query-43aa53a3114022a494a7a6bd011729c1
I am interested in contributing protein-small molecule binding data from our BindingDB databaseDear Wikidata community My lab runs the BindingDB database of protein-small molecule binding affinity data, bindingdb.org, and we are interested in contributing our data to WikiData. We have about 2 million measurements of binding between about 8,000 different proteins and 900K small molecules. The data come from scientific articles and US Patents. Many of the data come with a CC BY attribution license. Another big subset comes with a CC BY-SA license. We can treat these two sets differently, if needed. The proteins are outfitted with UniProt IDs and/or protein sequences. The small molecules have SMILES strings and InChI strings, and we can generate other identifiers for them if needed. The scientific articles are identifiable with DOIs, and the US Patent are identifiable with US Patent numbers. So it should be fairly straightforward to link our data in with other WikiData using these identifiers. Would these data be a good fit to Wikidata? 13:57, 6 January 2021 (UTC)) talk (Mkg001Thanks, instead.the WikiProject's talk page. Please post on couldn't be pinged has more than 50 participants and WikiProject Molecular biology PS You can see the >9,700 already existing statements with this query, so there is another type of duplicate to avoid: 10:20, 7 January 2021 (UTC)) talk (SCIdude, except your data is already digital, why not learn from them? Best wishes, have fun with Wikidata. --Wikidata:WikiProject_Chemistry/Natural_products Reference where Reference is the WD item of the paper. So you face similar task as the recently started (P248)stated in B, and as reference the statement (P129)physically interacts with Most important procedure-wise would be to avoid creating duplicate substances at all costs. Any protein in WD has a unique UniProt ID so any non-existing ID will need creation. Small molecules in WD have unique InChi keys (modulo exceptions) so any substance with InChi key not in WD is good to create. The central addition will be a statement A 17:48, 6 January 2021 (UTC)❫ ✉ ❪ChristianKlAs far as licenses go, there's a general question to what extend this is simply factual data that isn't protected or whether it is protected. Wikidata itself is cc-zero, and I think there's a good case to be made that the factual nature of the data allows the import and thus it would be great to have the data in Wikidata.
Use at
- https://query.wikidata.org/sparql
PREFIX wikibase: <http://wikiba.se/ontology#>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX bd: <http://www.bigdata.com/rdf#>
SELECT DISTINCT ?item1 ?item1Label ?item2 ?item2Label
{
?item1 wdt:P129 ?item2
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}