connect_gene_using_spoke_api.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "b0d0ebdc",
   "metadata": {},
   "source": [
    "## @author: Karthik Soman"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fcf5fa1e",
   "metadata": {},
   "source": [
    "## Click the badge below to run it in binder"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "aec1e1c3",
   "metadata": {},
   "source": [
    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/BaranziniLab/spoke_api_demo/main?labpath=connect_gene_using_spoke_api.ipynb)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "c46d8e7b",
   "metadata": {},
   "outputs": [],
   "source": [
    "import requests\n",
    "import pandas as pd\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e23ac061",
   "metadata": {},
   "source": [
    "## Custom functions for API call"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "1caa09b4",
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_api_resp(END_POINT, params=None):\n",
    "    URI = BASE_URI + END_POINT\n",
    "    if params:\n",
    "        return requests.get(URI, params=params)\n",
    "    else:\n",
    "        return requests.get(URI)\n",
    "    \n",
    "    \n",
    "\n",
    "def get_phenotype_nbrs(gene_name, params=None):\n",
    "    END_POINT = '{}/{}/{}/{}'.format(NBR_END_POINT, NODE_TYPE, ATTRIBUTE, gene_name)\n",
    "    result = get_api_resp(END_POINT, params=params)\n",
    "    neighbors = result.json()\n",
    "    disease_nbr_names = list(filter(None, list(map(lambda x:x['data']['properties']['name'] if x['data']['neo4j_type'] == 'Disease' else None, neighbors))))\n",
    "    symptom_nbr_names = list(filter(None, list(map(lambda x:x['data']['properties']['name'] if x['data']['neo4j_type'] == 'Symptom' else None, neighbors))))\n",
    "    phenotype_names = disease_nbr_names +  symptom_nbr_names\n",
    "\n",
    "    disease_nbr_ids = list(filter(None, list(map(lambda x:x['data']['id'] if x['data']['neo4j_type'] == 'Disease' else None, neighbors))))\n",
    "    symptom_nbr_ids = list(filter(None, list(map(lambda x:x['data']['id'] if x['data']['neo4j_type'] == 'Symptom' else None, neighbors))))\n",
    "    phenotype_ids = disease_nbr_ids + symptom_nbr_ids\n",
    "\n",
    "    phenotype_df = pd.DataFrame(zip(phenotype_ids, phenotype_names), columns=['phenotype_id', 'phenotype_name'])\n",
    "\n",
    "    nbr_edge_list = []\n",
    "    for item in neighbors:\n",
    "        try:\n",
    "            if (item['data']['source'] in phenotype_ids): \n",
    "                nbr_edge_list.append((item['data']['source'], item['data']['properties']))\n",
    "            elif (item['data']['target'] in phenotype_ids):\n",
    "                nbr_edge_list.append((item['data']['target'], item['data']['properties']))\n",
    "        except:\n",
    "            continue\n",
    "\n",
    "    nbr_edge_df = pd.DataFrame(nbr_edge_list, columns=['phenotype_id', 'properties'])\n",
    "    phenotype_nbr_df = pd.merge(phenotype_df, nbr_edge_df, on='phenotype_id').drop('phenotype_id', axis=1)\n",
    "    return list(phenotype_nbr_df.to_records(index=False))\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a5d3229c",
   "metadata": {},
   "source": [
    "## API parameters"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "d4bba595",
   "metadata": {},
   "outputs": [],
   "source": [
    "BASE_URI = 'https://spoke.rbvi.ucsf.edu'\n",
    "NBR_END_POINT = '/api/v1/neighborhood/'\n",
    "\n",
    "\n",
    "API_PARAMS = {\n",
    "    'cutoff_DaG_diseases_sources': ['knowledge', 'experiments', 'textmining'],\n",
    "    'cutoff_DaG_textmining': 3,\n",
    "}\n",
    "\n",
    "NODE_TYPE = 'Gene'\n",
    "ATTRIBUTE = 'name'\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0421f96a",
   "metadata": {},
   "source": [
    "## Input Gene name to get the corresponding associated phenotype\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "98e29798",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 37.6 ms, sys: 4.9 ms, total: 42.5 ms\n",
      "Wall time: 348 ms\n"
     ]
    }
   ],
   "source": [
    "%%time\n",
    "\n",
    "gene_name = 'BRCA2'\n",
    "\n",
    "phenotype_nbrs = get_phenotype_nbrs(gene_name, params=API_PARAMS)\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "548ce4e4",
   "metadata": {},
   "source": [
    "## Printing the extracted neighbors as Markdown"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "3cb8e4b1",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/markdown": [
       "### Phenotypes associated with the gene BRCA2 in SPOKE:\n",
       "\n",
       "1. **nephroblastoma**\n",
       "   - Sources: OMIM\n",
       "   - O_inheritance: AD,SOMATIC\n",
       "   - O_modifiers: \n",
       "\n",
       "2. **intestinal cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:10155\n",
       "   - Diseases_scores: 6.049\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.024\n",
       "\n",
       "3. **large intestine cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:5672\n",
       "   - Diseases_scores: 6.035\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.018\n",
       "\n",
       "4. **attention deficit hyperactivity disorder**\n",
       "   - Source: HPO\n",
       "\n",
       "5. **embryonal tumor with multilayered rosettes, C19MC-altered**\n",
       "   - Source: HPO\n",
       "\n",
       "6. **melancholic depression**\n",
       "   - Source: HPO\n",
       "\n",
