SPARQL queries
All organisms containing compound for which a given MeSh id has been reported.
Change MeSH Id according to https://meshb.nlm.nih.gov/search
displayed as a treemap
compounds in organisms who have a parent taxon with a given taxon name
compounds in organisms who have a parent taxon with a given taxon name - grouped and counted
compounds in organisms who have a parent taxon with a given taxon name - with mf and accurate mass
compounds displaying a found in a taxon property
idsm powered !!!
genus counting indole substrutcures
This SPAQRL query is based on a proposition of Jakub Galgonek jakub.galgonek@uochb.cas.cz (https://idsm.elixir-czech.cz/) and adapted by Pierre-Marie Allard (pierre-marie.allard@unige.ch) It returns an order list of organisms known to produce chemical compounds having an indolic moiety. The organisms are aggregated at the parent taxon level, and the list is ordered by number of compound occurence in the parent t
all molecules isolated by author X
https://w.wiki/32D6 https://w.wiki/32$m
count of the authors having isolated a given scaffold
compare authors by count of compound
https://w.wiki/32Vb https://w.wiki/32Vk (bar-chart)
compare authors by count of compound (substructure-refinable)
compare authors by count of compound (structuresimilarity-refinable)
https://w.wiki/32Vg (indolic)
https://w.wiki/32Vj (bubblechart - indolic) https://w.wiki/32Vi (bubblechart - tropanic)
count of authors isolating substances with a given role
all distinct article/substances/org for a given biological role
all disticnt antibiotics
drug-prot interaction
SELECT DISTINCT ?parent_taxon ?parent_taxon_name ?compound ?interaction ?compoundLabel ?geneLabel ?biological_processLabel ?diseaseLabel WHERE {
#?compound wdt:P2868 ?mesh.
#?mesh wdt:P486 "D000962".
?compound wdt:P235 ?inchikey.
{
?compound p:P703 ?statement.
?statement ps:P703 ?taxon.
?taxon wdt:P171 ?parent_taxon.
OPTIONAL { ?taxon wdt:P171 ?parent_taxon. }
OPTIONAL { ?parent_taxon wdt:P225 ?parent_taxon_name. }
{
?statement prov:wasDerivedFrom ?ref.
?ref pr:P248 ?reference.
?reference wdt:P356 ?reference_doi;
wdt:P1476 ?reference_title.
}
#?compound p:P129 ?interaction.
#?interaction wdt: wd:Q21119831.
?compound wdt:P129 ?gene_product . # drug interacts with a gene_product
?gene wdt:P688 ?gene_product . # gene_product (usually a protein) is a product of a gene (a region of DNA)
?disease wdt:P2293 ?gene . # genetic association between disease and gene
?disease wdt:P279* wd:Q12078 . # limit to cancers wd:Q12078 (the * operator runs up a transitive relation..)
?gene_product wdt:P682 ?biological_process . #add information about the GO biological processes that the gene is related to
?biological_process (wdt:P361|wdt:P279)* wd:Q14599311.
}
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
GROUP BY ?parent_taxon ?parent_taxon_name ?compound ?interaction ?compoundLabel ?geneLabel ?biological_processLabel ?diseaseLabel
#ORDER BY DESC (?count)
Generic LOTUS queries
https://w.wiki/$Q$ https://w.wiki/$R3 https://w.wiki/$RD apparently working ! https://w.wiki/$RR with wd: for structure and org https://w.wiki/$RU wd: for everyone ...still ok https://w.wiki/$SF full monty
Sachem non-permanent endpoint
https://idsm.elixir-czech.cz:2443/sachem/#/search
Sachem grand parents https://w.wiki/32Wz
Retrun compound present in invasive species
https://w.wiki/32fa https://w.wiki/32fc
check taxon for a givin INChikey (regex)
chemotax graph queries
https://w.wiki/32q9 https://w.wiki/32qC
to tweet
All the compounds found in the Streptomyces avermitilis taxon and the references documenting this link. https://w.wiki/33V$
We can remove the references to get all unique compounds found in the Streptomyces coelicolor
All the biological taxa where the chemical compound erysodine is found in. https://w.wiki/33WA
all compounds produced by a given taxon or group of taxa (including children taxa) which have a described bioactivity :
resumed as treemap https://w.wiki/3YMt