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List of works by Susanna-Assunta Sansone

'Omics data sharing

scientific article

A design framework and exemplar metrics for FAIRness

article published in 2017

A design framework and exemplar metrics for FAIRness

scientific article

A research data management (RDM) community for ELIXIR

scientific article published on 30 September 2024

A sea of standards for omics data: sink or swim?

scientific article (publication date: 2014)

A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group

scientific article published on January 2006

Addendum: The FAIR Guiding Principles for scientific data management and stewardship

article by Mark D Wilkinson et al published 19 March 2019 in Scientific Data

Agenda of the “BioSharing workshop – Bringing catalogues of bio-resource and standards together”

Agenda of the “BioSharing workshop – Unifying Bio-Resources Descriptors”

Agenda of the “BioSharing workshop – Unifying Bio-Resources Descriptors”

An open data ecosystem for cell migration research

scientific article

An open letter on microarray data from the MGED Society

scientific article published on November 2004

Annotation of environmental OMICS data: application to the transcriptomics domain

scientific article

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

scientific article

ArrayExpress--a public repository for microarray gene expression data at the EBI

scientific article

ArrayExpress--a public repository for microarray gene expression data at the EBI

scientific article (publication date: 2003)

ArrayExpress: a public database of gene expression data at EBI.

scientific article

Author Correction: Evaluating FAIR maturity through a scalable, automated, community-governed framework

scientific article published on 21 October 2019

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

scientific article (publication date: 5 February 2014)

BioSharing Overview

BioSharing: Harnessing Metadata Standards For The Data Commons

BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences

scientific article

COVID-19 pandemic reveals the peril of ignoring metadata standards

scientific article published on 19 June 2020

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access

scientific article

Community standards for open cell migration data

scientific article published on 01 May 2020

Community-driven governance of FAIRness assessment: an open issue, an open discussion

scientific article published on 6 September 2023

Conceptualizing a Genomics Software Institute (GSI)

scientific article (publication date: 19 March 2012)

Consent insufficient for data release-Response

scientific article published on 01 May 2019

DATS, the data tag suite to enable discoverability of datasets

scientific article

DATS: the data tag suite to enable discoverability of datasets

Data discovery with DATS: exemplar adoptions and lessons learned.

scientific article published on 8 December 2017

Data standards can boost metabolomics research, and if there is a will, there is a way

scientific article

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

scientific article (publication date: 2011)

DataMed - an open source discovery index for finding biomedical datasets

scientific article published on 13 January 2018

DataMed: Finding useful data across multiple biomedical data repositories

scholarly article published 17 December 2016

Database development in toxicogenomics: issues and efforts

scientific article

Databases and Standardisation of Reporting Methods for Metabolic Studies

Defining best practice for microarray analyses in nutrigenomic studies.

scientific article

Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action

scientific article

Development of FuGO: an ontology for functional genomics investigations

scientific article published on January 2006

Discovering and linking public omics data sets using the Omics Discovery Index.

scientific article

EBI metagenomics--a new resource for the analysis and archiving of metagenomic data

scientific article

ELIXIR and Toxicology: a community in development

ELIXIR and Toxicology: a community in development

scientific article published on 3 October 2023

Empowering industrial research with shared biomedical vocabularies

scientific article (publication date: November 2011)

Enabling reusability of plant phenomic datasets with MIAPPE 1.1.

scientific article published on 14 March 2020

Erratum to: COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access

scholarly article published in Metabolomics

Establishing reporting standards for metabolomic and metabonomic studies: a call for participation

scientific article published on January 2006

Evaluating FAIR maturity through a scalable, automated, community-governed framework

scientific article published on 20 September 2019

Evaluating FAIR-Compliance Through an Objective, Automated, Community-Governed Framework

Experiment design driven FAIRification of omics data matrices, an exemplar

scientific article published on 12 December 2019

FAIR Convergence Matrix: Optimizing the Reuse of Existing FAIR-Related Resources

FAIR Principles: Interpretations and Implementation Considerations

scholarly article

FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources

scientific article published on 30 October 2019

FAIRsharing as a community approach to standards, repositories and policies

scientific article published on 01 April 2019

FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies

Facilitating the development of controlled vocabularies for metabolomics technologies with text mining

scientific article

Finding useful data across multiple biomedical data repositories using DataMed.

scientific article

Foreword to the special issue on the Fifth Genomic Standards consortium workshop

scientific article published in June 2008

Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 working group

scientific article published on 9 November 2020

Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 working group

scientific article published on 26 May 2021

From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics

scientific article

From peer-reviewed to peer-reproduced: a role for data standards, models and computational workflows in scholarly publishing

Genomic Standards Consortium Projects

article

Genomic standards consortium projects

scientific article

Helping the Consumers and Producers of Standards, Repositories and Policies to Enable FAIR Data

High-quality science requires high-quality open data infrastructure.

scientific article

ISA API: An open platform for interoperable life science experimental metadata

scientific article published on 16 September 2021

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

scientific article (publication date: 15 September 2010)

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

scientific article (publication date: 20 March 2017)

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

scientific article

Interoperable and scalable data analysis with microservices: Applications in Metabolomics

Interoperable and scalable data analysis with microservices: Applications in Metabolomics

