74 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...

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.

Larsgw/Citation.Js V0.3.1

Lars Willighagen & Egon Willighagen
Added Options parameter in parseInput and parseInputAsync Option for max parsing chain length Option to generate parsing chain data in _graph property Option to force type when parsing Changed Options API in Cite and Cite.async Cite(data, outputOptions) // BECOMES Cite(data, { ...parsingOptions, output: outputOptions }) Author ordinal in Wikidata props is now a property _ordinal instead of an array element Parsing invalid dates now returns input as literal date instead of an empty date-parts Refactored...

Larsgw/Citation.Js V0.3.3

Lars Willighagen & Egon Willighagen
Added A lot of Wikidata entry type mappings Support for option-less piping stdin -> stdout in the CLI Changed Greatly improve name parsing Wikidata entry type default is now book to align with, among other things, BibTeX Fixed Unknown Wikidata entry type now actually defaults to something CLI now uses the API changed in 0.3.1

Larsgw/Citation.Js V0.3.3

Lars Willighagen & Egon Willighagen
Added A lot of Wikidata entry type mappings Support for option-less piping stdin -> stdout in the CLI Changed Greatly improve name parsing Wikidata entry type default is now book to align with, among other things, BibTeX Fixed Unknown Wikidata entry type now actually defaults to something CLI now uses the API changed in 0.3.1

Larsgw/Citation.Js V0.3.2

Lars Willighagen & Egon Willighagen
Added New Wikidata field mappings (see #76) Changed BibTeX name field output now uses reverse notation Main parsing function aliases/shortcuts: Cite.normalise() -> Cite.input() Cite.normaliseAsync() -> Cite.inputAsync()

Publication Year

  • 2017
    74

Data Centers

  • figshare Academic Research System
    46
  • ZENODO - Research. Shared.
    25
  • PeerJ
    2
  • National Cancer Institute, Bioconductor
    1