57 Works

Collaborative research: about licensing, waiving, and ownership

Egon Willighagen
Research collaborations are hampered by copyright law. While these laws are aimed at solving sustainability of writing and later other creative processes, and nowadays knowledge too, the make it harder in a time where research is funded with on temporary projects. This article discusses some of the aspects involved, though the legal foundations are only minimally brought up. One critical aspect is the role of consortium agreements. It also outlines how open licenses can simplify...

Collaborative research: about licensing, waiving, and ownership

Egon Willighagen
Research collaborations are hampered by copyright law. While these laws are aimed at solving sustainability of writing and later other creative processes, and nowadays knowledge too, the make it harder in a time where research is funded with on temporary projects. This article discusses some of the aspects involved, though the legal foundations are only minimally brought up. One critical aspect is the role of consortium agreements. It also outlines how open licenses can simplify...

Open Science: what's next?

Egon Willighagen
Presentation given at the National Plan Open Science meeting in Delft, 2017-05-29.

Open Science: what's next?

Egon Willighagen
Presentation given at the National Plan Open Science meeting in Delft, 2017-05-29.

Accessing biological data with semantic web technologies

Egon Willighagen
Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness show advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows. Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be use in...

Accessing biological data in R with semantic web technologies

Egon Willighagen
Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness shows advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows. Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be used in...

Accessing biological data in R with semantic web technologies

Egon Willighagen
Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness show advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows. Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be use in...

Accessing biological data in R with semantic web technologies

Egon Willighagen
Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness shows advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows. Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be used in...

Capturing reuse in altmetrics

Egon Willighagen
A brief idea

Scholia And Scientometrics With Wikidata

Finn Årup Nielsen, Daniel Mietchen & Egon Willighagen
Scholia is a tool to handle scientific bibliographic information through Wikidata. The Scholia Web service creates on-the-fly scholarly profiles for researchers, organizations, journals, publishers, individual scholarly works, and for research topics. To collect the data, it queries the SPARQL-based Wikidata Query Service. Among several display formats available in Scholia are lists of publications for individual researchers and organizations, publications per year, employment timelines, as well as coauthor and topic networks and citation graphs. The Python...

Scholia And Scientometrics With Wikidata

Finn Årup Nielsen, Daniel Mietchen & Egon Willighagen
Scholia is a tool to handle scientific bibliographic information through Wikidata. The Scholia Web service creates on-the-fly scholarly profiles for researchers, organizations, journals, publishers, individual scholarly works, and for research topics. To collect the data, it queries the SPARQL-based Wikidata Query Service. Among several display formats available in Scholia are lists of publications for individual researchers and organizations, publications per year, employment timelines, as well as coauthor and topic networks and citation graphs. The Python...

Deliverable Report D1.1 Requirements Analysis And Systems Design

Barry Hardy Markus Hegi
The objective of WP 1 is, to enable the communication between the eNanoMapper project and the wider nanosafety community and to ensure the alignment of the objectives of eNanoMapper with the needs of the community. At the start of the project, an extensive requirements analysis was conducted and based on the results, an overall system design was worked out. The process was based on the methodology of Contextual Design and included five steps, each building...

Deliverable Report D2.1 Framework And Infrastructure For Ontology Development, Versioning And Dissemination

Egon Willighagen Janna Hastings
The eNanoMapper project aims to build an ontology and database to collate and describe data relevant for “safe by design” engineered nanomaterial development. Work Package 2 of this effort will develop and disseminate a comprehensive ontology for the nanosafety domain, encompassing nanomaterials and all information relating to their characterization, as well as relevant experimental paradigms, biological interactions and safety information. This deliverable report describes the technical infrastructure that has been created in order to support...

A ScienceOpen collection of NanoSafety Cluster publications

Egon Willighagen, Iseult Lynch & Stephanie Dawson
Preprint describing a ScienceOpen collection of literature generated by NanoSafety Cluster projects.

A ScienceOpen collection of NanoSafety Cluster publications

Egon Willighagen, Iseult Lynch & Stephanie Dawson
Preprint describing a ScienceOpen collection of literature generated by NanoSafety Cluster projects.

