diff --git a/src/App.vue b/src/App.vue
index 202b5a008e4674a6cddf97e52cd224f723a1eede..794fed2460215195e33b711ebe8ec1c7d756be49 100644
--- a/src/App.vue
+++ b/src/App.vue
@@ -267,8 +267,8 @@ export default {
},
members: [],
- pid: "o:582674",
- //pid: "o:582678",thhis is the assay one
+ pid: "o:584804",
+
piddoc: {},
collection: "",
sampleCollection: "",
@@ -834,8 +834,11 @@ export default {
this.form.sections[2].categories[2].fields.push(
fields.getField("0-Small-molecule")
);
+ this.form.sections[2].categories[2].fields.push(
+ fields.getField("0-Organism-assayTarget")
+ );
var organism_assayTarget = fields.getField("0-Organism");
- organism_assayTarget.type = "skos:Concept";
+
organism_assayTarget.label = "Assay Target Organism";
organism_assayTarget.subjectType = "organism_assayTarget";
organism_assayTarget.visible = false;
@@ -849,7 +852,8 @@ export default {
var cell_organism_assayTarget = fields.getField("0-Cellular-organism");
//cell_organism_assayTarget.description = ["Cellular organism", "Organism"];
cell_organism_assayTarget.label = "Assay Target Cellular Organism";
- cell_organism_assayTarget.subjectType = "cellular_organism_assayTarget";
+ cell_organism_assayTarget.type =
+ "pharmaWien:cellular_organism_assayTarget";
cell_organism_assayTarget.category = ["organismAssayTarget"];
// cell_organism_assayTarget.topcategory = "assayTarget";
cell_organism_assayTarget.visible = false;
@@ -859,7 +863,8 @@ export default {
var viruses_organism_assayTarget = fields.getField("0-Viruses");
//viruses_organism_assayTarget.description = ["Viruses", "Organism"];
viruses_organism_assayTarget.label = "Assay Target Viruses";
- viruses_organism_assayTarget.subjectType = "viruses_assayTarget";
+ viruses_organism_assayTarget.type =
+ "pharmaWien:viruses_organism_assayTarget";
// cell_organism_assayTarget.topcategory = "assayTarget";
viruses_organism_assayTarget.category = ["organismAssayTarget"];
@@ -870,7 +875,8 @@ export default {
var viroids_organism_assayTarget = fields.getField("0-Viroids");
//viroids_organism_assayTarget.description = ["Viroids", "Organism"];
viroids_organism_assayTarget.label = "Assay Target Viroids";
- viroids_organism_assayTarget.subjectType = "viroids_assayTarget";
+ viroids_organism_assayTarget.subjectType =
+ "pharmaWien:viroids_organism_assayTarget";
viroids_organism_assayTarget.category = ["organismAssayTarget"];
// cell_organism_assayTarget.topcategory = "assayTarget";
viroids_organism_assayTarget.visible = false;
diff --git a/src/components/display/pharma_display/PhDJsonld.vue b/src/components/display/pharma_display/PhDJsonld.vue
index 2065a1544fca0877fc730e87166c7a977d5d4de8..5c42badf50b582da142fd5303faf9a34fce9dbd9 100644
--- a/src/components/display/pharma_display/PhDJsonld.vue
+++ b/src/components/display/pharma_display/PhDJsonld.vue
@@ -453,7 +453,7 @@ export default {
n_subjects[i].data = subjects[i];
}
- //console.log("pharmaData", n_subjects);
+ console.log("pharmaData", n_subjects);
return n_subjects;
}
},
@@ -548,6 +548,7 @@ export default {
var elem = this.pharmaData.filter(
pharmaData => pharmaData.category === cat
);
+
return elem;
},
getSelectionElem: function(categ, selection) {
diff --git a/src/components/input/pharma-input-fields/PhInputForm.vue b/src/components/input/pharma-input-fields/PhInputForm.vue
index d4e61954f42a10da7be72f15a34bf712caf540d3..554088bd59b745405a1e1407d5ef6dd73c9a4ce8 100644
