DFGFO-OLS.ipynb

{
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  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Jupyter Notebooks Prototypes on how to use Ontology Look-up Service API to navidate the [DFG-Fachsystematik-Ontology](https://github.com/tibonto/DFG-Fachsystematik-Ontology)\n",
    "\n",
    "## Links\n",
    "* **DFGFO at TIB Terminology Service (OLS) frontend** https://service.tib.eu/ts4tib/ontologies/dfgfo\n",
    "* **DFGFO at TIB Terminology Service (OLS) API** https://service.tib.eu/ts4tib/api/ontologies/dfgfo\n",
    "* **DFGFO root terms at TIB Terminology Service (OLS) API** https://service.tib.eu/ts4tib/api/ontologies/dfgfo/terms/roots\n",
    "\n",
    "## Notebooks\n",
    "* extract the DFGFO relations tree - so it can be used in drop-down menus to select an appropriate subject\n",
    "* extract the DFGFO relations tree from a *non root term*: of the sub-disciplines of Chemistry ([https://github.com/tibonto/dfgfo/31](https://service.tib.eu/ts4tib/ontologies/dfgfo/terms?iri=https%3A%2F%2Fgithub.com%2Ftibonto%2Fdfgfo%2F31&viewMode=All&siblings=true))\n",
    "* given any DFGFO subject extract all its ancestors\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "import requests\n",
    "from urllib.parse import quote_plus\n",
    "from pprint import pprint\n",
    "\n",
    "####################################\n",
    "# imports - global vars - utility functions\n",
    "####################################\n",
    "\n",
    "tib_ols_api = 'https://service.tib.eu/ts4tib/api/'\n",
    "ontology_rootterms = tib_ols_api + 'ontologies/dfgfo/terms/roots'\n",
    "\n",
    "\n",
    "def url_double_quote(url):\n",
    "    # NOTE: OLS API IRIs have to be double quoted see https://www.ebi.ac.uk/ols/docs/api\n",
    "    quoted_url = quote_plus(quote_plus(url)) \n",
    "    return quoted_url\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "* Life Sciences - id: 2\n",
      "  * Biology - id: 21\n",
      "    * Plant Sciences - id: 202\n",
      "      * Plant Cell and Developmental Biology - id: 202-06\n",
      "      * Plant Genetics - id: 202-07\n",
      "      * Plant Physiology - id: 202-04\n",
      "      * Plant Biochemistry and Biophysics - id: 202-05\n",
      "      * Ecology and Biodiversity of Plants and Ecosystems - id: 202-02\n",
      "      * Organismic Interactions, Chemical Ecology and Microbiomes of Plant Systems - id: 202-03\n",
      "      * Evolution and Systematics of Plants and Fungi - id: 202-01\n",
      "    * Basic Research in Biology and Medicine - id: 201\n",
      "      * Bioinformatics and Theoretical Biology - id: 201-07\n",
      "      * General Genetics and Functional Genome Biology - id: 201-05\n",
      "      * Developmental Biology - id: 201-06\n",
      "      * Cell Biology - id: 201-03\n",
      "      * Structural Biology - id: 201-04\n",
      "      * Biochemistry - id: 201-01\n",
      "      * Biophysics - id: 201-02\n",
      "    * Zoology - id: 203\n",
      "      * Evolutionary Cell and Developmental Biology (Zoology) - id: 203-06\n",
      "      * Animal Physiology and Biochemistry - id: 203-05\n",
      "      * Evolution, Anthropology - id: 203-02\n",
      "      * Systematics and Morphology (Zoology) - id: 203-01\n",
      "      * Sensory and Behavioural Biology - id: 203-04\n",
      "      * Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions - id: 203-03\n",
      "  * Medicine - id: 22\n",
      "    * Microbiology, Virology and Immunology - id: 204\n",
      "      * Parasitology and Biology of Tropical Infectious Disease Pathogens - id: 204-06\n",
      "      * Medical Microbiology and Mycology, Hygiene, Molecular Infection Biology - id: 204-03\n",
      "      * Microbial Ecology and Applied Microbiology - id: 204-02\n",
      "      * Immunology - id: 204-05\n",
      "      * Virology - id: 204-04\n",
      "      * Metabolism, Biochemistry and Genetics of Microorganisms - id: 204-01\n",
      "    * Neurosciences - id: 206\n",
      "      * Human Cognitive and Systems Neuroscience - id: 206-08\n",
