From 28a2cc6b65ad911c9cb562f14dbf4fff8b9b78c1 Mon Sep 17 00:00:00 2001
From: isah <isabelle.herbauts@univie.ac.at>
Date: Wed, 17 Jun 2020 18:00:15 +0200
Subject: [PATCH] diplay fixed (but bioasssay)
---
src/App.vue | 57 +++++--
.../display/pharma_display/PhDJsonld.vue | 147 ++++++++++++------
.../display/pharma_display/PhDMetadata.vue | 2 +
src/components/input/PhSubmit.vue | 2 +-
.../input/pharma-input-fields/PhInputForm.vue | 11 +-
src/utils/fields.js | 121 +++++++-------
6 files changed, 220 insertions(+), 120 deletions(-)
diff --git a/src/App.vue b/src/App.vue
index 7986c17..f50b6ee 100644
--- a/src/App.vue
+++ b/src/App.vue
@@ -258,7 +258,7 @@ export default {
emptyForm: {},
members: [],
fullmembers: [],
- pid: "o:589601",
+ pid: "o:589444",
piddoc: {},
collection: "",
sampleCollection: "",
@@ -723,7 +723,7 @@ export default {
this.form.sections[1].fields.push(fields.getField("file"));
- //push to biassay
+ //push to bioassay
this.form.sections[2].categories[2].fields.push(
fields.getField("0-Assay-title")
@@ -775,23 +775,29 @@ export default {
var uniprot_assayTarget = fields.getField("1-Uniprot");
uniprot_assayTarget.label = "Assay Target Uniprot record";
- uniprot_assayTarget.type = "pharmaWien:uniprot_protein_assayTarget";
+ uniprot_assayTarget.type = "pharmaWien:assayTarget_uniprot";
uniprot_assayTarget.category = ["assayTarget"];
+ uniprot_assayTarget.subcategory = ["assay target protein"];
var isoform_assayTarget = fields.getField("1-Isoform");
isoform_assayTarget.label = "Assay Target Isoform";
- isoform_assayTarget.type = "pharmaWien:assayTarget_isoform_protein";
+ isoform_assayTarget.type = "pharmaWien:assayTarget__proteinIsoform";
isoform_assayTarget.category = ["assayTarget"];
+ isoform_assayTarget.subcategory = ["assay target protein isoform"];
var seqAlt_assayTarget = fields.getField("1-Protein-sequence-alteration");
seqAlt_assayTarget.label = "Assay Target Protein sequence alteration";
- seqAlt_assayTarget.type = "pharmaWien:assayTarget_seqAlt_protein";
+ seqAlt_assayTarget.type = "pharmaWien:assayTarget_proteinSeqAlt";
seqAlt_assayTarget.category = ["assayTarget"];
+ seqAlt_assayTarget.subcategory = [
+ "assay target Protein sequence alteration"
+ ];
var protMod_assayTarget = fields.getField("1-Protein-modification");
protMod_assayTarget.label = "Assay Target Protein Modification";
- protMod_assayTarget.type = "pharmaWien:assayTarget_protMod_protein";
+ protMod_assayTarget.type = "pharmaWien:assayTarget_proteinProtMod";
protMod_assayTarget.category = ["assayTarget"];
+ protMod_assayTarget.subcategory = ["assay target Protein Modification"];
this.form.sections[2].categories[2].fields.push(uniprot_assayTarget);
this.form.sections[2].categories[2].fields.push(isoform_assayTarget);
this.form.sections[2].categories[2].fields.push(seqAlt_assayTarget);
@@ -802,26 +808,30 @@ export default {
gene_assayTarget.type = "pharmaWien:assayTarget_geneId";
gene_assayTarget.category = ["assayTarget"];
