okay, busy day. multiple things to finish today. one, my script to extend and improve the chemistry in #wikidata with better typing (e.g. ions), add mass (https://www.wikidata.org/wiki/Property:P2067), and a bit more. The code still is in my online open notebook at https://github.com/egonw/ons-wikidata/blob/master/Wikidata/createWDitemsFromSMILES.groovy and soon with the new features
So, at the #dagstuhl meeting we continued exploring CXSMILES for compound classes (report pending, blog post https://chem-bla-ics.blogspot.com/2022/08/biology-acps-lipids-cheminformatics-and.html) and I've been adding some more CXSMILES recently, for fatty acyl ACPs and polymers. For the last, there are ~160 candidate #wikidata entries that can use CXSMILES too: https://w.wiki/5aTd
Fwd: "BridgeDb NWO grant update #4: Bioregistry.io and a BioSB workshop" https://chem-bla-ics.blogspot.com/2022/07/bridgedb-nwo-grant-update-4.html #openscience #bridgedb #wikidata
a new lipid metabolism pathway in WikiPathways contains a lot of LIPID MAPS identifiers that we do not have in #wikidata yet. Using Bacting I am adding a bunch of them.
new: "The LOTUS initiative for open knowledge management in natural products research" https://chem-bla-ics.blogspot.com/2022/05/new-lotus-initiative-for-open-knowledge.html https://doi.org/10.7554/elife.70780 #wikidata #openscience
new paper: "CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community" https://pubs.acs.org/doi/10.1021/acs.jcim.2c00268
this morning I attended a FAIRplus Cookbook bookdash session. This cookbook has a growing number of short recipes on how to make your research output a bit more FAIR. https://faircookbook.elixir-europe.org/ I filed an official pull request for the recipe how to add external identifiers to #wikidata and proposed a recipe on how to convert IUPAC names to InChIKeys (see WIP https://github.com/egonw/the-fair-cookbook/pull/11)
I actually wrote this on Twitter for Twitter users interested in migrating to #Mastodon but maybe this tweetorial describes how to use #Wikidata to find co-authors on Mastodon :) https://threadreaderapp.com/thread/1519193166188007424.html Have fun!
in the past week I have started annotating CAS registry numbers in #wikidata with references to indicate CAS Common Chemistry https://w.wiki/3AGr This, in turn, is starting to be used to validate the CAS numbers in the English Wikidata (I can reports for other langauges too, tho) #chemistry #openscience #AmericanChemicalSociety
help me get NMRShiftDb compound identifiers into #wikidata: https://www.wikidata.org/wiki/Wikidata:Property_proposal/NMRShiftDB_Structure_ID
happy to have contributed to this new work (preprint): "Open Natural Products Research: Curation and Dissemination of Biological Occurrences of Chemical Structures through #Wikidata" https://www.biorxiv.org/content/10.1101/2021.02.28.433265v1
new paper: "A protocol for adding knowledge to #Wikidata: aligning resources on human coronaviruses" https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-020-00940-y (blog will follow)
Chem/Bio/Stats/SemWeb, @the_cdk, @wikipathways, @bigcat_um, @MaastrichtU (these tweets are personal)
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