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Application development Benchmark Bioinformatics Biological networks BioPAX Collaborative research Cytoscape Data Analysis Database Data integration Data Market Platform Dendritic cells Experiment annotation Gene expression Gene regulation geographic information Immunology Knowledge Management Life Sciences Microarrays Ontologies Pathogen Host Interaction Pathways Reasoning Semantic Analysis Semantic Web Translational Research Triplestore User Interaction Visualization Web Science WikiCategories
- Biomedical knowledge bases and infrastructures (4)
- Biomedical ontologies and representation of Biological Pathways (3)
- Book chapters (1)
- EditedBy (6)
- Journal Papers (11)
- Lived (1)
- Newsletters (1)
- Ontology based data analysis (2)
- Proceedings (7)
- Publications (1)
- Talks (5)
- Tutorials (5)
- Visualisation and User Interaction on the Semantic Web (3)
- Workshops (6)
Author Archives: sgtp
Toward Open Linked Gene Mutation Data
Achille Zappa, Andrea Splendiani and Paolo Romano Towards linked open gene mutations data http://www.biomedcentral.com/1471-2105/13/S4/S7 Background With the advent of high-throughput technologies, a great wealth of variation data is being produced. Such information may constitute the basis for correlation analyses between … Continue reading
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Semantic Web Applications and Tools for the Life Sciences: SWAT4LS 2010 BMC Bioinformatics Research Supplement Edited by Albert Burger, Adrian Paschke, Paolo Romano, M Scott Marshall and Andrea Splendiani Available at http://www.biomedcentral.com/1471-2105/13/S1/S1 Abstract As Semantic Web technologies mature and new … Continue reading
Gauging triple stores with actual biological data
Vladimir Mironov, Nirmala Seethappan, Ward Blondé, Erick Antezana, Andrea Splendiani and Martin Kuiper. Gauging triple stores with actual biological data. http://www.biomedcentral.com/1471-2105/13/S1/S3 Abstract Background: Semantic Web technologies have been developed to overcome the limitations of the current Web and conventional data … Continue reading
Knowledge sharing and collaboration in translational research, and the DC-THERA Directory
Andrea Splendiani, Michaela Gündel, Jonathan M Austyn, Duccio Cavalieri, Ciro Scognamiglio, Marco Brandizi. Knowledge sharing and collaboration in translational research, and the DC-THERA Directory. http://bib.oxfordjournals.org/content/early/2011/10/02/bib.bbr051.full.pdf Abstract Biomedical research relies increasingly on large collections of data sets and knowledge whose generation, … Continue reading
Biomedical Semantics in the Semantic Web
At BioHackathon Symposium, Aug 21st 2001, Kyoto.
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SWAT4LS 2011
I have organized the 4th edition of SWAT4LS (Semantic Web Applications and Tools for Life Sciences) in London, from the 6th to the 9th of December 2011, which took place athe University of London Union and at the Wellcome Trust … Continue reading
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Lost in translation: data integration tools meet the Semantic Web (experiences from the Ondex project)
Andrea Splendiani, Chris J Rawlings, Shao-Chih Kuo, Robert Stevens, Phillip Lord Lost in translation: data integration tools meet the Semantic Web (experiences from the Ondex project) Presented at DEIT (Data Engineering and Internet Technology) 2011 (Conference Record # 17831, IEEE … Continue reading
Posted in Proceedings
Tagged Semantic Analysis, Semantic Web, User Interaction, Visualization
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Biomedical Semantics in the Semantic Web
Andrea Splendiani, Albert Burger, Adrian Paschke, Paolo Romano, M. Scott Marshall. Biomedical Semamtics in the Semantic Web (commentary) http://www.jbiomedsem.com/content/2/S1/S1 Abstract The Semantic Web offers an ideal platform for representing and linking biomedical information, which is a prerequisite for the development … Continue reading
BMC JBS Special Issue on Semantic Web Applications and Tools for Life Sciences, 2009
Semantic Web Applications and Tools for Life Sciences, 2009 BMC Bioinformatics Research Supplement Edited by Andrea Splendiani, Albert Burger, Adrian Paschke, Paolo Romano and M. Scott Marshall Available at http://www.jbiomedsem.com/supplements/2/S1