--- a/src/components/input/pharma-input-fields/PhInputForm.vue
+++ b/src/components/input/pharma-input-fields/PhInputForm.vue
@@ -186,7 +186,7 @@
:text="'skos:prefLabel'"
:nested="['@value']"
v-on:input-select="f.value=$event;updateSubfields(f.multiplicable,c.fields,f)"
- :freeText="{'@type': [f.subjectType],'skos:prefLabel': [{'@value':''}]}"
+ :freeText="{'@type': [f.type],'skos:prefLabel': [{'@value':''}]}"
></ph-selection>
</v-flex>
@@ -569,9 +569,9 @@ export default {
}
}
return w;
- }
+ },
- /*selectInput: function(f, event) {
+ selectInput: function(f, event) {
if (event) {
f.value = event["@id"];
if (event["@type"]) {
@@ -595,7 +595,7 @@ export default {
f["skos:prefLabel"] = [];
}
this.$emit("form-input-" + f.component, f);
- },*/
+ }
},
mounted: function() {
this.$store.dispatch("loadLanguages");
diff --git a/src/store/modules/vocabulary.js b/src/store/modules/vocabulary.js
index 7b638d212b847b1475ab7200be23e1859427f101..bfd1fe8affac8244f45e10198e67bfbee2ce8ea6 100644
--- a/src/store/modules/vocabulary.js
+++ b/src/store/modules/vocabulary.js
@@ -497,7 +497,7 @@ const state = {
assay_organism: {
terms: [
{
- "@type": "skos:Concept",
+ "@type": "pharmaWien:assayOrg",
"skos:prefLabel": [
{
"@value": "Cellular organism",
@@ -507,7 +507,7 @@ const state = {
"skos:exactMatch": ["http://purl.obolibrary.org/obo/NCBITaxon_131567"]
},
{
- "@type": "skos:Concept",
+ "@type": "pharmaWien:assayOrg",
"skos:prefLabel": [
{
"@value": "Viruses",
@@ -517,7 +517,42 @@ const state = {
"skos:exactMatch": ["http://purl.obolibrary.org/obo/NCBITaxon_10239"]
},
{
- "@type": "skos:Concept",
+ "@type": "pharmaWien:assayOrg",
+ "skos:prefLabel": [
+ {
+ "@value": "Viroids",
+ "@language": "eng"
+ }
+ ],
+ "skos:exactMatch": ["http://purl.obolibrary.org/obo/NCBITaxon_12884"]
+ }
+ ],
+ loaded: true
+ },
+ assayTarget_organism: {
+ terms: [
+ {
+ "@type": "pharmaWien:assayOrg_assayTarget",
+ "skos:prefLabel": [
+ {
+ "@value": "Cellular organism",
+ "@language": "eng"
+ }
+ ],
+ "skos:exactMatch": ["http://purl.obolibrary.org/obo/NCBITaxon_131567"]
+ },
+ {
+ "@type": "pharmaWien:assayOrg_assayTarget",
+ "skos:prefLabel": [
+ {
+ "@value": "Viruses",
+ "@language": "eng"
+ }
+ ],
+ "skos:exactMatch": ["http://purl.obolibrary.org/obo/NCBITaxon_10239"]
+ },
+ {
+ "@type": "pharmaWien:assayOrg_assayTarget",
"skos:prefLabel": [
{
"@value": "Viroids",
@@ -527,13 +562,12 @@ const state = {
"skos:exactMatch": ["http://purl.obolibrary.org/obo/NCBITaxon_12884"]
}
],
-
loaded: true
},
assay_detection: {
terms: [
{
- "@type": "skos:Concept",
+ "@type": "pharmaWien:assayDetection",
"skos:prefLabel": [
{
"@value": "Physical detection method",
@@ -543,7 +577,7 @@ const state = {
"skos:exactMatch": ["http://www.bioassayontology.org/bao#BAO_0000035"]
},
{
- "@type": "skos:Concept",
+ "@type": "pharmaWien:assayDetection",
"skos:prefLabel": [
{
"@value": "Detection instrument",
diff --git a/src/utils/fields.js b/src/utils/fields.js
index a83a58dcb0ec151e793651caf94643b5ff72e2c5..4d5fc7edd9e2712356faf6741288a17cfcf5cf9f 100644
--- a/src/utils/fields.js
+++ b/src/utils/fields.js
@@ -216,7 +216,7 @@ const fields = [
id: "1-Isoform",
predicate: "dcterms:subject",
type: "pharmaWien:isoform_protein",
- subjectType: "isoform",
+ //subjectType: "isoform",
label: "Isoform:",
value: "",
required: false,
