211 Works

Metabolite BridgeDb ID Mapping Database (20161106)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 145, and Wikidata (5 November 2016) as data sources. See the attached QC for more details on the changes.

Metabolite BridgeDb ID Mapping Database (20161106)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 145, and Wikidata (5 November 2016) as data sources. See the attached QC for more details on the changes.

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.

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

Nanotoxicity from Ionization Enthalpy

Egon Willighagen
Data from the "Using nano-QSAR to predict the cytotoxicity of metal oxide nanoparticles" paper in Nature Nanotechnology (doi:10.1038/nnano.2011.10) showing the main finding.

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 (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.

Resource Types

  • Dataset
    60
  • Text
    55
  • Software
    48
  • Collection
    32
  • Image
    9
  • Other
    5
  • Audiovisual
    2

Publication Year

  • 2017
    62
  • 2016
    47
  • 2015
    54
  • 2014
    23
  • 2013
    16
  • 2012
    7
  • 2011
    2

Data Centers

  • figshare Academic Research System
    125
  • ZENODO - Research. Shared.
    71
  • Faculty of 1000 Research Ltd
    6
  • PeerJ
    6
  • ResearchGate
    2
  • National Cancer Institute, Bioconductor
    1