Suggest-EDAM-Annotation.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 106,
   "metadata": {},
   "outputs": [],
   "source": [
    "import json\n",
    "import io\n",
    "\n",
    "from rdflib import ConjunctiveGraph, RDFS, Namespace, URIRef, BNode, Literal\n",
    "from rdflib.namespace import RDF\n",
    "\n",
    "#import networkx as nx\n",
    "#from nxpd import draw\n",
    "\n",
    "g = ConjunctiveGraph()\n",
    "g.bind('prov', Namespace('http://www.w3.org/ns/prov#'))\n",
    "g.bind('p-plan', Namespace('http://purl.org/net/p-plan#'))\n",
    "g.bind('dc', Namespace('http://dcterms/'))\n",
    "g.bind('nb-core', Namespace('http://bise-eu.info/core-ontology#'))\n",
    "\n",
    "nb_core = Namespace(\"http://bise-eu.info/core-ontology#\")\n",
    "pplan = Namespace(\"http://purl.org/net/p-plan#\")\n",
    "bise = Namespace(\"http://biii.eu/node/\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 1. Load the EDAM Bioimaging ontology"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 107,
   "metadata": {},
   "outputs": [],
   "source": [
    "def load_rdf(filename):\n",
    "    with io.open(filename,'r',encoding='utf8') as f:\n",
    "        g.load(f, format='turtle')  \n",
    "        \n",
    "def load_remote_rdf(url):\n",
    "    g.load(url, format='turtle')\n",
    "    \n",
    "def load_remote_owl(url):\n",
    "    g.load(url, format='xml')\n",
    "\n",
    "\n",
    "def load_owl(filename):\n",
    "    with io.open(filename,'r',encoding='utf8') as f:\n",
    "        g.load(f, format='xml')  \n",
    "\n",
    "#with open('test.json', 'r') as data_file:\n",
    "#    data_str = data_file.read()\n",
    "#try:\n",
    "#    data = json.loads(data_str)\n",
    "#except json.decoder.JSONDecodeError as e:\n",
    "#    print(\"parsing ERROR \"+e.msg)\n",
    "\n",
    "#import requests\n",
    "#r = requests.get('http://test.biii.eu/wfsteps?_format=json') \n",
    "#print(json.dumps(r.json(), indent=4))\n",
    "#data = r.json()\n",
    "\n",
    "#load_remote_rdf('https://raw.githubusercontent.com/NeuBIAS/bise-core-ontology/master/data-dumps/latest/neubias-latest.ttl')\n",
    "#load_owl('./bise-linked-data-webapp/static/data/EDAM-bioimaging_alpha03.owl')\n",
    "load_remote_owl('https://github.com/edamontology/edam-bioimaging/raw/master/releases/EDAM-bioimaging_alpha06.owl')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 2. Indexing all synonyms and labels associated to EDAM concepts"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 108,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "    \"Geometric distortion correction\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__R3BGvVm77d5vFMF6f28ZiW\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Lens distortion correction\"\n",
      "        ]\n",
      "    },\n",
      "    \"Electron cryotomography\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RDCjx86atJP685sX1zrE2ia\",\n",
      "        \"exact_syn\": [\n",
      "            \"CryoET\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"CET\"\n",
      "        ],\n",
      "        \"broad_syn\": [\n",
      "            \"CryoTEM\"\n",
      "        ]\n",
      "    },\n",
      "    \"Binary format\": {\n",
      "        \"uri\": \"http://edamontology.org/format_Binary_format\"\n",
      "    },\n",
      "    \"Smoothing\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Image_smoothing\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Gaussian filtering\"\n",
      "        ],\n",
      "        \"related_syn\": [\n",
      "            \"Blurring\"\n",
      "        ]\n",
      "    },\n",
      "    \"Serial block-face scanning electron microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RByvmgDpAo4FOrMdvTm1gwR\",\n",
      "        \"exact_syn\": [\n",
      "            \"SBF SEM\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"3View\\u00ae\"\n",
      "        ]\n",
      "    },\n",
      "    \"Live sample imaging\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RL4rPCXlIu9uzNrGcbcSNp\",\n",
      "        \"broad_syn\": [\n",
      "            \"Dynamic imaging\"\n",
      "        ]\n",
      "    },\n",
      "    \"Light-sheet microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_Light-sheet_microscopy\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Swept confocally-aligned planar excitation microscopy (SCAPE)\"\n",
      "        ],\n",
      "        \"related_syn\": [\n",
      "            \"Bessel Beam Lightsheet Microscopy\"\n",
      "        ]\n",
      "    },\n",
      "    \"Fourier-transform infrared spectroscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Fourier-transform_infrared_spectroscopy\",\n",
      "        \"exact_syn\": [\n",
      "            \"FTIR\"\n",
      "        ]\n",
      "    },\n",
      "    \"Model-based segmentation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation____Model-based_segmentation\"\n",
      "    },\n",
      "    \"Image analysis\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_3443\",\n",
      "        \"narrow_syn\": [\n",
      "            \"General image analysis\"\n",
      "        ]\n",
      "    },\n",
      "    \"DIC microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RNFOzq5E0ZVBh5Euhn06rn\",\n",
      "        \"exact_syn\": [\n",
      "            \"Differential interference contrast microscopy\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Nomarski interferential contrast (NIC)\"\n",
      "        ]\n",
      "    },\n",
      "    \"is identifier of\": {\n",
      "        \"uri\": \"http://edamontology.org/is_identifier_of\"\n",
      "    },\n",
      "    \"Volume rendering\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Volume_rendering\"\n",
      "    },\n",
      "    \"Image correction\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__R7MFwdgojfmkZ07yWbdcda0\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Instrument aberration correction\"\n",
      "        ],\n",
      "        \"related_syn\": [\n",
      "            \"Image preprocessing\"\n",
      "        ]\n",
      "    },\n",
      "    \"Pixel classification\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Pixel_classification\",\n",
      "        \"exact_syn\": [\n",
      "            \"Pixel labeling\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Semantic image segmentation\"\n",
      "        ]\n",
      "    },\n",
      "    \"Image bit depth\": {\n",
      "        \"uri\": \"http://edamontology.org/data__RDcwcMJia2DgGNXx2JKa8Oc\"\n",
      "    },\n",
      "    \"Dark-field microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__R89wYXZ2735GXdn4m4GOT9n\"\n",
      "    },\n",
      "    \"Intravital imaging\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_____Intravital_imaging\"\n",
      "    },\n",
      "    \"Connected-component analysis\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_____Connected-component_analysis\"\n",
      "    },\n",
      "    \"Tomography\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_3452\"\n",
      "    },\n",
      "    \"Object detection\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__RBNng13hEB0CJD5VzSKqrfB\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Object localisation\"\n",
      "        ]\n",
      "    },\n",
      "    \"Affine registration\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__RLtOI0poPsYRHzgXbAcr2E\",\n",
      "        \"exact_syn\": [\n",
      "            \"Affine image registration\"\n",
      "        ]\n",
      "    },\n",
      "    \"Ex-vivo imaging\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RB4unXFUWvdBe91ihVAA9rR\"\n",
      "    },\n",
      "    \"Conversion\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_3434\"\n",
      "    },\n",
      "    \"Adaptive microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Self-adjusting_microscopy\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Intelligent microscopy\"\n",
      "        ]\n",
      "    },\n",
      "    \"Object tracking\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Image_tracking\",\n",
      "        \"exact_syn\": [\n",
      "            \"Tracking\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Trajectory extraction\"\n",
      "        ]\n",
      "    },\n",
      "    \"Image generation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__RDFFD5jBfUw74a3vJeBAGB1\",\n",
      "        \"exact_syn\": [\n",
      "            \"Image synthesis\"\n",
      "        ]\n",
      "    },\n",
      "    \"has output\": {\n",
      "        \"uri\": \"http://edamontology.org/has_output\",\n",
      "        \"related_syn\": [\n",
      "            \"OBO_REL:has_participant\"\n",
      "        ]\n",
      "    },\n",
      "    \"Confocal fluorescence microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__Rn8MnorStmqIkNlAVZWBc0\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Laser scanning microscopy (LSM)\"\n",
