Susanna-Assunta Sansone

Publications of Susanna-Assunta Sansone

• Toward interoperable bioscience data.

  Authors: Susanna-Assunta Sansone, Philippe Rocca-Serra, Dawn Field, Eamonn Maguire, Chris Taylor, Oliver Hofmann, Hong Fang, Steffen Neumann, Weida Tong, Linda Amaral-Zettler [......] Dorothy Reilly, Magali Roux, Caroline E Shamu, Catherine A Shang, Christoph Steinbeck, Anne Trefethen, Bryn Williams-Jones, Katherine Wolstencroft, Ioannis Xenarios, Winston Hide

  Nature genetics. 02/2012; 44(2):121-6.

  To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture.To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision.

• Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting.

  Authors: Larisa N Soldatova, Susanna-Assunta Sansone, Michel Dumontier, Nigam H Shah

  Journal of biomedical semantics. 01/2012; 3 Suppl 1:I1.

  Over the 14 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine andOver the 14 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The seven papers selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data from wikis, innovative methods of annotating and mining electronic health records, advances in annotating web documents and biomedical literature, quality control of ontology alignments, and the ontology support for predictive models about toxicity and open access to the toxicity data.

• The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons.

  Authors: Shannan J Ho Sui, Kimberly Begley, Dorothy Reilly, Brad Chapman, Ray McGovern, Philippe Rocca-Sera, Eamonn Maguire, Gabriel M Altschuler, Terah A A Hansen, Ramakrishna Sompallae, Andrei Krivtsov, Ramesh A Shivdasani, Scott A Armstrong, Aedín C Culhane, Mick Correll, Susanna-Assunta Sansone, Oliver Hofmann, Winston Hide

  Nucleic acids research. 11/2011; 40(Database issue):D984-91.

  Mounting evidence suggests that malignant tumors are initiated and maintained by a subpopulation of cancerous cells with biological properties similar to those of normal stem cells. However,Mounting evidence suggests that malignant tumors are initiated and maintained by a subpopulation of cancerous cells with biological properties similar to those of normal stem cells. However, descriptions of stem-like gene and pathway signatures in cancers are inconsistent across experimental systems. Driven by a need to improve our understanding of molecular processes that are common and unique across cancer stem cells (CSCs), we have developed the Stem Cell Discovery Engine (SCDE)-an online database of curated CSC experiments coupled to the Galaxy analytical framework. The SCDE allows users to consistently describe, share and compare CSC data at the gene and pathway level. Our initial focus has been on carefully curating tissue and cancer stem cell-related experiments from blood, intestine and brain to create a high quality resource containing 53 public studies and 1098 assays. The experimental information is captured and stored in the multi-omics Investigation/Study/Assay (ISA-Tab) format and can be queried in the data repository. A linked Galaxy framework provides a comprehensive, flexible environment populated with novel tools for gene list comparisons against molecular signatures in GeneSigDB and MSigDB, curated experiments in the SCDE and pathways in WikiPathways. The SCDE is available at http://discovery.hsci.harvard.edu.

• The Genomic Standards Consortium.

  Authors: Dawn Field, Linda Amaral-Zettler, Guy Cochrane, James R Cole, Peter Dawyndt, George M Garrity, Jack Gilbert, Frank Oliver Glöckner, Lynette Hirschman, Ilene Karsch-Mizrachi [......] Nikos Kyrpides, Folker Meyer, Inigo San Gil, Susanna-Assunta Sansone, Lynn M Schriml, Peter Sterk, Tatiana Tatusova, David W Ussery, Owen White, John Wooley

  PLoS biology. 06/2011; 9(6):e1001088.

  A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise itsA vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic Standards Consortium (GSC), an open-membership organization that drives community-based standardization activities, Here we provide a short history of the GSC, provide an overview of its range of current activities, and make a call for the scientific community to join forces to improve the quality and quantity of contextual information about our public collections of genomes, metagenomes, and marker gene sequences.

• Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

  Authors: Pelin Yilmaz, Renzo Kottmann, Dawn Field, Rob Knight, James R Cole, Linda Amaral-Zettler, Jack A Gilbert, Ilene Karsch-Mizrachi, Anjanette Johnston, Guy Cochrane [......] James M Tiedje, Doyle V Ward, George M Weinstock, Doug Wendel, Owen White, Andrew Whiteley, Andreas Wilke, Jennifer R Wortman, Tanya Yatsunenko, Frank Oliver Glöckner

  Nature biotechnology. 05/2011; 29(5):415-20.

  Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce aHere we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmental packages' apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

• The genomic standards consortium: bringing standards to life for microbial ecology.

  Authors: Pelin Yilmaz, Jack A Gilbert, Rob Knight, Linda Amaral-Zettler, Ilene Karsch-Mizrachi, Guy Cochrane, Yasukazu Nakamura, Susanna-Assunta Sansone, Frank Oliver Glöckner, Dawn Field

  The ISME journal. 04/2011; 5(10):1565-7.

• Overcoming the ontology enrichment bottleneck with Quick Term Templates.

  Authors: Philippe Rocca-Serra, Alan Ruttenberg, Martin J. O'Connor, Patricia L. Whetzel, Daniel Schober, Jay Greenbaum, Mélanie Courtot, Ryan R. Brinkman, Susanna-Assunta Sansone, Richard H. Scheuermann, Bjoern Peters

  Applied Ontology. 01/2011; 6:13-22.

• Towards BioDBcore: a community-defined information specification for biological databases.

  Authors: Pascale Gaudet, Amos Bairoch, Dawn Field, Susanna-Assunta Sansone, Chris F. Taylor, Teresa K. Attwood, Alex Bateman, Judith A. Blake, Carol J. Bult, J. Michael Cherry [......] Lorna Richardson, Philippe Rocca-Serra, Paul N. Schofield, Damian Smedley, Christopher Southan, Tin Wee Tan, Tatiana A. Tatusova, Patricia L. Whetzel, Owen White, Chisato Yamasaki

  Nucleic Acids Research. 01/2011; 39:7-10.

• Selected papers from the 13th Annual Bio-Ontologies Special Interest Group Meeting.

  Authors: Larisa N Soldatova, Susanna-Assunta Sansone, Susie M Stephens, Nigam H Shah

  Journal of biomedical semantics. 01/2011; 2 Suppl 2:I1.

  Over the years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the application of ontologies and more generally the organisation,Over the years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the application of ontologies and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The ten papers selected for this supplement are extended versions of the original papers presented at the 2010 SIG. The papers span a wide range of topics including practical solutions for data and knowledge integration for translational medicine, hypothesis based querying , understanding kidney and urinary pathways, mining the pharmacogenomics literature; theoretical research into the orthogonality of biomedical ontologies, the representation of diseases, the representation of research hypotheses, the combination of ontologies and natural language processing for an annotation framework, the generation of textual definitions, and the discovery of gene interaction networks.

• Towards BioDBcore: a community-defined information specification for biological databases.

  Authors: Pascale Gaudet, Amos Bairoch, Dawn Field, Susanna-Assunta Sansone, Chris Taylor, Teresa K Attwood, Alex Bateman, Judith A Blake, Carol J Bult, J Michael Cherry [......] Lorna Richardson, Philippe Rocca-Serra, Paul N Schofield, Damian Smedley, Christopher Southan, Tin Wee Tan, Tatiana Tatusova, Patricia L Whetzel, Owen White, Chisato Yamasaki

  Nucleic acids research. 01/2011; 39(Database issue):D7-10.

  The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provideThe present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases.

• Data standards for Omics data: the basis of data sharing and reuse.

  Authors: Stephen A Chervitz, Eric W Deutsch, Dawn Field, Helen Parkinson, John Quackenbush, Phillipe Rocca-Serra, Susanna-Assunta Sansone, Christian J Stoeckert, Chris F Taylor, Ronald Taylor, Catherine A Ball

  Methods in molecular biology (Clifton, N.J.). 01/2011; 719:31-69.

