78 Works

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 (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 (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.

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 (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 (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.

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 (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.

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.

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 V0.3.2

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()

Larsgw/Citation.Js V0.3.0

Lars Willighagen & Egon Willighagen
Release v0.3.0.

Larsgw/Citation.Js: V0.3.4

Lars Willighagen, Egon Willighagen & Johannes Wienke
Citation.js converts formats like BibTeX, Wikidata JSON and ContentMine JSON to CSL-JSON to convert to other formats like APA, Vancouver and back to BibTeX. Changed Updated README Fixed Command sequence normalisation in BibTeX BibTeX test case output

Larsgw/Citation.Js: V0.3.4

Lars Willighagen, Egon Willighagen & Johannes Wienke
Citation.js converts formats like BibTeX, Wikidata JSON and ContentMine JSON to CSL-JSON to convert to other formats like APA, Vancouver and back to BibTeX. Changed Updated README Fixed Command sequence normalisation in BibTeX BibTeX test case output

Enanomapper/Ontologies: Final Release Of Enanomapper Ontology

JKChang, Janna Hastings, Egon Willighagen, Fehrhart & Lrieswijk
v4.0 of the eNanoMapper Ontology (ENM) covers 10,881 classes, compared with 8407 classes in version 3. What's new in eNM V4.0: 162 New modelling-related terms selected by NTUA have been added to cover experimental and calculated (image analysis and algorithm-derived) descriptors. Around 200 new terms have been added as a result of input from the NanoSafety Cluster Community (NANoREG, Nano WG and NECID etc.). As a byproduct of the development of the eNanoMapper Ontology, interaction...

Resource Types

  • Software
    25
  • Text
    23
  • Collection
    17
  • Dataset
    10
  • Image
    3

Publication Year

  • 2017
    78

Registration Year

  • 2018
    3
  • 2017
    75

Data Centers

  • figshare Academic Research System
    47
  • ZENODO - Research. Shared.
    29
  • National Cancer Institute, Bioconductor
    1
  • University of Cambridge
    1