      "        ]\n",
      "    },\n",
      "    \"Landmark assignment\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__RDggamr21qZlMqkQmyOdC7l\",\n",
      "        \"exact_syn\": [\n",
      "            \"Reference point assignment\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Fiducial placement\"\n",
      "        ]\n",
      "    },\n",
      "    \"Image time series\": {\n",
      "        \"uri\": \"http://edamontology.org/data__RCMgLYJyn9WJyCc3bA23xT1\",\n",
      "        \"exact_syn\": [\n",
      "            \"Time-series image\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Video sequence\"\n",
      "        ]\n",
      "    },\n",
      "    \"hdf5\": {\n",
      "        \"uri\": \"http://edamontology.org/format_hdf5\",\n",
      "        \"exact_syn\": [\n",
      "            \"h5\"\n",
      "        ]\n",
      "    },\n",
      "    \"Hide in subset\": {\n",
      "        \"uri\": \"http://edamontology.org/hide_in_subset\"\n",
      "    },\n",
      "    \"Tomographic reconstruction\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__R1NVO6hpWWcs99UiEFiOfK\",\n",
      "        \"exact_syn\": [\n",
      "            \"Tomography reconstruction\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Filtered back projection\"\n",
      "        ]\n",
      "    },\n",
      "    \"Scientific visualisation\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Scientific_visualisation\",\n",
      "        \"exact_syn\": [\n",
      "            \"Scientific visualization\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Interactive visual analysis\"\n",
      "        ]\n",
      "    },\n",
      "    \"dat\": {\n",
      "        \"uri\": \"http://edamontology.org/format_dat\",\n",
      "        \"exact_syn\": [\n",
      "            \".dat\"\n",
      "        ]\n",
      "    },\n",
      "    \"Object feature extraction\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Feature_extraction\",\n",
      "        \"exact_syn\": [\n",
      "            \"Feature detection\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"scale-invariant feature transform\"\n",
      "        ]\n",
      "    },\n",
      "    \"Documentation\": {\n",
      "        \"uri\": \"http://edamontology.org/documentation\",\n",
      "        \"related_syn\": [\n",
      "            \"Specification\"\n",
      "        ]\n",
      "    },\n",
      "    \"Digital pathology\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_____Digital_pathology\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Digital histopathology\"\n",
      "        ],\n",
      "        \"related_syn\": [\n",
      "            \"Telepathology\"\n",
      "        ]\n",
      "    },\n",
      "    \"Regular expression\": {\n",
      "        \"uri\": \"http://edamontology.org/regex\"\n",
      "    },\n",
      "    \"X-ray microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_____X-ray_microscopy\"\n",
      "    },\n",
      "    \"Image processing\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Image_processing\",\n",
      "        \"exact_syn\": [\n",
      "            \"Image transformation\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Image postprocessing\"\n",
      "        ],\n",
      "        \"related_syn\": [\n",
      "            \"Image manipulation\"\n",
      "        ]\n",
      "    },\n",
      "    \"Plunge freezing\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RMctC69gGv9qYqwKCXxeLF\"\n",
      "    },\n",
      "    \"Phase imaging\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Phase_imaging\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Ptychography\"\n",
      "        ]\n",
      "    },\n",
      "    \"Image annotation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_3553\"\n",
      "    },\n",
      "    \"Single-photon emission computed tomography\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RBkRgSi7js0c70kjiPgYTgR\",\n",
      "        \"related_syn\": [\n",
      "            \"SPECT\"\n",
      "        ]\n",
      "    },\n",
      "    \"Expansion microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_____Expansion_microscopy\",\n",
      "        \"exact_syn\": [\n",
      "            \"ExM\"\n",
      "        ]\n",
      "    },\n",
      "    \"Texture extraction\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Texture_extraction\",\n",
      "        \"exact_syn\": [\n",
      "            \"Texture feature extraction\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Inverse Difference Moment\"\n",
      "        ]\n",
      "    },\n",
      "    \"Dense image annotation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation______Dense_annotation\"\n",
      "    },\n",
      "    \"Sample clearing\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Sample_clearing\",\n",
      "        \"narrow_syn\": [\n",
      "            \"cleared tissue\"\n",
      "        ]\n",
      "    },\n",
      "    \"is output of\": {\n",
      "        \"uri\": \"http://edamontology.org/is_output_of\",\n",
      "        \"related_syn\": [\n",
      "            \"OBO_REL:participates_in\"\n",
      "        ]\n",
      "    },\n",
      "    \"Media type\": {\n",
      "        \"uri\": \"http://edamontology.org/media_type\",\n",
      "        \"narrow_syn\": [\n",
      "            \"MIME type\"\n",
      "        ]\n",
      "    },\n",
      "    \"Evolutionary algorithm\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Evolutionary_algorithm\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Genetic algorithm\"\n",
      "        ]\n",
      "    },\n",
      "    \"Photoablation\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Photoablation\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Laser ablation\"\n",
      "        ]\n",
      "    },\n",
      "    \"Editing\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_3096\"\n",
      "    },\n",
      "    \"Image characteristics\": {\n",
      "        \"uri\": \"http://edamontology.org/data__R80aNLt4YY02ByptWQa2yrY\",\n",
      "        \"related_syn\": [\n",
      "            \"Image metadata\"\n",
      "        ]\n",
      "    },\n",
      "    \"Cell lineage extraction\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_____Cell_lineage_extraction\"\n",
      "    },\n",
      "    \"Imaging flow cytometry\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Imaging_flow_cytometry\",\n",
      "        \"exact_syn\": [\n",
      "            \"IFC\"\n",
      "        ]\n",
      "    },\n",
      "    \"Array tomography\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_____Array_tomography\"\n",
      "    },\n",
      "    \"Spatial image resolution\": {\n",
      "        \"uri\": \"http://edamontology.org/data__R9yc0jq1eJBgmvEQwMcRSUS\"\n",
      "    },\n",
      "    \"Radiometric properties\": {\n",
      "        \"uri\": \"http://edamontology.org/data__RCjZhkavxxifpvdNiasVVCc\"\n",
      "    },\n",
      "    \"Transmission light microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__R9P5gEAm1wic4R2PcZ7ZpPA\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Widefield transmission light microscopy\"\n",
      "        ]\n",
      "    },\n",
      "    \"Bioluminescence imaging\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RDvZSyRAcr8fonKvKdVoXw2\",\n",
      "        \"exact_syn\": [\n",
      "            \"BLI\"\n",
      "        ]\n",
      "    },\n",
      "    \"Laser microdissection\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Laser_microdissection\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Laser capture microdissection (LCM)\"\n",
      "        ]\n",
      "    },\n",
      "    \"Overlay\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Overlay\"\n",
      "    },\n",
      "    \"Image reconstruction\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Image_reconstruction\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Image restoration\"\n",
      "        ]\n",
      "    },\n",
      "    \"Edge detection\": {\n",
      "        \"uri\": \"http://edamontology.org/operation____Edge_detection\"\n",
      "    },\n",
      "    \"Localisation markers\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_____Fiducial_markers\",\n",
      "        \"exact_syn\": [\n",
      "            \"Landmarks\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Localisation beads\"\n",
      "        ],\n",
      "        \"related_syn\": [\n",
      "            \"Finder grids\"\n",
      "        ]\n",
      "    },\n",
      "    \"Distribution-based clustering\": {\n",
      "        \"uri\": \"http://edamontology.org/operation______Distribution-based_clustering\"\n",
      "    },\n",
      "    \"Image registration\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Image_registration\",\n",
