228 Works

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

A genetic switch

Egon Willighagen
Reaction acting as genetic switch, catalyzed by hydrogen peroxide. Published inĀ Govan, J. M., McIver, A. L., Riggsbee, C. & Deiters, A. Hydrogen peroxide induced activation of gene expression in mammalian cells using boronate estrone derivatives. Angewandte Chemie International Edition n/a (2012). URL http://dx.doi.org/10.1002/anie.201203222.

Metabolite BridgeDb ID Mapping Database (20160910)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 142, and Wikidata (7 September 2016) as data sources. This release includes names of compounds in ChEBI, useful for drawing new metabolic pathways in PathVisio.
See the attached QC for more details on the changes.

Metabolite BridgeDb ID Mapping Database (20160910)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 142, and Wikidata (7 September 2016) as data sources. This release includes names of compounds in ChEBI, useful for drawing new metabolic pathways in PathVisio.
See the attached QC for more details on the changes.

Metabolite BridgeDb ID Mapping Database (20161012)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 144, and Wikidata (12 October 2016) as data sources. This release includes names of compounds in ChEBI, useful for drawing new metabolic pathways in PathVisio.
See the attached QC for more details on the changes.

Metabolite BridgeDb ID Mapping Database (20161012)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 144, and Wikidata (12 October 2016) as data sources. This release includes names of compounds in ChEBI, useful for drawing new metabolic pathways in PathVisio.
See the attached QC for more details on the changes.

NanoWiki 4

Egon Willighagen
Added more source annotation and SMILES info for many materialsm and physchem endpoints are now annotated with ontology terms. Furthermore, nanomaterials can now be typed with a specific ontology term, such as the JRC representative test materials.

NanoWiki (release 4)

Egon Willighagen
Added more source annotation and SMILES info for many materialsm and physchem endpoints are now annotated with ontology terms. Furthermore, nanomaterials can now be typed with a specific ontology term, such as the JRC representative test materials.

NanoWiki (release 3)

Egon Willighagen
Third release of the NanoWiki dataset. This release extends the Linked Data feature, introducing owl:sameAs and skos:closeMatch. The first is used in the new ChEMBL bundle with a few derived fullerenes. A GEO bundle has also been added. Most nanomaterials are now linked directly to articles (with DOIs). The data now describes 420 nanomaterials with 900 measurements (physchem and bioassay data) from 43 research articles.

NanoWiki (release 3)

Egon Willighagen
Third release of the NanoWiki dataset. This release extends the Linked Data feature, introducing owl:sameAs and skos:closeMatch. The first is used in the new ChEMBL bundle with a few derived fullerenes. A GEO bundle has also been added. Most nanomaterials are now linked directly to articles (with DOIs). The data now describes 420 nanomaterials with 900 measurements (physchem and bioassay data) from 43 research articles.

Metabolite BridgeDb ID Mapping Database (20160605)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 140, and Wikidata (4 June 2016) as data sources.
This release fixes storing of ChEBI identifiers in both alternative forms and adds names from Wikidata, useful for drawing new metabolic pathways in PathVisio.
See the attached QC for more details on the changes.

Metabolite BridgeDb ID Mapping Database (20160605)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 140, and Wikidata (4 June 2016) as data sources.
This release fixes storing of ChEBI identifiers in both alternative forms and adds names from Wikidata, useful for drawing new metabolic pathways in PathVisio.
See the attached QC for more details on the changes.

Publication Year

  • 2017
    74
  • 2016
    50
  • 2015
    56
  • 2014
    23
  • 2013
    16
  • 2012
    7
  • 2011
    2

Data Centers

  • figshare Academic Research System
    132
  • ZENODO - Research. Shared.
    81
  • Faculty of 1000 Research Ltd
    6
  • PeerJ
    6
  • ResearchGate
    2
  • National Cancer Institute, Bioconductor
    1