Jakub Galgonek

We are continuously working on improving our Integrated Database of Small Molecules that employs Semantic Web technologies and is accessible at idsm.elixir-czech.cz. Recently, we achieved a nice rating on YummyData, which monitors SPARQL endpoints: yummydata.org/endpoint.

#IDSM (the small-molecule database developed by @ELIXIRCZ) now also allows you to search for small molecules by their mass spectrum via #SPARQL. doi.org/10.1093/bioinf…

As a member of @ELIXIRCZ, we would like to introduce you to our new review on making relational databases accessible via #SPARQL. doi.org/10.1186/s13321…

Using one query to link @ELIXIRCZ a idsm/sachem #SPARQL endpoint having #MolMeDB with @SwissLipids is fantastic. Connecting membranes to lipids data and on to @rhea,@uniprot and @chebit is real #FAIR #BioHackEU21

UniProt release 2021_04 is out with 225,578,953 proteins! Read the headline: ZTGC: bacteriophages reinvent the DNA alphabet and catch up on all our updates at uniprot.org/news/2021/11/1…

Our new @ELIXIRCZ paper on the Integrated Database of Small Molecules: "IDSM ChemWebRDF: SPARQLing small-molecule datasets" jcheminf.biomedcentral.com/articles/10.11…

new: "IDSM ChemWebRDF: SPARQLing small-molecule datasets" jcheminf.biomedcentral.com/articles/10.11…

@egonwillighagen @emblebi @bigcat_UM @ChEMBL Happy to have ChEMBL #sparql back via the IDSM endpoint @ELIXIRCZ. Try our queries at snorql.nextprot.org #chemistry #compchem #drugdesign @egonwillighagen @JGalgonek

IDSM - Integrated Database of Small Molecules idsm.elixir-czech.cz youtu.be/09WwGtEMraw

@egonwillighagen @jervenbolleman @emblebi @bigcat_UM @ChEMBL @ELIXIRCZ @uniprot @rhea_db @ISBSIB @sparql No, the preprint is not available, but maybe you saw the paper as CHIN-D-21-00004.

@egonwillighagen @jervenbolleman @emblebi @bigcat_UM @ChEMBL @ELIXIRCZ @uniprot @rhea_db @ISBSIB @sparql Yes, I can confirm that the text is correct. Nevertheless, just for completeness, IDSM supports also chemical similarity searching.

@jervenbolleman @egonwillighagen @emblebi @bigcat_UM @ChEMBL @ELIXIRCZ @uniprot @rhea_db @ISBSIB @sparql Great, thank you. The SPARQL endpoint corresponding to the ChemWeb application (idsm.elixir-czech.cz/chemweb/) and containing ChEMBL data is idsm.elixir-czech.cz/sparql/endpoin…. We already submitted a paper describing it in detail. We hope that it will be published soon.

@JGalgonek @egonwillighagen @emblebi @bigcat_UM @ChEMBL @ELIXIRCZ @uniprot @rhea_db @ISBSIB I didn't know that :D I will reinstate the #ChEMBL examples on @uniprot @sparql to point to your work.

@jervenbolleman @egonwillighagen @emblebi @bigcat_UM @ChEMBL @ELIXIRCZ @uniprot @rhea_db @ISBSIB Actually, the ChEMBL 27.0 dataset is already included in the IDSM SPARQL endpoint and the ChemWeb application.

@egonwillighagen @emblebi @bigcat_UM @ChEMBL It would be wonderful to have @chembl #sparql back. Especially in combination with the @ELIXIRCZ #idsm substructure search and idsm.elixir-czech.cz/chemweb/ the #federated queries with @uniprot and @rhea_db endpoints at @ISBSIB

@egonwillighagen The 1st digit is a Sgroup type: 0=none, 1=SRU type, 2=monomer, 3=copolymer, 4=modification, 5=crosslink, 6=Mer type. The 2nd digit is a Sgroup subtype: 0=none, 1=alternating, 2=random, 3=block. The 3rd digits is a connectivity: 0=none, 1=head-to-tail, 2=head-to-head, 3=unknown.