Egon Willighagen
Joined 9 November 2012
| Babel user information | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| ||||||||||
| Users by language |
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) .
- Somewhere in September 2024 I passed the 7 millionth edit. Since the previous landmark, it has been mostly citations (between existing Wikidata items for scholarly articles) and annotation of retracted articles.
Chemistry has my main interest, metabolites particularly, but I am interested in science at large, including the process and the history.
Doing these days
editThings 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
- 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
editAccepted 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
editShape 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)
- Wikimedia list article (E450)
Curation lists
editBots
editI have started developing a bot to working on metabolic pathways related information.
Based on a request, I have created a third account, again ending with "bot". These two accounts are defunct.
Finished/Retired/Paused tasks
edit- manually copying four physicochemical properties from Basic laboratory and industrial chemicals: A CRC quick reference handbook (Q22236188): melting point (P2101), boiling point (P2102), electric dipole moment (P2201), and ionization energy (P2260)* added missing mass (P2067) annotations for chemical compounds
- 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