@@ -234,7 +234,7 @@ const fields = [
id: "1-Protein-sequence-alteration",
predicate: "dcterms:subject",
type: "pharmaWien:proteinSequenceAlteration_protein",
- subjectType: "ProteinSequenceAlteration",
+ //subjectType: "ProteinSequenceAlteration",
label: "Protein Sequence alteration:",
value: "",
required: false,
@@ -252,7 +252,7 @@ const fields = [
id: "1-Protein-modification",
predicate: "dcterms:subject",
type: "pharmaWien:proteinModifaction_protein",
- subjectType: "ProteinModifaction",
+ //subjectType: "ProteinModifaction",
label: "Protein modifaction:",
value: "",
required: false,
@@ -712,6 +712,7 @@ const fields = [
ontology: "mondo",
topId: "MONDO_0000001",
ontClass: "",
+ category: ["disease"],
//ontClass: "MONDO_0000001",
//ontClass: "MONDO_0000620",
//baseurl: "http://purl.obolibrary.org/obo/",
@@ -1031,6 +1032,7 @@ const fields = [
ontClass: "NCIT_C16847",
topId: "NCIT_C16847",
description: "Research technique:",
+ category: ["technique"],
freefield: true,
infoRef:
"http://www.ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C20368",
@@ -1051,6 +1053,7 @@ const fields = [
ontClass: "NCIT_C19160",
topId: "NCIT_C19160",
freefield: true,
+ category: ["discipline"],
description: "Occupation or Discipline:",
infoRef: "http://purl.obolibrary.org/obo/NCIT_C19160",
info: "Info here "
@@ -1250,6 +1253,27 @@ const fields = [
"The organism related to the target / meta-target of the bioassay. It includes both bacterium and eukaryote.",
infoRef: "BAO:0000551"
},
+ {
+ id: "0-Organism-assayTarget",
+ predicate: "dcterms:subject",
+ type: "skos:Concept",
+ //subjectType: "AssayOrganism:",
+ label: "Assay Target Organism",
+ description: "Organism",
+ value: "",
+ component: "selection",
+ freefield: false,
+ commit: true,
+ visible: false,
+ vocabulary: "assayTarget_organism",
+ stateVoc: "organism_assay_target",
+ category: ["assayTarget"],
+ subcategory: ["organismAssayTarget"],
+ multiplicable: true,
+ info:
+ "The organism related to the target / meta-target of the bioassay. It includes both bacterium and eukaryote.",
+ infoRef: "BAO:0000551"
+ },
{
id: "0-Cellular-organism",
predicate: "dcterms:subject",
@@ -1424,7 +1448,7 @@ const fields = [
id: "0-detection",
predicate: "dcterms:subject",
type: "skos:Concept",
- subjectType: "assay_detection",
+ //subjectType: "assay_detection",
label: "Detection method:",
description: "selection",
value: "",
@@ -1446,8 +1470,8 @@ const fields = [
{
id: "0-detection_method",
predicate: "dcterms:subject",
- type: "skos:Concept",
- subjectType: "physical_detection_method",
+ type: "pharmaWien:physicalDetectionMethod",
+ //subjectType: "physical_detection_method",
label: "Physical detection method:",
value: "",
required: false,
@@ -1466,8 +1490,8 @@ const fields = [
{
id: "0-detection_instrument",
predicate: "dcterms:subject",
- type: "skos:Concept",
- subjectType: "detection_instrument",
+ type: "pharmaWien:physicalDetectionInstrument",
+ //subjectType: "detection_instrument",
label: "Detection instrument:",
value: "",
required: false,
@@ -1585,7 +1609,7 @@ export default {
},
getFieldbySubject: function(subject) {
for (var i = 0; i < fields.length; i++) {
- if (fields[i]["subjectType"] === subject) {
+ if (fields[i]["type"] === subject) {
var field = JSON.parse(JSON.stringify(fields[i]));
field.id = field.id + "_" + uuid.generate();
return field;