List of works - James Malone

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

scientific article

ArrayExpress update--trends in database growth and links to data analysis tools

scientific article (publication date: 2013)

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

scientific article

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data

scientific article

Modeling sample variables with an Experimental Factor Ontology

scientific article

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

scientific article

Modeling biomedical experimental processes with OBI

scientific article

The EBI RDF platform: linked open data for the life sciences

scientific article

Gene expression atlas at the European bioinformatics institute

scientific article

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments

scientific article

Open Targets: a platform for therapeutic target identification and validation

scientific article

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

scientific article

The Ontology for Biomedical Investigations

scientific article

CLO: The cell line ontology

scientific article

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

scientific article

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation

scientific article

Ten Simple Rules for Selecting a Bio-ontology

scientific article

Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation

scientific article

MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB.

scientific article

The health care and life sciences community profile for dataset descriptions

scientific article (publication date: 2016)

The cellular microscopy phenotype ontology

scientific article published on 18 May 2016

Measuring the level of activity in community built bio-ontologies

scientific article published on 25 April 2012

Contributions of the EMERALD project to assessing and improving microarray data quality

scientific article

Translating standards into practice - one Semantic Web API for Gene Expression

scientific article published on 24 March 2012

Automating generation of textual class definitions from OWL to English.

scientific article

MIRO: guidelines for minimum information for the reporting of an ontology

scientific article published on 18 January 2018

Matching disease and phenotype ontologies in the ontology alignment evaluation initiative

scientific article

Webulous and the Webulous Google Add-On - a web service and application for ontology building from templates

scientific article published on January 1, 2016

Anatomy ontologies and potential users: bridging the gap

scientific article published on 09 August 2011

The health care and life sciences community profile for dataset descriptions

article published in 2016

A Simple Standard for Sharing Ontological Mappings (SSSOM)

preprint published on 15 December 2021

Ten quick tips for biocuration

scientific article published on 02 May 2019

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)

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

scientific article

Collaborative Ontology Development Using the Webulous Architecture and Google App

article

Semantic Web Atlas: Putting Gene Expression Data into Biological Context

article

The health care and life sciences community profile for dataset descriptions

scholarly article

List of works by James Malone

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

ArrayExpress update--trends in database growth and links to data analysis tools

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data

Modeling sample variables with an Experimental Factor Ontology

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

Modeling biomedical experimental processes with OBI

The EBI RDF platform: linked open data for the life sciences

Gene expression atlas at the European bioinformatics institute

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments

Open Targets: a platform for therapeutic target identification and validation

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

The Ontology for Biomedical Investigations

CLO: The cell line ontology

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

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation

Ten Simple Rules for Selecting a Bio-ontology

Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation

MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB.

The health care and life sciences community profile for dataset descriptions

The cellular microscopy phenotype ontology

Measuring the level of activity in community built bio-ontologies

Contributions of the EMERALD project to assessing and improving microarray data quality

Translating standards into practice - one Semantic Web API for Gene Expression

Automating generation of textual class definitions from OWL to English.

MIRO: guidelines for minimum information for the reporting of an ontology

Matching disease and phenotype ontologies in the ontology alignment evaluation initiative

Webulous and the Webulous Google Add-On - a web service and application for ontology building from templates

Anatomy ontologies and potential users: bridging the gap

The health care and life sciences community profile for dataset descriptions

A Simple Standard for Sharing Ontological Mappings (SSSOM)

Ten quick tips for biocuration

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

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

Collaborative Ontology Development Using the Webulous Architecture and Google App

Semantic Web Atlas: Putting Gene Expression Data into Biological Context

The health care and life sciences community profile for dataset descriptions

The health care and life sciences community profile for dataset descriptions