      "      * Biological Psychiatry - id: 206-09\n",
      "      * Cognitive, Systems and Behavioural Neurobiology - id: 206-04\n",
      "      * Experimental Models for the Understanding of Nervous System Diseases - id: 206-05\n",
      "      * Molecular and Cellular Neurology and Neuropathology - id: 206-06\n",
      "      * Clinical Neurosciences; Neurosurgery and Neuroradiology - id: 206-07\n",
      "      * Developmental Neurobiology - id: 206-01\n",
      "      * Molecular Biology and Physiology of Neurons and Glial Cells - id: 206-02\n",
      "      * Experimental and Theoretical Network Neuroscience - id: 206-03\n",
      "      * Clinical Psychiatry, Psychotherapy, Child and Adolescent Psychiatry - id: 206-10\n",
      "      * Ophthalmology - id: 206-11\n",
      "    * Medicine - id: 205\n",
      "      * Radiology, Nuclear Medicine, Radiotherapy, Radiobiology - id: 205-30\n",
      "      * Clinical Infectiology and Tropical Medicine - id: 205-31\n",
      "      * Medical Physics, Biomedical Technology - id: 205-32\n",
      "      * Anatomy - id: 205-33\n",
      "      * Otolaryngology - id: 205-29\n",
      "      * Pediatric and Adolescent Medicine - id: 205-20\n",
      "      * General and Visceral Surgery - id: 205-25\n",
      "      * Cardiac and Vascular Sugery - id: 205-26\n",
      "      * Orthopaedics, Traumatology, Reconstructive Surgery - id: 205-27\n",
      "      * Dentistry, Oral Surgery - id: 205-28\n",
      "      * Gynaecology and Obstetrics - id: 205-21\n",
      "      * Clinical Immunology and Allergology - id: 205-22\n",
      "      * Reproductive Medicine, Urology - id: 205-23\n",
      "      * Biogerontology and Geriatric Medicine - id: 205-24\n",
      "      * Rheumatology - id: 205-18\n",
      "      * Dermatology - id: 205-19\n",
      "      * Hematology, Oncology - id: 205-14\n",
      "      * Gastroenterology - id: 205-15\n",
      "      * Nephrology - id: 205-16\n",
      "      * Endocrinology, Diabetology, Metabolism - id: 205-17\n",
      "  * Agriculture, Forestry and Veterinary Medicine - id: 23\n",
      "    * Agriculture, Forestry and Veterinary Medicine - id: 207\n",
      "      * Ecology of Land Use - id: 207-04\n",
      "      * Plant Cultivation, Plant Nutrition, Agricultural Technology - id: 207-03\n",
      "      * Plant Breeding and Plant Pathology - id: 207-02\n",
      "      * Soil Sciences - id: 207-01\n",
      "      * Veterinary Medical Science - id: 207-08\n",
      "      * Animal Breeding, Animal Nutrition, Animal Husbandry - id: 207-07\n",
      "      * Forestry - id: 207-06\n",
      "      * Agricultural Economics, Agricultural Policy, Agricultural Sociology - id: 207-05\n",
      "* Humanities and Social Sciences - id: 1\n",
      "  * Humanities - id: 11\n",
      "    * History - id: 102\n",
      "      * Medieval History - id: 102-01\n",
      "      * Early Modern History - id: 102-02\n",
      "      * Modern and Current History - id: 102-03\n",
      "      * History of Science - id: 102-04\n",
      "      * Musicology - id: 103-02\n",
      "      * Theatre and Media Studies - id: 103-03\n",
      "      * Art History - id: 103-01\n",
      "    * Literary Studies - id: 105\n",
      "      * Medieval German Literature - id: 105-01\n",
      "      * European and American Literature - id: 105-03\n",
      "      * Modern German Literature - id: 105-02\n",
      "      * General and Comparative Literature and Cultural Studies - id: 105-04\n",
      "    * Linguistics - id: 104\n",
      "      * Individual Linguistics - id: 104-02\n",
      "      * General and Comparative Linguistics, Typology, Non-European Languages - id: 104-01\n",
      "      * Applied Linguistics, Experimental Linguistics, Computational Linguistics - id: 104-04\n",
      "      * Historical Linguistics - id: 104-03\n",
      "    * Theology - id: 107\n",
      "      * Protestant Theology - id: 107-01\n",
      "      * Roman Catholic Theology - id: 107-02\n",