  To facilitate sharing of Omics data, many groups of scientists have been working to establish the relevant data standards. The main components of data sharing standards are experiment descriptionTo facilitate sharing of Omics data, many groups of scientists have been working to establish the relevant data standards. The main components of data sharing standards are experiment description standards, data exchange standards, terminology standards, and experiment execution standards. Here we provide a survey of existing and emerging standards that are intended to assist the free and open exchange of large-format data.

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

  Authors: 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, Susanna-Assunta Sansone

  Bioinformatics (Oxford, England). 09/2010; 26(18):2354-6.

  The first open source software suite for experimentalists and curators that (i) assists in the annotation and local management of experimental metadata from high-throughput studies employing one or aThe first open source software suite for experimentalists and curators 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 users to uptake community-defined checklists and ontologies; and (iii) facilitates submission to international public repositories. Availability and Implementation: Software, documentation, case studies and implementations at http://www.isa-tools.org.

• Selected papers from the 12th annual Bio-Ontologies meeting.

  Authors: Larisa N Soldatova, Phillip Lord, Susanna-Assunta Sansone, Susie M Stephens, Nigam H Shah

  Journal of biomedical semantics. 01/2010; 1 Suppl 1:I1.

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• Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010.

  Authors: Lynette Hirschman, Peter Sterk, Dawn Field, John Wooley, Guy Cochrane, Jack Gilbert, Eugene Kolker, Nikos Kyrpides, Folker Meyer, Ilene Mizrachi, Yasukazu Nakamura, Susanna-Assunta Sansone, Lynn Schriml, Tatiana Tatusova, Owen White, Pelin Yilmaz

  Standards in genomic sciences. 01/2010; 2(3):357-60.

  This report summarizes the M3 Workshop held at the January 2010 Pacific Symposium on Biocomputing. The workshop, organized by Genomic Standards Consortium members, included five contributed talks, aThis report summarizes the M3 Workshop held at the January 2010 Pacific Symposium on Biocomputing. The workshop, organized by Genomic Standards Consortium members, included five contributed talks, a series of short presentations from stakeholders in the genomics standards community, a poster session, and, in the evening, an open discussion session to review current projects and examine future directions for the GSC and its stakeholders.

• Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop.

  Authors: Carsten Kettner, Dawn Field, Susanna-Assunta Sansone, Chris Taylor, Jan Aerts, Nigel Binns, Andrew Blake, Cedrik M Britten, Ario de Marco, Jennifer Fostel [......] Sandra Orchard, Helen Parkinson, William Piel, Shoba Ranganathan, Philippe Rocca-Serra, Annapaola Santarsiero, David Shotton, Peter Sterk, Andreas Untergasser, Patricia L Whetzel

  Standards in genomic sciences. 01/2010; 3(3):259-66.

  This report summarizes the proceedings of the second workshop of the 'Minimum Information for Biological and Biomedical Investigations' (MIBBI) consortium held on Dec 1-2, 2010 in Rüdesheim, GermanyThis report summarizes the proceedings of the second workshop of the 'Minimum Information for Biological and Biomedical Investigations' (MIBBI) consortium held on Dec 1-2, 2010 in Rüdesheim, Germany through the sponsorship of the Beilstein-Institute. MIBBI is an umbrella organization uniting communities developing Minimum Information (MI) checklists to standardize the description of data sets, the workflows by which they were generated and the scientific context for the work. This workshop brought together representatives of more than twenty communities to present the status of their MI checklists and plans for future development. Shared challenges and solutions were identified and the role of MIBBI in MI checklist development was discussed. The meeting featured some thirty presentations, wide-ranging discussions and breakout groups. The top outcomes of the two-day workshop as defined by the participants were: 1) the chance to share best practices and to identify areas of synergy; 2) defining a series of tasks for updating the MIBBI Portal; 3) reemphasizing the need to maintain independent MI checklists for various communities while leveraging common terms and workflow elements contained in multiple checklists; and 4) revision of the concept of the MIBBI Foundry to focus on the creation of a core set of MIBBI modules intended for reuse by individual MI checklist projects while maintaining the integrity of each MI project. Further information about MIBBI and its range of activities can be found at http://mibbi.org/.