+ gene_assayTarget.subcategory = ["assay Target gene ID"];
var geneMod_assayTarget = fields.getField("1-Gene-modification");
geneMod_assayTarget.label = "Assay Target Gene Modification";
-
geneMod_assayTarget.type = "pharmaWien:assayTarget_geneMod";
geneMod_assayTarget.category = ["assayTarget"];
+ geneMod_assayTarget.subcategory = ["assay target gene modification"];
this.form.sections[2].categories[2].fields.push(gene_assayTarget);
this.form.sections[2].categories[2].fields.push(geneMod_assayTarget);
var nacid_assayTarget = fields.getField("1-Nucleic-acid-type");
nacid_assayTarget.label = "Assay Target Nucleic Acid Type";
- nacid_assayTarget.type = "pharmaWien:assayTarget_type_nucleicAcid";
+ nacid_assayTarget.type = "pharmaWien:assayTarget_nucleicAcidType";
nacid_assayTarget.category = ["assayTarget"];
nacid_assayTarget.description = "Nucleic Acid";
+ nacid_assayTarget.subcategory = ["assay target Nucleic Acid Type"];
var refSeq_assayTarget = fields.getField("1-RefSeq-accession");
refSeq_assayTarget.label = "Assay Target RefSeq accession:";
- refSeq_assayTarget.type = "pharmaWien:assayTarget_refSeq_nucleicAcid";
+ refSeq_assayTarget.type =
+ "pharmaWien:assayTarget_nucleicAcidRefSeqAccession";
refSeq_assayTarget.category = ["assayTarget"];
refSeq_assayTarget.description = "Nucleic Acid";
+ refSeq_assayTarget.subcategory = ["assay target RefSeq accession"];
this.form.sections[2].categories[2].fields.push(nacid_assayTarget);
this.form.sections[2].categories[2].fields.push(refSeq_assayTarget);
var PFAM_assayTarget = fields.getField("1-PFAM-accession");
@@ -829,34 +839,45 @@ export default {
PFAM_assayTarget.type = "pharmaWien:assayTarget_PFAM";
PFAM_assayTarget.category = ["assayTarget"];
+ PFAM_assayTarget.subcategory = ["assay target PFAM"];
this.form.sections[2].categories[2].fields.push(PFAM_assayTarget);
var uniprotsub_assayTarget = fields.getField("1-Uniprot");
uniprotsub_assayTarget.label =
"Assay Target Protein Subunit Uniprot record";
- uniprotsub_assayTarget.type = "pharmaWien:assayTarget_uniprot_protSub";
+ uniprotsub_assayTarget.type = "pharmaWien:assayTarget_protSub";
uniprotsub_assayTarget.category = ["assayTarget"];
uniprotsub_assayTarget.description = "Protein Subunit";
+ uniprotsub_assayTarget.subcategory = ["assay target protein subunit"];
var isoformsub_assayTarget = fields.getField("1-Isoform");
isoformsub_assayTarget.label = "Assay Target Protein Subunit Isoform";
- isoformsub_assayTarget.type = "pharmaWien:assayTarget_isoform_protSub";
+ isoformsub_assayTarget.type = "pharmaWien:assayTarget_protSubIsoform";
isoformsub_assayTarget.category = ["assayTarget"];
isoformsub_assayTarget.description = "Protein Subunit";
+ isoformsub_assayTarget.subcategory = [
+ "assay Target protein subunit isoform"
+ ];
var seqAltsub_assayTarget = fields.getField(
"1-Protein-sequence-alteration"
);
seqAltsub_assayTarget.label =
"Assay Target Protein Subunit sequence alteration";
- seqAltsub_assayTarget.type = "pharmaWien:assayTarget_seqAlt_protSub";
+ seqAltsub_assayTarget.type = "pharmaWien:assayTarget_protSubSeqAlt";
seqAltsub_assayTarget.category = ["assayTarget"];
+ seqAltsub_assayTarget.subcategory = [
+ "assay Target Protein Subunit sequence alteration"
+ ];
seqAltsub_assayTarget.description = "Protein Subunit";
var protModsub_assayTarget = fields.getField("1-Protein-modification");
protModsub_assayTarget.label =
"Assay Target Protein Subunit modification";
- protModsub_assayTarget.type = "pharmaWien:assayTarget_protMod_protSub";
+ protModsub_assayTarget.type = "pharmaWien:assayTarget_protSubMod";
protModsub_assayTarget.category = ["assayTarget"];
+ protModsub_assayTarget.subcategory = [
+ "Assay Target Protein Subunit modification"
+ ];
protModsub_assayTarget.description = "Protein Subunit";
this.form.sections[2].categories[2].fields.push(uniprotsub_assayTarget);
this.form.sections[2].categories[2].fields.push(isoformsub_assayTarget);
@@ -868,8 +889,11 @@ export default {
protcomplex_assayTarget.label =
"Assay Target Protein Complex-Portal Accession";
protcomplex_assayTarget.type =
- "pharmaWien:assayTarget_portalAcc_protComplex";
+ "pharmaWien:assayTarget_protComplexPortalAcc";
protcomplex_assayTarget.category = ["assayTarget"];
+ protcomplex_assayTarget.subcategory = [
+ "ssay Target Protein Complex-Portal Accession"
+ ];
this.form.sections[2].categories[2].fields.push(protcomplex_assayTarget);
this.form.sections[2].categories[2].fields.push(
fields.getField("0-carbohydrate")
@@ -924,11 +948,14 @@ export default {
viroids_organism_assayTarget
);
var cell_line_assayTarget = fields.getField("0-cell-line");
- cell_line_assayTarget.label = "Assay Target Cell line (cellosaurus)";
+ cell_line_assayTarget.label = "Assay Target Cell line";
cell_line_assayTarget.type = "pharmaWien:assayTarget_cellosaurus";
cell_line_assayTarget.visible = false;
cell_line_assayTarget.category = ["assayTarget"];
+ cell_line_assayTarget.subcategory = [
+ "Assay Target Cell line (cellosaurus)"
+ ];
this.form.sections[2].categories[2].fields.push(cell_line_assayTarget);
this.form.sections[2].categories[2].fields.push(
diff --git a/src/components/display/pharma_display/PhDJsonld.vue b/src/components/display/pharma_display/PhDJsonld.vue
index 9907e2d..fd8c09d 100644
--- a/src/components/display/pharma_display/PhDJsonld.vue
+++ b/src/components/display/pharma_display/PhDJsonld.vue
@@ -413,27 +413,31 @@
<v-toolbar-title class="font-weight-light">{{categ.label}}</v-toolbar-title>
</v-layout>
</v-toolbar>
-
<template v-if="categ.fields.length>0">
- <v-card v-for="(l,index) in categ.fields" :key="l['@type']+'field'+index">
+
+ <v-card v-for="l in categ.fields" :key="l.category+'field'">
<v-layout v-if="l">
-
+
<v-flex xs11>
-
- <p-d-skos-preflabel
- v-if="getSkosexactMatch(l)==undefined"
- :o="l"
- :key="l+index+'pharmafreesubject'"
- ></p-d-skos-preflabel>
+ <v-card v-for="(inputf,index) in l.fields" :key="index+'subjectField'">
+
+ <p-d-skos-preflabel