      "    * Social and Cultural Anthropology, Non-European Cultures, Jewish Studies and Religious Studies - id: 106\n",
      "      * Asian Studies - id: 106-02\n",
      "      * Social and Cultural Anthropology and Ethnology - id: 106-01\n",
      "      * Islamic Studies, Arabian Studies, Semitic Studies - id: 106-04\n",
      "      * African, American and Oceania Studies - id: 106-03\n",
      "      * Religious Studies and Jewish Studies - id: 106-05\n",
      "    * Philosophy - id: 108\n",
      "      * History of Philosophy - id: 108-01\n",
      "      * Theoretical Philosophy - id: 108-02\n",
      "      * Practical Philosophy - id: 108-03\n",
      "    * Ancient Cultures - id: 101\n",
      "      * Prehistory and World Archaeology - id: 101-01\n",
      "      * Egyptology and Ancient Near Eastern Studies - id: 101-05\n",
      "      * Classical Archaeology - id: 101-04\n",
      "      * Ancient History - id: 101-03\n",
      "      * Classical Philology - id: 101-02\n",
      "  * Social and Behavioural Sciences - id: 12\n",
      "    * Jurisprudence - id: 113\n",
      "      * Public Law - id: 113-03\n",
      "      * Criminal Law - id: 113-04\n",
      "      * Criminology - id: 113-05\n",
      "      * Principles of Law and Jurisprudence - id: 113-01\n",
      "      * Private Law - id: 113-02\n",
      "    * Psychology - id: 110\n",
      "      * Differential, Clinical and Medical Psychology, Methodology - id: 110-05\n",
      "      * Social Psychology, Industrial and Organisational Psychology - id: 110-04\n",
      "      * General, Cognitive and Mathematical Psychology - id: 110-01\n",
      "      * Developmental and Educational Psychology - id: 110-03\n",
      "      * Biological Psychology and Cognitive Neuroscience - id: 110-02\n",
      "    * Economics - id: 112\n",
      "      * Economic Policy, Applied Economics - id: 112-02\n",
      "      * Business Administration - id: 112-03\n",
      "      * Statistics and Econometrics - id: 112-04\n",
      "      * Economic and Social History - id: 112-05\n",
      "      * Economic Theory - id: 112-01\n",
      "    * Social Sciences - id: 111\n",
      "      * Empirical Social Research - id: 111-02\n",
      "      * Sociological Theory - id: 111-01\n",
      "      * Political Science - id: 111-04\n",
      "      * Communication Sciences - id: 111-03\n",
      "    * Educational Research - id: 109\n",
      "      * General Education and History of Education - id: 109-01\n",
      "      * Educational Research on Socialisation, Welfare and Professionalism Research - id: 109-04\n",
      "      * Education Systems and Educational Institutions - id: 109-03\n",
      "      * General and Domain-Specific Teaching and Learning - id: 109-02\n",
      "* Engineering Sciences - id: 4\n",
      "  * Mechanical and Industrial Engineering - id: 41\n",
      "    * Mechanics and Constructive Mechanical Engineering - id: 402\n",
      "      * Mechanics - id: 402-02\n",
      "      * Lightweight Construction, Textile Technology - id: 402-03\n",
      "      * Acoustics - id: 402-04\n",
      "      * Engineering Design, Machine Elements, Product Development - id: 402-01\n",
      "    * Production Technology - id: 401\n",
      "      * Metal-Cutting and Abrasive Manufacturing Engineering - id: 401-01\n",
      "      * Primary Shaping and Reshaping Technology, Additive Manufacturing - id: 401-02\n",
      "      * Joining and Separation Technology - id: 401-03\n",
      "      * Plastics Engineering - id: 401-04\n",
      "      * Production Systems, Operations Management, Quality Management and Factory Planning - id: 401-05\n",
      "      * Production Automation - id: 401-06\n",
      "  * Thermal Engineering/ Process Engineering - id: 42\n",
      "    * Fluid Mechanics, Technical Thermodynamics and Thermal Energy Engineering - id: 404\n",
      "      * Fluid Mechanics - id: 404-03\n",
      "      * Technical Thermodynamics - id: 404-02\n",
      "      * Energy Process Engineering - id: 404-01\n",
      "      * Hydraulic and Turbo Engines and Piston Engines - id: 404-04\n",
