228 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...

Ambit.Js: Release 0.0.2

Egon Willighagen
Second release: extended support for the Substance API initial support for the Bundle API examples online at http://enanomapper.github.io/ambit.js/ API documentation online at http://enanomapper.github.io/ambit.js/api/

Bodr: Bodr 10

Egon Willighagen
Release notes are available from: http://chem-bla-ics.blogspot.co.uk/2013/08/the-blue-obelisk-data-repositorys-10.html

Metabolite BridgeDb ID Mapping Database (20161227)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 146, and Wikidata (26 December 2016) as data sources. See the attached QC for more details on the changes.

Metabolite BridgeDb ID Mapping Database (20161227)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 146, and Wikidata (26 December 2016) as data sources. See the attached QC for more details on the changes.

WikiPathways SD file (v.2)

Egon Willighagen
Second release of a Structure Data File (SDF) containing metabolites found in WikiPathways. The file is created with SMILES strings from Wikidata based on the ID mappings to metabolites in the pathways, and converted into a SD file with CDK 1.5.14.

WikiPathways SD file (v.2)

Egon Willighagen
Second release of a Structure Data File (SDF) containing metabolites found in WikiPathways. The file is created with SMILES strings from Wikidata based on the ID mappings to metabolites in the pathways, and converted into a SD file with CDK 1.5.14.

Metabolite BridgeDb ID Mapping Database (20170504)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 151, and Wikidata (4 May 2017) as data sources. No significant changes, and just updated mappings. See the attached QC for more details on the changes.

Metabolite BridgeDb ID Mapping Database (20170504)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 151, and Wikidata (4 May 2017) as data sources. No significant changes, and just updated mappings. See the attached QC for more details on the changes.

Metabolite BridgeDb ID Mapping Database (20171008)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6 (26 August 2017), ChEBI 156, and Wikidata (8 October 2017) as data sources. No significant changes but just updated data.
If you use this data in your research, please cite that data set, and the BridgeDb, ChEBI, and HMDB articles.

Metabolite BridgeDb ID Mapping Database (20171008)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6 (26 August 2017), ChEBI 156, and Wikidata (8 October 2017) as data sources. No significant changes but just updated data.
If you use this data in your research, please cite that data set, and the BridgeDb, ChEBI, and HMDB articles.

Metabolite BridgeDb ID Mapping Database (20171203)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 4.0 (3 December 2017), ChEBI 158, and Wikidata (3 December 2017) as data sources. No significant changes but just updated data.
If you use this data in your research, please cite this data set, and the BridgeDb, ChEBI, and HMDB articles.

Metabolite BridgeDb ID Mapping Database (20170408)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 150, and Wikidata (8 April 2017) as data sources. No significant changes, and just updated mappings. See the attached QC for more details on the changes.

Metabolite BridgeDb ID Mapping Database (20170408)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 150, and Wikidata (8 April 2017) as data sources. No significant changes, and just updated mappings. See the attached QC for more details on the changes.

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.

Metabolite BridgeDb ID Mapping Database (20170826)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6 (26 August 2017), ChEBI 154, and Wikidata (26 August 2017) as data sources. Two significant changes: Mappings to the EPA CompTox Dashboard have been added (about 36 thousand) and it is using a newer HMDB 3.6 version with many more compounds. If you experience problems, please report on the project page. See the attached QC for more details on the changes.
If you use this data in...

Metabolite BridgeDb ID Mapping Database (20170826)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6 (26 August 2017), ChEBI 154, and Wikidata (26 August 2017) as data sources. Two significant changes: Mappings to the EPA CompTox Dashboard have been added (about 36 thousand) and it is using a newer HMDB 3.6 version with many more compounds. If you experience problems, please report on the project page. See the attached QC for more details on the changes.
If you use this data in...

Metabolite BridgeDb ID Mapping Database (20170709)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 153, and Wikidata (9 July 2017) as data sources. No significant changes, and just updated mappings. See the attached QC for more details on the changes.

Metabolite BridgeDb ID Mapping Database (20170709)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 153, and Wikidata (9 July 2017) as data sources. No significant changes, and just updated mappings. See the attached QC for more details on the changes.

Metabolite BridgeDb ID Mapping Database (20170621)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 152, and Wikidata (21 June 2017) as data sources. No significant changes, and just updated mappings. See the attached QC for more details on the changes.

Metabolite BridgeDb ID Mapping Database (20170621)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 152, and Wikidata (21 June 2017) as data sources. No significant changes, and just updated mappings. See the attached QC for more details on the changes.

Metabolite BridgeDb ID Mapping Database (20170621)

Egon Willighagen
BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 152, and Wikidata (21 June 2017) as data sources. No significant changes, and just updated mappings. 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