       "7. **cerebral primitive neuroectodermal tumor**\n",
       "   - Source: HPO\n",
       "\n",
       "8. **uterine cancer**\n",
       "   - Source: HPO\n",
       "\n",
       "9. **dysgraphia**\n",
       "   - Source: HPO\n",
       "\n",
       "10. **thyroid cancer**\n",
       "   - Source: HPO\n",
       "\n",
       "11. **rectal benign neoplasm**\n",
       "   - Source: HPO\n",
       "\n",
       "12. **thyroid gland disease**\n",
       "   - Source: HPO\n",
       "\n",
       "13. **pituitary cancer**\n",
       "   - Source: HPO\n",
       "\n",
       "14. **skin cancer**\n",
       "   - Source: HPO\n",
       "\n",
       "15. **neurotic disorder**\n",
       "   - Source: HPO\n",
       "\n",
       "16. **pituitary carcinoma**\n",
       "   - Source: HPO\n",
       "\n",
       "17. **Ewing sarcoma**\n",
       "   - Source: HPO\n",
       "\n",
       "18. **neuroblastoma**\n",
       "   - Source: HPO\n",
       "\n",
       "19. **skin benign neoplasm**\n",
       "   - Source: HPO\n",
       "\n",
       "20. **intracranial hypertension**\n",
       "   - Source: HPO\n",
       "\n",
       "21. **medulloepithelioma**\n",
       "   - Source: HPO\n",
       "\n",
       "22. **thyroid gland carcinoma**\n",
       "   - Source: HPO\n",
       "\n",
       "23. **agnosia**\n",
       "   - Source: HPO\n",
       "\n",
       "24. **pituitary adenoma**\n",
       "   - Source: HPO\n",
       "\n",
       "25. **agraphia**\n",
       "   - Source: HPO\n",
       "\n",
       "26. **rectum cancer**\n",
       "   - Source: HPO\n",
       "\n",
       "27. **lingual-facial-buccal dyskinesia**\n",
       "   - Source: HPO\n",
       "\n",
       "28. **visual epilepsy**\n",
       "   - Source: HPO\n",
       "\n",
       "29. **speech disorder**\n",
       "   - Source: HPO\n",
       "\n",
       "30. **hepatocellular carcinoma**\n",
       "   - Source: HPO\n",
       "\n",
       "31. **stomach cancer**\n",
       "   - Source: HPO\n",
       "\n",
       "32. **thyroid adenoma**\n",
       "   - Source: HPO\n",
       "\n",
       "33. **melancholia**\n",
       "   - Source: HPO\n",
       "\n",
       "34. **epilepsy**\n",
       "   - Source: HPO\n",
       "\n",
       "35. **migraine**\n",
       "   - Source: HPO\n",
       "\n",
       "36. **lung squamous cell carcinoma**\n",
       "   - Sources: GWAS\n",
       "   - Gwas_pvalue: 1e-15\n",
       "\n",
       "37. **estrogen-receptor negative breast cancer**\n",
       "   - Sources: GWAS\n",
       "   - Gwas_pvalue: 2e-13\n",
       "\n",
       "38. **lung carcinoma**\n",
       "   - Sources: GWAS\n",
       "   - Gwas_pvalue: 2e-19\n",
       "\n",
       "39. **squamous cell carcinoma**\n",
       "   - Sources: GWAS\n",
       "   - Gwas_pvalue: 5e-20\n",
       "\n",
       "40. **organ system cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:0050686, MedlinePlus, MedlinePlus, MedlinePlus, MedlinePlus\n",
       "   - Diseases_scores: 7.809, CURATED, CURATED, CURATED, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge, knowledge, knowledge, knowledge\n",
       "   - Diseases_confidences: 3.905, 5.0, 5.0, 5.0, 5.0\n",
       "\n",
       "41. **hepatobiliary system cancer**\n",
       "   - Diseases_identifiers: MedlinePlus\n",
       "   - Diseases_scores: CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: knowledge\n",
       "   - Diseases_confidences: 5.0\n",
       "\n",
       "42. **breast disease**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:3463, MedlinePlus\n",
       "   - Diseases_scores: 7.913, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge\n",
       "   - Diseases_confidences: 3.956, 5.0\n",
       "\n",
       "43. **malignant ovarian surface epithelial-stromal neoplasm**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:2151\n",
       "   - Diseases_scores: 6.195\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.098\n",
       "\n",
       "44. **carcinoma**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:305, MedlinePlus\n",
       "   - Diseases_scores: 6.797, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge\n",
       "   - Diseases_confidences: 3.398, 5.0\n",
       "\n",
       "45. **gastrointestinal system cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:3119, MedlinePlus\n",
       "   - Diseases_scores: 6.204, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge\n",
       "   - Diseases_confidences: 3.102, 5.0\n",
       "\n",
       "46. **cholangiocarcinoma**\n",
       "   - Diseases_identifiers: MedlinePlus\n",
       "   - Diseases_scores: CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: knowledge\n",
       "   - Diseases_confidences: 5.0\n",
       "\n",
       "47. **ovarian carcinoma**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:4001\n",
       "   - Diseases_scores: 6.182\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.091\n",
       "\n",
       "48. **ovary epithelial cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:2152\n",
       "   - Diseases_scores: 6.559\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.279\n",
       "\n",
       "49. **male reproductive organ cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:3856, MedlinePlus\n",
       "   - Diseases_scores: 6.528, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge\n",
       "   - Diseases_confidences: 3.264, 5.0\n",
       "\n",
       "50. **syndrome**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:225\n",