Semantic Web Applications and Tools for Life Sciences 2010
Semantic Web and Tools for Life Sciences 2010 Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS-2010), Berlin, Germany, December 10, 2010. Edited by: Albert Burger, M. Scott Marshall, Paolo Romano, Adrian Paschke, Andrea Splendiani … Continue reading
wikiMap
wikiMap is a very, very simple project. It is a tiny bit of the Phibase project, and it is basically a beginner exercise in Javascript. Said that, it does something nice, it shows on a map which countries related to … Continue reading
Mining the Internet for scientific discoveries (Position paper)
Shao Chih Kuo, Andrea Splendiani, Michael Defoin-Platel, Chris Rawlings Mining the Internet for Scientific Discoveries Proceedings of the First Workshop on Mining the Future Internet (MIFI-2010) Berlin, Germany, September 20th, 2010
BioPAX
I’ve been involved since 2005 with BioPAX, which I first approached in search a suitable knowledge base to develop pathway analysis methods. I have been mostly focused on “consuming” BioPAX, which has meant debugging of the specification and some tools … Continue reading
DC-RESEARCH.EU
DC-RESEARCH.EU is a system that aims at representing the communication and know-how proper of a research networks. DC-RESEARCH.EU has been developed in the context of the network DC-THERA by Leaf Bioscience s.r.l., in collaboration with other participants in the network. DC-RESEARCH.EU stores synthetic … Continue reading
Ontology based Data Analysis
More information coming (hopefully) soon!
Posted in Ontology based data analysis
Tagged Data Analysis, Ontologies, Semantic Web
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PHI-Base
I am involved in the re-design of the Host Pathogen Interaction database PHI-BASE, where I have devised a new information model and a new database schema. Rather than focusing on “storing” the data, the new information model makes explicit the … Continue reading
Ondex
I’m currently working on Ondex, in the context of the Ondex SABR project. Ondex is a data integration software aimed at the molecular biology domain. It provides tools to map databases to the Ondex data structure, tools for the integration, … Continue reading
DC-ATLAS, a Systems Biology Resource to Dissect Receptor Specific Signal Transduction in Dendritic Cells
Duccio Cavalieri1, Damariz Rivero, Luca Beltrame, Sonja I. Buschow, Enrica Calura, Lisa Rizzetto, Sandra Gessani, Maria C. Gauzzi, Walter Reith, Andreas Baur, Roberto Bonaiuti, Marco Brandizi, Carlotta De Filippo, Ugo D’Oro, Sorin Draghici, Isabelle Dunand-Sauthier, Evelina Gatti, Francesca Granucci, Michaela … Continue reading
The Genopolis Microarray Database
The Genopolis Microarray Database originated as custom microarray database project for Affymetrix GeneChip data, supporting an homogeneous community studying dendritic cells differentiation. It is based on an object model MAGEcompliant, and provides support for MIAME annotation, export to ArrayExpress as … Continue reading
Semantic Web/Linking/CV WorkGroup: next steps ?
Talk @COMBINE meeting, on next step of the BioPAX SemWeb Working Group. Edinburgh, Thursday October 7th, 2010. Info and slides are available here.
Use of semantic web resources in computational biology and bioinformatics
Tutorial at ECCB 2010 by Andrea Splendiani and Paolo Romano Use of semantic web resources in computational biology and bioinformatics Full description available on the ECCB site.
Posted in Tutorials
Tagged Application development, Bioinformatics, Life Sciences, Semantic Web
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The BioPAX community standard for pathway data sharing
The BioPAX community standard for pathway data sharing Emek Demir, Michael P Cary, Suzanne Paley, Ken Fukuda, Christian Lemer, Imre Vastrik, Guanming Wu, Peter D’Eustachio, Carl Schaefer, Joanne Luciano, Frank Schacherer, Irma Martinez-Flores, Zhenjun Hu, Veronica Jimenez-Jacinto, Geeta Joshi-Tope, Kumaran … Continue reading
Introduction to the development of Biomedical Semantic Web applications
Three day course by Emanuele della Valle, Andrea Splendiani, Paolo Romano Introduzione allo sviluppo di applicazioni basate su Semantic Web in ambito biomedico Link to the course page (in Italian).
