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

https://w.wiki/xMN

all molecules isolated by author X

https://w.wiki/32D6 https://w.wiki/32$m

count of the authors having isolated a given scaffold

https://w.wiki/32DF

compare authors by count of compound

https://w.wiki/32Vb https://w.wiki/32Vk (bar-chart)

compare authors by count of compound (substructure-refinable)

https://w.wiki/32Vd

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

https://w.wiki/32Vr

all distinct article/substances/org for a given biological role

https://w.wiki/32Vu

all disticnt antibiotics

https://w.wiki/32Vv

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)

https://w.wiki/32j3

chemotax graph queries

https://w.wiki/32q9 https://w.wiki/32qC

https://w.wiki/32qN

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

https://w.wiki/33WG

All the biological taxa where the chemical compound erysodine is found in. https://w.wiki/33WA

molecules found within vegetables

https://w.wiki/4EAh

molecules found within toxic plants

https://w.wiki/4EAw

mlecules in IUCN threatned species

https://w.wiki/4EGg

https://w.wiki/4EHQ

looking for molecules present in old species according to life span

https://w.wiki/4EH8 https://w.wiki/4EHB

with preclass

https://w.wiki/4EHD

and prepreclass

at all levels https://w.wiki/4EHH

at a single level

https://w.wiki/4EHJ

classed by chem classes https://w.wiki/4EHP

Messing around with pathways

https://w.wiki/4EK7

original query

https://w.wiki/4EK9

highest mountains in Switzerland

https://w.wiki/4EKE

all biologist with a twitter account

https://w.wiki/4EKW

strictly biologists https://w.wiki/4EKM

educated in Switzerland

https://w.wiki/4EKk

example for prsenattion UniFr

https://w.wiki/4EMf All compounds + ref for S. coelicolor

https://w.wiki/4EMo (bioact listed)

Compounds from species wuth given IUCN status and lifespan

https://w.wiki/4EMw

compounds in taxa and children filtered by SMILES pattern regex

https://w.wiki/4JWv

Melochia genus query

https://w.wiki/4VYy

IDSM queries

PREFIX sachem: http://bioinfo.uochb.cas.cz/rdf/v1.0/sachem# PREFIX rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# PREFIX bd: http://www.bigdata.com/rdf# PREFIX wd: http://www.wikidata.org/entity/ PREFIX wdt: http://www.wikidata.org/prop/direct/ PREFIX wdtn: http://www.wikidata.org/prop/direct-normalized/ PREFIX p: http://www.wikidata.org/prop/ PREFIX prov: http://www.w3.org/ns/prov# PREFIX ps: http://www.wikidata.org/prop/statement/ PREFIX pr: http://www.wikidata.org/prop/reference/ PREFIX endpoint: https://idsm.elixir-czech.cz/sparql/endpoint/

#title (Private): Which are the available referenced structure-organism pairs on Wikidata? (example limited to 1000 results) SELECT DISTINCT ?structure ?structure_inchikey ?taxon ?taxon_name ?reference ?reference_doi WHERE { ?structure wdt:P235 ?structure_inchikey; # get the inchikey p:P703[ # statement found in taxon ps:P703 ?taxon; # get the taxon (prov:wasDerivedFrom/pr:P248) ?reference ]. # get the reference ?taxon wdt:P225 ?taxon_name. # get the taxon scientific name ?reference wdt:P356 ?reference_doi. # get the reference DOI } LIMIT 10

PREFIX rdfs: http://www.w3.org/2000/01/rdf-schema# PREFIX sachem: http://bioinfo.uochb.cas.cz/rdf/v1.0/sachem# PREFIX endpoint: https://idsm.elixir-czech.cz/sparql/endpoint/

SELECT * WHERE { SERVICE endpoint:chebi { ?COMPOUND sachem:substructureSearch [ sachem:query "CC(=O)Oc1ccccc1C(O)=O" ] } ?COMPOUND rdfs:label ?o }

title: Compounds of the Melochia genus bearing the quinoline substructure

https://w.wiki/4wbY

all articles documenting found in taxonn Prop by authors of a given country

https://w.wiki/4z7M

PREFIX rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# PREFIX jlw: https://www.sinergiawolfender.org/jlw/ PREFIX rdfs: http://www.w3.org/2000/01/rdf-schema# PREFIX wd: http://www.wikidata.org/entity/ PREFIX wdt: http://www.wikidata.org/prop/direct/ PREFIX p: http://www.wikidata.org/prop/ PREFIX ps: http://www.wikidata.org/prop/statement/ PREFIX prov: http://www.w3.org/ns/prov# PREFIX pr: http://www.wikidata.org/prop/reference/ PREFIX wikibase: http://wikiba.se/ontology# PREFIX bd: http://www.bigdata.com/rdf# PREFIX wdraw: http://www.wikidata.org/ PREFIX vit: https://www.sinergiawolfender.org/vit/

