User:Egon Willighagen
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Open Scientist, very much involved in the Blue Obelisk (Q4420286) 
movement, Egon Willighagen (Q20895241) in the Wikidata database. Co-submitter of the Enabling Open Science: Wikidata for Research (Wiki4R) (Q26707522) .[1]
[2] Also contributed to the Scholia project.[3] Participating in Wikidata since July 2013.[4] I practice open notebook science and my Wikidata notebooks can be found at https://github.com/egonw/ons-wikidata
Seven years later, on September 19th 2020, I made my 1 millionth edit. Later milestones:
- in November 2021 the 2 millionth edit was made, adding a SwissLipids (Q41165322)
identifier - on April 8th 2023 I made the 3 millionth edit around the topic of per- and polyfluoroalkyl substances (Q648037)
- thanks to a big effort to add missing mass (P2067) annotations for chemical compounds, I made my 4 millionth edit in August 2023.
- my 5 millionth edit was in December 2023, for a batch of citations to retracted articles (ht OpenCitations (Q29279836) ). Earlier this week I marked ~7000 articles in Wikidata as retracted, based on CrossRef Retraction Watch (Q17078233) data
- April 19, 2024: my 6 millionth edit. Part of a big batch of citations from and to articles from the LOTUS Initiative data, linking metabolites to taxons. See The LOTUS initiative for open knowledge management in natural products research (Q112143478) .
Chemistry has my main interest, metabolites particularly, but I am interested in science at large, including the process and the history.
Doing these days[edit]
Things I am doing or interested in in Wikidata right now include:
- adding SMILES (and a bit more) for Wikidata pages that do not have it, while Wikipedia has a ChemBox: https://w.wiki/8iUp
- manually copying four physicochemical properties from Basic laboratory and industrial chemicals: A CRC quick reference handbook (Q22236188):
- added missing mass (P2067) annotations for chemical compounds
- retracted articles (and citations to them) (without adding new articles)
- Wikidata:WikiCite/Citation_Typing_Ontology
- Scholia (Q45340488) (particularly topic, citation links)
- contribute to Wikidata:WikiProject Chemistry and Wikidata:WikiProject COVID-19
- working with PubChem (Q278487) on depositing chemical structures in Wikidata in PubChem
- working with Cambridge Crystallographic Data Centre (Q5025404) on their identifiers in Wikidata and a small data deposit
Events[edit]
- BioHackathon Europe 2023 (Q118733318) , Oct/Nov 2023
- SWAT4HCLS 2023 (Q116458604) Hackathon, 16 February 2023
- LD4-Wikidata Group Call: Wikidata Queries around the SARS-CoV-2 virus and pandemic, 10th January 2023
- BioHackathon Europe 2022 (Q112064986)
- Wikidata 10th Birthday in Utrecht, the Netherlands
- BioHackathon Europe 2021 (Q109379355) , hacked on KNCV Van Marumpenning (Q110544180) and WikiProject_Elixir
- 13th International SWAT4HCLS conference (Q110499790)
- VOGIN, 2021
- WikidataCon, 2019, Berlin, Germany: Cheminformatics to improve Wikidata on chemical compounds
- 11th International SWAT4HCLS conference (Q56236021) , 2018 December 3-6, Antwerp, Belgium
- WikiProject Wikidata for Research Meetup, 2018 June 17-19, Berlin, Germany
- 11th International Conference on Chemical Structures (Q47501229) , 2018 May 27-31, Noordwijkerhout, The Netherlands (abstract, poster)
- Festival van Talent, 2018 March 24, Eindhoven, The Netherlands
- Open Science: the National Plan and you, 2017 May 29, Delft, The Netherlands
Proposals[edit]
Accepted Properties[edit]
- nanopublication identifier (P12545) (proposal)
- CSD Refcode (P11375) (proposal)
- CXSMILES (P10718) (proposal)
- OpenAlex ID (P10283) (proposal)
- NMRShiftDB structure ID (P9405) (proposal)
- SwissLipids ID (P8691) (proposal, constraint violations)
- Linked Open Data Cloud ID (P8605) (proposal)
- MassBank accession ID (P6689) (proposal)
- SPLASH (P4964) (proposal)
- MetaboLights Compound ID (P3890) (proposal)
- CORDIS Project ID (P3400) (proposal)
- DSSTox substance ID (P3117) (proposal)
- PubChem Substance ID (SID) (P2153) (proposal)
- WikiPathways ID (P2410) (proposal)
Shape expressions[edit]
Shape expressions are a nice way to formally document the structure of data. In Wikidata these are covered by EntitySchema. I started a few of them:
- university teacher (E44)
- university (E45)
- chemical element (E46)
- racemic mixture (E47)
- lipid (E232)
- protein family (E233)
- chemical compound (E239)
- natural product (E240)
- stereoisomer (E241)
- chemical compound with CAS registry number (E298)
- chemical compound with validated CAS registry number (E299)
- Open Science & Scholarship Community (E318)
- blog planet (E405)
- type of a chemical entity (E406)
- podcast (E418)
- podcast presenter (E419)
- podcast episode (E420)
- podcast series season (E421)
- Apple Podcast (E425)
Curation lists[edit]
Bots[edit]
User:UreomiczBot[edit]
I have started developing a bot to working on metabolic pathways related information.