       "   - Diseases_scores: 6.794\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.397\n",
       "\n",
       "51. **physical disorder**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:0080015, MedlinePlus, UniProtKB-KW\n",
       "   - Diseases_scores: 6.239, CURATED, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge, knowledge\n",
       "   - Diseases_confidences: 3.12, 5.0, 4.0\n",
       "\n",
       "52. **congenital hypoplastic anemia**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:1342, MedlinePlus, UniProtKB-KW\n",
       "   - Diseases_scores: 7.057, CURATED, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge, knowledge\n",
       "   - Diseases_confidences: 3.528, 5.0, 4.0\n",
       "\n",
       "53. **bile duct disease**\n",
       "   - Diseases_identifiers: MedlinePlus\n",
       "   - Diseases_scores: CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: knowledge\n",
       "   - Diseases_confidences: 5.0\n",
       "\n",
       "54. **prostate disease**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:47, MedlinePlus\n",
       "   - Diseases_scores: 6.513, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge\n",
       "   - Diseases_confidences: 3.257, 5.0\n",
       "\n",
       "55. **cell type cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:0050687, MedlinePlus\n",
       "   - Diseases_scores: 6.881, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge\n",
       "   - Diseases_confidences: 3.44, 5.0\n",
       "\n",
       "56. **reproductive system disease**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:15, MedlinePlus, MedlinePlus\n",
       "   - Diseases_scores: 7.654, CURATED, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge, knowledge\n",
       "   - Diseases_confidences: 3.827, 5.0, 5.0\n",
       "\n",
       "57. **pancreas disease**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:26\n",
       "   - Diseases_scores: 6.296\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.148\n",
       "\n",
       "58. **disease of anatomical entity**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:7, MedlinePlus, MedlinePlus, MedlinePlus, MedlinePlus, MedlinePlus, UniProtKB-KW\n",
       "   - Diseases_scores: 7.512, CURATED, CURATED, CURATED, CURATED, CURATED, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge, knowledge, knowledge, knowledge, knowledge, knowledge\n",
       "   - Diseases_confidences: 3.756, 5.0, 5.0, 5.0, 5.0, 5.0, 4.0\n",
       "\n",
       "59. **reproductive organ cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:193, MedlinePlus, MedlinePlus\n",
       "   - Diseases_scores: 7.721, CURATED, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge, knowledge\n",
       "   - Diseases_confidences: 3.86, 5.0, 5.0\n",
       "\n",
       "60. **sporadic breast cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:8029\n",
       "   - Diseases_scores: 6.763\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.381\n",
       "\n",
       "61. **Fanconi anemia**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:13636, MedlinePlus, UniProtKB-KW\n",
       "   - Diseases_scores: 7.109, CURATED, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge, knowledge\n",
       "   - Diseases_confidences: 3.555, 5.0, 4.0\n",
       "\n",
       "62. **Lynch syndrome**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:3883\n",
       "   - Diseases_scores: 6.732\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.366\n",
       "\n",
       "63. **adenocarcinoma**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:299, MedlinePlus\n",
       "   - Diseases_scores: 6.125, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge\n",
       "   - Diseases_confidences: 3.063, 5.0\n",
       "\n",
       "64. **bile duct adenocarcinoma**\n",
       "   - Diseases_identifiers: MedlinePlus\n",
       "   - Diseases_scores: CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: knowledge\n",
       "   - Diseases_confidences: 5.0\n",
       "\n",
       "65. **autosomal dominant disease**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:0050736\n",
       "   - Diseases_scores: 6.694\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.347\n",
       "\n",
       "66. **male reproductive system disease**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:48, MedlinePlus\n",
       "   - Diseases_scores: 6.516, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge\n",
       "   - Diseases_confidences: 3.258, 5.0\n",
       "\n",
       "67. **female breast cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:0050671\n",
       "   - Diseases_scores: 6.103\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.051\n",
       "\n",
       "68. **bilateral breast cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:6741\n",
       "   - Diseases_scores: 6.590\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.295\n",
       "\n",
       "69. **bile duct carcinoma**\n",
       "   - Diseases_identifiers: MedlinePlus\n",
       "   - Diseases_scores: CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: knowledge\n",
       "   - Diseases_confidences: 5.0\n",
       "\n",
       "70. **cystadenocarcinoma**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:3111\n",
       "   - Diseases_scores: 6.111\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.056\n",
       "\n",
       "71. **thoracic cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:5093, MedlinePlus\n",
