary: The first open source software suite that; (i) assists in the annotation and local management of experimental metadata from high-throughput studies employing one or a combination of omics and other technologies, (ii) empowers experimentalists and curators to use community-defined checklists and ontologies, and (iii) facilitates submission to international public repositories.

Philippe Rocca-Serra, Marco Brandizi, Eamonn Maguire, Nataliya Sklyar, Chris Taylor, Kimberly Begley, Dawn Field, Stephen Harris, Winston Hide, Oliver Hofmann, Steffen Neumann, Peter Sterk , Weida Tong  and Susanna-Assunta Sansone

Availability and Implementation: Software, documentation, case studies and implementations at: http://isatab.sourceforge.net/

Contact: isatools@googlegroups.com

Associate Editor: Dr. Jonathan Wren

Full content available here.

DC-THERA Directory, a Knowledge Management System for the support of the European Dendritic Cell Immunology Community

[dc-research.eu logo]Abstract. DC-THERA Directory is a web portal to support collaboration, communication and knowledge sharing within DC-THERA, a community focused on immunology. We show how we have faced the problem of repres- enting and managing highly heterogeneous and interconnected knowledge. One aspect of the application interface is the search and navigation through web ontologies. Another aspect is the dynamic representation of information entities having variable sets of properties. These results have been achieved by adopting a modelling approach that combines traditional object-oriented modelling with a triple-based knowledge representation. We discuss advantages of such an approach, especially for what concerns the possible future integration of other information sources.

(Late) notes from ISWC 2008

I've eventually found time to review the notes from the last International Semantic Web Conference conference and put them in a clean document. Yes, it's a bit late, but I like to put this here and maybe someone will still find it interesting.

If you like the longer reading, please see the slides below. If you're looking for just short impressions, I can summarize them as follows.

ArrayExpress update–from an archive of functional genomics experiments to the atlas of gene expression

ArrayExpress http://www.ebi.ac.uk/arrayexpress consists of three components: the ArrayExpress Repository-a public archive of functional genomics experiments and supporting data, the ArrayExpress Warehouse-a database of gene expression profiles and other bio-measurements and the ArrayExpress Atlas-a new summary database and meta-analytical tool of ranked gene expression across multiple experiments and different biological conditions. The Repository contains data from over 6000 experiments comprising approximately 200 000 assays, and the database doubles in size every 15 months. The majority of the data are array based, but other data types are included, most recently-ultra high-throughput sequencing transcriptomics and epigenetic data. The Warehouse and Atlas allow users to query for differentially expressed genes by gene names and properties, experimental conditions and sample properties, or a combination of both. In this update, we describe the ArrayExpress developments over the last two years.

http://view.ncbi.nlm.nih.gov/pubmed/19015125

CiteXplore

The First RSBI (ISA-TAB) Workshop: "Can a Simple Format Work for Complex Studies?"

This article summarizes the motivation for, and the proceedings of, the first ISA-TAB workshop held December 6-8, 2007, at the EBI, Cambridge, UK. This exploratory workshop, organized by members of the Microarray Gene Expression Data (MGED) Society's Reporting Structure for Biological Investigations (RSBI) working group, brought together a group of developers of a range of collaborative systems to discuss the use of a common format to address the pressing need of reporting and communicating data and metadata from biological, biomedical, and environmental studies employing combinations of genomics, transcriptomics, proteomics, and metabolomics technologies along with more conventional methodologies. The expertise of the participants comprised database development, data management, and hands-on experience in the development of data communication standards. The workshop's outcomes are set to help formalize the proposed Investigation, Study, Assay (ISA)-TAB tab-delimited format for representing and communicating experimental metadata. This article is part of the special issue of OMICS on the activities of the Genomics Standards Consortium (GSC).

http://dx.doi.org/10.1089/omi.2008.0019
CiteXplore

Managing Microarray Knowledge with the Semantic Web

[MannOnto, relatedAssertions] Geeez! Eventually I have submitted the thesis and given the defense presentation! My PhD project is about representing the results coming from microarray data analysis. I represent concepts like: sets of differentially expressed genes, results from clustering algorithms, claims about the role of genes in a biological pathway. I use Semantic Web technologies and an OWL model (ontology) to provide a formal representation of such knowledge. All is focused on assertions (e.g.: "IL2 is expressed under LPS infection condition"), which may be supported by experimental evidence (e.g.: a data set) or other kinds of evaluations, including ranking and comments from the users. Moreover, users and their roles (e.g.: is an expert on Immunology) may be considedered, especially for ranking the assertions. I have also developed a demo, based on the Makna Semantic Wiki.





 

PhD project, yet another ontology

I have reviewed the OWL file once more. I have done it after analysis of study cases and considerations on making useful inference with OWL. Details are reported in the doc.

A Database for Genomic Expression Data Management

This is the project that made me discover the charm of Bioinformatics, Microarrays and Biology. Here you can find:

PhD project, new version of the Ontology and Updates

I've reviewed the ontology, in favour of something rather simpler.

PhD, Progress report of Mar 2006

Now I am working on my project from the EBI. This is a progress report where I show the application of the Semantic Web to my stuff.