Hallo JMP-Community,
Ich muss anhand einer eindeutigen Kennung biologische Informationen von der öffentlichen Website des Human Protein Atlas abrufen.
Bisher kann ich die JSON-Datei mithilfe des folgenden einfachen Codes problemlos von der Website abrufen und analysieren.
Names DEfault to Here (1);
ID = "ENSG00000108691";
HTM_c = "https://www.proteinatlas.org/XXX.json";
HTM_str = Substitute (HTM_c, "XXX", ID);
request = New HTTP Request (URL (HTM_str), Method ("Get"));
temp = request << send ();
js_par = Parse JSON (temp);
Das Problem tritt auf, wenn ich versuche, nur einen ausgewählten Teil des JSON-Dokuments zu sammeln (siehe Anhang):
1) Der Befehl „js_par << Get Keys“ ruft nur die Schlüssel der obersten Ebene ab, sodass „Unterschlüssel“ nicht verfügbar sind
2) Der Befehl „js_par << Get Values“ gibt nicht die tatsächlichen Werte zurück, sondern das Format der Daten-„Container“
Wie kann ich also das JSON-Dokument aufschlüsseln, um den Abruf bestimmter Schlüssel und Werte zu ermöglichen?
Jeder Hinweis wäre willkommen.
Danke schön.
Am besten,
TS
Prüfen Sie, ob der JSON-Importassistent das tut, was Sie brauchen. Es gibt mehrere Möglichkeiten, es anzugreifen; So könnte eine JSL-Lösung aussehen
dt = open("z:/ENSG00000108691.json",guess("huge", stack(1)),jsonwizard(0));
Ändern Sie die 0 in eine 1, um den Assistentendialog anzuzeigen.
Diese Datei scheint 8 Datensätze mit der besten Schätzauswahl zu haben. Wenn dies nicht Ihren Erwartungen entspricht, möchten Sie möglicherweise über die GUI manuell auswählen, was Sie möchten. Ich bin mir jedoch nicht sicher, ob Sie viel mehr tun können, als nicht benötigte Spalten zu entfernen.
(Datei -> Öffnen, Erweiterung .json auswählen, Daten mithilfe der Vorschau auswählen, öffnen.)
json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.json (and XML) dialogs are almost identical.JSON- (und XML-)Dialoge sind nahezu identisch.
Tatsächlich ist es nach der Neuformatierung (Visual Studio-Code hat funktioniert) wahrscheinlich sinnvoller, Stack(0) zu verwenden und 1 Zeile zu erhalten. Jede Spalte ist eine Liste von Attributen für diese Spalte (ich vermute). Die Synonymspalte hat 8 Möglichkeiten. Die Proteinklasse hat 5 Möglichkeiten. Sie sollten nicht wie im ersten Beispiel gezeigt an Zeilen ausgerichtet werden. Ich vermute, dass dies nicht beabsichtigt war.
Die Tabelle enthält Ausdrucksspalten anstelle von Zeichenspalten mit Trennzeichen, wenn Sie danach fragen:
[
{
"Gene": "CCL2",
"Gene synonym": [
"GDCF-2",
"HC11",
"MCAF",
"MCP-1",
"MCP1",
"MGC9434",
"SCYA2",
"SMC-CF"
],
"Ensembl": "ENSG00000108691",
"Gene description": "C-C motif chemokine ligand 2",
"Uniprot": [
"P13500"
],
"Chromosome": "17",
"Position": "34255274-34257208",
"Protein class": [
"Cancer-related genes",
"Candidate cardiovascular disease genes",
"Human disease related genes",
"Plasma proteins",
"Predicted secreted proteins"
],
"Biological process": [
"Chemotaxis",
"Inflammatory response"
],
"Molecular function": [
"Cytokine"
],
"Disease involvement": [
"Cancer-related genes"
],
"Evidence": "Evidence at protein level",
"HPA evidence": "Evidence at protein level",
"UniProt evidence": "Evidence at protein level",
"NeXtProt evidence": "Evidence at protein level",
"RNA tissue specificity": "Tissue enhanced",
"RNA tissue distribution": "Detected in all",
"RNA tissue specificity score": null,
"RNA tissue specific nTPM": {
"urinary bladder": "726.7"
},
"RNA single cell type specificity": "Cell type enhanced",
"RNA single cell type distribution": "Detected in many",
"RNA single cell type specificity score": null,
"RNA single cell type specific nTPM": {
"Ductal cells": "2990.5",
"Exocrine glandular cells": "1242.1",
"Pancreatic endocrine cells": "1696.3",
"Secretory cells": "2061.7",
"Smooth muscle cells": "1284.8"
},
"RNA cancer specificity": "Low cancer specificity",
"RNA cancer distribution": "Detected in all",
"RNA cancer specificity score": null,
"RNA cancer specific FPKM": null,
"RNA brain regional specificity": "Low region specificity",
"RNA brain regional distribution": "Detected in all",
"RNA brain regional specificity score": null,
"RNA brain regional specific nTPM": null,
"RNA blood cell specificity": "Group enriched",