      "    * Process Engineering, Technical Chemistry - id: 403\n",
      "      * Technical Chemistry - id: 403-02\n",
      "      * Chemical and Thermal Process Engineering - id: 403-01\n",
      "      * Biological Process Engineering - id: 403-04\n",
      "      * Mechanical Process Engineering - id: 403-03\n",
      "  * Materials Science and Engineering - id: 43\n",
      "    * Materials Science - id: 406\n",
      "      * Computer-Aided Design of Materials and Simulation of Materials Behaviour from Atomic to Microscopic Scale - id: 406-04\n",
      "      * Biomaterials - id: 406-02\n",
      "      * Thermodynamics and Kinetics as well as Properties of Phases and Microstructure of Materials - id: 406-03\n",
      "      * Synthesis and Properties of Functional Materials - id: 406-01\n",
      "    * Materials Engineering - id: 405\n",
      "      * Coating and Surface Technology - id: 405-03\n",
      "      * Mechanical Properties of Metallic Materials and their Microstructural Origins - id: 405-04\n",
      "      * Metallurgical, Thermal and Thermomechanical Treatment of Materials - id: 405-01\n",
      "      * Materials in Sintering Processes and Generative Manufacturing Processes - id: 405-02\n",
      "      * Glass, Ceramics and Derived Composites - id: 405-05\n",
      "      * Polymeric and Biogenic Materials and Derived Composites - id: 405-06\n",
      "  * Computer Science, Systems and  Electrical Engineering - id: 44\n",
      "    * Electrical Engineering and Information Technology - id: 408\n",
      "      * Electronic Semiconductors, Components, Circuits, Systems - id: 408-01\n",
      "      * Electrical Energy Generation, Distribution, Application - id: 408-03\n",
      "      * Communications, High-Frequency and Network Technology, Theoretical Electrical Engineering - id: 408-02\n",
      "    * Systems Engineering - id: 407\n",
      "      * Human Factors, Ergonomics, Human-Machine Systems - id: 407-05\n",
      "      * Biomedical Systems Technology - id: 407-06\n",
      "      * Microsystems - id: 407-03\n",
      "      * Traffic and Transport Systems, Logistics, Intelligent and Automated Traffic - id: 407-04\n",
      "      * Automation, Control Systems, Robotics, Mechatronics, Cyber Physical Systems - id: 407-01\n",
      "      * Measurement Systems - id: 407-02\n",
      "    * Computer Science - id: 409\n",
      "      * Information Systems, Process and Knowledge Management - id: 409-06\n",
      "      * Interactive and Intelligent Systems, Image and Language Processing, Computer Graphics and Visualisation - id: 409-05\n",
      "      * Massively Parallel and Data-Intensive Systems - id: 409-08\n",
      "      * Computer Architecture and Embedded Systems - id: 409-07\n",
      "      * Software Engineering and Programming Languages - id: 409-02\n",
      "      * Theoretical Computer Science - id: 409-01\n",
      "      * Operating, Communication, Database and Distributed Systems - id: 409-04\n",
      "      * Security and Dependability - id: 409-03\n",
      "  * Construction Engineering and Architecture - id: 45\n",
      "    * Construction Engineering and Architecture - id: 410\n",
      "      * Geotechnics, Hydraulic Engineering - id: 410-06\n",
      "      * Applied Mechanics, Statics and Dynamics - id: 410-05\n",
      "      * Structural Engineering, Building Informatics and Construction Operation - id: 410-04\n",
      "      * Construction Material Sciences, Chemistry, Building Physics - id: 410-03\n",
      "      * Urbanism, Spatial Planning, Transportation and Infrastructure Planning, Landscape Planning - id: 410-02\n",
      "      * Architecture, Building and Construction History, Construction Research, Sustainable Building Technology - id: 410-01\n",
      "* Natural Sciences - id: 3\n",
      "  * Chemistry - id: 31\n",
      "    * Physical Chemistry - id: 323\n",
      "      * Physical Chemistry of Molecules, Liquids and Interfaces, Biophysical Chemistry - id: 323-01\n",
      "    * Chemical Solid State and Surface Research - id: 322\n",