SWAT4LS-2010
The Third edition of SWAT4LS, Semantic Web Applications and Tools for Life Sciences was held in Berlin on Dec. 10th, 2010. The workshop was preceded by two days of hackathon and tutorials. The program of the Workshop can be seen … Continue reading
Semantic Web Applications and Tools for Life Sciences 2009
Semantic Web Applications and Tools for Life Sciences 2009 Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS-2009), Amsterdam, The Netherlands, November 20, 2009. Edited by: M. Scott Marshall, Albert Burger, Paolo Romano, Adrian Paschke, … Continue reading
SWAT4LS-2009
Following the success of the first edition, we have organized the second edition of SWAT4LS (Semantic Web and Tools for Life Sciences), which was held in Amsterdam on November 20th, 2009. This year M.Scott Marshall joined the organizers group. Proceedings … Continue reading
DC-THERA Directory, a Knowledge Management System for the support of the European Dendritic Cell Immunology Community (Demo paper)
Marco Brandizi, Michaela Gündel, Ciro Scognamiglio and Andrea Splendiani DC-THERA Directory, a Knowledge Management System for the support of the European Dendritic Cell Immunology Community (Demo paper) In Proceedings of Semantic Applications and Tools for Life Sciences (SWAT4LS 2009)
Posted in Proceedings
Tagged Collaborative research, Data integration, Database, Dendritic cells, Semantic Web
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BioPAX is from Venus, the Semantic Web is from Mars
Talk at BioPAX f2f meeting, NYC, 11-13 November 2009
Toward a new paradigm for user interaction on the semantic web to support life sciences investigation
In Proceedings of the Sixth International Workshop on Semantic Web User Interaction, 2009 Continue reading
Visualization and analysis of biological networks on the Semantic Web
At BioHackathon Symposium, Tokyo, Feb 10th 2010.
BMC Bioinformatics Special Issue on Semantic Web Applications and Tools for Life Sciences, 2008
Semantic Web Applications and Tools for Life Sciences, 2008 BMC Bioinformatics Research Supplement Edited by Albert Burger, Paolo Romano, Adrian Paschke and Andrea Splendiani Available at http://www.biomedcentral.com/1471-2105/10?issue=S10
The DC-THERA Directory: a semantic-web based approach to the management of collaborative research projects
The DC-THERA Directory: a semantic-web based approach to the management of collaborative research projects in Link.92 Newsletter
Posted in Newsletters
Tagged Collaborative research, Data integration, Dendritic cells, Knowledge Management
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Nettab 2009: Collaborative Bioinformatics Research and Development
Together with Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti and Paolo Romano, I have co-organized and co-chaired, the Nettab 2009 workshop, with focus on on Collaborative Bioinformatics Research and Development. The workshop was held in Catania, 10-13 June 2009. More information … Continue reading
The DC-THERA Directory: A Knowledge Management System to Support Collaboration on Dendritic Cell and Immunology Research
Michaela Guendel, Ciro Scognamiglio, Marco Brandizi and Andrea Splendiani The DC-THERA Directory: A Knowledge Management System to Support Collaboration on Dendritic Cell and Immunology Research In Proceedings of the Nettab Workshop, (Network Tools and Applications in Biology, Collaborative Bioinformatics Research … Continue reading
Posted in Proceedings
Tagged Collaborative research, Dendritic cells, Knowledge Management, Ontologies, Semantic Web
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Combined CellML SBGN SBO BioPAX MIASE Workshop
“BioPAX for semantic web based data integration”, talk at Combined CellML SBGN SBO BioPAX MIASE Workshop, 5-9 April 2009, Wahieke Island (NZ).
SWAT4LS-2008
I have co-organized and co-chaired the workshop: Semantic Web Applications and Tools for Life Sciences (SWAT4LS), together with Paolo Romano, Albert Burger and Adrian Pashcke. The workshop was held at Edinburgh e-Science center, on November 23rd. Here is a link … Continue reading
Semantic Web Applications and Tools for Life Sciences SWAT4LS 2008
Semantic Web Applications and Tools for Life Sciences SWAT4LS 2008 Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS) Edinburgh, United Kingdom, November 28, 2008. Edited by Albert Burger, Adrian Paschke, Paolo Romano, Andrea Splendiani … Continue reading
Semantic Web Application and Tools for Life Sciences, 2008 – Introduction
Albert Burger, Paolo Romano, Adrian Paschke, Andrea Splendiani Semantic Web Application and Tools for Life Sciences, 2008 – Introduction BMC Bioinformatics 2009, 10 (S10), S1
I-Atlas 2008
Together with Duccio Cavalieri, I have co-organized and co-chaired I-ATLAS, Internatonal Workshop on Gene Signalling Pathway Analysis and Representation for the Dendritic Cell. The workshop was held in Florence, 13-14 November 2008.