• Modeling biomedical experimental processes with OBI.

  Authors: Ryan R Brinkman, Mélanie Courtot, Dirk Derom, Jennifer M Fostel, Yongqun He, Phillip Lord, James Malone, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Larisa N Soldatova, Christian J Stoeckert, Jessica A Turner, Jie Zheng

  Journal of biomedical semantics. 01/2010; 1 Suppl 1:S7.

  ABSTRACT : BACKGROUND : Experimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. TheseABSTRACT : BACKGROUND : Experimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. These difficulties impose limitations on data exchange and information retrieval. RESULTS : The Ontology for Biomedical Investigations (OBI), developed as a global, cross-community effort, provides a resource that represents biomedical investigations in an explicit and integrative framework. Here we detail three real-world applications of OBI, provide detailed modeling information and explain how to use OBI. CONCLUSION : We demonstrate how OBI can be applied to different biomedical investigations to both facilitate interpretation of the experimental process and increase the computational processing and integration within the Semantic Web. The logical definitions of the entities involved allow computers to unambiguously understand and integrate different biological experimental processes and their relevant components. AVAILABILITY : OBI is available at http://purl.obolibrary.org/obo/obi/2009-11-02/obi.owl.

• Megascience. 'Omics data sharing.

  Authors: Dawn Field, Susanna-Assunta Sansone, Amanda Collis, Tim Booth, Peter Dukes, Susan K Gregurick, Karen Kennedy, Patrik Kolar, Eugene Kolker, Mary Maxon, Siân Millard, Alexis-Michel Mugabushaka, Nicola Perrin, Jacques E Remacle, Karin Remington, Philippe Rocca-Serra, Chris F Taylor, Mark Thorley, Bela Tiwari, John Wilbanks

  Science (New York, N.Y.). 10/2009; 326(5950):234-6.

• Survey-based naming conventions for use in OBO Foundry ontology development.

  Authors: Daniel Schober, Barry Smith, Suzanna Lewis, Waclaw Kusnierczyk, Jane Lomax, Chris Mungall, Chris Taylor, Philippe Rocca-Serra, Susanna-Assunta Sansone

  BMC bioinformatics. 05/2009; 10(1):125.

  ABSTRACT: BACKGROUND: A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration ofABSTRACT: BACKGROUND: A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. RESULTS: We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. CONCLUSIONS: Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data.

• Survey-based naming conventions for use in OBO Foundry ontology development.

  Authors: Daniel Schober, Barry Smith, Suzanna E. Lewis, Waclaw Kusnierczyk, Jane Lomax, Chris Mungall, Chris F. Taylor, Philippe Rocca-Serra, Susanna-Assunta Sansone

  BMC Bioinformatics. 01/2009; 10.

• Towards interoperable reporting standards for omics data: hopes and hurdles.

  Authors: Susanna-Assunta Sansone, Philippe Rocca-Serra, Dawn Field, Chris F Taylor, Weida Tong, Marco Brandizi, Eamonn Maguire, Nataliya Sklyar

  Summit on translational bioinformatics. 01/2009; 2009:112-5.

  As the size and complexity of scientific datasets and the corresponding information stores grow, standards for collecting, describing, formatting, submitting and exchanging information are playing anAs the size and complexity of scientific datasets and the corresponding information stores grow, standards for collecting, describing, formatting, submitting and exchanging information are playing an increasingly active role. Several initiatives occupy strategic positions in the international scenario, both within and across domains. However, the job of harmonising reporting standards is still very much a work in progress; both software interoperability and the data integration remain challenging as things stand. The status quo with respect to standardization initiatives is summarized here, with particular emphasis on the motivation for, and the challenges of, ongoing synergistic activities amongst the academic community focused on the creation of truly interoperable standards. Groups generating standards should engage with ongoing cross-domain activities to simplify the integration of heterogeneous data sets to the greatest possible extent.