      "      * Physical Chemistry of Solids and Surfaces, Material Characterisation - id: 322-02\n",
      "      * Solid State and Surface Chemistry, Material Synthesis - id: 322-01\n",
      "    * Biological Chemistry and Food Chemistry - id: 325\n",
      "      * Biological and Biomimetic Chemistry - id: 325-01\n",
      "      * Food Chemistry - id: 325-02\n",
      "    * Analytical Chemistry - id: 324\n",
      "      * Analytical Chemistry - id: 324-01\n",
      "    * Theoretical Chemistry - id: 327\n",
      "      * Molecules, Materials, Surfaces - id: 327-02\n",
      "      * Electron Structure, Dynamics, Simulation - id: 327-01\n",
      "    * Polymer Research - id: 326\n",
      "      * Experimental and Theoretical Physics of Polymers - id: 326-02\n",
      "      * Preparatory and Physical Chemistry of Polymers - id: 326-01\n",
      "      * Polymer Materials - id: 326-03\n",
      "    * Molecular Chemistry - id: 321\n",
      "      * Inorganic Molecular Chemistry - Synthesis and Characterisation - id: 321-01\n",
      "      * Organic Molecular Chemistry - Synthesis and Characterisation - id: 321-02\n",
      "  * Physics - id: 32\n",
      "    * Astrophysics and Astronomy - id: 311\n",
      "      * Astrophysics and Astronomy - id: 311-01\n",
      "    * Statistical Physics, Soft Matter, Biological Physics, Nonlinear Dynamics - id: 310\n",
      "      * Statistical Physics, Soft Matter, Biological Physics, Nonlinear Dynamics - id: 310-01\n",
      "    * Particles, Nuclei and Fields - id: 309\n",
      "      * Nuclear and Elementary Particle Physics, Quantum Mechanics, Relativity, Fields - id: 309-01\n",
      "    * Optics, Quantum Optics and Physics of Atoms, Molecules and Plasmas - id: 308\n",
      "      * Optics, Quantum Optics, Atoms, Molecules, Plasmas - id: 308-01\n",
      "    * Condensed Matter Physics - id: 307\n",
      "      * Theoretical Condensed Matter Physics - id: 307-02\n",
      "      * Experimental Condensed Matter Physics - id: 307-01\n",
      "  * Mathematics - id: 33\n",
      "    * Mathematics - id: 312\n",
      "      * Mathematics - id: 312-01\n",
      "  * Geosciences - id: 34\n",
      "    * Geology and Palaeontology - id: 314\n",
      "      * Geology and Palaeontology - id: 314-01\n",
      "    * Atmospheric Science, Oceanography and Climate Research - id: 313\n",
      "      * Atmospheric Science - id: 313-01\n",
      "      * Oceanography - id: 313-02\n",
      "    * Mineralogy, Petrology and Geochemistry - id: 316\n",
      "      * Mineralogy, Petrology and Geochemistry - id: 316-01\n",
      "    * Geophysics and Geodesy - id: 315\n",
      "      * Geodesy, Photogrammetry, Remote Sensing, Geoinformatics, Cartography - id: 315-02\n",
      "      * Geophysics - id: 315-01\n",
      "    * Water Research - id: 318\n",
      "      * Hydrogeology, Hydrology, Limnology, Urban Water Management, Water Chemistry, Integrated Water Resources Management - id: 318-01\n",
      "    * Geography - id: 317\n",
      "      * Physical Geography - id: 317-01\n",
      "      * Human Geography - id: 317-02\n"
     ]
    }
   ],
   "source": [
    "\n",
    "####################################\n",
    "# extract the DFGFO relations tree from OLS API #\n",
    "# output prints class tree indented further down each level #\n",
    "# the term['label'] and term['short_form'] (short identifier) are printed # \n",
    "# the term['iri'] is ommited but could also be printed/used # \n",
    "####################################\n",
    "\n",
    "\n",
    "def get_terms_from_root(api_url, level):\n",
    "    # calls OLS API on ontology terms \n",
    "    # prints the terms of a given level \n",
    "    # and requests the terms parent, recursively \n",
    "    apirequest = requests.get(api_url)\n",
    "    apiresponse = apirequest.json() \n",
    "    if '_embedded' in apiresponse.keys():\n",
    "        terms = apiresponse['_embedded']['terms']\n",
    "        for term in terms:\n",