User:Ureomics and User:UreomicsBot[edit]
Based on a request, I have created a third account, again ending with "bot". These two accounts are defunct.
Finished/Retired/Paused tasks[edit]
- annotating (existing) articles in Wikidata if retracted with the new CrossRef data dump of Retraction Watch (Q17078233)
- get the history of highly cited (cheminformatics) literature into Wikidata, including citation networks
- make sure all metabolites in WikiPathways (Q7999828) are found in Wikidata[5]
- adding LIPID MAPS ID (P2063) identifiers based on InChIKey match
- adding SwissLipids ID (P8691) identifiers based on InChIKey match
- Compounds with (canonical SMILES) that can have a CXSMILES
- EurJOC journal article that were published under a different journal name
- JCIM journal article that were published under a different journal name (See also Scholia and this list of most cited, misclassified JCICS article)
- added the JRC representative nanomaterial (Q47461491) and literature that discusses them
- adding compounds (neutral, full stereochemistry) from PubChemLite tier0 and tier1 (Q75998504)
- adding compounds that may be interesting to be explored as Zika drug leads
- porting pKa (P1117) data from the DrugMet database (finished)
- adding DSSTox substance ID (P3117) identifiers using QuickStatements (Q20084080) commands created with Bioclipse (Q1769726) from Creative Commons CC0 License (Q6938433) data on Figshare (Q17013516) (finished)
- make sure all human metabolites in the RECON model (see Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2 (Q28487717) ) are found in Wikidata
- adding CAS Registry Number (P231) in a local data set to define the chemical identity it captures
- curation of PubChem IDs
- get mass spectra linked to using CCZero InChIKey-SPLASH data
- Wikidata:Wiki-wetenschappers
- general statistics and my statistics
Authority control[edit]
| Authority control |
- ↑ Mietchen, Daniel et al. (2015). Enabling Open Science: Wikidata for Research. Zenodo. http://dx.doi.org/10.5281/zenodo.13906
- ↑ Mietchen, Daniel et al. (2015). Enabling Open Science: Wikidata for Research. Research Ideas and Outcomes 1: e7573. http://dx.doi.org/10.3897/rio.1.e7573
- ↑ Nielsen, Finn Å., Mietchen, Daniel Willighagen, Egon, 'Scholia and scientometrics with Wikidata', (2017). https://arxiv.org/abs/1703.04222
- ↑ https://www.wikidata.org/w/index.php?title=User:Egon_Willighagen&oldid=54749158
- ↑ Slenter, D. N., Kutmon, M., Hanspers, K., Riutta, A., Windsor, J., Nunes, N., Mélius, J., Cirillo, E., Coort, S. L., Digles, D., Ehrhart, F., Giesbertz, P., Kalafati, M., Martens, M., Miller, R., Nishida, K., Rieswijk, L., Waagmeester, A., Eijssen, L. M. T., Evelo, C. T., Pico, A. R., Willighagen, E. L., Jan. 2018. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. Nucleic Acids Research. http://dx.doi.org/10.1093/nar/gkx1064