      "        \"exact_syn\": [\n",
      "            \"Image alignment\"\n",
      "        ]\n",
      "    },\n",
      "    \"k-nearest neighbours\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______k-nearest_neighbours\",\n",
      "        \"exact_syn\": [\n",
      "            \"k-NN\"\n",
      "        ]\n",
      "    },\n",
      "    \"Operation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_0004\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Computational procedure\"\n",
      "        ],\n",
      "        \"broad_syn\": [\n",
      "            \"Function\"\n",
      "        ],\n",
      "        \"related_syn\": [\n",
      "            \"sumo:Function\"\n",
      "        ]\n",
      "    },\n",
      "    \"Sample embedding\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Sample_embedding\"\n",
      "    },\n",
      "    \"Frequency-domain analysis\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__RBYLqCqN4rP7Jy5m5mxpTeM\",\n",
      "        \"exact_syn\": [\n",
      "            \"Analysis in the frequency domain\"\n",
      "        ],\n",
      "        \"related_syn\": [\n",
      "            \"Wavelet transform\"\n",
      "        ]\n",
      "    },\n",
      "    \"Image enhancement\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Image_enhancement\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Image restoration\"\n",
      "        ]\n",
      "    },\n",
      "    \"Time-lapse data\": {\n",
      "        \"uri\": \"http://edamontology.org/data_Time-lapse_data\"\n",
      "    },\n",
      "    \"2D image\": {\n",
      "        \"uri\": \"http://edamontology.org/data_2D_dataset\"\n",
      "    },\n",
      "    \"Artificial intelligence\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Artificial_intelligence\",\n",
      "        \"exact_syn\": [\n",
      "            \"AI\"\n",
      "        ]\n",
      "    },\n",
      "    \"Multi-photon microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RBKlmE9DGTZwEwxw0juThGg\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Three-photon excitation microscopy\"\n",
      "        ]\n",
      "    },\n",
      "    \"Support vector machine\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Support_vector_machine\",\n",
      "        \"exact_syn\": [\n",
      "            \"SVM\"\n",
      "        ]\n",
      "    },\n",
      "    \"Fluorescence recovery after photobleaching\": {\n",
      "        \"uri\": \"http://edamontology.org/topic___Fluorescence_recovery_after_photobleaching\",\n",
      "        \"exact_syn\": [\n",
      "            \"FRAP\"\n",
      "        ],\n",
      "        \"related_syn\": [\n",
      "            \"Inverse fluorescence recovery after photobleaching (iFRAP)\"\n",
      "        ]\n",
      "    },\n",
      "    \"is format of\": {\n",
      "        \"uri\": \"http://edamontology.org/is_format_of\",\n",
      "        \"related_syn\": [\n",
      "            \"OBO_REL:quality_of\"\n",
      "        ]\n",
      "    },\n",
      "    \"Alignment construction\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_2928\"\n",
      "    },\n",
      "    \"Instrument distortion characteristics\": {\n",
      "        \"uri\": \"http://edamontology.org/data____Instrument_distortion_characteristics\",\n",
      "        \"exact_syn\": [\n",
      "            \"Lens distortion characteristics\"\n",
      "        ]\n",
      "    },\n",
      "    \"Warping\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Warping\"\n",
      "    },\n",
      "    \"Stereoscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Stereoscopy\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Stereoscopics\"\n",
      "        ]\n",
      "    },\n",
      "    \"Decision tree\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Decision_tree\",\n",
      "        \"exact_syn\": [\n",
      "            \"Decision tree learning\"\n",
      "        ]\n",
      "    },\n",
      "    \"Optical projection tomography\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Optical_Projection_Tomography\",\n",
      "        \"exact_syn\": [\n",
      "            \"Optical tomography\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"optical-ECT\"\n",
      "        ]\n",
      "    },\n",
      "    \"Created in\": {\n",
      "        \"uri\": \"http://edamontology.org/created_in\"\n",
      "    },\n",
      "    \"Volume\": {\n",
      "        \"uri\": \"http://edamontology.org/data_Volume\"\n",
      "    },\n",
      "    \"Image data properties\": {\n",
      "        \"uri\": \"http://edamontology.org/data_Image_geometry\"\n",
      "    },\n",
      "    \"Atomic force microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_____Atomic_force_microscopy\",\n",
      "        \"exact_syn\": [\n",
      "            \"AFM\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Scanning force microscopy\"\n",
      "        ]\n",
      "    },\n",
      "    \"Single molecule localisation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__R8EfungVXA0oQM2Ac7YY5eu\",\n",
      "        \"exact_syn\": [\n",
      "            \"Single molecule localization\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"STORM image reconstruction\"\n",
      "        ]\n",
      "    },\n",
      "    \"Bright-field microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RDdX0TswBVhmWiS1dI3pghN\"\n",
      "    },\n",
      "    \"Supervised learning\": {\n",
      "        \"uri\": \"http://edamontology.org/topic___Supervised_learning\"\n",
      "    },\n",
      "    \"Ultrasonography\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RBHw300pzIYcttGsAmIZvk5\",\n",
      "        \"exact_syn\": [\n",
      "            \"diagnostic sonography\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Ultrasound imaging\"\n",
      "        ]\n",
      "    },\n",
      "    \"Plant image analysis\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_____Plant_image_analysis\",\n",
      "        \"broad_syn\": [\n",
      "            \"Plant image informatics\"\n",
      "        ]\n",
      "    },\n",
      "    \"Sample preparation\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__ReQzVVVh0IPyN0c1V5wQVO\"\n",
      "    },\n",
      "    \"Greyscale\": {\n",
      "        \"uri\": \"http://edamontology.org/data_Greyscale\"\n",
      "    },\n",
      "    \"Microtomy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Microtomy\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Ultra-microtomy\"\n",
      "        ]\n",
      "    },\n",
      "    \"Region-proposal network\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Region-proposal_network\",\n",
      "        \"exact_syn\": [\n",
      "            \"RBF network\"\n",
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      "    },\n",
      "    \"Feature enhancement\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Edge_detection\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Edge enhancement\"\n",
      "        ]\n",
      "    },\n",
      "    \"Manual segmentation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation______Manual_segmentation\"\n",
      "    },\n",
      "    \"Pixel-based colocalisation analysis\": {\n",
      "        \"uri\": \"http://edamontology.org/operation___Pixel-based_colocalisation\",\n",
      "        \"exact_syn\": [\n",
      "            \"Pixel-based colocalization analysis\"\n",
      "        ]\n",
      "    },\n",
      "    \"Fluorescence lifetime imaging microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic___Fluorescence_lifetime_imaging\",\n",
      "        \"exact_syn\": [\n",
      "            \"FLIM\"\n",
      "        ]\n",
      "    },\n",
      "    \"Analysis\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_2945\"\n",
      "    },\n",
      "    \"Light field microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_____Light_field_microscopy\"\n",
      "    },\n",
      "    \"Airyscan\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Airyscan\"\n",
      "    },\n",
      "    \"Image segmentation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Image_segmentation\"\n",
      "    },\n",
      "    \"Medical imaging\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Medical_imaging\"\n",
      "    },\n",
      "    \"Sample thinning\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Sample_thinning\"\n",
      "    },\n",
      "    \"Montage\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Montage\"\n",
      "    },\n",
      "    \"Geometrical transformation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Geometrical_transform\"\n",
      "    },\n",
      "    \"Sparse image annotation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation______Sparse_annotation\"\n",
      "    },\n",