+ v-if="getSkosexactMatch(inputf)==undefined"
+ :p="getLabel(inputf['@type'])"
+ :o="inputf"
+ :key="inputf+index+'pharmafreesubject'"
+ ></p-d-skos-preflabel>
- <ph-d-metadata
- v-if="getSkosexactMatch(l)"
- :o="l"
- :p="p"
- :key="l+index+'pharmasubject'"
- ></ph-d-metadata>
- <v-divider></v-divider>
+ <ph-d-metadata
+ v-if="getSkosexactMatch(inputf)"
+ :o="inputf"
+ :p="p"
+ :key="index+'pharmasubject'"
+ ></ph-d-metadata>
+ <v-divider></v-divider>
+ </v-card>
</v-flex>
+
</v-layout>
</v-card>
</template>
@@ -446,8 +450,7 @@
</v-toolbar>
<template v-if="categ.subcategory.length>0">
-
- <v-card v-for="l in categ.subcategory" :key="l.category+'field'">
+ <v-card v-for="l in categ.subcategory" :key="l.category+'field'">
<v-layout v-if="l">
<v-flex xs1 class="subheading">
<div class="text-xs-center">
@@ -457,7 +460,7 @@
<v-flex xs11>
<v-card v-for="(inputf,index) in l.fields" :key="index+'subjectField'">
-
+
<p-d-skos-preflabel
v-if="getSkosexactMatch(inputf)==undefined"
:p="getLabel(inputf['@type'])"
@@ -477,6 +480,8 @@
</v-layout>
</v-card>
+
+
</template>
</v-card>
</template>
@@ -665,9 +670,6 @@ export default {
});
if (jsonTypeArray.length > 0) {
- //for (var k = 0; k < jsonTypeArray.length; k++) {
- // console.log("jsonTypeArray", jsonTypeArray[k]);
- //}
//find first whether there is a subcategory
if (formFieldsFiltered[j].subcategory) {
//the category is formFieldsFiltered[j].category
@@ -701,16 +703,76 @@ export default {
} else {
jsonStructured[result].subcategory = [
{
- category: formFieldsFiltered[j].subcategory[0],
+ category: n_subcat,
id: formFieldsFiltered[j].infoRef,
fields: jsonTypeArray
}
];
}
+ } else {
+ //a quick fix but it's not pretty!!!
+ //check if those are any of the bioassay categories - the way i structured this code is not adapted yet to those subfields
+ if (
+ n_categ === "assayOrganism" ||
+ n_categ === "assayTarget" ||
+ n_categ === "assayDetection"
+ ) {
+ var findAssay = jsonStructured.findIndex(
+ obj => obj.category === "assay"
+ );
+ if (jsonStructured[findAssay].subcategory) {
+ var r = jsonStructured[findAssay].subcategory.findIndex(
+ obj => obj.category === n_subcat
+ );
+
+ if (r >= 0) {
+ for (var n = 0; n < jsonTypeArray.length; n++) {
+ jsonStructured[findAssay].subcategory[r].fields.push(
+ jsonTypeArray[n]
+ );
+ }
+ } else {
+ jsonStructured[findAssay].subcategory.push({
+ category: n_subcat,
+ id: formFieldsFiltered[j].infoRef,
+ fields: jsonTypeArray
+ });
+ }
+ } else {
+ if (n_categ === "assayOrganism") {
+ jsonStructured[findAssay].subcategory = [
+ {
+ category: "Assay organism",
+ id: formFieldsFiltered[j].infoRef,
+ fields: jsonTypeArray
+ }
+ ];
+ }
+ if (n_categ === "assayTarget") {
+ jsonStructured[findAssay].subcategory = [
+ {
+ category: "Assay Target",
+ id: formFieldsFiltered[j].infoRef,
+ fields: jsonTypeArray
+ }
+ ];
+ }
+ if (n_categ === "assayDetection") {
+ jsonStructured[findAssay].subcategory = [
+ {
+ category: "Detection",