    "            ols_term_url = term['_links']['self']['href']\n",
    "            # print(ols_term_url)\n",
    "            print(f\"{' ' * level * 2}* {term['label']} - id: {term['short_form']}\")\n",
    "            if 'children' in term['_links'].keys():\n",
    "                api_children_url = term['_links']['children']['href']\n",
    "                get_terms_from_root(api_url=api_children_url, level=level+1)\n",
    "                \n",
    "\n",
    "get_terms_from_root(api_url=ontology_rootterms, level=0) \n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "* Chemistry - id: 31\n",
      "    * Physical Chemistry - id: 323\n",
      "        * Physical Chemistry of Molecules, Liquids and Interfaces, Biophysical Chemistry - id: 323-01\n",
      "    * Chemical Solid State and Surface Research - id: 322\n",
      "        * Physical Chemistry of Solids and Surfaces, Material Characterisation - id: 322-02\n",
      "        * Solid State and Surface Chemistry, Material Synthesis - id: 322-01\n",
      "    * Biological Chemistry and Food Chemistry - id: 325\n",
      "        * Biological and Biomimetic Chemistry - id: 325-01\n",
      "        * Food Chemistry - id: 325-02\n",
      "    * Analytical Chemistry - id: 324\n",
      "        * Analytical Chemistry - id: 324-01\n",
      "    * Theoretical Chemistry - id: 327\n",
      "        * Molecules, Materials, Surfaces - id: 327-02\n",
      "        * Electron Structure, Dynamics, Simulation - id: 327-01\n",
      "    * Polymer Research - id: 326\n",
      "        * Experimental and Theoretical Physics of Polymers - id: 326-02\n",
      "        * Preparatory and Physical Chemistry of Polymers - id: 326-01\n",
      "        * Polymer Materials - id: 326-03\n",
      "    * Molecular Chemistry - id: 321\n",
      "        * Inorganic Molecular Chemistry - Synthesis and Characterisation - id: 321-01\n",
      "        * Organic Molecular Chemistry - Synthesis and Characterisation - id: 321-02\n"
     ]
    }
   ],
   "source": [
    "####################################\n",
    "# Extract the relations tree from a *non root term*: ie. start from Chemistry - IRI: https://github.com/tibonto/dfgfo/31 \n",
    "# does not start '/api/ontologies/dfgfo/terms/roots' but from 'ontologies/dfgfo/terms/TERMIRI'\n",
    "####################################\n",
    "\n",
    "def get_children_terms(ols_api, term_iri, level):\n",
    "    # calls OLS API on an ontology term\n",
    "    # prints the terms of a given level \n",
    "    # and requests the terms children, recursively\n",
    "    \n",
    "    term_iri = url_double_quote(url=term_iri) \n",
    "    term_api_url = ols_api + '/ontologies/dfgfo/terms/' + term_iri \n",
    "    apirequest = requests.get(term_api_url)\n",
    "    apiresponse = apirequest.json()\n",
    "    has_children = apiresponse['has_children']\n",
    "    short_form =  apiresponse['short_form']\n",
    "    label = apiresponse['label']\n",
    "    print(f\"{' ' * level * 4}* {label} - id: {short_form}\")\n",
    "    if has_children == True:\n",
    "        children_link = apiresponse['_links']['children']['href']\n",
    "        apichildrenrequest = requests.get(children_link)\n",
    "        apichildrenresponse = apichildrenrequest.json()\n",
    "        children = apichildrenresponse['_embedded']['terms']\n",
    "        for i, child in enumerate(children):\n",
    "            get_children_terms(ols_api=ols_api, term_iri=child['iri'], level=level+1)\n",
    "\n",
    "        \n",
    "get_children_terms(ols_api='https://service.tib.eu/ts4tib/api',\n",
    "                   term_iri='https://github.com/tibonto/dfgfo/31',\n",
    "                   level=0) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "Get parents of: https://github.com/tibonto/dfgfo/31\n",
      "*    Chemistry - id: 31\n",
      "*   Natural Sciences - id: 3\n",
      "--------------------------------------\n",
      "\n",
      "Get parents of: https://github.com/tibonto/dfgfo/401-03\n",
      "*    Joining and Separation Technology - id: 401-03\n",