"RNA blood cell distribution": "Detected in some",
"RNA blood cell specificity score": "6",
"RNA blood cell specific nTPM": {
"classical monocyte": "7.6",
"eosinophil": "3.1"
},
"RNA blood lineage specificity": "Group enriched",
"RNA blood lineage distribution": "Detected in many",
"RNA blood lineage specificity score": "6",
"RNA blood lineage specific nTPM": {
"granulocytes": "3.1",
"monocytes": "7.6"
},
"RNA cell line specificity": "Low cancer specificity",
"RNA cell line distribution": "Detected in many",
"RNA cell line specificity score": null,
"RNA cell line specific nTPM": null,
"RNA tissue cell type enrichment": [
"Pancreas - Ductal cells"
],
"RNA mouse brain regional specificity": "Low region specificity",
"RNA mouse brain regional distribution": "Detected in some",
"RNA mouse brain regional specificity score": null,
"RNA mouse brain regional specific nTPM": null,
"RNA pig brain regional specificity": "Group enriched",
"RNA pig brain regional distribution": "Detected in all",
"RNA pig brain regional specificity score": "4",
"RNA pig brain regional specific nTPM": {
"midbrain": "13.1",
"spinal cord": "52.4"
},
"Antibody": [
"CAB013676",
"HPA019163"
],
"Reliability (IH)": "Approved",
"Reliability (Mouse Brain)": null,
"Reliability (IF)": "Approved",
"Subcellular location": [
"Golgi apparatus",
"Vesicles"
],
"Secretome location": "Secreted to blood",
"Secretome function": "Chemokine",
"CCD Protein": "NA",
"CCD Transcript": "NA",
"Blood concentration - Conc. blood IM [pg\/L]": 323000,
"Blood concentration - Conc. blood MS [pg\/L]": null,
"Blood expression cluster": null,
"Tissue expression cluster": "Cluster 7: Adipose tissue - Mixed function",
"Brain expression cluster": "Cluster 12: Non-specific - Vasculature",
"Cell line expression cluster": "Cluster 49: HMC-1 - Innate immune response",
"Single cell expression cluster": "Cluster 48: Smooth muscle cells - Signal transduction",
"Interactions": 4,
"Subcellular main location": [
"Golgi apparatus"
],
"Subcellular additional location": [
"Vesicles"
],
"Antibody RRID": {
"CAB013676": null,
"HPA019163": "AB_1846179"
},
"Pathology prognostics - Breast cancer": {
"prognostic type": "favorable",
"is_prognostic": false,
"p_val": "6.43e-2"
},
"Pathology prognostics - Cervical cancer": {
"prognostic type": "unfavorable",
"is_prognostic": false,
"p_val": "4.14e-2"
},
"Pathology prognostics - Colorectal cancer": {
"prognostic type": "unfavorable",
"is_prognostic": false,
"p_val": "4.78e-2"
},
"Pathology prognostics - Endometrial cancer": {
"prognostic type": "favorable",
"is_prognostic": false,
"p_val": "5.57e-2"
},
"Pathology prognostics - Glioma": {
"prognostic type": "unfavorable",
"is_prognostic": false,
"p_val": "2.37e-3"
},
"Pathology prognostics - Head and neck cancer": {
"prognostic type": "unfavorable",
"is_prognostic": false,
"p_val": "8.64e-2"
},
"Pathology prognostics - Liver cancer": {
"prognostic type": "favorable",
"is_prognostic": false,
"p_val": "2.78e-2"
},
"Pathology prognostics - Lung cancer": {
"prognostic type": "unfavorable",
"is_prognostic": false,
"p_val": "7.53e-2"
},
"Pathology prognostics - Melanoma": {
"prognostic type": "unfavorable",
"is_prognostic": false,
"p_val": "2.90e-1"
},
"Pathology prognostics - Ovarian cancer": {
"prognostic type": "favorable",
"is_prognostic": false,
"p_val": "1.19e-1"
},
"Pathology prognostics - Pancreatic cancer": {
"prognostic type": "favorable",
"is_prognostic": false,
"p_val": "9.33e-2"
},
"Pathology prognostics - Prostate cancer": {
"prognostic type": "favorable",
"is_prognostic": false,
"p_val": "2.65e-1"
},
"Pathology prognostics - Renal cancer": {
"prognostic type": "unfavorable",
"is_prognostic": true,
"p_val": "4.51e-4"
},
"Pathology prognostics - Stomach cancer": {
"prognostic type": "unfavorable",
"is_prognostic": false,
"p_val": "1.33e-1"
},
"Pathology prognostics - Testis cancer": {
"prognostic type": "unfavorable",
"is_prognostic": false,
"p_val": "2.50e-2"
},
"Pathology prognostics - Thyroid cancer": {
"prognostic type": "unfavorable",
"is_prognostic": false,
"p_val": "1.81e-1"
},
"Pathology prognostics - Urothelial cancer": {
"prognostic type": "unfavorable",
"is_prognostic": false,
"p_val": "4.92e-2"
}
}
]