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Fix #424
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@henrietteharmse
henrietteharmse committed Jul 20, 2023
1 parent f4b369f commit 3ce067b
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Showing 10 changed files with 273 additions and 47 deletions.
7 changes: 6 additions & 1 deletion backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1SearchController.java
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Expand Up @@ -216,7 +216,12 @@ public void search(
if (fieldList.contains("id")) outDoc.put("id", JsonHelper.getString(json, "id"));
if (fieldList.contains("iri")) outDoc.put("iri", JsonHelper.getString(json, "iri"));
if (fieldList.contains("ontology_name")) outDoc.put("ontology_name", JsonHelper.getString(json, "ontologyId"));
if (fieldList.contains("label")) outDoc.put("label", JsonHelper.getStrings(json, "label"));
if (fieldList.contains("label")) {
var label = outDoc.put("label", JsonHelper.getStrings(json, "label"));
if(label!=null) {
outDoc.put("label", label);
}
}
if (fieldList.contains("description")) outDoc.put("description", JsonHelper.getStrings(json, "definition"));
if (fieldList.contains("short_form")) outDoc.put("short_form", JsonHelper.getStrings(json, "shortForm"));
if (fieldList.contains("obo_id")) outDoc.put("obo_id", JsonHelper.getStrings(json, "curie"));
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4 changes: 3 additions & 1 deletion backend/src/main/java/uk/ac/ebi/spot/ols/repository/transforms/LocalizationTransform.java
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Expand Up @@ -187,7 +187,9 @@ public static JsonObject localizeLinkedEntities(JsonObject linkedEntities, Strin
JsonObject entityProps = linkedEntities.getAsJsonObject(entityIri);
JsonObject entityPropsRes = new JsonObject();
for(String k : entityProps.keySet()) {
entityPropsRes.add(k, localizeValueWithFallbacks(entityProps.get(k), lang));
var val = localizeValueWithFallbacks(entityProps.get(k), lang);
if(val!=null)
entityPropsRes.add(k, val);
}
res.add(entityIri, entityPropsRes);
}
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50 changes: 50 additions & 0 deletions dataload/configs/ado.json
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@@ -0,0 +1,50 @@
{
"name": "OBO Foundry",
"title": "The OBO Foundry",
"markdown": "kramdown",
"highlighter": "rouge",
"baseurl": "/",
"imgurl": "/images",
"repo": "https://github.com/OBOFoundry/OBOFoundry.github.io/",
"repo_src": "https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/",
"author": {
"name": "OBO Technical WG"
},
"ontologies": [
{
"activity_status": "active",
"contact": {
"email": "alpha.tom.kodamullil@scai.fraunhofer.de",
"github": "akodamullil",
"label": "Alpha Tom Kodamullil",
"orcid": "0000-0001-9896-3531"
},
"dependencies": [
{
"id": "bfo"
}
],
"description": "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities that demonstrate the network of the understanding on Alzheimer's disease and can be readily applied for text mining.",
"domain": "health",
"homepage": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO",
"id": "ado",
"layout": "ontology_detail",
"license": {
"label": "CC BY 4.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "https://creativecommons.org/licenses/by/4.0/"
},
"ontology_purl": "http://purl.obolibrary.org/obo/ado.owl",
"preferredPrefix": "ADO",
"products": [
{
"id": "ado.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/ado.owl"
}
],
"repository": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO",
"title": "Alzheimer's Disease Ontology",
"tracker": "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO/issues"
}
]
}
2 changes: 1 addition & 1 deletion dataload/extras/orcid2level/dependency-reduced-pom.xml
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Expand Up @@ -2,7 +2,7 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>uk.ac.ebi.spot</groupId>
<artifactId>orcid-extractor</artifactId>
<artifactId>orcid2level</artifactId>
<version>1.0-SNAPSHOT</version>
<build>
<plugins>
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24 changes: 23 additions & 1 deletion dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/DefinitionAnnotator.java
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Expand Up @@ -3,6 +3,7 @@
import uk.ac.ebi.rdf2json.OntologyGraph;
import uk.ac.ebi.rdf2json.OntologyNode;
import uk.ac.ebi.rdf2json.annotators.helpers.PropertyCollator;
import uk.ac.ebi.rdf2json.properties.PropertyValue;

public class DefinitionAnnotator {

Expand All @@ -27,6 +28,27 @@ public static Set<String> getDefinitionProperties(OntologyGraph graph) {
}

public static void annotateDefinitions(OntologyGraph graph) {
PropertyCollator.collateProperties(graph, "definition", getDefinitionProperties(graph), List.of());
collateProperties(graph, "definition", getDefinitionProperties(graph));
}

private static void collateProperties(OntologyGraph graph, String destProp, Collection<String> sourceProps) {

for(String id : graph.nodes.keySet()) {
OntologyNode c = graph.nodes.get(id);