The Gene Regulation Ontology (GRO): Design Principles and Use Case
E. Beisswanger, V. Lee, Kim JJ, Rebholz-Schumann D, A. Splendiani, O. Dameron, Schulz S, U Hahn. The Gene Regulation Ontology (GRO): Design Principles and Use Cases Stud Health Technol Inform. 2008;136:9-14 Abstract The Gene Regulation Ontology (GRO) is designed as … Continue reading
Applications of Semantic Web Methodologies and Techniques to Biology and Bioinformatics
by Paolo Romano and Andrea Splendiani Tutorial at Reasoning Web 2008 Summer School. Lecturer notes published in Springer LNCS. Preprint version available here
Posted in Tutorials
Tagged Application development, Bioinformatics, Life Sciences, Semantic Web
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Applications of Semantic Web Methodologies and Techniques to Biology and Bioinformatics
in Reasoning Web 2008, by Paolo Romano and Andrea Splendiani Continue reading
RDFScape: Semantic Web meets Systems Biology
Splendiani A RDFScape: Semantic Web meets Systems Biology (selected In IMIA Yearbook of Medical Informatics) BMC Bioinformatics 2008 Apr 25, 9 (S4):S6 Abstract BACKGROUND The recent availability of high-throughput data in molecular biology has increased the need for a formal … Continue reading
Beat
Beat is platform for the matching and enrichment of ontologies, which was first implemented in the context of the Bootstrep project. It was aimed at providing a platform where several tasks related to ontology alignment/enrichment can be modularly composed. I … Continue reading
RDFScape
RDFScape originated as an attempt to “merge” Cytoscape, a popular network analysis software, with Semantic Web technologies. In its original design, RDFScape was including a variety of experimental features: Cytoscape-based interactive visual interface for RDF-based knowledge bases Interactive visual SPARQL … Continue reading
The Genopolis Microarray Database
Splendiani A, Brandizi B, Even G, Beretta O, Pavelka N, Pelizzola M, Foti M, Mauri G, Ricciardi-Castagnoli P. The Genopolis Microarray Database BMC Bioinformatics 2007 Mar 8, 8(Suppl 1):S22 Abstract Background Gene expression databases are key resources for microarray data … Continue reading
Integration of ontologies and high-throughput data in bioinformatics
Integration of ontologies and high-throughput data in bioinformatics (PhD Thesis) Available here
Posted in Publications
Tagged BioPAX, Data Analysis, Database, Microarrays, Semantic Web
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Semantic browsing of pathway ontologies and biological networks with RDFScape (working paper)
In Dagstuhl proceedings, 2006 Continue reading
Posted in Proceedings
Tagged Bioinformatics, Cytoscape, Ontologies, Pathways, Reasoning, Semantic Web
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Ontology based analysis of experimental data (position paper)
In proceedings of the Uncertainty Reasoning for the Semantic Web Workshop, 2005 Continue reading
Network-based Analysis resources
Network-based Analysis resources, In EMBO Course “Making Sense out of Transcriptomes”, University of Milano-Bicocca, February 14-19, 2005. Slides from the tutorial are available here.
A power law global error model for the identification of differentially expressed genes in microarray data
Pavelka N, Pelizzola M, Vizzardelli C, Capozzoli M, Splendiani A, Granucci F, Ricciardi-Castagnoli P. A power law global error model for the identification of differentially expressed genes in microarray data BMC Bioinformatics. 2004 Dec 17;5(1):203 Abstract Background High-density oligonucleotide microarray … Continue reading
An introduction to Microarray Databases (Tutorial)
At the Embo Course on Functional Genomics, University of Milano Bicocca, 2003. The pdf of the presentation is available here.