      "    \"Temporal properties\": {\n",
      "        \"uri\": \"http://edamontology.org/data__R7sy3JByrUsyKaGNYQ1eSQF\"\n",
      "    },\n",
      "    \"Machine learning\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_3474\",\n",
      "        \"exact_syn\": [\n",
      "            \"ML\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
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      "        \"related_syn\": [\n",
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      "        ]\n",
      "    },\n",
      "    \"Trajectory analysis\": {\n",
      "        \"uri\": \"http://edamontology.org/operation___Trajectory_analysis\",\n",
      "        \"related_syn\": [\n",
      "            \"Displacement analysis\"\n",
      "        ]\n",
      "    },\n",
      "    \"Superpixel extraction\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_____Superpixel_extraction\",\n",
      "        \"exact_syn\": [\n",
      "            \"Supervoxel extraction\"\n",
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      "    },\n",
      "    \"Wound-healing analysis\": {\n",
      "        \"uri\": \"http://edamontology.org/operation___Wound-healing_analysis\"\n",
      "    },\n",
      "    \"Neuron image analysis\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_Neuron_image_analysis\",\n",
      "        \"narrow_syn\": [\n",
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      "        ],\n",
      "        \"broad_syn\": [\n",
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      "    },\n",
      "    \"Natural language processing\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_0218\"\n",
      "    },\n",
      "    \"Photoacoustic tomography\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__R9WwNqEL8rvkyBPk7GkDTYh\",\n",
      "        \"exact_syn\": [\n",
      "            \"PAT\"\n",
      "        ],\n",
      "        \"broad_syn\": [\n",
      "            \"Photoacoustic imaging\"\n",
      "        ]\n",
      "    },\n",
      "    \"Bayesian statistics\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Bayesian_statistics\"\n",
      "    },\n",
      "    \"In-silico reconstruction\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__R96toeNl9iMp8oqv9augU84\",\n",
      "        \"broad_syn\": [\n",
      "            \"3D reconstruction\"\n",
      "        ]\n",
      "    },\n",
      "    \"Freeze fracturing\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RbM6PZFI9i5lG4gzAySn0c\",\n",
      "        \"exact_syn\": [\n",
      "            \"Freeze-fracture\"\n",
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      "    },\n",
      "    \"Optical sectioning tomography\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_____Micro-optical_sectioning_tomography\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Two-photon micro-optical sectioning microscopy\"\n",
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      "    },\n",
      "    \"img\": {\n",
      "        \"uri\": \"http://edamontology.org/format_img\",\n",
      "        \"exact_syn\": [\n",
      "            \".img\"\n",
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      "    },\n",
      "    \"Cryofixation\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__R77vfEkRqjIenYUqhDPvdkM\",\n",
      "        \"exact_syn\": [\n",
      "            \"Cryo-fixation\"\n",
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      "    },\n",
      "    \"Region properties\": {\n",
      "        \"uri\": \"http://edamontology.org/data__RCRp3XI62rYeU9aZHw4yBvj\"\n",
      "    },\n",
      "    \"Soft X-ray tomography\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_____Soft_x-ray_tomography\",\n",
      "        \"exact_syn\": [\n",
      "            \"SXT\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Cryo-SXT\"\n",
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      "    },\n",
      "    \"Collective object tracking\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__RBUpi1JSczmHQSf8Q8fDzG5\",\n",
      "        \"related_syn\": [\n",
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      "    },\n",
      "    \"has function\": {\n",
      "        \"uri\": \"http://edamontology.org/has_function\",\n",
      "        \"related_syn\": [\n",
      "            \"OBO_REL:bearer_of\"\n",
      "        ]\n",
      "    },\n",
      "    \"Intensity-based registration\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_____Intensity-based_registration\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Area-based registration\"\n",
      "        ]\n",
      "    },\n",
      "    \"nD image\": {\n",
      "        \"uri\": \"http://edamontology.org/data_4D_dataset\"\n",
      "    },\n",
      "    \"Critical-point drying\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__R9PtYz3fOHhRsnKnQzFIXff\",\n",
      "        \"exact_syn\": [\n",
      "            \"CPD\"\n",
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      "    },\n",
      "    \"Random forest\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Random_forest\",\n",
      "        \"exact_syn\": [\n",
      "            \"Random decision forest\"\n",
      "        ]\n",
      "    },\n",
      "    \"Deformable registration\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__RCPVGO34XrwrJasQ5yWBg9k\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Elastic registration\"\n",
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      "    },\n",
      "    \"Image fusion\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_____Image_fusion\"\n",
      "    },\n",
      "    \"Detector bias correction\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__RDlueIjODveP3FyOknVAqo5\",\n",
      "        \"narrow_syn\": [\n",
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      "    },\n",
      "    \"Image crop\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__Rhb4iyLUQWY4HnhPpuqNNI\"\n",
      "    },\n",
      "    \"Computed tomography\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RxfmHE99gOkUOOML5krfsJ\",\n",
      "        \"exact_syn\": [\n",
      "            \"CAT scan\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"High-resolution micro-CT\"\n",
      "        ],\n",
      "        \"related_syn\": [\n",
      "            \"High-resolution X-ray tomography\"\n",
      "        ]\n",
      "    },\n",
      "    \"xml\": {\n",
      "        \"uri\": \"http://edamontology.org/format_xml\",\n",
      "        \"exact_syn\": [\n",
      "            \".xml\"\n",
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      "    },\n",
      "    \"vsi\": {\n",
      "        \"uri\": \"http://edamontology.org/format_vsi\",\n",
      "        \"exact_syn\": [\n",
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      "    },\n",
      "    \"Particle tracking\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Particle_tracking\"\n",
      "    },\n",
      "    \"Tissue image analysis\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_Digital_histology\",\n",
      "        \"exact_syn\": [\n",
      "            \"Digital histology\"\n",
      "        ],\n",
      "        \"broad_syn\": [\n",
      "            \"Tissue image informatics\"\n",
      "        ]\n",
      "    },\n",
      "    \"Shape features extraction\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Shape_features\",\n",
      "        \"exact_syn\": [\n",
      "            \"Shape feature extraction\"\n",
      "        ],\n",
      "        \"related_syn\": [\n",
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      "        ]\n",
      "    },\n",
      "    \"Optimisation or refinement\": {\n",
      "        \"uri\": \"http://edamontology.org/operation___Optimisation_or_refinement\",\n",
      "        \"exact_syn\": [\n",
      "            \"Optimization or refinement\"\n",
      "        ]\n",
      "    },\n",
      "    \"Artificial neural network\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Artificial_neural_network\",\n",
      "        \"exact_syn\": [\n",
      "            \"ANN\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Dense neural network\"\n",
      "        ]\n",
      "    },\n",
      "    \"Cryo electron microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Cryo_electron_microscopy\"\n",
      "    },\n",
      "    \"In-vivo imaging\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__R8XUtD89JCyeUaaVebe9Mkw\"\n",
      "    },\n",
      "    \"Synthetic image generation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__R9FvNkpDIaqZQhLVlPsHisj\",\n",
      "        \"exact_syn\": [\n",
      "            \"Image simulation\"\n",
      "        ]\n",
      "    },\n",
      "    \"sm2\": {\n",
      "        \"uri\": \"http://edamontology.org/format_sm2\",\n",
      "        \"exact_syn\": [\n",
      "            \".sm2\"\n",