+ id: formFieldsFiltered[j].infoRef,
+ fields: jsonTypeArray
+ }
+ ];
+ }
+ }
+ }
}
} else {
//the category is formFieldsFiltered[j].category
// if it exists, push to it, otherwise create it
+
var n_categ = formFieldsFiltered[j].category[0];
//check if it exists already
@@ -719,39 +781,26 @@ export default {
);
if (result >= 0) {
- /* if (jsonStructured[result].subcategory) {
- var r = jsonStructured[result].subcategory.findIndex(
- obj => obj.category === n_subcat
- );
- console.log(
- "n_sub r",
- r,
- "formFieldsFiltered[j].infoRef",
- formFieldsFiltered[j].infoRef
- );
- if (r >= 0) {
- jsonStructured[result].subcategory[r].fields.push(
- jsonTypeArray[0]
- );
- } else {
- jsonStructured[result].subcategory.push({
- category: n_subcat,
- id: formFieldsFiltered[j].infoRef,
- fields: jsonTypeArray
- });
+ jsonStructured[result].fields.push({
+ category: formFieldsFiltered[j].label,
+ id: formFieldsFiltered[j].infoRef,
+ fields: jsonTypeArray
+ });
+ } else {
+ jsonStructured[result].fields = [
+ {
+ category: "my cat",
+ id: formFieldsFiltered[j].infoRef,
+ fields: jsonTypeArray
}
- } else {*/
- jsonStructured[result].fields = jsonTypeArray;
- // category: n_categ,
- // id: formFieldsFiltered[j].infoRef,
- // fields: jsonTypeArray
- //};
+ ];
}
}
}
}
}
this.pharma = jsonStructured;
+
return jsonStructured;
},
diff --git a/src/components/display/pharma_display/PhDMetadata.vue b/src/components/display/pharma_display/PhDMetadata.vue
index 58824f4..6dbc8ae 100644
--- a/src/components/display/pharma_display/PhDMetadata.vue
+++ b/src/components/display/pharma_display/PhDMetadata.vue
@@ -229,6 +229,8 @@ export default {
})
.catch(function(error) {
+ self.data = self.o;
+
console.error(error);
});
}
diff --git a/src/components/input/PhSubmit.vue b/src/components/input/PhSubmit.vue
index bd4869b..8cfce64 100644
--- a/src/components/input/PhSubmit.vue
+++ b/src/components/input/PhSubmit.vue
@@ -10,7 +10,7 @@
</template>
</v-tab>
<v-tab ripple @click="updatePrettyPrint()">Metadata preview</v-tab>
- <v-tab v-if="templating" ripple @click="loadTemplates()">Templates</v-tab>
+ <!-- <v-tab v-if="templating" ripple @click="loadTemplates()">Templates</v-tab>-->
</v-tabs>
<v-tabs-items v-model="activetab">
diff --git a/src/components/input/pharma-input-fields/PhInputForm.vue b/src/components/input/pharma-input-fields/PhInputForm.vue
index ff4dd46..33477fc 100644
--- a/src/components/input/pharma-input-fields/PhInputForm.vue
+++ b/src/components/input/pharma-input-fields/PhInputForm.vue
@@ -190,7 +190,7 @@
:freeText="{'@type': [f.type],'skos:prefLabel': [{'@value':''}]}"
></ph-selection>
</v-flex>
-
+
<v-layout
row
wrap
@@ -595,6 +595,10 @@ export default {
var sub = [];
if (el.subcategory) {
+ for (var catt in arr) {
+ if (arr[catt].category[0] === el.subcategory[0]) {
+ }
+ }
sub = arr.filter(function(a) {
if (a.category) {
return a.category[0] === el.subcategory[0];
@@ -635,6 +639,7 @@ export default {
}
}
} else {
+ //WHAT"S UP HERE???