A ScienceOpen collection of NanoSafety Cluster publications

Egon Willighagen, Iseult Lynch & Stephanie Dawson
Preprint describing a ScienceOpen collection of literature generated by NanoSafety Cluster projects.

How to Use Chipster for Bioinformatics Analysis of Nanomaterial-Based Omics Data

Penny Nymark, Friederike Ehrhart & Egon Willighagen
This tutorial will get you started on the basic use of the bioinformatics tool Chipster, an alternative to ArrayAnalysis.org described in other eNM tutorials. It will guide you through the import of microarray data (Affymetrix .CEL files), quality checks, normalization, pre-processing, basic statistical analyses methods and visualization of your data. Chipster is not specific to the nanosafety field, but this tutorial will be focused on the specific needs of nanotoxicological research. Chipster is an open...

How to Use Chipster for Bioinformatics Analysis of Nanomaterial-Based Omics Data

Penny Nymark, Friederike Ehrhart & Egon Willighagen
This tutorial will get you started on the basic use of the bioinformatics tool Chipster, an alternative to ArrayAnalysis.org described in other eNM tutorials. It will guide you through the import of microarray data (Affymetrix .CEL files), quality checks, normalization, pre-processing, basic statistical analyses methods and visualization of your data. Chipster is not specific to the nanosafety field, but this tutorial will be focused on the specific needs of nanotoxicological research. Chipster is an open...

Extending WikiPathways to Improve Educational Capabilities

Jacob Windsor, Egon Willighagen & Anders Riutta
This thesis represents my work at the Maastricht Science Programme, Maastricht University to create "pathway stories" for WikiPathways.

Extending WikiPathways to Improve Educational Capabilities

Jacob Windsor, Egon Willighagen & Anders Riutta
This thesis represents my work at the Maastricht Science Programme, Maastricht University to create "pathway stories" for WikiPathways.

Deliverable Report D5.6 User Application For Conformance To Reporting And Curation Standards

Jiakang Chang Linda Rieswijk
The eNanoMapper project aims to build an ontology and database to collate and describe data relevant for “safe by design” engineered nanomaterial development. Within the nanosafety domain several projects have initiated the development of standards for data reporting and curation. With this deliverable we show how the ontology can be used to test the data completeness within the eNanoMapper database, according to these approved standards, which is tested with the use of SPARQL queries. To...

Deliverable Report D2.2 Ontology Content Types And Existing Community Efforts

Gareth Owen Janna Hastings
The eNanoMapper project aims to build an ontology and database to collate and describe data relevant for “safe by design” engineered nanomaterial development. Work Package 2 of this effort will develop and disseminate a comprehensive ontology for the nanosafety domain, encompassing nanomaterials and all information relating to their characterization, as well as relevant experimental paradigms, biological interactions and safety information. This deliverable report describes the primary content areas within the nanomaterial safety domain which need...

Deliverable Report D2.3 Ontology Initial Release

Egon Willighagen Janna Hastings
The eNanoMapper project aims to build an ontology and database to collate and describe data relevant for “safe by design” engineered nanomaterial development. Work Package 2 of this effort is developing and disseminating a comprehensive ontology for the nanosafety domain, encompassing nanomaterials and all information relating to their characterization, as well as relevant experimental paradigms, biological interactions and safety information. This deliverable report describes the initial release of the ontology, including the content and organization,...

Poster: Visualizing metabolomics data in directed biological networks

Martina Kutmon, Ryan Miller, Denise Slenter, Chris Evelo & Egon Willighagen
We developed a new solution to visualize the biological pathways involved in sparse metabolomics data. Using knowledge from two pathway resources and ontology-based approaches, we can show the directed networks between active metabolites from metabolomics data. The data from both resources is made interoperable by collapsing metabolites in the pathways into single nodes in the biological networks using ontological approaches. This explicit ontological linking allows for precise biological interpretation of the paths. By using Neo4j...

Publication Year

  • 2017
    24
  • 2016
    12
  • 2015
    13
  • 2014
    6
  • 2013
    1
  • 2012
    1

Data Centers

  • ZENODO - Research. Shared.
    27
  • figshare Academic Research System
    21
  • PeerJ
    6
  • ResearchGate
    2
  • Faculty of 1000 Research Ltd
    1