      "        ]\n",
      "    },\n",
      "    \"High-throughput screening\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______High_throughput_screening\",\n",
      "        \"exact_syn\": [\n",
      "            \"HTS\"\n",
      "        ]\n",
      "    },\n",
      "    \"Contrasting method\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Contrasting\"\n",
      "    },\n",
      "    \"Molecular imaging\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Molecular_Imaging\"\n",
      "    },\n",
      "    \"Chromatic aberration correction\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__RDr8xcZEa4L3mZsslmhhee8\",\n",
      "        \"related_syn\": [\n",
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      "    },\n",
      "    \"Re-scan confocal microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Re-scan_confocal_microscopy\",\n",
      "        \"exact_syn\": [\n",
      "            \"RCM\"\n",
      "        ],\n",
      "        \"related_syn\": [\n",
      "            \"Re-Scan\"\n",
      "        ]\n",
      "    },\n",
      "    \"Light microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_3385\",\n",
      "        \"exact_syn\": [\n",
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      "    },\n",
      "    \"Super-resolution microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_Super-resolution_microscopy\",\n",
      "        \"exact_syn\": [\n",
      "            \"SR microscopy\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"High resolution microscopy\"\n",
      "        ]\n",
      "    },\n",
      "    \"Object counting\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Cell_counting\"\n",
      "    },\n",
      "    \"Array-based detection microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RBsSZve5PnQFO3scMDWo9f0\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Area-capturing microscopy\"\n",
      "        ],\n",
      "        \"related_syn\": [\n",
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      "        ]\n",
      "    },\n",
      "    \"Data augmentation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation______Data_augmentation\"\n",
      "    },\n",
      "    \"Object trajectory\": {\n",
      "        \"uri\": \"http://edamontology.org/data_Trajectory\"\n",
      "    },\n",
      "    \"csv\": {\n",
      "        \"uri\": \"http://edamontology.org/format_csv\"\n",
      "    },\n",
      "    \"X-ray microtomography\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Computed_microtomography\",\n",
      "        \"exact_syn\": [\n",
      "            \"\\u00b5CT\"\n",
      "        ]\n",
      "    },\n",
      "    \"Phase-contrast microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RtBCcu7zJiS0phrbR2HzAI\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Phase imaging\"\n",
      "        ],\n",
      "        \"related_syn\": [\n",
      "            \"Quantitative phase-contrast imaging\"\n",
      "        ]\n",
      "    },\n",
      "    \"Density-based clustering\": {\n",
      "        \"uri\": \"http://edamontology.org/operation______Density-based_clustering\"\n",
      "    },\n",
      "    \"Active contours\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Active_contours\",\n",
      "        \"exact_syn\": [\n",
      "            \"Active contour model\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Snakes\"\n",
      "        ]\n",
      "    },\n",
      "    \"Object shape\": {\n",
      "        \"uri\": \"http://edamontology.org/data__RPhipiN98zgq3wqXj4ESkT\"\n",
      "    },\n",
      "    \"Annotation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_0226\"\n",
      "    },\n",
      "    \"Focused ion beam scanning electron microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__R9zg34pnGmTyzPidJj9vfJt\",\n",
      "        \"exact_syn\": [\n",
      "            \"FIBSEM\"\n",
      "        ]\n",
      "    },\n",
      "    \"Image validation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation___Image_validation\"\n",
      "    },\n",
      "    \"Object classification\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__RyCFuPLOeGxpcGjYbWcWWD\",\n",
      "        \"exact_syn\": [\n",
      "            \"Semantic object classification\"\n",
      "        ]\n",
      "    },\n",
      "    \"Cell tracking\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Cell_tracking\"\n",
      "    },\n",
      "    \"Ridge detection\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_____Ridge_detection\"\n",
      "    },\n",
      "    \"Validation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation___Validation\"\n",
      "    },\n",
      "    \"Semi-automatic segmentation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation______Semi-automatic_segmentation\"\n",
      "    },\n",
      "    \"Photomanipulation\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Photomanipulation\"\n",
      "    },\n",
      "    \"Reinforcement learning\": {\n",
      "        \"uri\": \"http://edamontology.org/topic___Reinforcement_learning\"\n",
      "    },\n",
      "    \"Image sensor characteristics\": {\n",
      "        \"uri\": \"http://edamontology.org/data____Image_sensor_characteristics\"\n",
      "    },\n",
      "    \"Dilation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Dilation\",\n",
      "        \"exact_syn\": [\n",
      "            \"Dilatation\"\n",
      "        ]\n",
      "    },\n",
      "    \"jpg\": {\n",
      "        \"uri\": \"http://edamontology.org/format_jpg\",\n",
      "        \"exact_syn\": [\n",
      "            \".jpg\"\n",
      "        ]\n",
      "    },\n",
      "    \"Object-based colocalisation analysis\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Image_colocalization\",\n",
      "        \"exact_syn\": [\n",
      "            \"Object-based colocalization analysis\"\n",
      "        ]\n",
      "    },\n",
      "    \"Image classification\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Image_classification\"\n",
      "    },\n",
      "    \"Detector gain correction\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__RCi5QWhY2hXnO46smg6bHRQ\"\n",
      "    },\n",
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      "    },\n",
      "    \"Time\": {\n",
      "        \"uri\": \"http://edamontology.org/data_Time\"\n",
      "    },\n",
      "    \"High-pressure freezing\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RkSYwMcVWG5FCi4BaWDMaJ\"\n",
      "    },\n",
      "    \"Image visualisation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Image_visualisation\",\n",
      "        \"exact_syn\": [\n",
      "            \"Rendering\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Lookup table\"\n",
      "        ]\n",
      "    },\n",
      "    \"Homogeneity extraction\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Homogeneity\"\n",
      "    },\n",
      "    \"Example\": {\n",
      "        \"uri\": \"http://edamontology.org/example\"\n",
      "    },\n",
      "    \"ims\": {\n",
      "        \"uri\": \"http://edamontology.org/format_ims\",\n",
      "        \"exact_syn\": [\n",
      "            \".ims\"\n",
      "        ]\n",
      "    },\n",
      "    \"Regression\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_2423\"\n",
      "    },\n",
      "    \"Isolated object tracking\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__RDsrmC9l0bZw9kGJzGMCyY8\"\n",
      "    },\n",
      "    \"Point spread function\": {\n",
      "        \"uri\": \"http://edamontology.org/data____Point_spread_function\",\n",
      "        \"exact_syn\": [\n",
      "            \"PSF\"\n",
      "        ]\n",
      "    },\n",
      "    \"Structured illumination microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RC91JqkkQnsmvg8zuG6Td7q\",\n",
      "        \"exact_syn\": [\n",
      "            \"SIM\"\n",
      "        ],\n",
      "        \"related_syn\": [\n",
      "            \"iSIM\"\n",
      "        ]\n",
      "    },\n",
      "    \"tif\": {\n",
      "        \"uri\": \"http://edamontology.org/format_tif\"\n",
      "    },\n",
      "    \"In-vitro imaging\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__R7WRbf9Y8ySw9QWPwAjzcUa\"\n",
      "    },\n",
      "    \"Near-field scanning optical microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_____Near-field_scanning_optical_microscopy\",\n",
      "        \"exact_syn\": [\n",
      "            \"NSOM\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Scattering-type scanning near-field optical microscopy\"\n",
      "        ]\n",
      "    },\n",
      "    \"Spot detection\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Spot_extraction\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Seed point detection\"\n",
      "        ]\n",
      "    },\n",