       "   - Diseases_scores: 7.916, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge\n",
       "   - Diseases_confidences: 3.958, 5.0\n",
       "\n",
       "72. **female reproductive organ cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:120, MedlinePlus\n",
       "   - Diseases_scores: 7.745, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge\n",
       "   - Diseases_confidences: 3.873, 5.0\n",
       "\n",
       "73. **thoracic disease**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:0060118, MedlinePlus\n",
       "   - Diseases_scores: 7.912, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge\n",
       "   - Diseases_confidences: 3.956, 5.0\n",
       "\n",
       "74. **malignant adenoma**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:0080364\n",
       "   - Diseases_scores: 6.104\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.052\n",
       "\n",
       "75. **serous cystadenocarcinoma**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:3114\n",
       "   - Diseases_scores: 6.124\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.062\n",
       "\n",
       "76. **genetic disease**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:630\n",
       "   - Diseases_scores: 6.433\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.217\n",
       "\n",
       "77. **autosomal genetic disease**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:0050739\n",
       "   - Diseases_scores: 6.724\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.362\n",
       "\n",
       "78. **Li-Fraumeni syndrome**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:3012\n",
       "   - Diseases_scores: 6.134\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.067\n",
       "\n",
       "79. **disease**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:4, MedlinePlus, MedlinePlus, MedlinePlus, MedlinePlus, MedlinePlus, UniProtKB-KW\n",
       "   - Diseases_scores: 7.501, CURATED, CURATED, CURATED, CURATED, CURATED, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge, knowledge, knowledge, knowledge, knowledge, knowledge\n",
       "   - Diseases_confidences: 3.751, 5.0, 5.0, 5.0, 5.0, 5.0, 4.0\n",
       "\n",
       "80. **male breast cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:1614\n",
       "   - Diseases_scores: 7.010\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.505\n",
       "\n",
       "81. **aplastic anemia**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:12449, MedlinePlus, UniProtKB-KW\n",
       "   - Diseases_scores: 6.906, CURATED, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge, knowledge\n",
       "   - Diseases_confidences: 3.453, 5.0, 4.0\n",
       "\n",
       "82. **monogenic disease**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:0050177\n",
       "   - Diseases_scores: 6.672\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.336\n",
       "\n",
       "83. **disease of cellular proliferation**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:14566, MedlinePlus, MedlinePlus, MedlinePlus, MedlinePlus, UniProtKB-KW\n",
       "   - Diseases_scores: 7.798, CURATED, CURATED, CURATED, CURATED, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge, knowledge, knowledge, knowledge, knowledge\n",
       "   - Diseases_confidences: 3.899, 5.0, 5.0, 5.0, 5.0, 4.0\n",
       "\n",
       "84. **bile duct cancer**\n",
       "   - Diseases_identifiers: MedlinePlus\n",
       "   - Diseases_scores: CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: knowledge\n",
       "   - Diseases_confidences: 5.0\n",
       "\n",
       "85. **malignant cystadenoma**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:60004\n",
       "   - Diseases_scores: 6.111\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.056\n",
       "\n",
       "86. **gonadal disease**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:2277, MedlinePlus\n",
       "   - Diseases_scores: 7.773, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge\n",
       "   - Diseases_confidences: 3.887, 5.0\n",
       "\n",
       "87. **hereditary breast ovarian cancer syndrome**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:5683\n",
       "   - Diseases_scores: 7.843\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.921\n",
       "\n",
       "88. **female reproductive system disease**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:229, MedlinePlus\n",
       "   - Diseases_scores: 7.673, CURATED\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining, knowledge\n",
       "   - Diseases_confidences: 3.837, 5.0\n",
       "\n",
       "89. **endocrine gland cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:170\n",
       "   - Diseases_scores: 6.286\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_sources: textmining\n",
       "   - Diseases_confidences: 3.143\n",
       "\n",
       "90. **germ cell cancer**\n",
       "   - Source: HPO\n",
       "\n",
       "91. **gemistocytic astrocytoma**\n",
       "   - Source: HPO\n",
       "\n",
       "92. **hypertrophic cardiomyopathy**\n",
       "   - Source: HPO\n",
       "\n",
       "93. **astroblastoma**\n",
       "   - Source: HPO\n",
       "\n",
       "94. **astigmatism**\n",
       "   - Source: HPO\n",
       "\n",
       "95. **kidney disease**\n",
       "   - Source: HPO\n",
       "\n",
       "96. **microphthalmia**\n",
       "   - Source: HPO\n",
       "\n",