SELECT ?chemical_compound ?compoundLabel ?queried_taxa ?queried_taxaLabel ?queried_taxall ?queried_taxallLabel ?pfcode WHERE {

SERVICE https://query.wikidata.org/sparql { VALUES ?queried_taxa { wd:Q310915 } { ?chemical_compound p:P703 ?stmt.# We selecte chemical classes having the found in taxon statement ?queried_taxall wdt:P171* ?queried_taxa. ?stmt ps:P703 ?queried_taxall. # and the restrict the found in taxon statement to match our queried taxa } ?chemical_compound rdfs:label ?compoundLabel. ?queried_taxa rdfs:label ?queried_taxaLabel. ?queried_taxall rdfs:label ?queried_taxallLabel.

FILTER (LANG(?compoundLabel) = "en") . # filter for English FILTER (LANG(?queried_taxaLabel) = "en") . FILTER (LANG(?queried_taxallLabel) = "en") . }

?pfcode jlw:is_from_plant_part ?plant_part; vit:has_taxon ?taxon.

?taxon jlw:has_wd_QID ?queried_taxall.

}

SELECT ?chemical_compound ?mf ?mf_formatted ?compoundLabel ?queried_taxa ?queried_taxaLabel ?queried_taxall ?queried_taxallLabel ?pfcode ?labprocess ?feature ?sirius_formula ?sirius_formula_string WHERE {

SERVICE https://query.wikidata.org/sparql { VALUES ?queried_taxa { wd:Q310915 } { ?chemical_compound p:P703 ?stmt.# We selecte chemical classes having the found in taxon statement OPTIONAL { ?chemical_compound wdt:P231 ?cas. } OPTIONAL { ?chemical_compound wdt:P233 ?smiles_canonical. } OPTIONAL { ?chemical_compound wdt:P234 ?inchi. } OPTIONAL { ?chemical_compound wdt:P592 ?chembl. } OPTIONAL { ?chemical_compound wdt:P662 ?pubchem. } OPTIONAL { ?chemical_compound wdt:P683 ?chebi. } OPTIONAL { ?chemical_compound wdt:P2017 ?smiles_isomeric. } OPTIONAL { ?chemical_compound wdt:P274 ?mf. } OPTIONAL { ?chemical_compound wdt:P2067 ?mass. } #BIND (Private)(LCASE(STR(?mf)) as ?lowmf) #BIND (Private)(REPLACE(STR(?mf),"₀₁₂₃₄₅₆₇₈₉","B") AS ?mf_b) . BIND(REPLACE(REPLACE(REPLACE(REPLACE(REPLACE(REPLACE(REPLACE(REPLACE(REPLACE(REPLACE(STR(?mf),"₀","0"),"₁","1"),"₂","2"),"₃","3"),"₄","4"),"₅","5"),"₆","6"),"₇","7"),"₈","8"),"₉","9") AS ?mf_formatted) .

?queried_taxall wdt:P171* ?queried_taxa.
?stmt ps:P703 ?queried_taxall. # and the restrict the found in taxon statement to match our queried taxa

} ?chemical_compound rdfs:label ?compoundLabel. ?queried_taxa rdfs:label ?queried_taxaLabel. ?queried_taxall rdfs:label ?queried_taxallLabel.

FILTER (LANG(?compoundLabel) = "en") . # filter for English FILTER (LANG(?queried_taxaLabel) = "en") . FILTER (LANG(?queried_taxallLabel) = "en") . }

?pfcode jlw:is_from_plant_part ?plant_part; jlw:has_lab_process ?labprocess; vit:has_taxon ?taxon. ?labprocess jlw:has_MZmine_chromatogram ?mzmine_chromatogram .

?mzmine_chromatogram jlw:has_MZmine_feature ?feature .

?feature jlw:has_SIRIUS_formula ?sirius_formula.

?sirius_formula jlw:has_SIRIUS_formula_string ?sirius_formula_string.

?taxon jlw:has_wd_QID ?queried_taxall.

FILTER(?mf_formatted = ?sirius_formula_string) }

Compounds produced by plants endemic to New caledonia

https://w.wiki/57ap

cleaner with mass and mf

https://w.wiki/57hN

listing compounds in meals

https://w.wiki/5Bs7

https://w.wiki/5Bs9

Compounds of the Arachnida class

https://w.wiki/5Doy

Compounds from taxa and children clean

https://w.wiki/5LJf

References and occurences of Alstonine

https://w.wiki/5WXP

compare occurences in WD of entries with a given taxon id (OTL versus WFO)

https://w.wiki/5WYx

endpoints

https://www.wikidata.org/wiki/Wikidata:Lists/SPARQL_endpoints

quest query mod from Mietchen to compounds (not working)

Pay attention to edge cases

?ta rdfs:label ?n. FILTER (LANG(?n) = "en") . BIND(REPLACE(STR(?n),"@en","") AS ?n_formatted) .