      "    \"Format\": {\n",
      "        \"uri\": \"http://edamontology.org/format_1915\",\n",
      "        \"narrow_syn\": [\n",
      "            \"File format\"\n",
      "        ],\n",
      "        \"broad_syn\": [\n",
      "            \"Data model\"\n",
      "        ]\n",
      "    },\n",
      "    \"has identifier\": {\n",
      "        \"uri\": \"http://edamontology.org/has_identifier\"\n",
      "    },\n",
      "    \"Machine learning-based data generation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation______Machine_learning-based_data_generation\"\n",
      "    },\n",
      "    \"Image scanning microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Image_Scanning_Microscopy\",\n",
      "        \"exact_syn\": [\n",
      "            \"ISM\"\n",
      "        ]\n",
      "    },\n",
      "    \"Region texture\": {\n",
      "        \"uri\": \"http://edamontology.org/data__RDz7WLs6GBWl7rPjqfjKBT0\"\n",
      "    },\n",
      "    \"Ablation\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Ablation\",\n",
      "        \"narrow_syn\": [\n",
      "            \"FIB\"\n",
      "        ]\n",
      "    },\n",
      "    \"Image radiometric noise characteristics\": {\n",
      "        \"uri\": \"http://edamontology.org/data__R7Vdp7H5PzNJiqA7JaEEPrJ\"\n",
      "    },\n",
      "    \"Sample immobilisation\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Sample_fixation\",\n",
      "        \"exact_syn\": [\n",
      "            \"Sample fixation\"\n",
      "        ]\n",
      "    },\n",
      "    \"Sample staining\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Staining\"\n",
      "    },\n",
      "    \"Skeletonisation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Skeletonization\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Medial axis transform\"\n",
      "        ]\n",
      "    },\n",
      "    \"Pattern recognition\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__RDetoixS3xEu0agR2CebaoB\"\n",
      "    },\n",
      "    \"Selective plane illumination microscopy reconstruction\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__RBPObKBKIMwjdLygBOlvojW\"\n",
      "    },\n",
      "    \"Image radiometric noise\": {\n",
      "        \"uri\": \"http://edamontology.org/data__RDr5D5pOVdnB8hASL1LG8HH\"\n",
      "    },\n",
      "    \"Image formation characteristics\": {\n",
      "        \"uri\": \"http://edamontology.org/data____Image_formation_characteristics\"\n",
      "    },\n",
      "    \"Fluctuation based microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic___Fluctuation_based_microscopy\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Super resolution radial fluctuations (SRRF)\"\n",
      "        ]\n",
      "    },\n",
      "    \"Obsolete since\": {\n",
      "        \"uri\": \"http://edamontology.org/obsolete_since\"\n",
      "    },\n",
      "    \"Scanning electron microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RBZsLMTdyuEDtVe2fge61l0\",\n",
      "        \"exact_syn\": [\n",
      "            \"SEM\"\n",
      "        ]\n",
      "    },\n",
      "    \"Image\": {\n",
      "        \"uri\": \"http://edamontology.org/data_Image\",\n",
      "        \"exact_syn\": [\n",
      "            \"Image data\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Voxel-based image\"\n",
      "        ]\n",
      "    },\n",
      "    \"Intensity\": {\n",
      "        \"uri\": \"http://edamontology.org/data_Intensity\"\n",
      "    },\n",
      "    \"Top-hat transform\": {\n",
      "        \"uri\": \"http://edamontology.org/operation____Top-hat_transform\",\n",
      "        \"exact_syn\": [\n",
      "            \"White top-hat transform\"\n",
      "        ],\n",
      "        \"broad_syn\": [\n",
      "            \"Hat transform\"\n",
      "        ],\n",
      "        \"related_syn\": [\n",
      "            \"Black top-hat transform\"\n",
      "        ]\n",
      "    },\n",
      "    \"Near-infrared branding\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_____Near-infrared_branding\"\n",
      "    },\n",
      "    \"Optical coherence tomography\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Optical_Coherence_Tomography\",\n",
      "        \"exact_syn\": [\n",
      "            \"OCT\"\n",
      "        ]\n",
      "    },\n",
      "    \"Image convolution\": {\n",
      "        \"uri\": \"http://edamontology.org/operation___Image_convolution\",\n",
      "        \"exact_syn\": [\n",
      "            \"Linear shift invariant image filtering\"\n",
      "        ]\n",
      "    },\n",
      "    \"Traction force microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_____Traction_force_microscopy\"\n",
      "    },\n",
      "    \"Rotation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Rotation\"\n",
      "    },\n",
      "    \"Parameter optimisation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation___Parameter_optimisation\",\n",
      "        \"exact_syn\": [\n",
      "            \"Parameter optimization\"\n",
      "        ]\n",
      "    },\n",
      "    \"Positron emission tomography\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RDos3h5yRfjhLUcOImDOFgB\",\n",
      "        \"narrow_syn\": [\n",
      "            \"PET\"\n",
      "        ]\n",
      "    },\n",
      "    \"Distance transform\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Distance_transform\"\n",
      "    },\n",
      "    \"Scanning transmission electron microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RXLeVr0cHSXzTSRyO5zwZD\",\n",
      "        \"exact_syn\": [\n",
      "            \"STEM\"\n",
      "        ]\n",
      "    },\n",
      "    \"Fluorescence microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_Fluorescent_microscopy\"\n",
      "    },\n",
      "    \"1D image\": {\n",
      "        \"uri\": \"http://edamontology.org/data_1D_dataset\"\n",
      "    },\n",
      "    \"Region growing\": {\n",
      "        \"uri\": \"http://edamontology.org/operation____Region_growing\",\n",
      "        \"broad_syn\": [\n",
      "            \"Region-based segmentation\"\n",
      "        ]\n",
      "    },\n",
      "    \"Image stitching\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Image_stitching\",\n",
      "        \"related_syn\": [\n",
      "            \"Mosaic\"\n",
      "        ]\n",
      "    },\n",
      "    \"Surface rendering\": {\n",
      "        \"uri\": \"http://edamontology.org/operation____Surface_rendering\"\n",
      "    },\n",
      "    \"Illumination correction\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Illumination_correction\",\n",
      "        \"exact_syn\": [\n",
      "            \"Flat field correction\"\n",
      "        ]\n",
      "    },\n",
      "    \"Fixed sample imaging\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__RBNoPZIOvBhdWGe8mFNpoWQ\"\n",
      "    },\n",
      "    \"Photonic force microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_____Photon_force_microscopy\",\n",
      "        \"exact_syn\": [\n",
      "            \"PFM\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Force sensing optical tweezers\"\n",
      "        ]\n",
      "    },\n",
      "    \"Colour\": {\n",
      "        \"uri\": \"http://edamontology.org/data_Colour\",\n",
      "        \"narrow_syn\": [\n",
      "            \"rgb\"\n",
      "        ]\n",
      "    },\n",
      "    \"Optical transfer function\": {\n",
      "        \"uri\": \"http://edamontology.org/data____Optical_transfer_function\",\n",
      "        \"exact_syn\": [\n",
      "            \"OTF\"\n",
      "        ]\n",
      "    },\n",
      "    \"Spatial properties\": {\n",
      "        \"uri\": \"http://edamontology.org/data__R7Xr4YLUfGpHoI3FnAzgMnA\"\n",
      "    },\n",
      "    \"Second-harmonic imaging microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_____Second-harmonic_imaging_microscopy\",\n",
      "        \"exact_syn\": [\n",
      "            \"SHIM\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Third harmonic generation (THG)\"\n",
      "        ]\n",
      "    },\n",
      "    \"Centroid-based clustering\": {\n",
      "        \"uri\": \"http://edamontology.org/operation______Centroid-based_clustering\"\n",
      "    },\n",
      "    \"Statistics\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_Statistics\"\n",
      "    },\n",
      "    \"Multimodal imaging\": {\n",
      "        \"uri\": \"http://edamontology.org/topic____Multimodal_imaging\",\n",
      "        \"exact_syn\": [\n",
      "            \"Multisensor imaging\"\n",
      "        ],\n",
      "        \"narrow_syn\": [\n",
      "            \"Correlative imaging\"\n",
      "        ]\n",
      "    },\n",
      "    \"hdr\": {\n",