// skip bnodes
if(c.uri == null)
continue;

for(String prop : sourceProps) {
List<PropertyValue> values = c.properties.getPropertyValues(prop);
if(values != null) {
for(PropertyValue value : values) {
c.properties.addProperty(destProp, value);
}
}
}
}

}
}
59 changes: 57 additions & 2 deletions dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/LabelAnnotator.java
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Expand Up @@ -3,6 +3,8 @@
import uk.ac.ebi.rdf2json.OntologyGraph;
import uk.ac.ebi.rdf2json.OntologyNode;
import uk.ac.ebi.rdf2json.annotators.helpers.PropertyCollator;
import uk.ac.ebi.rdf2json.properties.PropertyValue;
import uk.ac.ebi.rdf2json.properties.PropertyValueLiteral;

public class LabelAnnotator {

Expand All @@ -12,7 +14,8 @@ public static Set<String> getLabelProperties(OntologyGraph graph) {
List.of(
"http://www.w3.org/2000/01/rdf-schema#label",
"http://purl.org/dc/elements/1.1/title",
"http://purl.org/dc/terms/title"
"http://purl.org/dc/terms/title",
"http://www.w3.org/2004/02/skos/core#prefLabel"
)
);

Expand All @@ -26,6 +29,58 @@ public static Set<String> getLabelProperties(OntologyGraph graph) {
}

public static void annotateLabels(OntologyGraph graph) {
PropertyCollator.collateProperties(graph, "label", getLabelProperties(graph), List.of("shortForm"));
collateProperties(graph, "label", getLabelProperties(graph), List.of("shortForm"));
}

private static void collateProperties(OntologyGraph graph, String destProp, Collection<String> sourceProps, Collection<String> fallbackProps) {

long startTime3 = System.nanoTime();

for(String id : graph.nodes.keySet()) {
OntologyNode c = graph.nodes.get(id);

// skip bnodes
if(c.uri == null)
continue;

boolean hasEnglishValue = false;

for(String prop : sourceProps) {
List<PropertyValue> values = c.properties.getPropertyValues(prop);
if(values != null) {
for(PropertyValue value : values) {
c.properties.addProperty(destProp, value);
if(!isNonEnglishValue(graph, value))
hasEnglishValue = true;
}
}
}

if(!hasEnglishValue) {
for(String prop : fallbackProps) {
List<PropertyValue> values = c.properties.getPropertyValues(prop);
if (values != null) {
for (PropertyValue value : values) {
c.properties.addProperty(destProp, value);
}
}
}
}
}

long endTime3 = System.nanoTime();
System.out.println("collate properties from " + sourceProps + " and fallback " + fallbackProps + " into " + destProp + ": " + ((endTime3 - startTime3) / 1000 / 1000 / 1000));


}

private static boolean isNonEnglishValue(OntologyGraph graph, PropertyValue value) {
if(value.getType() == PropertyValue.Type.LITERAL) {
PropertyValueLiteral literal = (PropertyValueLiteral) value;
if( !literal.getLang().equals("") && !literal.getLang().equals("en")) {
return true;
}
}
return false;
}
}
23 changes: 22 additions & 1 deletion dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/SynonymAnnotator.java
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Expand Up @@ -30,6 +30,27 @@ public static Set<String> getSynonymProperties(OntologyGraph graph) {
}

public static void annotateSynonyms(OntologyGraph graph) {
PropertyCollator.collateProperties(graph, "synonym", getSynonymProperties(graph), List.of());
collateProperties(graph, "synonym", getSynonymProperties(graph));
}

private static void collateProperties(OntologyGraph graph, String destProp, Collection<String> sourceProps) {

for(String id : graph.nodes.keySet()) {
OntologyNode c = graph.nodes.get(id);

// skip bnodes
if(c.uri == null)
continue;

for(String prop : sourceProps) {
List<PropertyValue> values = c.properties.getPropertyValues(prop);
if(values != null) {
for(PropertyValue value : values) {
c.properties.addProperty(destProp, value);
}
}
}
}