Interoperable and scalable data analysis with microservices: Applications in Metabolomics

scientific article published in 2019

Machine actionable metadata models

scientific article published in 2022

Mapping Subjects and Domains across the Humanities and Natural Sciences in FAIRsharing ⬇️

Measures for interoperability of phenotypic data: minimum information requirements and formatting

scientific article

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10

scientific article (publication date: 25 December 2010)

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

scientific article (publication date: 25 December 2010)

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

scientific article

Meeting Report: BioSharing at ISMB 2010

scientific article (publication date: 4 December 2010)

Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 2010

scientific article (publication date: 4 December 2010)

Meeting report: EU-US Workshop on Molecular Signatures of DNA Damage-Induced Stress Responses. Cortona, Italy, 26-30 September 2003

scientific article published on 01 June 2004

Meeting report: Validation of toxicogenomics-based test systems: ECVAM-ICCVAM/NICEATM considerations for regulatory use.

scientific article

Meeting report: the fifth Genomic Standards Consortium (GSC) workshop

scientific article published in June 2008

MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data

scientific article (publication date: 2013)

MetaboLights: towards a new COSMOS of metabolomics data management

scientific article (publication date: October 2012)

Metabolomics standards initiative: ontology working group work in progress

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)

scientific article

Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach

scientific article

Modeling biomedical experimental processes with OBI

scientific article

Omics Discovery Index - Discovering and Linking Public Omics Datasets

On the evolving portfolio of community-standards and data sharing policies: turning challenges into new opportunities

scientific article (publication date: 12 July 2012)

OntoMaton: a bioportal powered ontology widget for Google Spreadsheets

scientific article published on 24 December 2012

Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates

Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates

Perspectives on Data Sharing and the New NIH policy from the European Union

scientific article published in 2022

PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud

PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud

scholarly article by Kristian Peters et al published 7 December 2018 in GigaScience

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

scientific article (publication date: August 2008)

Publishing descriptions of non-public clinical datasets: guidance for researchers, repositories, editors and funding organisations

scientific article published on 30 June 2015

Publishing descriptions of non-public clinical datasets: proposed guidance for researchers, repositories, editors and funding organisations

scientific article published on 22 June 2016

Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference

scientific article (publication date: 2012)

Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012

scientific article (publication date: 25 May 2012)

Selected papers from the 12th annual Bio-Ontologies meeting

scientific article

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

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

scientific article (publication date: 24 April 2012)

Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting

scientific article (publication date: 15 April 2013)

Semantic concept schema of the linear mixed model of experimental observations

scientific article published on 27 February 2020

Standard reporting requirements for biological samples in metabolomics experiments: environmental context

article by Norman Morrison et al published 24 August 2007 in Metabolomics

Standardization Initiatives in the (eco)toxicogenomics domain: a review

scientific article published on January 2004

Standardizing data

scientific article published on February 2013

Standards and infrastructure for managing experimental metadata

Standards for microarray data: an open letter

scientific article

Submission of microarray data to public repositories

scientific article

Summary recommendations for standardization and reporting of metabolic analyses

scientific article published on 01 July 2005

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

scientific article (publication date: 27 April 2009)

TeSS: a platform for discovering life science training opportunities

scientific article published on 11 February 2020

The ArrayExpress gene expression database: a software engineering and implementation perspective

scientific article published on 25 November 2004

The FAIR Cookbook - the essential resource for and by FAIR doers

scientific article published on 19 May 2023

The FAIR Guiding Principles for scientific data management and stewardship

scientific article (publication date: 15 March 2016)

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics

article

The Genomic Standards Consortium

scientific article (publication date: June 2011)

The MGED Ontology: a resource for semantics-based description of microarray experiments

scientific article published on 21 January 2006

The MetaboLights repository: curation challenges in metabolomics

scientific article (publication date: 2013)

The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness

scientific article (publication date: 30 July 2012)

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

scientific article published in November 2007

The Ontology for Biomedical Investigations

scientific article

The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again

scientific article

The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework

scientific article

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

scientific article published on 24 November 2011

The carcinoGENOMICS project: critical selection of model compounds for the development of omics-based in vitro carcinogenicity screening assays

scientific article published on 26 April 2008

The center for expanded data annotation and retrieval

scientific article

The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?".

scientific article

The future of metabolomics in ELIXIR

scientific article published in 2017

The future of metabolomics in ELIXIR.

scientific article

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

scientific article (publication date: October 2011)

The international MAQC Society launches to enhance reproducibility of high-throughput technologies

scientific article published in December 2017

The minimum information about a genome sequence (MIGS) specification

scientific article

The use of concept maps during knowledge elicitation in ontology development processes--the nutrigenomics use case

scientific article (publication date: 25 May 2006)

Toward a standards-compliant genomic and metagenomic publication record

scientific article

Toward interoperable bioscience data

scientific article (publication date: 27 January 2012)

Toward unrestricted use of public genomic data:

scientific article

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

scientific article

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

scientific article (publication date: 2011)

Towards interoperable reporting standards for omics data: hopes and hurdles

scientific article (publication date: March 2009)

Visual compression of workflow visualizations with automated detection of macro motifs

scientific article published in December 2013

Wrestling with SUMO and bio-ontologies

scientific article

linkedISA: semantic representation of ISA-Tab experimental metadata

scientific article

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