}
}
// } else {
@@ -666,7 +671,7 @@ export default {
this.$emit("form-input-" + f.component, f);
},
warning: function(section) {
- console.log("in warning", section);
+ //console.log("in warning", section);
if (typeof section === "undefined") {
//console.log("undefined");
} else {
@@ -690,7 +695,7 @@ export default {
for (var f in fields) {
if (fields[f].warning === true) {
w = true;
- console.log("field", fields[f].label, "is missing");
+ //console.log("field", fields[f].label, "is missing");
}
}
}
diff --git a/src/utils/fields.js b/src/utils/fields.js
index 66186c0..001f299 100644
--- a/src/utils/fields.js
+++ b/src/utils/fields.js
@@ -530,7 +530,6 @@ const fields = [
multiplicable: false,
visible: true,
category: ["life"],
-
vocabulary: "life",
info:
"Life NCIT:C142142 Thee biochemical phenomenon that distinguishes organisms from inorganic matter. It is characterized by growth, metabolism, and reproduction. [ NCI ]",
@@ -751,14 +750,14 @@ const fields = [
{
id: "4-Anatomical-category",
predicate: "dcterms:subject",
- type: "skos:Concept",
+ type: "pharmaWien:anatomicalCat",
//subjectType: "Anatomical Category:",
label: "Anatomical Category:",
value: "",
component: "selection",
-
commit: true,
visible: true,
+ category: ["anatomicalCategory"],
vocabulary: "anatomical_category",
stateVoc: "anatomical_category",
info: "OMIT:0001001",
@@ -1134,6 +1133,7 @@ const fields = [
required: false,
removable: false,
category: ["assay"],
+
label: "Assay title:",
value: "",
component: "text-field",
@@ -1156,6 +1156,7 @@ const fields = [
component: "text-field",
multiline: true,
category: ["assay"],
+
info:
"This includes the methodology used to perform a particular bioassay and is found on the PubChem website associated with each assay ID (AID). It includes the assay components and the order in which they were added, the incubation times, detection method and the kit used, etc.",
infoRef: "http://www.bioassayontology.org/bao#BAO_0000523",
@@ -1174,6 +1175,7 @@ const fields = [
commit: true,
visible: true,
category: ["assay"],
+ subcategory: ["Assay type"],
vocabulary: "bioassay_type",
stateVoc: "bioassay_type",
info: "",
@@ -1194,6 +1196,7 @@ const fields = [
ontology: "bao",
ontClass: "BAO_0000015",
category: ["assay"],
+ subcategory: ["Bioassay category:"],
topId: "BAO_0000015",
description: "Bioassay category:",
info:
@@ -1216,6 +1219,7 @@ const fields = [
topId: "BAO_0000019",
description: "Assay format:",
category: ["assay"],
+ subcategory: ["Bioassay format:"],
info:
"Assay format is a conceptualization of assays based on the biological and / or chemical features of the experimental system. For example assay formats include biochemical assays - referring to assays with purified protein, cell-based - referring to assays in whole cells, or organism-based - referring to assays performed in an organism.",
infoRef: "http://www.bioassayontology.org/bao#BAO_0000019",
@@ -1237,6 +1241,8 @@ const fields = [
//category: ["assay"],
topId: "BAO_0002202",
description: "Assay design method:",
+ category: ["assay"],
+ subcategory: ["Bioassay design method:"],
info:
"The assay design method describes how a biological or physical process screened / investigated in the model system is translated into a detectable signal. This relates to the technology / technologies used to make the assay system work, i.e. enable that the screened process can be detected. It typically involves some manipulation of the (biological) model system to detect the process of interest.",
infoRef: "http://www.bioassayontology.org/bao#BAO_0002202",
@@ -1254,6 +1260,7 @@ const fields = [
freefield: true,
component: "ext-service",
category: ["assay"],
+ subcategory: ["Computational method:"],
ontology: "bao",
//baseurl: "http://www.bioassayontology.org/bao#",
ontClass: "BAO_0002094",
@@ -1278,6 +1285,7 @@ const fields = [