SERVICE wikibase:mwapi { bd:serviceParam wikibase:endpoint "www.wikidata.org"; wikibase:api "Generator"; mwapi:generator "search"; mwapi:gsrsearch ?n_formatted ; mwapi:gsrlimit "max". ?i wikibase:apiOutputItem mwapi:title. } ?i wdt:P1476 ?ti . #MINUS (Private) {?i wdt:P921 ?ta } #MINUS (Private) {?i wdt:P921 [wdt:P171* ?ta ] } FILTER (REGEX(LCASE(?ti) LCASE(CONCAT( "\" "b" ?n_formatted ,"\" "b")))) FILTER (!REGEX(LCASE(?ti) LCASE(CONCAT( ?n_formatted ,"-")))) FILTER (!REGEX(LCASE(?ti) LCASE(CONCAT( ?n_formatted ,"(.)virus")))) FILTER (!REGEX(LCASE(?ti) LCASE(CONCAT( "pseudo(.?)" ?n_formatted)))) } } AS %i WHERE { INCLUDE %i INCLUDE %t BIND (SUBSTR(?ti STRLEN(STRBEFORE(REPLACE(?ti ?n "=HELP=" "i") "=HELP=")) +1 STRLEN(?n_formatted)) AS ?a) }

No error but no results neither

?ta rdfs:label ?n. FILTER (LANG(?n) = "en") . BIND(REPLACE(STR(?n),"@en","") AS ?n_formatted) .

} LIMIT 100 } AS %t WITH { SELECT ?i ?n_formatted ?ta ?ti WHERE { INCLUDE %t

SERVICE wikibase:mwapi { bd:serviceParam wikibase:endpoint "www.wikidata.org"; wikibase:api "Generator"; mwapi:generator "search"; mwapi:gsrsearch ?n_formatted ; mwapi:gsrlimit "max". ?i wikibase:apiOutputItem mwapi:title. } ?i wdt:P1476 ?ti . #MINUS (Private) {?i wdt:P921 ?ta } #MINUS (Private) {?i wdt:P921 [wdt:P171* ?ta ] } FILTER (REGEX(LCASE(?ti) LCASE(CONCAT( "\" "b" ?n_formatted ,"\" "b")))) FILTER (!REGEX(LCASE(?ti) LCASE(CONCAT( ?n_formatted ,"-")))) FILTER (!REGEX(LCASE(?ti) LCASE(CONCAT( ?n_formatted ,"(.)virus")))) FILTER (!REGEX(LCASE(?ti) LCASE(CONCAT( "pseudo(.?)" ?n)))) } } AS %i WHERE { INCLUDE %i INCLUDE %t BIND (SUBSTR(?ti STRLEN(STRBEFORE(REPLACE(?ti ?n_formatted "=HELP=" "i") "=HELP=")) +1 STRLEN(?n_formatted)) AS ?a) }

Works !!!

adapted from Daniel Mietchen https://w.wiki/5a7K

SELECT DISTINCT ?n_formatted (CONCAT( REPLACE(STR(?i) ".Q" "Q") "|P921|" REPLACE(STR(?ta) ".Q" "Q") "|P1932|" (CONCAT("\"" ?a "\"")) "|S887|Q69652283") AS ?QuickStatements) WITH { SELECT DISTINCT ?ta ?n_formatted WHERE { SERVICE bd:sample { ?ta wdt:P31 wd:Q11173 . bd:serviceParam bd:sample.limit 5000 } ?ta p:P703 ?stmt. ?stmt ps:P703 ?taxa. ?ta rdfs:label ?n. FILTER (LANG(?n) = "en") . BIND(REPLACE(STR(?n),"@en","") AS ?n_formatted) . } LIMIT 25 } AS %t WITH { SELECT ?i ?n_formatted ?ta ?ti WHERE { INCLUDE %t SERVICE wikibase:mwapi { bd:serviceParam wikibase:endpoint "www.wikidata.org"; wikibase:api "Generator"; mwapi:generator "search"; mwapi:gsrsearch ?n_formatted ; mwapi:gsrlimit "max". ?i wikibase:apiOutputItem mwapi:title. } ?i wdt:P1476 ?ti . MINUS {?i wdt:P921 ?ta } #MINUS (Private) {?i wdt:P921 [wdt:P171* ?ta ] } #FILTER (Private) (REGEX(LCASE(?ti) LCASE(CONCAT( "\" "b" ?n_formatted ,"\" "b")))) #FILTER (Private) (!REGEX(LCASE(?ti) LCASE(CONCAT( ?n_formatted ,"-")))) #FILTER (Private) (!REGEX(LCASE(?ti) LCASE(CONCAT( ?n_formatted ,"(.)virus")))) #FILTER (Private) (!REGEX(LCASE(?ti) LCASE(CONCAT( "pseudo(.?)" ?n)))) } } AS %i WHERE { INCLUDE %i INCLUDE %t BIND (SUBSTR(?ti STRLEN(STRBEFORE(REPLACE(?ti ?n_formatted "=HELP=" "i") "=HELP=")) +1 STRLEN(?n_formatted)) AS ?a) }

https://w.wiki/5a8b

escaping dangling meta chracters https://w.wiki/5a8g

with taxa and compound

Adapted from Daniel Mietchen https://w.wiki/5a7K

SELECT DISTINCT (CONCAT( REPLACE(STR(?i) ".Q" "Q") "|P921|" REPLACE(STR(?ta) ".Q" "Q") "|P1932|" (CONCAT("\"" ?a "\"")) "|S887|Q69652283") AS ?QuickStatements) WITH { SELECT DISTINCT ?ta ?n_formatted WHERE { SERVICE bd:sample { ?ta wdt:P31 wd:Q11173 . bd:serviceParam bd:sample.limit 5000 } ?ta p:P703 ?stmt. ?stmt ps:P703 ?taxa. ?ta rdfs:label ?n. FILTER (LANG(?n) = "en") . BIND(REPLACE(REPLACE(REPLACE(STR(?n),"@en",""),"\+",""),"\-","") AS ?n_formatted) . } LIMIT 25 } AS %t WITH { SELECT ?i ?n_formatted ?ta ?ti WHERE { INCLUDE %t SERVICE wikibase:mwapi { bd:serviceParam wikibase:endpoint "www.wikidata.org"; wikibase:api "Generator"; mwapi:generator "search"; mwapi:gsrsearch ?n_formatted; mwapi:gsrlimit "max". ?i wikibase:apiOutputItem mwapi:title. } ?i wdt:P1476 ?ti . MINUS {?i wdt:P921 ?ta } } } AS %i WITH { SELECT ?j ?taxa ?ta ?ti WHERE { INCLUDE %t SERVICE wikibase:mwapi { bd:serviceParam wikibase:endpoint "www.wikidata.org"; wikibase:api "Generator"; mwapi:generator "search"; mwapi:gsrsearch ?taxa; mwapi:gsrlimit "max". ?j wikibase:apiOutputItem mwapi:title. } ?j wdt:P1476 ?ti . MINUS {?j wdt:P921 ?taxa } } } AS %j WHERE { INCLUDE %i INCLUDE %j INCLUDE %t BIND (SUBSTR(?ti STRLEN(STRBEFORE(REPLACE(?ti ?n_formatted "=HELP=" "i") "=HELP=")) +1 STRLEN(?n_formatted)) AS ?a) }

Using filter EXISTS

https://w.wiki/5a8t

https://w.wiki/5a9B

Curating query

Adapted from Daniel Mietchen https://w.wiki/5a7K

SELECT DISTINCT ?taxa ?taxaLabel ?taxa_chem ?taxa_chemLabel ?ta ?taLabel ?ti (CONCAT( REPLACE(STR(?ta) ".Q" "Q") "|P703|" REPLACE(STR(?taxa) ".Q" "Q") "|S248|" REPLACE(STR(?i) ".*Q" "Q")) AS ?QuickStatements) WITH { SELECT DISTINCT ?ta ?n_formatted ?taxa_chem WHERE { SERVICE bd:sample { ?ta wdt:P31 wd:Q11173 . bd:serviceParam bd:sample.limit 25000 } OPTIONAL { ?ta p:P703 ?stmt. } OPTIONAL { ?stmt ps:P703 ?taxa_chem. } ?ta rdfs:label ?n. FILTER (LANG(?n) = "en") . BIND(REPLACE(REPLACE(REPLACE(STR(?n),"@en",""),"\+",""),"\-","") AS ?n_formatted) . } LIMIT 30 } AS %t WITH { SELECT ?i ?n_formatted ?ta ?ti ?taxa WHERE { INCLUDE %t SERVICE wikibase:mwapi { bd:serviceParam wikibase:endpoint "www.wikidata.org"; wikibase:api "Generator"; mwapi:generator "search"; mwapi:gsrsearch ?n_formatted ; mwapi:gsrlimit "max". ?i wikibase:apiOutputItem mwapi:title. } ?i wdt:P1476 ?ti . ?i wdt:P921 ?taxa. ?taxa wdt:P105 wd:Q7432. FILTER (?taxa != ?taxa_chem) } } AS %i WHERE { INCLUDE %i INCLUDE %t BIND (SUBSTR(?ti STRLEN(STRBEFORE(REPLACE(?ti ?n_formatted "=HELP=" "i") "=HELP=")) +1 STRLEN(?n_formatted)) AS ?a) SERVICE wikibase:label { bd:serviceParam wikibase:language "en". } }

https://w.wiki/5a9T

https://w.wiki/5a9g

Solanum genus compounds

https://w.wiki/5h8g

Solanum and erythroxylum genus compounds

https://w.wiki/5h9f

Solanum and erythroxylum and Apocynaceae genus compounds

https://w.wiki/5h9p

Manager

Limit by journal

https://w.wiki/5imt Scorfi shiny version https://w.wiki/5imj

filter papers which do not have found in taxon

https://w.wiki/5ipT

10 papers (random) from journal of natural products

https://w.wiki/5ity

10 papers (random) from phytochemistry

https://w.wiki/5it$

Restricting quest queries to journals and taxa

Adapted from Daniel Mietchen https://w.wiki/5a7K

SELECT DISTINCT #(CONCAT( #REPLACE (Private)(STR(?ta) ".Q" "Q") "|P703|" REPLACE(STR(?taxa) ".Q" "Q") "|S248|" REPLACE(STR(?i) ".Q" "Q")) AS ?QuickStatements) WITH { SELECT DISTINCT ?ta ?n_formatted ?taxa_chem WHERE { #SERVICE (Private) bd:sample { ?ta wdt:P31 wd:Q11173 . bd:serviceParam bd:sample.limit 1000 } ?ta wdt:P31 wd:Q11173 . SERVICE bd:sample { ?taxa_int wdt:P171 wd:Q173756 . bd:serviceParam bd:sample.limit 2000 } ?taxa_chem wdt:P171 ?taxa_int . #?taxa_chem (wdt:P171) wd:Q173756 . ?ta p:P703 ?stmt. ?stmt ps:P703 ?taxa_chem. ?ta rdfs:label ?n. FILTER (LANG(?n) = "en") . BIND(REPLACE(REPLACE(REPLACE(STR(?n),"@en",""),"\+",""),"\-","") AS ?n_formatted) . } LIMIT 40 } AS %t WITH { SELECT ?i ?n_formatted ?ta ?ti ?taxa ?taxa_chem WHERE { INCLUDE %t SERVICE wikibase:mwapi { bd:serviceParam wikibase:endpoint "www.wikidata.org"; wikibase:api "Generator"; mwapi:generator "search"; mwapi:gsrsearch ?n_formatted ; mwapi:gsrlimit "max". ?i wikibase:apiOutputItem mwapi:title. } VALUES ?ref_journal { wd:Q1884753 wd:Q165584 } ?i wdt:P1433 ?ref_journal. ?i wdt:P1476 ?ti . ?i wdt:P921 ?taxa. ?taxa wdt:P105 wd:Q7432. #?taxa (wdt:P171) wd:Q173756 . FILTER (?taxa != ?taxa_chem) . } } AS %i WHERE { INCLUDE %i INCLUDE %t BIND (SUBSTR(?ti STRLEN(STRBEFORE(REPLACE(?ti ?n_formatted "=HELP=" "i") "=HELP=")) +1 STRLEN(?n_formatted)) AS ?a) SERVICE wikibase:label { bd:serviceParam wikibase:language "en". } }

Compounds and ref from the Actinobacteria phylum

https://w.wiki/5kCC with Chembl ids

https://w.wiki/5kDz

NP with drug interactions

https://w.wiki/5o9R

Query for simon

https://w.wiki/5rxD

Researcher in the field of X working in an organisation located in country Z filter by sex Y

https://w.wiki/65F4

Organisms containing 7-methyl-2,3,5,7a-tetrahydro-1H-pyrrolizin-1-ol

SMILES CC1=CCN2CCC(O)C12

Aggregate producing organisms at the superior taxa level

count and order descending https://w.wiki/6w6J

Return all referenced pairs metadata

https://w.wiki/6w7R

Count individual compounds

https://w.wiki/6w7S = 369

Organisms containing 7-methyl-2,3,5,7a-tetrahydro-1H-pyrrolizine-1,1-diol

SMILES CC1=CCN2CCC(O)(O)C12

Aggregate producing organisms at the superior taxa level

count and order descending https://w.wiki/6w6R

Return all referenced pairs metadata

https://w.wiki/6w7L

Count individual compounds

https://w.wiki/6w7N = 0

Organisms containing 7-methyl-2,3,5,7a-tetrahydro-1H-pyrrolizine-1,3-diol

SMILES CC1=CCN2C(O)CC(O)C12

Aggregate producing organisms at the superior taxa level

count and order descending https://w.wiki/6w6T

Return all referenced pairs metadata

https://w.wiki/6w7G

Count individual compounds

https://w.wiki/6w7H = 0

Organisms containing 1-hydroxy-7-methyl-1,2,3,4,5,7a-hexahydropyrrolizin-4-ium-4-olate

SMILES CC1=CC[N+]2([O-])CCC(O)C12

Aggregate producing organisms at the superior taxa level

count and order descending https://w.wiki/6w6a

Return all referenced pairs metadata

https://w.wiki/6w73

Count individual compounds

https://w.wiki/6w77 = 45

containing taxa + ref for a given IK

SELECT ?compound ?InChIKey ?taxon ?taxonLabel ?reference ?referenceLabel WITH { SELECT ?queryKey ?srsearch ?filter WHERE { VALUES ?queryKey { "KWIUHFFTVRNATP" } BIND (CONCAT(substr( $queryKey,1,14) " haswbstatement:P235") AS ?srsearch) BIND (CONCAT("^" substr($ queryKey,1,14)) AS ?filter) } } AS %comps WITH { SELECT ?compound ?InChIKey WHERE { INCLUDE %comps SERVICE wikibase:mwapi { bd:serviceParam wikibase:endpoint "www.wikidata.org"; wikibase:api "Search"; mwapi:srsearch ?srsearch; mwapi:srlimit "max". ?compound wikibase:apiOutputItem mwapi:title. } ?compound wdt:P235 ?InChIKey . FILTER (REGEX(STR(?InChIKey) ?filter)) } } AS %compounds WHERE { INCLUDE %compounds { ?compound p:P703 ?stmt. ?stmt ps:P703 ?taxon. } OPTIONAL { ?stmt prov:wasDerivedFrom ?ref. ?ref pr:P248 ?reference. }
SERVICE wikibase:label { bd:serviceParam wikibase:language "en". } } LIMIT 10000

SELECT ?compound ?InChIKey ?taxon ?taxonLabel ?reference ?referenceLabel WITH { SELECT ?queryKey ?srsearch ?filter WHERE { VALUES ?queryKey { "KWIUHFFTVRNATP" } BIND (CONCAT(substr( $queryKey,1,14) " haswbstatement:P235") AS ?srsearch) BIND (CONCAT("^" substr($ queryKey,1,14)) AS ?filter) } } AS %comps WITH { SELECT ?compound ?InChIKey WHERE { INCLUDE %comps SERVICE wikibase:mwapi { bd:serviceParam wikibase:endpoint "www.wikidata.org"; wikibase:api "Search"; mwapi:srsearch ?srsearch; mwapi:srlimit "max". ?compound wikibase:apiOutputItem mwapi:title. } ?compound wdt:P235 ?InChIKey . FILTER (REGEX(STR(?InChIKey) ?filter)) } } AS %compounds WHERE { INCLUDE %compounds VALUES ?taxon { wd:Q1303946 } { ?compound p:P703 ?stmt. ?stmt ps:P703 ?taxon. } OPTIONAL { ?stmt prov:wasDerivedFrom ?ref. ?ref pr:P248 ?reference. #?reference wdt:P921 ?main_subject. #?main_subject ps:P921 ?taxon_ref. } #FILTER (Private) ( ?taxon = ?match) SERVICE wikibase:label { bd:serviceParam wikibase:language "en". } } LIMIT 10000

https://query.wikidata.org/index.html#%23Goats%0ASELECT%20%3Fitem%20%3FitemLabel%20%0AWHERE%20%0A%7B%0A%20%20%3Fitem%20wdt%3AP31%20wd%3AQ2934.%0A%20%20SERVICE%20wikibase%3Alabel%20%7B%20bd%3AserviceParam%20wikibase%3Alanguage%20%22%5BAUTO_LANGUAGE%5D%2Cen%22.%20%7D%0A%7D

https://query.wikidata.org/embed.html#%23Goats%0ASELECT%20%3Fitem%20%3FitemLabel%20%0AWHERE%20%0A%7B%0A%20%20%3Fitem%20wdt%3AP31%20wd%3AQ2934.%0A%20%20SERVICE%20wikibase%3Alabel%20%7B%20bd%3AserviceParam%20wikibase%3Alanguage%20%22%5BAUTO_LANGUAGE%5D%2Cen%22.%20%7D%0A%7D

Cleaned queryies cpds per taxa

https://w.wiki/7WL3

Filter by atoms in MF

https://w.wiki/7WL9

With a regex substring in the mf

https://w.wiki/7WLb

Wd all

https://w.wiki/7Woz

Most described taxon

Excluding humans + only at the species level

https://w.wiki/7YDr

sr WD by MF

https://w.wiki/9AAN

same with refs

https://w.wiki/9AAe

Genome

proteome metabolome

https://w.wiki/9qZT

2024.07.12 2024-07-12 09:47 > 1'755'037

Qlever LOTUS chemical count

https://qlever.cs.uni-freiburg.de/wikidata/0Slm8l

227,090 "227090"^^http://www.w3.org/2001/XMLSchema#int

Qlever LOTUS chemical count with Isomeric SMILES

https://qlever.cs.uni-freiburg.de/wikidata/wnFz75

172,598 "172598"^^http://www.w3.org/2001/XMLSchema#int

Qlever LOTUS organisms count

https://qlever.cs.uni-freiburg.de/wikidata/1e5Rdg

37,471

Qlever LOTUS organisms count with taxon name

https://qlever.cs.uni-freiburg.de/wikidata/f0F9Y4

37,461 "37461"^^http://www.w3.org/2001/XMLSchema#int

Mind the famous WD graph split regarding scholarly articles

Why is that not working https://w.wiki/Eexo 5 min

eyes

Antiviral chlorinated daphnane diterpenoid orthoesters from the bark and wood of Trigonostemon cherrieri scientific article published on 29 August 2012 www.wikidata.org

For https://www.wikidata.org/wiki/Q40275796 5 min

Egon because all the scholarly articles moved to a different SPARQL endpoint #wikidataSplit (Private) 4 min

While that https://w.wiki/Eexs works 4 min

for https://www.wikidata.org/wiki/Q103883147 4 min

Egon e.g. use https://w.wiki/Eext 4 min

heart

ahhh the famous Split 4 min

Egon or...

https://w.wiki/Eexz 2 min

Thanks, i'll note these down once for all. Not the first time that I forget this split

Count molecule-taxon-ref tuples in LOTUS

https://qlever.dev/wikidata/q3SRt7

List molecule-taxon-ref tuples in LOTUS

https://qlever.dev/wikidata/HqZC6p

MetrinKG

Tripartie interaction with Betula + wd lookup

https://qlever.earthmetabolome.org/metrin-kg/swBuop

Same with Taxonomy lookup

https://qlever.earthmetabolome.org/metrin-kg/WayY7B

Same no wd taxon retrioeval

https://qlever.earthmetabolome.org/metrin-kg/BBQxuv

2) All direct interactions involving Betula (everything, no tripartite constraint) This answers: “Do I have all interaction records that touch Betula at all?” (Useful to compare against what subset ends up in tripartite chains.)

https://qlever.earthmetabolome.org/metrin-kg/5PGcG8

Directional Interaction Type Summary for a Fixed Taxon (Local Aggregation Only)

Short Description This query summarizes all direct interactions involving a fixed taxon in the EMI knowledge graph. It counts interaction statements grouped by interaction type and explicitly separates cases where the fixed taxon acts as source versus target. The query runs entirely locally (no federated Wikidata calls), ensuring fast execution while providing a directional interaction profile of the selected taxon.

https://qlever.earthmetabolome.org/metrin-kg/ORAG5S

MetrinkG

https://qlever.earthmetabolome.org/metrin-kg/0tB2id

Which plants eat plants ?

Directional Interaction Network of a Fixed Taxon with Taxonomic Enrichment

Short Description This query retrieves all direct interactions involving a fixed taxon, explicitly indicating for each row whether the fixed taxon acts as source or target in the interaction. It returns the interaction type label, the interacting partner taxon, and the taxon-level source/target assignments. Both the fixed and partner taxa are enriched via federated Wikidata queries with taxonomic metadata (scientific name P225, family, and domain), enabling directional ecological network analysis with hierarchical taxonomic context. https://qlever.earthmetabolome.org/metrin-kg/YRhcG1

Fix taxon - all interactions - all targets -eats - plants

This query allows to fix a taxon (using WDQID) retrieve all interacting organisms and all plants connected to the interacting organisms by a eat relationship. https://qlever.earthmetabolome.org/metrin-kg/7kz9Uf

Tripartite Ecological Interaction and Plant Metabolite Retrieval for a Fixed Taxon

Short Description

This query retrieves a multi-level ecological network centered on a fixed taxon. It:

Identifies all taxa interacting with the fixed taxon (any interaction type).
Retrieves taxa eaten by those interacting taxa (RO_0002470).
Filters the eaten taxa to a specified clade (currently Archaeplastida / plants).
Enriches all taxa (fixed, interacting, eaten) with taxonomic metadata from Wikidata (taxon name, family, domain).
Retrieves all chemical compounds (wdt:P703) reported to be produced by the eaten taxa, including their Wikidata QID, English label, canonical SMILES (P233), and mass (P2067). The query combines local ecological interaction data (EMI graph) with federated Wikidata queries using role-separated SERVICE blocks to optimize performance and avoid timeouts.

https://qlever.earthmetabolome.org/metrin-kg/sDLjL0

Frequency Ranking of Sub-400 Da Plant Metabolites in the Trophic Network of a Fixed Taxon

Short Description This query constructs a two-step ecological network centered on a fixed taxon: (1) it retrieves all taxa interacting with the fixed taxon (any interaction type), and (2) identifies taxa they eat via RO_0002470 (eats). The eaten taxa are restricted to a specified clade (currently Archaeplastida / plants). For each such plant taxon, the query retrieves chemical compounds reported as produced by that taxon (wdt:P703), filters compounds with molecular mass (P2067) below 400 Da, and aggregates results by compound QID. The output ranks compounds by the number of distinct producing plant taxa, thereby identifying the most taxonomically widespread low-molecular-weight metabolites within the trophic neighborhood of the fixed taxon_ref.

https://qlever.earthmetabolome.org/metrin-kg/5pioIC

Directional Interaction–Herbivory Chain with Plant Metabolite Enrichment for a Fixed Taxon

Short Description This query constructs a two-step ecological interaction chain centered on a fixed taxon: any taxon → (any interaction where fixed taxon is target) → fixed taxon → (eats) → plant taxon The left-hand taxa are not restricted to parasitoids; they include all taxa that interact with the fixed taxon as a target, regardless of interaction type. The query: Retrieves all taxa interacting with the fixed taxon as target (any relation type) Identifies plant taxa eaten by the fixed taxon (RO_0002470) Restricts eaten taxa to plants (Archaeplastida lineage) Enriches all taxa (left, fixed, plant) with Wikidata taxonomy (scientific name P225, family, domain) Retrieves chemical compounds (P703) produced by the eaten plant taxa, including canonical SMILES (P233) and molecular mass (P2067) This enables analysis of interaction context and downstream herbivory–metabolite networks centered on a chosen intermediary taxon.

https://qlever.earthmetabolome.org/metrin-kg/hwyrI9

Configurable Interaction–Herbivory Chain with Plant Metabolite Enrichment

Short Description This query constructs a directional ecological chain centered on a fixed intermediary taxon: any taxon → (selected interaction types, fixed taxon as target) → fixed taxon → (eats) → plant taxon The left interaction is configurable via a VALUES block, allowing restriction to specific RO relations (e.g., pathogenOf, allelopathOf, parasiteOf, preysOn). The query: Retrieves taxa interacting with the fixed taxon under selected relation types Identifies plant taxa eaten by the fixed taxon (RO_0002470) Filters eaten taxa to Archaeplastida (plants) Enriches all taxa (left, fixed, plant) with Wikidata taxonomy (scientific name P225, family, domain) Retrieves chemical compounds (P703) produced by the eaten plant taxa, including canonical SMILES and molecular mass This enables targeted analysis of specific ecological interaction classes and their downstream herbivory–metabolite networks.

https://qlever.earthmetabolome.org/metrin-kg/dcnZT3

Plants Eaten by a Fixed Taxon with Plant Taxonomy and Produced Compounds

Short description This simplified query fixes one consumer taxon, retrieves all plant taxa it eats (RO_0002470), filters eaten taxa to Archaeplastida, enriches the consumer + plant taxa with Wikidata upper taxonomy (taxon name P225, family, domain), and returns all compounds produced by each eaten plant (P703) including label, canonical SMILES (P233), and mass (P2067).

Q2715913

Sub-400 Da Metabolites from Plants Eaten by a Fixed Taxon (Ranked by Producing Plant Count)

Short description This query fixes a consumer taxon, retrieves all plant taxa it eats (RO_0002470), restricts eaten taxa to Archaeplastida, and fetches chemical compounds produced by those plants (P703). It filters compounds with molecular mass (P2067) below 400 Da, aggregates by compound QID, and counts the number of distinct producing plant taxa to rank the most widespread low-molecular-weight metabolites in the trophic neighborhood of the fixed taxon.

https://qlever.earthmetabolome.org/metrin-kg/mixIFs

Tripartite Parasitoid–Herbivory–Plant Chains with Wikidata Taxonomy (Taxon-Level Join)

Short description This query extracts tripartite ecological chains where a taxon A is parasitoidOf taxon B (RO_0002208), and B eats a taxon C (RO_0002470), with C restricted to plants (Archaeplastida lineage via wdt:P171* wd:Q879246). The interaction graph is queried locally (EMI KG) and joined at the taxon level via emi:inTaxon to handle multiple sample nodes per taxon. The result table is enriched using role-split federated Wikidata lookups to return scientific name (P225), family, and domain for A, B, and the plant taxon.

https://qlever.earthmetabolome.org/metrin-kg/uXLCRi