      "*   Production Technology - id: 401\n",
      "*  Mechanical and Industrial Engineering - id: 41\n",
      "* Engineering Sciences - id: 4\n",
      "--------------------------------------\n",
      "\n",
      "Get parents of: https://github.com/tibonto/dfgfo/103-02\n",
      "*    Musicology - id: 103-02\n",
      "*   History - id: 102\n",
      "*  Humanities - id: 11\n",
      "* Humanities and Social Sciences - id: 1\n",
      "--------------------------------------\n",
      "\n",
      "Get parents of: https://github.com/tibonto/dfgfo/311\n",
      "*    Astrophysics and Astronomy - id: 311\n",
      "*   Physics - id: 32\n",
      "*  Natural Sciences - id: 3\n",
      "--------------------------------------\n"
     ]
    }
   ],
   "source": [
    "####################################\n",
    "# given any DFGFO subject extract all its ancestors # \n",
    "# starting at [https://github.com/tibonto/dfgfo/401-03](https://service.tib.eu/ts4tib/ontologies/dfgfo/terms?iri=https%3A%2F%2Fgithub.com%2Ftibonto%2Fdfgfo%2F401-03&viewMode=All&siblings=true) (Joining and Separation Technology)\n",
    "# extract ancestors\n",
    "####################################\n",
    "\n",
    "\n",
    "def get_parent_term(ols_api, term_iri, level):\n",
    "    # calls OLS API on an ontology term\n",
    "    # if the term is not a root: requests its parents\n",
    "    # for each parent (generaly just 1): get its iri, \n",
    "    # call the function again (recursevely) with the parent iri\n",
    "    term_iri = url_double_quote(url=term_iri) \n",
    "    term_api_url = ols_api + '/ontologies/dfgfo/terms/' + term_iri \n",
    "    apirequest = requests.get(term_api_url)\n",
    "    apiresponse = apirequest.json()\n",
    "    is_root = apiresponse['is_root']\n",
    "    short_form =  apiresponse['short_form']\n",
    "    label = apiresponse['label']\n",
    "    print(f\"* {' ' * int(level / 4)}{label} - id: {short_form}\")\n",
    "    if is_root == False:\n",
    "        parents_link = apiresponse['_links']['parents']['href']\n",
    "        # print(parents_link)\n",
    "        apiparentrenrequest = requests.get(parents_link)\n",
    "        apiparentresponse = apiparentrenrequest.json()\n",
    "        parents = apiparentresponse['_embedded']['terms']\n",
    "        # print(parents)        \n",
    "        for i, parent in enumerate(parents):\n",
    "            parent_iri = parent['iri']\n",
    "            # print(parent_iri)\n",
    "            # pprint(parent)\n",
    "            get_parent_term(ols_api=ols_api, term_iri=parent_iri, level=level-4)\n",
    "\n",
    "iri = 'https://github.com/tibonto/dfgfo/31'  # Chemistry 31\n",
    "print(f'\\nGet parents of: {iri}')\n",
    "get_parent_term(ols_api='https://service.tib.eu/ts4tib/api', \n",
    "                term_iri=iri, \n",
    "                level=12)\n",
    "print('--------------------------------------')\n",
    "\n",
    "iri = 'https://github.com/tibonto/dfgfo/401-03'  # Joining and Separation Technology 401-03\n",
    "print(f'\\nGet parents of: {iri}')\n",
    "get_parent_term(ols_api='https://service.tib.eu/ts4tib/api', \n",
    "                term_iri=iri, \n",
    "                level=12)\n",
    "print('--------------------------------------')\n",
    "\n",
    "iri = 'https://github.com/tibonto/dfgfo/103-02'  # Musicology 103-03\n",
    "print(f'\\nGet parents of: {iri}')\n",
    "get_parent_term(ols_api='https://service.tib.eu/ts4tib/api', \n",
    "                term_iri=iri, \n",
    "                level=12)\n",
    "print('--------------------------------------')\n",
    "\n",
    "iri = 'https://github.com/tibonto/dfgfo/311'  # Astrophysics and Astronomy 311\n",
    "print(f'\\nGet parents of: {iri}')\n",
    "get_parent_term(ols_api='https://service.tib.eu/ts4tib/api', \n",
    "                term_iri=iri, \n",
    "                level=12)\n",
    "print('--------------------------------------')\n",
    "\n"
   ]
  }
 ],
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