      "        \"uri\": \"http://edamontology.org/format_hdr\",\n",
      "        \"exact_syn\": [\n",
      "            \".hdr\"\n",
      "        ]\n",
      "    },\n",
      "    \"Raman imaging\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_____Raman_imaging\",\n",
      "        \"related_syn\": [\n",
      "            \"Coherent anti-Stokes Raman scattering microscopy (CARS)\"\n",
      "        ]\n",
      "    },\n",
      "    \"Computer vision\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Computer_vision\"\n",
      "    },\n",
      "    \"Fluorescence\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Fluorescence\"\n",
      "    },\n",
      "    \"Spatial coordinates\": {\n",
      "        \"uri\": \"http://edamontology.org/data____Spatial_coordinates\"\n",
      "    },\n",
      "    \"Fluorescence correlation spectroscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic___Fluorescence_correlative_spectroscopy\",\n",
      "        \"exact_syn\": [\n",
      "            \"FCS\"\n",
      "        ],\n",
      "        \"related_syn\": [\n",
      "            \"Fluorescence cross-correlation spectroscopy (FCCS)\"\n",
      "        ]\n",
      "    },\n",
      "    \"Watershed segmentation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Watershed\",\n",
      "        \"exact_syn\": [\n",
      "            \"Watershed-based segmentation\"\n",
      "        ],\n",
      "        \"broad_syn\": [\n",
      "            \"Watershed transformation\"\n",
      "        ]\n",
      "    },\n",
      "    \"Chemical fixation\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Chemical_fixation\"\n",
      "    },\n",
      "    \"Closing\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Closing\"\n",
      "    },\n",
      "    \"Confocal microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic__R9Cmje2ZUXyDW6aQAvFhwSM\",\n",
      "        \"exact_syn\": [\n",
      "            \"Confocal laser scanning microscopy (CLSM)\"\n",
      "        ]\n",
      "    },\n",
      "    \"Image data\": {\n",
      "        \"uri\": \"http://edamontology.org/data__RCOwaNKaK3gFcUhkjBq7aor\",\n",
      "        \"exact_syn\": [\n",
      "            \"Image\"\n",
      "        ]\n",
      "    },\n",
      "    \"Spectral image resolution\": {\n",
      "        \"uri\": \"http://edamontology.org/data__RDLZjniM2p9bxNi1Md2Vqv3\"\n",
      "    },\n",
      "    \"Clustering\": {\n",
      "        \"uri\": \"http://edamontology.org/operation___Clustering\",\n",
      "        \"exact_syn\": [\n",
      "            \"Cluster analysis\"\n",
      "        ]\n",
      "    },\n",
      "    \"stk\": {\n",
      "        \"uri\": \"http://edamontology.org/format_stk\",\n",
      "        \"exact_syn\": [\n",
      "            \".stk\"\n",
      "        ]\n",
      "    },\n",
      "    \"Frequency-domain transformation\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_____Frequency_domain\",\n",
      "        \"exact_syn\": [\n",
      "            \"Transformation into frequency domain\"\n",
      "        ],\n",
      "        \"related_syn\": [\n",
      "            \"Fast Fourier transform\"\n",
      "        ]\n",
      "    },\n",
      "    \"Optical flow analysis\": {\n",
      "        \"uri\": \"http://edamontology.org/operation_Optical_flow_analysis\"\n",
      "    },\n",
      "    \"Force microscopy\": {\n",
      "        \"uri\": \"http://edamontology.org/topic_____Force_microscopy\"\n",
      "    },\n",
      "    \"Rigid registration\": {\n",
      "        \"uri\": \"http://edamontology.org/operation__R9Vc5BV3ZMcLHEL6WEceXbY\",\n",
      "        \"exact_syn\": [\n",
      "            \"Rigid image registration\"\n",
      "        ]\n",
      "    },\n",
      "    \"Object velocity\": {\n",
      "        \"uri\": \"http://edamontology.org/data__R9P4sScuriz9yN8l827hrLo\",\n",
      "        \"exact_syn\": [\n",
      "            \"Object speed\"\n",
      "        ]\n",
      "    },\n",
      "    \"Instrument response function\": {\n",
      "        \"uri\": \"http://edamontology.org/data____Instrument_response_function\",\n",
      "        \"exact_syn\": [\n",
      "            \"IRF\"\n",
      "        ]\n",
      "    },\n",
      "    \"Instrument maintenance\": {\n",
      "        \"uri\": \"http://edamontology.org/topic______Instrument_maintenance\",\n",
      "        \"narrow_syn\": [\n",
      "            \"Instrument calibration\"\n",
      "        ],\n",
      "        \"related_syn\": [\n",
      "            \"Instrument setup\"\n",
      "        ]\n",
      "    }\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "import pandas as pd\n",
    "\n",
    "synonyms_query = \"\"\"\n",
    "    SELECT ?edam_class ?label ?related_syn ?narrow_syn ?exact_syn ?broad_syn WHERE {\n",
    "        ?edam_class rdfs:label ?label .\n",
    "        OPTIONAL {?edam_class oboInOwl:hasRelatedSynonym ?related_syn .}\n",
    "        OPTIONAL {?edam_class oboInOwl:hasNarrowSynonym ?narrow_syn .}\n",
    "        OPTIONAL {?edam_class oboInOwl:hasExactSynonym ?exact_syn .}\n",
    "        OPTIONAL {?edam_class oboInOwl:hasBroadSynonym ?broad_syn .}\n",
    "    } \n",
    "\"\"\"\n",
    "\n",
    "labels_index = {}\n",
    "exact_syn_index = {}\n",
    "narrow_syn_index = {}\n",
    "broad_syn_index = {}\n",
    "related_syn_index = {}\n",
    "\n",
    "edam_syn_index = {}\n",
    "\n",
    "results = g.query(synonyms_query)\n",
    "\n",
    "for r in results :\n",
    "#    print(r)\n",
    "    if r['label']:\n",
    "        labels_index[str(r['label'])] = str(r['edam_class'])\n",
    "        edam_syn_index[str(r['label'])] = {'uri': str(r['edam_class'])}\n",
    "    \n",
    "    if r['exact_syn']:\n",
    "        exact_syn_index[str(r['exact_syn'])] = str(r['edam_class'])\n",
    "        \n",
    "        if 'exact_syn' not in edam_syn_index[str(r['label'])].keys():\n",
    "            edam_syn_index[str(r['label'])]['exact_syn'] = [str(r['exact_syn'])]\n",
    "        else:\n",
    "            edam_syn_index[str(r['label'])]['exact_syn'].append(str(r['exact_syn']))\n",
    "        \n",
    "    if r['narrow_syn']:\n",
    "        narrow_syn_index[str(r['narrow_syn'])] = str(r['edam_class'])\n",
    "        \n",
    "        if 'narrow_syn' not in edam_syn_index[str(r['label'])].keys():\n",
    "            edam_syn_index[str(r['label'])]['narrow_syn'] = [str(r['narrow_syn'])]\n",
    "        else:\n",
    "            edam_syn_index[str(r['label'])]['narrow_syn'].append(str(r['narrow_syn']))\n",
    "            \n",
    "    if r['broad_syn']:\n",
    "        broad_syn_index[str(r['broad_syn'])] = str(r['edam_class'])\n",
    "        \n",
    "        if 'broad_syn' not in edam_syn_index[str(r['label'])].keys():\n",
    "            edam_syn_index[str(r['label'])]['broad_syn'] = [str(r['broad_syn'])]\n",
    "        else:\n",
    "            edam_syn_index[str(r['label'])]['broad_syn'].append(str(r['broad_syn']))\n",
    "            \n",
    "    if r['related_syn']:\n",
    "        related_syn_index[str(r['related_syn'])] = str(r['edam_class'])\n",
    "        \n",
    "        if 'related_syn' not in edam_syn_index[str(r['label'])].keys():\n",
    "            edam_syn_index[str(r['label'])]['related_syn'] = [str(r['related_syn'])]\n",
    "        else:\n",
    "            edam_syn_index[str(r['label'])]['related_syn'].append(str(r['related_syn']))\n",
    "            \n",
    "print(json.dumps(edam_syn_index, indent=4))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 3. Compute syntactic distance between a set of tags and synonyms\n",
    "the distance is is a floating number between 0 and 1. The weighted distance, not very meaningfull, is a weighted mean between distance considering this order of priority : label >> exact synonym >> narrow synonym >> broad synonym >> related synonym. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 119,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "****** Fourier transformation ******\n",
      "top-5 closest concept (based on labels)\n",
      "\tFourier-transform infrared spectroscopy: http://edamontology.org/topic______Fourier-transform_infrared_spectroscopy (d=0.8491841491841492)\n",
      "\tLinear transformation: http://edamontology.org/operation_Linear_transformation (d=0.7991822991822991)\n",
      "\tAffine transformation: http://edamontology.org/operation__R8ANfLkuHu47r739AkhxrId (d=0.7823189882013412)\n",
      "\tFrequency-domain transformation: http://edamontology.org/operation_____Frequency_domain (d=0.7467322999581063)\n",
      "\tGeometrical transformation: http://edamontology.org/operation_Geometrical_transform (d=0.7244509876088824)\n",
      "\n",
      "top-5 closest concept (based on exact synonyms)\n",
      "\tImage processing: http://edamontology.org/operation_Image_processing (d=0.7799242424242424)\n",