ontClass: "BAO_0000029",
topId: "BAO_0000029",
category: ["assay"],
+ subcategory: ["Assay screening campaign stage:"],
// baseurl: "http://www.bioassayontology.org/bao#",
description: "Assay screening campaign stage:",
info:
@@ -1287,7 +1295,7 @@ const fields = [
{
id: "0-Organism",
predicate: "dcterms:subject",
- type: "pharmaWien:assayOrg",
+ type: "pharmaWien:assayOrganism",
//subjectType: "AssayOrganism:",
label: "Bioassay organism",
//description: "selection",
@@ -1298,41 +1306,19 @@ const fields = [
visible: true,
vocabulary: "assay_organism",
stateVoc: "assay_organism",
- category: ["assay"],
+ category: ["assayOrganism"],
subcategory: ["assayOrganism"],
multiplicable: true,
info:
"The organism related to the target / meta-target of the bioassay. It includes both bacterium and eukaryote.",
infoRef: "http://www.bioassayontology.org/bao#BAO:0000551",
- description: "Bioassay organism:",
- },
- {
- id: "0-Organism-assayTarget",
- predicate: "dcterms:subject",
- type: "pharmaWien:assayTarget_organism",
- //subjectType: "AssayOrganism:",
- label: "Assay Target Organism",
- description: "Bioassay Target 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",
+ description: "selection",
},
{
id: "0-Cellular-organism",
predicate: "dcterms:subject",
- type: "pharmaWien:assayOrganism_CellularOrganism",
- //subjectType: "AssayCellularOrganism",
- label: "Cellular organism",
+ type: "pharmaWien:assayOrgCellular",
+ label: "Bioassay Cellular organism",
value: "",
required: false,
visible: false,
@@ -1341,17 +1327,16 @@ const fields = [
ontClass: "NCBITaxon_131567",
topId: "NCBITaxon_131567",
component: "ext-service",
- category: ["assay"],
- subcategory: ["assayOrganism"],
- description: "Bioassay organism:",
+ category: ["assayOrganism"],
+ subcategory: ["Cellular organism"],
+ description: "Cellular organism",
info: "",
},
{
id: "0-Viruses",
predicate: "dcterms:subject",
- type: "pharmaWien:assayOrganism_Viruses",
- //subjectType: "AssayViruses",
- label: "Viruses",
+ type: "pharmaWien:assayOrgViruses",
+ label: "Bioassay Viruses",
value: "",
required: false,
visible: false,
@@ -1360,17 +1345,16 @@ const fields = [
ontClass: "NCBITaxon_10239",
topId: "NCBITaxon_10239",
component: "ext-service",
- category: ["assay"],
- subcategory: ["assayOrganism"],
+ category: ["assayOrganism"],
+ subcategory: ["Viruses"],
description: "Viruses",
info: "",
},
{
id: "0-Viroids",
predicate: "dcterms:subject",
- type: "pharmaWien:assayOrganism_Viroids",
- //subjectType: "AssayViroids",
- label: "Viroids",
+ type: "pharmaWien:assayOrgViroids",
+ label: "Bioassay Viroids",
value: "",
freefield: true,
required: false,
@@ -1379,11 +1363,35 @@ const fields = [
ontClass: "NCBITaxon_12884",
topId: "NCBITaxon_12884",
component: "ext-service",
- category: ["assay"],
- subcategory: ["assayOrganism"],
+ category: ["assayOrganism"],
+ subcategory: ["Viroids"],
description: "Viroids",
+ infoRef: "NCBITaxon_12884",
info: "",
},
+ {
+ id: "0-Organism-assayTarget",
+ predicate: "dcterms:subject",
+ type: "pharmaWien:assayTargetOrganism",
+ //subjectType: "AssayOrganism:",
+ label: "Assay Target Organism",
+ description: "Bioassay Target 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-cell-line",
predicate: "dcterms:subject",
@@ -1397,6 +1405,8 @@ const fields = [
ontology: "cellosaurus",
ontClass: "",
treeview: false,
+ category: ["assay"],
+ subcategory: ["Cultured Cell"],
description: "Cultured Cell (cellosaurus)",
info:
"A cell in vitro that is or has been maintained or propagated as part of a cell culture. [ ReO:mhb ]",
@@ -1417,6 +1427,7 @@ const fields = [
visible: true,
vocabulary: "assay_target",
category: ["assayTarget"],
+ subcategory: ["assayTarget"],
stateVoc: "assay_target",
info: "",
//baseurl: "http://www.bioassayontology.org/bao#",
@@ -1438,6 +1449,7 @@ const fields = [
