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List of works by Mark D. Wilkinson

A design framework and exemplar metrics for FAIRness

article published in 2017

A design framework and exemplar metrics for FAIRness

scientific article

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

Analysis of a multilevel diagnosis decision support system and its implications: a case study

scientific article published on 23 December 2012

Applying Semantic Web Services to Bioinformatics: Experiences Gained, Lessons Learnt

article by Phillip Lord et al published 2004 in The Semantic Web – ISWC 2004: Third International Semantic Web Conference, Hiroshima, Japan, November 7-11, 2004. Proceedings

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

scientific article published on 21 October 2019

Automatic definition of robust microbiome sub-states in longitudinal data

Automatic definition of robust microbiome sub-states in longitudinal data

Automatic detection and resolution of measurement-unit conflicts in aggregated data

scientific article

Automatically exposing OpenLifeData via SADI semantic Web Services

scientific article

BioHackathon 2015: Semantics of data for life sciences and reproducible research

scientific article published on 24 February 2020

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

scientific article (publication date: 5 February 2014)

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

scientific article

BioMOBY successfully integrates distributed heterogeneous bioinformatics Web Services. The PlaNet exemplar case

scientific article published on May 2005

BioMOBY: an open source biological web services proposal

scientific article published on December 2002

BioMoby extensions to the Taverna workflow management and enactment software

scientific article

Bioinformatics Tools for Next-Generation RNA Sequencing Analysis

article published in 2014

Bioscientific Data Processing and Modeling

Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud

scientific article (publication date: 7 March 2017)

Common conditions of use elements. Atomic concepts for consistent and effective information governance

scientific article published on 8 May 2024

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

scientific article published on 6 September 2023

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

scientific article published in 2022

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

scientific article published on 23 December 2022

Comparison of ESTs from juvenile and adult phases of the giant unicellular green alga Acetabularia acetabulum

scientific article

Data-driven classification of the certainty of scholarly assertions

Data-driven classification of the certainty of scholarly assertions

Data-driven classification of the certainty of scholarly assertions

scientific article published on 21 April 2020

DataBiNS-Viz: A Web-Based Tool for Visualization of Non-Synonymous SNP Data

scholarly article by Fong Chun Chan et al published 17 July 2008 in Journal of Proteomics and Bioinformatics

DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs

scientific article published on 18 January 2007

Diagnostic Knowledge Extraction from MedlinePlus: An Application for Infectious Diseases

Enhanced reproducibility of SADI web service workflows with Galaxy and Docker

scientific article

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

Executing SADI services in Galaxy

scientific article

Extending and encoding existing biological terminologies and datasets for use in the reasoned semantic web.

scientific article published on 20 July 2012

FAIR Data Point: A FAIR-oriented approach for metadata publication

scientific article published in 2022

FAIR Principles: Interpretations and Implementation Considerations

scholarly article

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

Fast, cheap and out of control: a zero curation model for ontology development.

scientific article published on January 2006

Gbrowse Moby: a Web-based browser for BioMoby Services

scientific article

Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa

scientific article published on 01 December 2019

Genome-wide polyadenylation site mapping datasets in the rice blast fungus Magnaporthe oryzae

Genomics Data Resources: Frameworks and Standards ⬇️

scientific article published on January 1, 2012

Genquire: genome annotation browser/editor

scientific article published on October 2002

Getting your DUCs in a row - standardising the representation of Digital Use Conditions

scientific article published on 8 May 2024

Interoperability and FAIRness through a novel combination of Web technologies ⬇️

scientific article (publication date: 24 April 2017)

Interoperability and FAIRness through a novel combination of Web technologies

Interoperability and FAIRness through a novel combination of Web technologies

Interoperability and FAIRness through a novel combination of Web technologies

Interoperability with Moby 1.0--it's better than sharing your toothbrush!

scientific article

MECP2 variation in Rett syndrome - an overview of current coverage of genetic and phenotype data within existing databases

scholarly article from 2018

Moby and Moby 2: creatures of the deep (web).

scientific article published on 16 January 2009

Molecular characterization of a novel ssRNA ourmia-like virus from the rice blast fungus Magnaporthe oryzae

scientific article published on 17 November 2016

Nanopublishing Clinical Diagnoses: Tracking Diagnostic Knowledge Base Content and Utilization

OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

scientific article published on 4 January 2013

OWL-DL Domain-Models as Abstract Workflows

OWL2Perl: creating Perl modules from OWL class definitions

scientific article

Ontology engineering using volunteer labor

Optimization of Distributed SPARQL Queries Using Edmonds' Algorithm and Prim's Algorithm

Preparing Data at the Source to Foster Interoperability across Rare Disease Resources

scientific article published in January 2017

Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base ⬇️

scientific article

Quantitative evaluation of bias in PCR amplification and next-generation sequencing derived from metabarcoding samples.

scientific article published on 11 January 2015

RO-Crate Metadata Specification 1.1.1

academic document

Registries of Domain-Relevant Semantic Reference Models Help Bootstrap Interoperability in Domains with Fragmented Data Resources ⬇️

article by Marco Roos et al published 19 February 2017 in Proceedings of the 9th International Conference Semantic Web Applications and Tools for Life Sciences

Robust and automatic definition of microbiome states

scientific article published in 2019

SADI, SHARE, and the in silico scientific method

scientific article

SHARE: A Semantic Web Query Engine for Bioinformatics

SPARQL assist language-neutral query composer

scientific article

Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data

scientific article published on 15 March 2022

Semantically-Guided Workflow Construction in Taverna: The SADI and BioMoby Plug-Ins

Semi-automatic web service composition for the life sciences using the BioMoby semantic web framework

scientific article published on 04 March 2008

Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics

scientific article

Tag clouds for summarizing web search results

Temporal microbiome road-maps guided by perturbations

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications

scientific article

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

scientific article (publication date: 11 February 2013)

The Bioperl toolkit: Perl modules for the life sciences

scientific article

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*

scientific article (publication date: 21 August 2010)

The FAIR Guiding Principles for scientific data management and stewardship

scientific article (publication date: 15 March 2016)

The Life Sciences Semantic Web is full of creeps!

scientific article published on 9 August 2006

The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions

scientific article (publication date: 5 April 2013)

The SADI plug-in to IO informatics' sentient knowledge explorer

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation

scientific article

The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery ⬇️

scientific article published on 6 March 2014

The emergent discipline of health web science

scientific article

The generation challenge programme platform: semantic standards and workbench for crop science

scientific article

The relationship between host lifespan and pathogen reservoir potential: an analysis in the system Arabidopsis thaliana--cucumber mosaic virus

scientific article

Using a Novel Data Transformation Technique to Provide the EMBOSS Software Suite as Semantic Web Services

VPS13D Gene Variant Is Associated with Altered IL-6 Production and Mortality in Septic Shock.

scientific article

Vcsa1 gene peptides for the treatment of inflammatory and allergic reactions.

scientific article published on June 2007

Virulence- and signaling-associated genes display a preference for long 3′UTRs during rice infection and metabolic stress in the rice blast fungus

article

Web Services and the Semantic Web for Life Science Data

iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website

scientific article (publication date: 15 December 2006)

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