      "\tAffine registration: http://edamontology.org/operation__RLtOI0poPsYRHzgXbAcr2E (d=0.6849242424242424)\n",
      "\tFrequency-domain transformation: http://edamontology.org/operation_____Frequency_domain (d=0.6567871699450647)\n",
      "\tFilament tracing: http://edamontology.org/operation__R9Qf06vxvFj2UbAk7pW3IMG (d=0.6502886002886002)\n",
      "\tTomographic reconstruction: http://edamontology.org/operation__R1NVO6hpWWcs99UiEFiOfK (d=0.6494949494949495)\n",
      "\n",
      "top-5 closest concept (based on narrow synonyms)\n",
      "\tSingle molecule localisation: http://edamontology.org/operation__R8EfungVXA0oQM2Ac7YY5eu (d=0.6862470862470863)\n",
      "\tInstrument maintenance: http://edamontology.org/topic______Instrument_maintenance (d=0.6723484848484849)\n",
      "\tUltrasonography: http://edamontology.org/topic__RBHw300pzIYcttGsAmIZvk5 (d=0.6684796684796686)\n",
      "\tFluctuation based microscopy: http://edamontology.org/topic___Fluctuation_based_microscopy (d=0.6632357850228107)\n",
      "\tImage correction: http://edamontology.org/operation__R7MFwdgojfmkZ07yWbdcda0 (d=0.6612340510366826)\n",
      "\n",
      "top-5 closest concept (based on broad synonyms)\n",
      "\tNeuron image analysis: http://edamontology.org/topic_Neuron_image_analysis (d=0.6897653000594177)\n",
      "\tWatershed segmentation: http://edamontology.org/operation_Watershed (d=0.6897653000594177)\n",
      "\tIn-silico reconstruction: http://edamontology.org/topic__R96toeNl9iMp8oqv9augU84 (d=0.6313588372411901)\n",
      "\tPlant image analysis: http://edamontology.org/topic_____Plant_image_analysis (d=0.6224418093983312)\n",
      "\tRegion growing: http://edamontology.org/operation____Region_growing (d=0.613073593073593)\n",
      "\n",
      "top-5 closest concept (based on related synonyms)\n",
      "\tFrequency-domain transformation: http://edamontology.org/operation_____Frequency_domain (d=0.7760765550239235)\n",
      "\tChromatic aberration correction: http://edamontology.org/operation__RDr8xcZEa4L3mZsslmhhee8 (d=0.6578282828282828)\n",
      "\tFrequency-domain analysis: http://edamontology.org/operation__RBYLqCqN4rP7Jy5m5mxpTeM (d=0.6569998628822158)\n",
      "\tLocalisation markers: http://edamontology.org/topic_____Fiducial_markers (d=0.6456228956228957)\n",
      "\tComputed tomography: http://edamontology.org/topic__RxfmHE99gOkUOOML5krfsJ (d=0.6454124579124579)\n",
      "\n",
      "top-5 closest concept (based on weighted synonyms)\n",
      "\tFilament tracing: http://edamontology.org/operation__R9Qf06vxvFj2UbAk7pW3IMG (d=0.5886006388299703)\n",
      "\tTomographic reconstruction: http://edamontology.org/operation__R1NVO6hpWWcs99UiEFiOfK (d=0.5652234596679041)\n",
      "\tSingle molecule localisation: http://edamontology.org/operation__R8EfungVXA0oQM2Ac7YY5eu (d=0.5271950271950272)\n",
      "\tScientific visualisation: http://edamontology.org/topic______Scientific_visualisation (d=0.5197367789960383)\n",
      "\tMultimodal imaging: http://edamontology.org/topic____Multimodal_imaging (d=0.5167927336543321)\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "import jellyfish\n",
    "\n",
    "\n",
    "#tags = ['Filament track']\n",
    "tags = ['Fourier transformation']\n",
    "\n",
    "#iterate over tags\n",
    "for t in tags:\n",
    "    distances = [] \n",
    "    \n",
    "    #iterate over edam concepts and their synonyms\n",
    "    for k,v in edam_syn_index.items():\n",
    "        dist_es = []\n",
    "        dist_rs = []\n",
    "        dist_ns = []\n",
    "        dist_bs = []\n",
    "        #print(v)\n",
    "        #print(v.keys())\n",
    "        #print(f\"computing distance between <{t}> and <{k}>\")\n",
    "        #print(jellyfish.jaro_winkler(t,k))\n",
    "        \n",
    "        # distance with the concept label\n",
    "        d_label = jellyfish.jaro_winkler(t,k)\n",
    "        \n",
    "        # distance with all of the concept exact synonyms\n",
    "        if 'exact_syn' in v.keys():\n",
    "            for exact in v['exact_syn']:\n",
    "                dist_es.append(jellyfish.jaro_winkler(t,exact))\n",
    "                \n",
    "        # distance with all of the concept narrow synonyms\n",
    "        if 'narrow_syn' in v.keys():\n",
    "            for narrow in v['narrow_syn']:\n",
    "                dist_ns.append(jellyfish.jaro_winkler(t,narrow))\n",
    "                \n",
    "        # distance with all of the concept broad synonyms\n",
    "        if 'broad_syn' in v.keys():\n",
    "            for broad in v['broad_syn']:\n",
    "                dist_bs.append(jellyfish.jaro_winkler(t,broad))\n",
    "                \n",
    "        # distance with all of the concept related synonyms\n",
    "        if 'related_syn' in v.keys():\n",
    "            for related in v['related_syn']:\n",
    "                #print(f\"distance betwen {t} and {exact}\")\n",
    "                dist_rs.append(jellyfish.jaro_winkler(t,related))\n",
    "        \n",
    "        d_es, d_ns, d_bs, d_rs = [0,0,0,0]\n",
    "        \n",
    "        # for each kind of synonym we peak only the closest one\n",
    "        if len(dist_es) > 0:\n",
    "            d_es = sorted(dist_es, reverse=True)[0]\n",
    "        if len(dist_ns) > 0:\n",
    "            d_ns = sorted(dist_ns, reverse=True)[0]\n",
    "        if len(dist_bs) > 0:\n",
    "            d_bs = sorted(dist_bs, reverse=True)[0]\n",
    "        if len(dist_rs) > 0:\n",
    "            d_rs = sorted(dist_rs, reverse=True)[0]\n",
    "        \n",
    "        # we compute a weighted distance to consider all kinds of synonyms\n",
    "        weighted_d = ((10 * d_label) + (8 * d_es) + (5 * d_ns) + (3 * d_bs) + (1 * d_rs)) / (10 + 8 + 5 + 3 + 1)\n",
    "        #print(f\"weighted dist({t},{k}) = {weighted_d}\")\n",
    "        #print(f\"exact dist({t},{k}) = {d_es}\")\n",
    "        #print(f\"narrow dist({t},{k}) = {d_ns}\")\n",
    "        #print(f\"broad dist({t},{k}) = {d_bs}\")\n",
    "        #print(f\"related dist({t},{k}) = {d_rs}\")\n",
    "        distances.append({'tag': t, 'edam_concept': k, 'edam_concept_uri': v['uri'], \n",
    "                         'weighted_distance': weighted_d, \n",
    "                          'label_distance': d_label,\n",
    "                         'exact_distance': d_es,\n",
    "                         'narrow_distance': d_ns, \n",
    "                         'broad_distance': d_bs, \n",
    "                         'related_distance': d_rs})\n",
    "    \n",
    "    # after having screened all EDAM concepts, we print the top-5 suggestions. \n",
    "    print(f'****** {t} ******')\n",
    "              \n",
    "    print(\"top-5 closest concept (based on labels)\")\n",
    "    for c in sorted(distances, key = lambda x : (x['label_distance']), reverse=True)[0:5]:\n",
    "        print(f\"\\t{c['edam_concept']}: {c['edam_concept_uri']} (d={c['label_distance']})\")\n",
    "    print()\n",
    "              \n",
    "    print(\"top-5 closest concept (based on exact synonyms)\")\n",
    "    for c in sorted(distances, key = lambda x : (x['exact_distance']), reverse=True)[0:5]:\n",
    "        print(f\"\\t{c['edam_concept']}: {c['edam_concept_uri']} (d={c['exact_distance']})\")\n",
    "    print()\n",
    "              \n",
    "    print(\"top-5 closest concept (based on narrow synonyms)\")\n",
    "    for c in sorted(distances, key = lambda x : (x['narrow_distance']), reverse=True)[0:5]:\n",
    "        print(f\"\\t{c['edam_concept']}: {c['edam_concept_uri']} (d={c['narrow_distance']})\")\n",
    "    print()\n",
    "              \n",
    "    print(\"top-5 closest concept (based on broad synonyms)\")\n",
    "    for c in sorted(distances, key = lambda x : (x['broad_distance']), reverse=True)[0:5]:\n",
    "        print(f\"\\t{c['edam_concept']}: {c['edam_concept_uri']} (d={c['broad_distance']})\")\n",
    "    print()\n",
    "              \n",
    "    print(\"top-5 closest concept (based on related synonyms)\")\n",
    "    for c in sorted(distances, key = lambda x : (x['related_distance']), reverse=True)[0:5]:\n",
    "        print(f\"\\t{c['edam_concept']}: {c['edam_concept_uri']} (d={c['related_distance']})\")\n",
    "    print()\n",
    "              \n",
    "    print(\"top-5 closest concept (based on weighted synonyms)\")\n",
    "    for c in sorted(distances, key = lambda x : (x['weighted_distance']), reverse=True)[0:5]:\n",
    "        print(f\"\\t{c['edam_concept']}: {c['edam_concept_uri']} (d={c['weighted_distance']})\")\n",
    "    print()\n",
    "    print()"
   ]
  },
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   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
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  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
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