}
}
42 changes: 2 additions & 40 deletions dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/helpers/PropertyCollator.java
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Expand Up @@ -3,52 +3,14 @@
import uk.ac.ebi.rdf2json.OntologyNode;
import uk.ac.ebi.rdf2json.OntologyGraph;
import uk.ac.ebi.rdf2json.properties.PropertyValue;
import uk.ac.ebi.rdf2json.properties.PropertyValueBNode;
import uk.ac.ebi.rdf2json.properties.PropertyValueLiteral;

import java.util.Collection;
import java.util.List;

public class PropertyCollator {

public static void collateProperties(OntologyGraph graph, String destProp, Collection<String> sourceProps, Collection<String> fallbackProps) {

long startTime3 = System.nanoTime();

for(String id : graph.nodes.keySet()) {
OntologyNode c = graph.nodes.get(id);

// skip bnodes
if(c.uri == null)
continue;

boolean annotated = false;

for(String prop : sourceProps) {
List<PropertyValue> values = c.properties.getPropertyValues(prop);
if(values != null) {
for(PropertyValue value : values) {
c.properties.addProperty(destProp, value);
annotated = true;
}
}
}

if(!annotated) {
for(String prop : fallbackProps) {
List<PropertyValue> values = c.properties.getPropertyValues(prop);
if (values != null) {
for (PropertyValue value : values) {
c.properties.addProperty(destProp, value);
}
}
}
}
}

long endTime3 = System.nanoTime();
System.out.println("collate properties from " + sourceProps + " and fallback " + fallbackProps + " into " + destProp + ": " + ((endTime3 - startTime3) / 1000 / 1000 / 1000));


}
}


9 changes: 9 additions & 0 deletions testcases/localized-labels/label.json
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@@ -0,0 +1,9 @@
{
"ontologies": [
{
"id": "label",
"preferredPrefix": "label",
"ontology_purl": "./testcases/localized-labels/label.rdf"
}
]
}
100 changes: 100 additions & 0 deletions testcases/localized-labels/label.rdf
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@@ -0,0 +1,100 @@
<?xml version="1.0"?>
<rdf:RDF xmlns="http://www.ebi.ac.uk/ols4/testcase/label/"
xml:base="http://www.ebi.ac.uk/ols4/testcase/label/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
<owl:Ontology rdf:about="http://www.ebi.ac.uk/ols4/testcase/label">
<owl:versionIRI rdf:resource="http://www.ebi.ac.uk/ols4/testcase/label/v.0.0.1"/>
</owl:Ontology>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->




<!-- http://www.ebi.ac.uk/ols4/testcase/label#deProperty -->

<owl:ObjectProperty rdf:about="http://www.ebi.ac.uk/ols4/testcase/label#deProperty">
<rdfs:label xml:lang="de">de Lang</rdfs:label>
</owl:ObjectProperty>



<!-- http://www.ebi.ac.uk/ols4/testcase/label#enProperty -->

<owl:ObjectProperty rdf:about="http://www.ebi.ac.uk/ols4/testcase/label#enProperty">
<rdfs:label xml:lang="en">en label</rdfs:label>
</owl:ObjectProperty>



<!-- http://www.ebi.ac.uk/ols4/testcase/label#noLabelProperty -->

<owl:ObjectProperty rdf:about="http://www.ebi.ac.uk/ols4/testcase/label#noLabelProperty"/>



<!-- http://www.ebi.ac.uk/ols4/testcase/label#property -->

<owl:ObjectProperty rdf:about="http://www.ebi.ac.uk/ols4/testcase/label#property">
<rdfs:label>noLangProperty</rdfs:label>
</owl:ObjectProperty>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->




<!-- http://www.ebi.ac.uk/ols4/testcase/label#deLangClass -->

<owl:Class rdf:about="http://www.ebi.ac.uk/ols4/testcase/label#deLangClass">
<rdfs:label xml:lang="de">de lang class</rdfs:label>
</owl:Class>



<!-- http://www.ebi.ac.uk/ols4/testcase/label#enLabelClass -->

<owl:Class rdf:about="http://www.ebi.ac.uk/ols4/testcase/label#enLabelClass">
<rdfs:label xml:lang="en">en label class</rdfs:label>
</owl:Class>



<!-- http://www.ebi.ac.uk/ols4/testcase/label#noLabelClass -->

<owl:Class rdf:about="http://www.ebi.ac.uk/ols4/testcase/label#noLabelClass"/>



<!-- http://www.ebi.ac.uk/ols4/testcase/label#noLangClass -->

<owl:Class rdf:about="http://www.ebi.ac.uk/ols4/testcase/label#noLangClass">
<rdfs:comment></rdfs:comment>
<rdfs:label>no lang label class</rdfs:label>
</owl:Class>
</rdf:RDF>



<!-- Generated by the OWL API (version 4.5.24.2023-01-14T21:28:32Z) https://github.com/owlcs/owlapi -->

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