       "97. **gastrointestinal system disease**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:77, MedlinePlus\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_confidences: 3.09, 5.0\n",
       "   - Diseases_scores: 6.180, CURATED\n",
       "   - Source: HPO\n",
       "   - Diseases_sources: textmining, knowledge\n",
       "\n",
       "98. **hypertropia**\n",
       "   - Source: HPO\n",
       "\n",
       "99. **liver disease**\n",
       "   - Source: HPO\n",
       "\n",
       "100. **pathologic nystagmus**\n",
       "   - Source: HPO\n",
       "\n",
       "101. **leukopenia**\n",
       "   - Source: HPO\n",
       "\n",
       "102. **hypertension**\n",
       "   - Source: HPO\n",
       "\n",
       "103. **liver cancer**\n",
       "   - Source: HPO\n",
       "\n",
       "104. **arthropathy**\n",
       "   - Source: HPO\n",
       "\n",
       "105. **nervous system cancer**\n",
       "   - Source: HPO\n",
       "\n",
       "106. **kidney failure**\n",
       "   - Source: HPO\n",
       "\n",
       "107. **atrial heart septal defect**\n",
       "   - Source: HPO\n",
       "\n",
       "108. **aniridia**\n",
       "   - Source: HPO\n",
       "\n",
       "109. **visual impairment and progressive phthisis bulbi**\n",
       "   - Source: HPO\n",
       "\n",
       "110. **diabetes mellitus**\n",
       "   - Source: HPO\n",
       "\n",
       "111. **eye disease**\n",
       "   - Source: HPO\n",
       "\n",
       "112. **hematologic cancer**\n",
       "   - Source: HPO\n",
       "\n",
       "113. **paralytic ileus**\n",
       "   - Source: HPO\n",
       "\n",
       "114. **spontaneous ocular nystagmus**\n",
       "   - Source: HPO\n",
       "\n",
       "115. **Glanzmann's thrombasthenia**\n",
       "   - Source: HPO\n",
       "\n",
       "116. **ovarian cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:2394, MedlinePlus\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_confidences: 3.928, 5.0\n",
       "   - Diseases_scores: 7.857, CURATED\n",
       "   - Source: HPO\n",
       "   - Diseases_sources: textmining, knowledge\n",
       "\n",
       "117. **acute myeloid leukemia without maturation**\n",
       "   - Source: HPO\n",
       "\n",
       "118. **hypogonadism**\n",
       "   - Source: HPO\n",
       "\n",
       "119. **patent ductus arteriosus**\n",
       "   - Source: HPO\n",
       "\n",
       "120. **endocrine system disease**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:28, MedlinePlus\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_confidences: 3.789, 5.0\n",
       "   - Diseases_scores: 7.578, CURATED\n",
       "   - Source: HPO\n",
       "   - Diseases_sources: textmining, knowledge\n",
       "\n",
       "121. **bone marrow disease**\n",
       "   - Source: HPO\n",
       "\n",
       "122. **melanoma**\n",
       "   - Source: HPO\n",
       "\n",
       "123. **pilocytic astrocytoma**\n",
       "   - Source: HPO\n",
       "\n",
       "124. **hepatobiliary disease**\n",
       "   - Diseases_identifiers: MedlinePlus\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_confidences: 5.0\n",
       "   - Diseases_scores: CURATED\n",
       "   - Source: HPO\n",
       "   - Diseases_sources: knowledge\n",
       "\n",
       "125. **intestinal disease**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:5295\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_confidences: 3.027\n",
       "   - Diseases_scores: 6.053\n",
       "   - Source: HPO\n",
       "   - Diseases_sources: textmining\n",
       "\n",
       "126. **hematopoietic system disease**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:74, MedlinePlus, UniProtKB-KW\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_confidences: 3.12, 5.0, 4.0\n",
       "   - Diseases_scores: 6.241, CURATED, CURATED\n",
       "   - Source: HPO\n",
       "   - Diseases_sources: textmining, knowledge, knowledge\n",
       "\n",
       "127. **cleft palate**\n",
       "   - Source: HPO\n",
       "\n",
       "128. **spinal cord disease**\n",
       "   - Source: HPO\n",
       "\n",
       "129. **colon adenocarcinoma**\n",
       "   - Source: HPO\n",
       "\n",
       "130. **choanal atresia**\n",
       "   - Source: HPO\n",
       "\n",
       "131. **anemia**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:2355, MedlinePlus, UniProtKB-KW\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_confidences: 3.18, 5.0, 4.0\n",
       "   - Diseases_scores: 6.360, CURATED, CURATED\n",
       "   - Source: HPO\n",
       "   - Diseases_sources: textmining, knowledge, knowledge\n",
       "\n",
       "132. **congenital heart disease**\n",
       "   - Source: HPO\n",
       "\n",
       "133. **juvenile pilocytic astrocytoma**\n",
       "   - Source: HPO\n",
       "\n",
       "134. **azoospermia**\n",
       "   - Source: HPO\n",
       "\n",
       "135. **central nervous system cancer**\n",
       "   - Source: HPO\n",
       "\n",
       "136. **subependymal giant cell astrocytoma**\n",
       "   - Source: HPO\n",
       "\n",
       "137. **acute myeloid leukemia**\n",
       "   - Source: HPO\n",
       "\n",
       "138. **heart valve disease**\n",
       "   - Source: HPO\n",
       "\n",
       "139. **colon cancer**\n",
       "   - Source: HPO\n",
       "\n",
       "140. **Meckel's diverticulum**\n",
       "   - Source: HPO\n",
       "\n",
       "141. **heart septal defect**\n",
       "   - Source: HPO\n",
       "\n",
       "142. **lung disease**\n",
       "   - Source: HPO\n",
       "\n",
       "143. **exocrine pancreatic insufficiency**\n",
       "   - Source: HPO\n",
       "\n",
       "144. **cryptorchidism**\n",
       "   - Source: HPO\n",
       "\n",
       "145. **colorectal cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:9256\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_confidences: 3.015\n",
       "   - Diseases_scores: 6.030\n",
       "   - Source: HPO\n",
       "   - Diseases_sources: textmining\n",
       "\n",
       "146. **lymphatic system disease**\n",
       "   - Source: HPO\n",
       "\n",
       "147. **neuroectodermal tumor**\n",
       "   - Source: HPO\n",
       "\n",
       "148. **enterocele**\n",
       "   - Source: HPO\n",
       "\n",
       "149. **childhood cerebral astrocytoma**\n",
       "   - Source: HPO\n",
       "\n",
       "150. **cranial nerve palsy**\n",
       "   - Source: HPO\n",
       "\n",
       "151. **central nervous system disease**\n",
       "   - Source: HPO\n",
       "\n",
       "152. **colonic benign neoplasm**\n",
       "   - Source: HPO\n",
       "\n",
       "153. **protoplasmic astrocytoma**\n",
       "   - Source: HPO\n",
       "\n",
       "154. **anaplastic astrocytoma**\n",
       "   - Source: HPO\n",
       "\n",
       "155. **congenital vertical talus**\n",
       "   - Source: HPO\n",
       "\n",
       "156. **glioblastoma**\n",
       "   - Source: HPO\n",
       "\n",
       "157. **lung benign neoplasm**\n",
       "   - Source: HPO\n",
       "\n",
       "158. **biliary tract disease**\n",
       "   - Diseases_identifiers: MedlinePlus\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_confidences: 5.0\n",
       "   - Diseases_scores: CURATED\n",
       "   - Source: HPO\n",
       "   - Diseases_sources: knowledge\n",
       "\n",
       "159. **tetralogy of Fallot**\n",
       "   - Source: HPO\n",
       "\n",
       "160. **high grade glioma**\n",
       "   - Source: HPO\n",
       "\n",
       "161. **cardiomyopathy**\n",
       "   - Source: HPO\n",
       "\n",
       "162. **acute myeloid leukemia with maturation**\n",
       "   - Source: HPO\n",
       "\n",
       "163. **sideroblastic anemia**\n",
       "   - Source: HPO\n",
       "\n",
       "164. **leukemia**\n",
       "   - Source: HPO\n",
       "\n",
       "165. **mechanical strabismus**\n",
       "   - Source: HPO\n",
       "\n",
       "166. **childhood medulloblastoma**\n",
       "   - Source: HPO\n",
       "\n",
       "167. **cholestasis**\n",
       "   - Source: HPO\n",
       "\n",
       "168. **mixed glioma**\n",
       "   - Source: HPO\n",
       "\n",
       "169. **melanotic medulloblastoma**\n",
       "   - Source: HPO\n",
       "\n",
       "170. **dissociated nystagmus**\n",
       "   - Source: HPO\n",
       "\n",
       "171. **colorectal carcinoma**\n",
       "   - Source: HPO\n",
       "\n",
       "172. **urinary system benign neoplasm**\n",
       "   - Source: HPO\n",
       "\n",
       "173. **hydrocephalus**\n",
       "   - Source: HPO\n",
       "\n",
       "174. **adult medulloblastoma**\n",
       "   - Source: HPO\n",
       "\n",
       "175. **syndactyly**\n",
       "   - Source: HPO\n",
       "\n",
       "176. **malignant astrocytoma**\n",
       "   - Source: HPO\n",
       "\n",
       "177. **myelodysplastic syndrome**\n",
       "   - Source: HPO\n",
       "\n",
       "178. **obstructive hydrocephalus**\n",
       "   - Source: HPO\n",
       "\n",
       "179. **megacolon**\n",
       "   - Source: HPO\n",
       "\n",
       "180. **imperforate anus**\n",
       "   - Source: HPO\n",
       "\n",
       "181. **biliary tract cancer**\n",
       "   - Diseases_identifiers: MedlinePlus\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_confidences: 5.0\n",
       "   - Diseases_scores: CURATED\n",
       "   - Source: HPO\n",
       "   - Diseases_sources: knowledge\n",
       "\n",
       "182. **intestinal pseudo-obstruction**\n",
       "   - Source: HPO\n",
       "\n",
       "183. **ptosis**\n",
       "   - Source: HPO\n",
       "\n",
       "184. **Hirschsprung's disease**\n",
       "   - Source: HPO\n",
       "\n",
       "185. **oligohydramnios**\n",
       "   - Source: HPO\n",
       "\n",
       "186. **lens disease**\n",
       "   - Source: HPO\n",
       "\n",
       "187. **movement disease**\n",
       "   - Source: HPO\n",
       "\n",
       "188. **spina bifida**\n",
       "   - Source: HPO\n",
       "\n",
       "189. **clubfoot**\n",
       "   - Source: HPO\n",
       "\n",
       "190. **medullomyoblastoma**\n",
       "   - Source: HPO\n",
       "\n",
       "191. **duodenal atresia**\n",
       "   - Source: HPO\n",
       "\n",
       "192. **ovarian disease**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:1100, MedlinePlus\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_confidences: 3.905, 5.0\n",
       "   - Diseases_scores: 7.810, CURATED\n",
       "   - Source: HPO\n",
       "   - Diseases_sources: textmining, knowledge\n",
       "\n",
       "193. **fibrillary astrocytoma**\n",
       "   - Source: HPO\n",
       "\n",
       "194. **embryonal cancer**\n",
       "   - Source: HPO\n",
       "\n",
       "195. **communicating hydrocephalus**\n",
       "   - Source: HPO\n",
       "\n",
       "196. **germ cell and embryonal cancer**\n",
       "   - Source: HPO\n",
       "\n",
       "197. **cardiovascular system disease**\n",
       "   - Source: HPO\n",
       "\n",
       "198. **gliomatosis cerebri**\n",
       "   - Source: HPO\n",
       "\n",
       "199. **extrahepatic cholestasis**\n",
       "   - Source: HPO\n",
       "\n",
       "200. **kidney cancer**\n",
       "   - Source: HPO\n",
       "\n",
       "201. **tracheal disease**\n",
       "   - Source: HPO\n",
       "\n",
       "202. **thrombocytopenia**\n",
       "   - Source: HPO\n",
       "\n",
       "203. **giant cell glioblastoma**\n",
       "   - Source: HPO\n",
       "\n",
       "204. **cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:162, MedlinePlus, MedlinePlus, MedlinePlus, MedlinePlus, UniProtKB-KW\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_confidences: 3.903, 5.0, 5.0, 5.0, 5.0, 4.0\n",
       "   - Diseases_scores: 7.805, CURATED, CURATED, CURATED, CURATED, CURATED\n",
       "   - Source: HPO\n",
       "   - Diseases_sources: textmining, knowledge, knowledge, knowledge, knowledge, knowledge\n",
       "\n",
       "205. **pancreatic cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:1793\n",
       "   - Sources: DISEASES\n",
       "   - Diseases_confidences: 3.2\n",
       "   - Diseases_scores: 6.400\n",
       "   - Source: HPO\n",
       "   - Diseases_sources: textmining\n",
       "\n",
       "206. **cranial nerve disease**\n",
       "   - Source: HPO\n",
       "\n",
       "207. **breast carcinoma**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:3459\n",
       "   - Sources: DISEASES, GWAS\n",
       "   - Diseases_confidences: 3.32\n",
       "   - Gwas_pvalue: 3e-15\n",
       "   - Diseases_scores: 6.640\n",
       "   - Diseases_sources: textmining\n",
       "\n",
       "208. **breast cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:1612, MedlinePlus\n",
       "   - Sources: OMIM, DISEASES\n",
       "   - Diseases_confidences: 3.959, 5.0\n",
       "   - O_inheritance: AD,SOMATIC\n",
       "   - O_modifiers: SUSCEPTIBILITY\n",
       "   - Diseases_scores: 7.917, CURATED\n",
       "   - Diseases_sources: textmining, knowledge\n",
       "\n",
       "209. **medulloblastoma**\n",
       "   - Sources: OMIM\n",
       "   - O_inheritance: AD,AR,SOMATIC\n",
       "   - O_modifiers: \n",
       "\n",
       "210. **Fanconi anemia complementation group D1**\n",
       "   - Sources: OMIM\n",
       "   - O_inheritance: AR\n",
       "   - O_modifiers: \n",
       "\n",
       "211. **prostate cancer**\n",
       "   - Diseases_identifiers: https://diseases.jensenlab.org/Entity?documents=10&type1=9606&id1=ENSP00000369497&type2=-26&id2=DOID:10283, MedlinePlus\n",
       "   - Sources: OMIM, DISEASES\n",
       "   - Diseases_confidences: 3.259, 5.0\n",
       "   - O_inheritance: AD,XL,SOMATIC\n",
       "   - O_modifiers: \n",
       "   - Diseases_scores: 6.517, CURATED\n",
       "   - Diseases_sources: textmining, knowledge\n",
       "\n",
       "212. **Abnormality of the skin**\n",
       "   - Source: HPO\n",
       "\n",
       "213. **Muscle Hypotonia**\n",
       "   - Source: HPO\n",
       "\n",
       "214. **Headache**\n",
       "   - Source: HPO\n",
       "\n",
       "215. **Hyperkinesis**\n",
       "   - Source: HPO\n",
       "\n",
       "216. **Cognitive impairment**\n",
       "   - Source: HPO\n",
       "\n",
       "217. **Flexion contracture**\n",
       "   - Source: HPO\n",
       "\n",
       "218. **Hallucinations**\n",
       "   - Source: HPO\n",
       "\n",
       "219. **Basal cell carcinoma**\n",
       "   - Source: HPO\n",
       "\n",
       "220. **Memory Disorders**\n",
       "   - Source: HPO\n",
       "\n",
       "221. **Amaurosis Fugax**\n",
       "   - Source: HPO\n",
       "\n",
       "222. **Constipation**\n",
       "   - Source: HPO\n",
       "\n",
       "223. **Dysarthria**\n",
       "   - Source: HPO\n",
       "\n",
       "224. **Muscle Hypertonia**\n",
       "   - Source: HPO\n",
       "\n",
       "225. **Paresthesia**\n",
       "   - Source: HPO\n",
       "\n",
       "226. **Abnormality of the anterior pituitary**\n",
       "   - Source: HPO\n",
       "\n",
       "227. **Anorectal anomaly**\n",
       "   - Source: HPO\n",
       "\n",
       "228. **Hypesthesia**\n",
       "   - Source: HPO\n",
       "\n",
       "229. **Gastrointestinal hemorrhage**\n",
       "   - Source: HPO\n",
       "\n",
       "230. **Anxiety**\n",
       "   - Source: HPO\n",
       "\n",
       "231. **Behavioral abnormality**\n",
       "   - Source: HPO\n",
       "\n",
       "232. **Behavioral abnormality**\n",
       "   - Source: HPO\n",
       "\n",
       "233. **Abnormality of the nervous system**\n",
       "   - Source: HPO\n",
       "\n",
       "234. **Abnormal foot morphology**\n",
       "   - Source: HPO\n",
       "\n",
       "235. **Abdominal Pain**\n",
       "   - Source: HPO\n",
       "\n",
       "236. **Intrauterine growth retardation**\n",
       "   - Source: HPO\n",
       "\n",
       "237. **Scoliosis**\n",
       "   - Source: HPO\n",
       "\n",
       "238. **Aplasia/Hypoplasia of the mandible**\n",
       "   - Source: HPO\n",
       "\n",
       "239. **Deafness**\n",
       "   - Source: HPO\n",
       "\n",
       "240. **Hypoplasia of the ulna**\n",
       "   - Source: HPO\n",
       "\n",
       "241. **Micrognathia**\n",
       "   - Source: HPO\n",
       "\n",
       "242. **T-cell acute lymphoblastic leukemias**\n",
       "   - Source: HPO\n",
       "\n",
