List of works - Philippe Rocca-Serra

'Omics data sharing

scientific article

A Data Citation Roadmap for Scholarly Data Repositories ⬇️

journal article from 'bioRxiv' published in 2016

A call for an international network of genomic observatories (GOs)

scientific article

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

scientific article

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”

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

Bio-GraphIIn: a graph-based, integrative and semantically-enabled repository for life science experimental data

scientific article published on 11 February 2014

BioHackEU22 Project 22: Plant data exchange and standard interoperability

BioHackEU22 Report for Project 31: The What & How in data management: Improving connectivity between RDMkit and FAIR Cookbook

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

scientific article published on 03 May 2011

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

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

scientific article

Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies

scientific article (publication date: 3 February 2010)

Chemical effects in biological systems--data dictionary (CEBS-DD): a compendium of terms for the capture and integration of biological study design description, conventional phenotypes, and 'omics data

scientific article

Community standards for open cell migration data

scientific article published on 01 May 2020

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 storage: bringing us a step closer to data sharing?

scientific article published on June 2006

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

Defining best practice for microarray analyses in nutrigenomic studies

scientific article

Development of FuGO: an ontology for functional genomics investigations

scientific article published on January 2006

Discovering Data Access and Use Requirements Using the Data Tags Suite (DATS) Model

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

scientific article

ELIXIR and Toxicology: a community in development

scientific article published on 3 October 2023

ELIXIR biovalidator for semantic validation of life science metadata

scientific article published in 2022

Embedding standards in metabolomics: the Metabolomics Society data standards task group

Enabling reusability of plant phenomic datasets with MIAPPE 1.1.

scientific article published on 14 March 2020

EnsMart: a generic system for fast and flexible access to biological data

scientific article (publication date: 2004)

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

scholarly article published in Metabolomics

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

scientific article published on 20 September 2019

Experiment design driven FAIRification of omics data matrices, an exemplar

scientific article published on 12 December 2019

FAIR Principles: Interpretations and Implementation Considerations

scholarly article

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

Finding useful data across multiple biomedical data repositories using DataMed.

scientific article

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

Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud

Global analysis of human SARS-CoV-2 infection and host-virus interaction

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

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

scientific article published in 2019

Machine actionable metadata models

scientific article published in 2022

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

scientific article

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

scientific article (publication date: 25 December 2010)

Meeting Report: BioSharing at ISMB 2010

scientific article (publication date: 4 December 2010)

Meeting report: advancing practical applications of biodiversity ontologies

scientific article

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

scientific article (publication date: 2013)

MetaboLights: An Open-Access Database Repository for Metabolomics Data

scientific article

MetaboLights: towards a new COSMOS of metabolomics data management

scientific article (publication date: October 2012)

Metabolomics - the stethoscope for the 21st century

scientific article published on 03 December 2020

Metabolomics standards initiative: ontology working group work in progress

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

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

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

Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network

scientific article (publication date: June 2009)

PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud

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

PlatformTM, a standards-based data custodianship platform for translational medicine research

scientific article published on 13 August 2019

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

scientific article (publication date: August 2008)

Selected papers from the 16th Annual Bio-Ontologies Special Interest Group Meeting.

scientific article published on 3 June 2014

Semantic concept schema of the linear mixed model of experimental observations

scientific article published on 27 February 2020

Sharing and archiving nucleic acid structure mapping data

scientific article (publication date: July 2011)

Special issue on bio-ontologies and phenotypes

scientific article

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

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

scientific article (publication date: 27 April 2009)

Taxonomy-Based Glyph Design—with a Case Study on Visualizing Workflows of Biological Experiments

scientific article published on December 2012

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

scientific article published on 25 November 2004

The Data Tags Suite (DATS) model for discovering data access and use requirements

scientific article published on 01 February 2020

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

scientific article (publication date: 25 May 2006)

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop

scientific article published on 12 December 2016

Toward interoperable bioscience data

scientific article (publication date: 27 January 2012)

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)

Use cases, best practice and reporting standards for metabolomics in regulatory toxicology

scientific article published on 10 July 2019

Using pathway signatures as means of identifying similarities among microarray experiments

scientific article

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

graph2tab, a library to convert experimental workflow graphs into tabular formats

scientific article

linkedISA: semantic representation of ISA-Tab experimental metadata

scientific article

mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data

scientific article

mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics

scientific article published on 13 February 2019

nmrML: a community supported open data standard for the description, storage, and exchange of NMR data

scientific article published on 16 October 2017

List of works by Philippe Rocca-Serra

'Omics data sharing

A Data Citation Roadmap for Scholarly Data Repositories ⬇️

A call for an international network of genomic observatories (GOs)

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

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

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

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”

Annotation of environmental OMICS data: application to the transcriptomics domain

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

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

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

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

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

Bio-GraphIIn: a graph-based, integrative and semantically-enabled repository for life science experimental data

BioHackEU22 Project 22: Plant data exchange and standard interoperability

BioHackEU22 Report for Project 31: The What & How in data management: Improving connectivity between RDMkit and FAIR Cookbook

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

BioSharing Overview

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

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

Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies

Chemical effects in biological systems--data dictionary (CEBS-DD): a compendium of terms for the capture and integration of biological study design description, conventional phenotypes, and 'omics data

Community standards for open cell migration data

DATS, the data tag suite to enable discoverability of datasets

DATS: the data tag suite to enable discoverability of datasets

Data discovery with DATS: exemplar adoptions and lessons learned.

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

Data storage: bringing us a step closer to data sharing?

DataMed - an open source discovery index for finding biomedical datasets

DataMed: Finding useful data across multiple biomedical data repositories

Defining best practice for microarray analyses in nutrigenomic studies

Development of FuGO: an ontology for functional genomics investigations

Discovering Data Access and Use Requirements Using the Data Tags Suite (DATS) Model

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

ELIXIR and Toxicology: a community in development

ELIXIR and Toxicology: a community in development

ELIXIR biovalidator for semantic validation of life science metadata

Embedding standards in metabolomics: the Metabolomics Society data standards task group

Enabling reusability of plant phenomic datasets with MIAPPE 1.1.

EnsMart: a generic system for fast and flexible access to biological data

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

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

Experiment design driven FAIRification of omics data matrices, an exemplar

FAIR Principles: Interpretations and Implementation Considerations

FAIRsharing as a community approach to standards, repositories and policies

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

Finding useful data across multiple biomedical data repositories using DataMed.

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

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

Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud

Global analysis of human SARS-CoV-2 infection and host-virus interaction

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

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

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

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

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

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

Machine actionable metadata models

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

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

Meeting Report: BioSharing at ISMB 2010

Meeting report: advancing practical applications of biodiversity ontologies

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

MetaboLights: An Open-Access Database Repository for Metabolomics Data

MetaboLights: towards a new COSMOS of metabolomics data management

Metabolomics - the stethoscope for the 21st century

Metabolomics standards initiative: ontology working group work in progress

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

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

Modeling biomedical experimental processes with OBI

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

OntoMaton: a bioportal powered ontology widget for Google Spreadsheets

Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates