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Integrate col data #13

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Integrate col data #13

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726dfc8
added colIDs to taxon-concepts
nleanba Jul 24, 2024
a080cec
format
nleanba Jul 24, 2024
694baa8
show col IDs
nleanba Jul 24, 2024
e248a06
hide vernacular names if none present
nleanba Jul 24, 2024
0c76292
allow tc or col URIs as search queries
nleanba Jul 24, 2024
9b952ec
v2.3.0-0 preminor
nleanba Jul 25, 2024
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226 changes: 139 additions & 87 deletions SynonymGroup.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -67,10 +67,19 @@ type Treatments = {
dpr: Set<Treatment>;
cite: Set<Treatment>;
};

/**
* Describes a taxon-concept and why it is considered a synonym by synolib
*/
export type JustifiedSynonym = {
taxonConceptUri: string;
taxonName: TaxonName;
/** Human-readable authority */ taxonConceptAuthority?: string;
/**
* Catalogue of Life Taxon URIs
* @example `["https://www.catalogueoflife.org/data/taxon/TWFG"]`
*/
colID: string[];
justifications: JustificationSet;
treatments: Treatments;
loading: boolean;
Expand Down Expand Up @@ -162,6 +171,13 @@ export default class SynonymGroup implements AsyncIterable<JustifiedSynonym> {

private controller = new AbortController();

/**
* Constructs a SynonymGroup
*
* @param sparqlEndpoint SPARQL-Endpoint to query
* @param taxonName either a string of the form "Genus species infraspecific" (species & infraspecific names optional), or an URI of a http://filteredpush.org/ontologies/oa/dwcFP#TaxonConcept or a CoL taxon URI
* @param [ignoreRank=false] if taxonName is "Genus" of "Genus species", by default it will ony search for taxons of rank genus/species. If set to true, sub-taxa are also considered as staring points.
*/
constructor(
sparqlEndpoint: SparqlEndpoint,
taxonName: string,
Expand Down Expand Up @@ -366,26 +382,41 @@ SELECT DISTINCT ?url ?description WHERE {
taxonName: string,
): Promise<JustifiedSynonym[]> => {
if (fetchInit.signal.aborted) return Promise.resolve([]);
const [genus, species, subspecies] = taxonName.split(" ");
// subspecies could also be variety
// ignoreRank has no effect when there is a 'subspecies', as this is assumed to be the lowest rank & should thus not be able to return results in another rank
let taxonNameQuery = "";
if (taxonName.startsWith("http")) {
if (taxonName.includes("catalogueoflife.org")) {
taxonNameQuery =
`?tc <http://www.w3.org/2000/01/rdf-schema#seeAlso> <${taxonName}> .`;
} else {
taxonNameQuery = `BIND(<${taxonName}> as ?tc)`;
}
} else {
const [genus, species, subspecies] = taxonName.split(" ");
// subspecies could also be variety
// ignoreRank has no effect when there is a 'subspecies', as this is assumed to be the lowest rank & should thus not be able to return results in another rank
taxonNameQuery = `?tc dwc:genus "${genus}" .`;
if (species) taxonNameQuery += ` ?tc dwc:species "${species}" .`;
if (subspecies) {
taxonNameQuery +=
` ?tc (dwc:subspecies|dwc:variety) "${subspecies}" .`;
}
if (!subspecies && !ignoreRank) {
taxonNameQuery += ` ?tc dwc:rank "${
species ? "species" : "genus"
}" .`;
}
}
const query = `PREFIX cito: <http://purl.org/spar/cito/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>
PREFIX treat: <http://plazi.org/vocab/treatment#>
SELECT DISTINCT
?tn ?name ?tc (group_concat(DISTINCT ?auth; separator=" / ") as ?authority) (group_concat(DISTINCT ?aug;separator="|") as ?augs) (group_concat(DISTINCT ?def;separator="|") as ?defs) (group_concat(DISTINCT ?dpr;separator="|") as ?dprs) (group_concat(DISTINCT ?cite;separator="|") as ?cites) (group_concat(DISTINCT ?trtn;separator="|") as ?trtns) (group_concat(DISTINCT ?citetn;separator="|") as ?citetns)
?tn ?name ?tc (group_concat(DISTINCT ?auth; separator=" / ") as ?authority) (group_concat(DISTINCT ?colid; separator="|") as ?colids) (group_concat(DISTINCT ?aug;separator="|") as ?augs) (group_concat(DISTINCT ?def;separator="|") as ?defs) (group_concat(DISTINCT ?dpr;separator="|") as ?dprs) (group_concat(DISTINCT ?cite;separator="|") as ?cites) (group_concat(DISTINCT ?trtn;separator="|") as ?trtns) (group_concat(DISTINCT ?citetn;separator="|") as ?citetns)
WHERE {
?tc dwc:genus "${genus}";
treat:hasTaxonName ?tn;
${species ? `dwc:species "${species}";` : ""}
${subspecies ? `(dwc:subspecies|dwc:variety) "${subspecies}";` : ""}
${
ignoreRank || !!subspecies
? ""
: `dwc:rank "${species ? "species" : "genus"}";`
}
${taxonNameQuery}
?tc treat:hasTaxonName ?tn ;
a <http://filteredpush.org/ontologies/oa/dwcFP#TaxonConcept>.
OPTIONAL { ?tc <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?colid . }
?tn dwc:genus ?genus .
OPTIONAL { ?tn dwc:subGenus ?subgenus . }
OPTIONAL {
Expand Down Expand Up @@ -413,7 +444,7 @@ GROUP BY ?tn ?name ?tc`;
.then(
(json: SparqlJson) =>
json.results.bindings.filter((t) => (t.tc && t.tn))
.map((t) => {
.map((t): JustifiedSynonym => {
return {
taxonConceptUri: t.tc.value,
taxonName: makeTaxonName(
Expand All @@ -423,6 +454,11 @@ GROUP BY ?tn ?name ?tc`;
t.citetns?.value.split("|"),
),
taxonConceptAuthority: t.authority?.value,
colID: t.colids?.value.split("|").filter((s) =>
s.startsWith(
"https://www.catalogueoflife.org/data/taxon/",
)
),
justifications: new JustificationSet([
`${t.tc.value} matches "${taxonName}"`,
]),
Expand Down Expand Up @@ -450,10 +486,11 @@ PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>
PREFIX treat: <http://plazi.org/vocab/treatment#>
SELECT DISTINCT
?tc (group_concat(DISTINCT ?auth; separator=" / ") as ?authority) (group_concat(DISTINCT ?aug;separator="|") as ?augs) (group_concat(DISTINCT ?def;separator="|") as ?defs) (group_concat(DISTINCT ?dpr;separator="|") as ?dprs) (group_concat(DISTINCT ?cite;separator="|") as ?cites)
?tc (group_concat(DISTINCT ?auth; separator=" / ") as ?authority) (group_concat(DISTINCT ?colid; separator="|") as ?colids) (group_concat(DISTINCT ?aug;separator="|") as ?augs) (group_concat(DISTINCT ?def;separator="|") as ?defs) (group_concat(DISTINCT ?dpr;separator="|") as ?dprs) (group_concat(DISTINCT ?cite;separator="|") as ?cites)
WHERE {
?tc treat:hasTaxonName <${taxon.taxonName.uri}> .
OPTIONAL { ?tc dwc:scientificNameAuthorship ?auth . }
OPTIONAL { ?tc <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?colid . }
OPTIONAL { ?aug treat:augmentsTaxonConcept ?tc . }
OPTIONAL { ?def treat:definesTaxonConcept ?tc . }
OPTIONAL { ?dpr treat:deprecates ?tc . }
Expand Down Expand Up @@ -481,6 +518,9 @@ GROUP BY ?tc`;
taxonConceptUri: t.tc.value,
taxonName: taxon.taxonName,
taxonConceptAuthority: t.authority?.value,
colID: t.colids?.value.split("|").filter((s) =>
s.startsWith("https://www.catalogueoflife.org/data/taxon/")
),
justifications: new JustificationSet([{
toString: () =>
`${t.tc.value} has taxon name ${taxon.taxonName.uri}`,
Expand Down Expand Up @@ -508,7 +548,7 @@ PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>
PREFIX treat: <http://plazi.org/vocab/treatment#>
SELECT DISTINCT
?tn ?name ?tc (group_concat(DISTINCT ?auth; separator=" / ") as ?authority) (group_concat(DISTINCT ?justification; separator="|") as ?justs) (group_concat(DISTINCT ?aug;separator="|") as ?augs) (group_concat(DISTINCT ?def;separator="|") as ?defs) (group_concat(DISTINCT ?dpr;separator="|") as ?dprs) (group_concat(DISTINCT ?cite;separator="|") as ?cites) (group_concat(DISTINCT ?trtn;separator="|") as ?trtns) (group_concat(DISTINCT ?citetn;separator="|") as ?citetns)
?tn ?name ?tc (group_concat(DISTINCT ?auth; separator=" / ") as ?authority) (group_concat(DISTINCT ?colid; separator="|") as ?colids) (group_concat(DISTINCT ?justification; separator="|") as ?justs) (group_concat(DISTINCT ?aug;separator="|") as ?augs) (group_concat(DISTINCT ?def;separator="|") as ?defs) (group_concat(DISTINCT ?dpr;separator="|") as ?dprs) (group_concat(DISTINCT ?cite;separator="|") as ?cites) (group_concat(DISTINCT ?trtn;separator="|") as ?trtns) (group_concat(DISTINCT ?citetn;separator="|") as ?citetns)
WHERE {
?justification treat:deprecates <${taxon.taxonConceptUri}> ;
(treat:augmentsTaxonConcept|treat:definesTaxonConcept) ?tc .
Expand All @@ -522,6 +562,7 @@ WHERE {
}
BIND(CONCAT(?genus, COALESCE(CONCAT(" (",?subgenus,")"), ""), COALESCE(CONCAT(" ",?species), ""), COALESCE(CONCAT(" ", ?subspecies), ""), COALESCE(CONCAT(" var. ", ?variety), "")) as ?name)
OPTIONAL { ?tc dwc:scientificNameAuthorship ?auth . }
OPTIONAL { ?tc <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?colid . }
OPTIONAL { ?aug treat:augmentsTaxonConcept ?tc . }
OPTIONAL { ?def treat:definesTaxonConcept ?tc . }
OPTIONAL { ?dpr treat:deprecates ?tc . }
Expand All @@ -539,41 +580,46 @@ GROUP BY ?tn ?name ?tc`;
).then((
json: SparqlJson,
) =>
json.results.bindings.filter((t) => t.tc).map((t) => {
return {
taxonConceptUri: t.tc.value,
taxonName: makeTaxonName(
t.tn.value,
t.name?.value,
t.trtns?.value.split("|"),
t.citetns?.value.split("|"),
),
taxonConceptAuthority: t.authority?.value,
justifications: new JustificationSet(
t.justs?.value.split("|").map((url) => {
if (!this.treatments.has(url)) {
this.treatments.set(url, {
url,
details: getTreatmentDetails(url),
});
}
return {
toString: () =>
`${t.tc.value} deprecates ${taxon.taxonConceptUri} according to ${url}`,
precedingSynonym: taxon,
treatment: this.treatments.get(url),
};
}),
),
treatments: {
def: makeTreatmentSet(t.defs?.value.split("|")),
aug: makeTreatmentSet(t.augs?.value.split("|")),
dpr: makeTreatmentSet(t.dprs?.value.split("|")),
cite: makeTreatmentSet(t.cites?.value.split("|")),
} as Treatments,
loading: true,
};
}), (error) => {
json.results.bindings.filter((t) => t.tc).map(
(t): JustifiedSynonym => {
return {
taxonConceptUri: t.tc.value,
taxonName: makeTaxonName(
t.tn.value,
t.name?.value,
t.trtns?.value.split("|"),
t.citetns?.value.split("|"),
),
taxonConceptAuthority: t.authority?.value,
colID: t.colids?.value.split("|").filter((s) =>
s.startsWith("https://www.catalogueoflife.org/data/taxon/")
),
justifications: new JustificationSet(
t.justs?.value.split("|").map((url) => {
if (!this.treatments.has(url)) {
this.treatments.set(url, {
url,
details: getTreatmentDetails(url),
});
}
return {
toString: () =>
`${t.tc.value} deprecates ${taxon.taxonConceptUri} according to ${url}`,
precedingSynonym: taxon,
treatment: this.treatments.get(url),
};
}),
),
treatments: {
def: makeTreatmentSet(t.defs?.value.split("|")),
aug: makeTreatmentSet(t.augs?.value.split("|")),
dpr: makeTreatmentSet(t.dprs?.value.split("|")),
cite: makeTreatmentSet(t.cites?.value.split("|")),
} as Treatments,
loading: true,
};
},
), (error) => {
console.warn("SPARQL Error: " + error);
return [];
});
Expand All @@ -585,7 +631,7 @@ PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>
PREFIX treat: <http://plazi.org/vocab/treatment#>
SELECT DISTINCT
?tn ?name ?tc (group_concat(DISTINCT ?auth; separator=" / ") as ?authority) (group_concat(DISTINCT ?justification; separator="|") as ?justs) (group_concat(DISTINCT ?aug;separator="|") as ?augs) (group_concat(DISTINCT ?def;separator="|") as ?defs) (group_concat(DISTINCT ?dpr;separator="|") as ?dprs) (group_concat(DISTINCT ?cite;separator="|") as ?cites) (group_concat(DISTINCT ?trtn;separator="|") as ?trtns) (group_concat(DISTINCT ?citetn;separator="|") as ?citetns)
?tn ?name ?tc (group_concat(DISTINCT ?auth; separator=" / ") as ?authority) (group_concat(DISTINCT ?colid; separator="|") as ?colids) (group_concat(DISTINCT ?justification; separator="|") as ?justs) (group_concat(DISTINCT ?aug;separator="|") as ?augs) (group_concat(DISTINCT ?def;separator="|") as ?defs) (group_concat(DISTINCT ?dpr;separator="|") as ?dprs) (group_concat(DISTINCT ?cite;separator="|") as ?cites) (group_concat(DISTINCT ?trtn;separator="|") as ?trtns) (group_concat(DISTINCT ?citetn;separator="|") as ?citetns)
WHERE {
?justification (treat:augmentsTaxonConcept|treat:definesTaxonConcept) <${taxon.taxonConceptUri}> ;
treat:deprecates ?tc .
Expand All @@ -599,6 +645,7 @@ WHERE {
}
BIND(CONCAT(?genus, COALESCE(CONCAT(" (",?subgenus,")"), ""), COALESCE(CONCAT(" ",?species), ""), COALESCE(CONCAT(" ", ?subspecies), ""), COALESCE(CONCAT(" var. ", ?variety), "")) as ?name)
OPTIONAL { ?tc dwc:scientificNameAuthorship ?auth . }
OPTIONAL { ?tc <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?colid . }
OPTIONAL { ?aug treat:augmentsTaxonConcept ?tc . }
OPTIONAL { ?def treat:definesTaxonConcept ?tc . }
OPTIONAL { ?dpr treat:deprecates ?tc . }
Expand All @@ -616,41 +663,46 @@ GROUP BY ?tn ?name ?tc`;
).then((
json: SparqlJson,
) =>
json.results.bindings.filter((t) => t.tc).map((t) => {
return {
taxonConceptUri: t.tc.value,
taxonName: makeTaxonName(
t.tn.value,
t.name?.value,
t.trtns?.value.split("|"),
t.citetns?.value.split("|"),
),
taxonConceptAuthority: t.authority?.value,
justifications: new JustificationSet(
t.justs?.value.split("|").map((url) => {
if (!this.treatments.has(url)) {
this.treatments.set(url, {
url,
details: getTreatmentDetails(url),
});
}
return {
toString: () =>
`${t.tc.value} deprecates ${taxon.taxonConceptUri} according to ${url}`,
precedingSynonym: taxon,
treatment: this.treatments.get(url),
};
}),
),
treatments: {
def: makeTreatmentSet(t.defs?.value.split("|")),
aug: makeTreatmentSet(t.augs?.value.split("|")),
dpr: makeTreatmentSet(t.dprs?.value.split("|")),
cite: makeTreatmentSet(t.cites?.value.split("|")),
} as Treatments,
loading: true,
};
}), (error) => {
json.results.bindings.filter((t) => t.tc).map(
(t): JustifiedSynonym => {
return {
taxonConceptUri: t.tc.value,
taxonName: makeTaxonName(
t.tn.value,
t.name?.value,
t.trtns?.value.split("|"),
t.citetns?.value.split("|"),
),
taxonConceptAuthority: t.authority?.value,
colID: t.colids?.value.split("|").filter((s) =>
s.startsWith("https://www.catalogueoflife.org/data/taxon/")
),
justifications: new JustificationSet(
t.justs?.value.split("|").map((url) => {
if (!this.treatments.has(url)) {
this.treatments.set(url, {
url,
details: getTreatmentDetails(url),
});
}
return {
toString: () =>
`${t.tc.value} deprecates ${taxon.taxonConceptUri} according to ${url}`,
precedingSynonym: taxon,
treatment: this.treatments.get(url),
};
}),
),
treatments: {
def: makeTreatmentSet(t.defs?.value.split("|")),
aug: makeTreatmentSet(t.augs?.value.split("|")),
dpr: makeTreatmentSet(t.dprs?.value.split("|")),
cite: makeTreatmentSet(t.cites?.value.split("|")),
} as Treatments,
loading: true,
};
},
), (error) => {
console.warn("SPARQL Error: " + error);
return [];
});
Expand Down
16 changes: 12 additions & 4 deletions main.ts
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,15 @@ try {
for await (const synonym of synoGroup) {
console.log(
Colors.red(
` * Found synonym: ${tcName(synonym)} <${synonym.taxonConceptUri}>`,
` * Found synonym: ${tcName(synonym)} <${synonym.taxonConceptUri}>${
synonym.colID.length
? ` [CoL: ${
synonym.colID.map((id) =>
id.replace("https://www.catalogueoflife.org/data/taxon/", "")
).join(", ")
}]`
: ""
}`,
),
);
console.log(
Expand All @@ -30,9 +38,9 @@ try {
} <${synonym.taxonName.uri}>`,
),
);
synonym.taxonName.vernacularNames.then((v) =>
console.log(JSON.stringify(v))
);
synonym.taxonName.vernacularNames.then((v) => {
if (Object.getOwnPropertyNames(v).length) console.log(JSON.stringify(v));
});
for (const treatment of synonym.taxonName.treatments.aug) {
console.log(
Colors.gray(
Expand Down
4 changes: 2 additions & 2 deletions npm-package/package-lock.json
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2 changes: 1 addition & 1 deletion npm-package/package.json
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"name": "@factsmission/synogroup",
"version": "2.2.0",
"version": "2.3.0-0",
"description": "",
"main": "index.js",
"scripts": {
Expand Down