       "243. **Anorexia**\n",
       "   - Source: HPO\n",
       "\n",
       "244. **Abnormality of the cardiovascular system**\n",
       "   - Source: HPO\n",
       "\n",
       "245. **Splenomegaly**\n",
       "   - Source: HPO\n",
       "\n",
       "246. **Vision Disorders**\n",
       "   - Source: HPO\n",
       "\n",
       "247. **Neoplasm of the nervous system**\n",
       "   - Source: HPO\n",
       "\n",
       "248. **Lymphadenopathy**\n",
       "   - Source: HPO\n",
       "\n",
       "249. **Proptosis**\n",
       "   - Source: HPO\n",
       "\n",
       "250. **Neoplasm of the respiratory system**\n",
       "   - Source: HPO\n",
       "\n",
       "251. **Abnormal heart valve morphology**\n",
       "   - Source: HPO\n",
       "\n",
       "252. **Neoplasm of the genitourinary tract**\n",
       "   - Source: HPO\n",
       "\n",
       "253. **Intellectual Disability**\n",
       "   - Source: HPO\n",
       "\n",
       "254. **Abnormality of the eye**\n",
       "   - Source: HPO\n",
       "\n",
       "255. **Hypertelorism**\n",
       "   - Source: HPO\n",
       "\n",
       "256. **Weight Loss**\n",
       "   - Source: HPO\n",
       "\n",
       "257. **Fatigue**\n",
       "   - Source: HPO\n",
       "\n",
       "258. **Reflex, Abnormal**\n",
       "   - Source: HPO\n",
       "\n",
       "259. **Abnormality of the skin**\n",
       "   - Source: HPO\n",
       "\n",
       "260. **Diarrhea**\n",
       "   - Source: HPO\n",
       "\n",
       "261. **Back Pain**\n",
       "   - Source: HPO\n",
       "\n",
       "262. **Arteriovenous malformation**\n",
       "   - Source: HPO\n",
       "\n",
       "263. **Abnormality of the hand**\n",
       "   - Source: HPO\n",
       "\n",
       "264. **Abnormality of the pancreas**\n",
       "   - Source: HPO\n",
       "\n",
       "265. **Hypopigmentation of the skin**\n",
       "   - Source: HPO\n",
       "\n",
       "266. **Body Temperature Changes**\n",
       "   - Source: HPO\n",
       "\n",
       "267. **Neural tube defect**\n",
       "   - Source: HPO\n",
       "\n",
       "268. **Multiple cafe-au-lait spots**\n",
       "   - Source: HPO\n",
       "\n",
       "269. **Intrauterine growth retardation**\n",
       "   - Source: HPO\n",
       "\n",
       "270. **Abnormal thumb morphology**\n",
       "   - Source: HPO\n",
       "\n",
       "271. **Abnormality of chromosome stability**\n",
       "   - Source: HPO\n",
       "\n",
       "272. **Tracheoesophageal fistula**\n",
       "   - Source: HPO\n",
       "\n",
       "273. **Hip dislocation**\n",
       "   - Source: HPO\n",
       "\n",
       "274. **Cafe-au-Lait Spots**\n",
       "   - Source: HPO\n",
       "\n",
       "275. **Abnormality of the uterus**\n",
       "   - Source: HPO\n",
       "\n",
       "276. **Triphalangeal thumb**\n",
       "   - Source: HPO\n",
       "\n",
       "277. **Thinness**\n",
       "   - Source: HPO\n",
       "\n",
       "278. **Pain**\n",
       "   - Source: HPO\n",
       "\n",
       "279. **Hearing Loss**\n",
       "   - Source: HPO\n",
       "\n",
       "280. **Cataract**\n",
       "   - Source: HPO\n",
       "\n",
       "281. **Abnormality of the mouth**\n",
       "   - Source: HPO\n",
       "\n",
       "282. **Vision, Low**\n",
       "   - Source: HPO\n",
       "\n",
       "283. **Abnormality of the genitourinary system**\n",
       "   - Source: HPO\n",
       "\n",
       "284. **Hyperpigmentation of the skin**\n",
       "   - Source: HPO\n",
       "\n",
       "285. **Jaundice**\n",
       "   - Source: HPO\n",
       "\n",
       "286. **Hepatomegaly**\n",
       "   - Source: HPO\n",
       "\n",
       "287. **Fever**\n",
       "   - Source: HPO\n",
       "\n",
       "288. **Hematuria**\n",
       "   - Source: HPO\n",
       "\n",
       "289. **Pruritus**\n",
       "   - Source: HPO\n",
       "\n",
       "290. **Facial asymmetry**\n",
       "   - Source: HPO\n",
       "\n",
       "291. **Abnormality of the gastrointestinal tract**\n",
       "   - Source: HPO\n",
       "\n",
       "292. **Joint dislocation**\n",
       "   - Source: HPO\n",
       "\n"
      ],
      "text/plain": [
       "<IPython.core.display.Markdown object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "if len(phenotype_nbrs) > 0:\n",
    "    markdown_output = \"### Phenotypes associated with the gene {} in SPOKE:\\n\\n\".format(gene_name)\n",
    "    for idx, (phenotype, data) in enumerate(phenotype_nbrs, start=1):\n",
    "        markdown_output += f\"{idx}. **{phenotype}**\\n\"\n",
    "        for key, value in data.items():\n",
    "            if isinstance(value, list):\n",
    "                value = ', '.join(map(str, value))\n",
    "                markdown_output += f\"   - {key.capitalize()}: {value}\\n\"\n",
    "            else:\n",
    "                markdown_output += f\"   - {key.capitalize()}: {value}\\n\"\n",
    "        markdown_output += \"\\n\"\n",
    "else:\n",
    "    markdown_output = \"### Selected Gene name not found in SPOKE graph!\\n\"\n",
    "    markdown_output += \"### Either there will be a typo in the given Gene name or the Gene has a different name in SPOKE\"\n",
    "\n",
    "from IPython.display import Markdown\n",
    "display(Markdown(markdown_output))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "1263fb24",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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