freetext: true,
component: "ext-service",
category: ["assayTarget"],
+ subcategory: ["Assay target Small Molecule"],
description: "Small Molecule",
info: "NCIT:C48809",
},
@@ -1455,6 +1467,7 @@ const fields = [
topId: "GO_0110165",
component: "ext-service",
category: ["assayTarget"],
+ subcategory: ["Assay target cellular anatomical entity"],
freefield: true,
multiple: true,
description: "Cellular anatomical entity",
@@ -1477,6 +1490,7 @@ const fields = [
topId: "NCIT_C12801",
component: "ext-service",
category: ["assayTarget"],
+ subcategory: ["assay target Tissue"],
description: "Tissue",
info:
"An anatomical structure consisting of similarly specialized cells and intercellular matrix, aggregated according to genetically determined spatial relationships, performing a specific function. [ NCI ]",
@@ -1498,6 +1512,7 @@ const fields = [
topId: "CHEBI_16646",
component: "ext-service",
category: ["assayTarget"],
+ subcategory: ["Assay Target Carbohydrate"],
description: "Carbohydrate",
info:
"An anatomical structure consisting of similarly specialized cells and intercellular matrix, aggregated according to genetically determined spatial relationships, performing a specific function. [ NCI ]",
@@ -1506,20 +1521,20 @@ const fields = [
{
id: "0-detection",
predicate: "dcterms:subject",
- type: "pharmaWien:assay_detection",
+ type: "pharmaWien:assayDetection",
//subjectType: "assay_detection",
label: "Detection method:",
description: "selection",
value: "",
required: false,
visible: true,
-
freefield: false,
commit: true,
visible: true,
vocabulary: "assay_detection",
stateVoc: "assay_detection",
category: ["assayDetection"],
+ subcategory: ["Detection"],
multiplicable: true,
component: "selection",
info:
@@ -1529,7 +1544,7 @@ const fields = [
{
id: "0-detection_method",
predicate: "dcterms:subject",
- type: "pharmaWien:assay_physicalDetectionMethod",
+ type: "pharmaWien:assayPhysicalDetectionMethod",
//subjectType: "physical_detection_method",
label: "Physical detection method:",
value: "",
@@ -1542,6 +1557,7 @@ const fields = [
topId: "BAO_0000035",
component: "ext-service",
category: ["assayDetection"],
+ subcategory: ["Detection Method"],
description: "Physical detection method",
info: "",
infoRef: "http://www.bioassayontology.org/bao#BAO_0000035",
@@ -1562,6 +1578,7 @@ const fields = [
topId: "BAO_0000697",
component: "ext-service",
category: ["assayDetection"],
+ subcategory: ["Detection Instrument"],
description: "Detection instrument",
info: "",
infoRef: "http://www.bioassayontology.org/bao#BAO_0000697",
@@ -1641,11 +1658,11 @@ const predicateOrder = [
];
export default {
- getFields: function() {
+ getFields: function () {
return fields;
},
- getEditableFields: function() {
+ getEditableFields: function () {
var editable = fields.filter((item) => !item.readonly);
// hack: some bug in vuetify autocomplete can't handle the value property
var newarr = [];
@@ -1656,7 +1673,7 @@ export default {
}
return newarr;
},
- getField: function(id, ordergroup) {
+ getField: function (id, ordergroup) {
for (var i = 0; i < fields.length; i++) {
if (fields[i]["id"] === id) {
var field = JSON.parse(JSON.stringify(fields[i]));
@@ -1666,7 +1683,7 @@ export default {
}
}
},
- getFieldbySubject: function(subject) {
+ getFieldbySubject: function (subject) {
for (var i = 0; i < fields.length; i++) {
if (fields[i]["type"] === subject) {
var field = JSON.parse(JSON.stringify(fields[i]));
@@ -1675,7 +1692,7 @@ export default {
}
}
},
- getFieldsLabelsbyCateg: function(categ) {
+ getFieldsLabelsbyCateg: function (categ) {
var ar = [];
for (var i = 0; i < fields.length; i++) {
@@ -1690,7 +1707,7 @@ export default {
}
return ar;
},
- getPredicateOrder: function() {
+ getPredicateOrder: function () {
return predicateOrder;
},
};
--
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