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Update Compound.ipynb to use searchengine instead of mapr
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@will-moore
will-moore committed Nov 15, 2024
1 parent 77985ae commit bfa67b7
Showing 1 changed file with 33 additions and 64 deletions.
97 changes: 33 additions & 64 deletions Compound.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -103,20 +103,16 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"### Set up base URLS so can use shorter variable names later on"
"### Set up base URL so can use shorter variable names later on"
]
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
"URL = \"https://idr.openmicroscopy.org/mapr/api/{key}/?value={value}&case_sensitive=false&orphaned=true\"\n",
"SCREENS_PROJECTS_URL = \"https://idr.openmicroscopy.org/mapr/api/{key}/?value={value}&case_sensitive=false&id={compound_id}\"\n",
"PLATES_URL = \"https://idr.openmicroscopy.org/mapr/api/{key}/plates/?value={value}&id={screen_id}&case_sensitive=false\"\n",
"IMAGES_URL = \"https://idr.openmicroscopy.org/mapr/api/{key}/images/?value={value}&node={parent_type}&id={parent_id}&case_sensitive=false\"\n",
"ATTRIBUTES_URL = \"https://idr.openmicroscopy.org/webclient/api/annotations/?type=map&image={image_id}\""
"SEARCH_URL = \"https://idr-testing.openmicroscopy.org/searchengine/api/v1/resources/image/search/?key={key}&value={value}\""
]
},
{
Expand All @@ -138,16 +134,7 @@
},
"outputs": [],
"source": [
"TYPE = \"compound\"\n",
"KEYS = {TYPE:\n",
" (\"InChIKey\",\n",
" \"PubChem InChIKey\",\n",
" \"Compound Concentration (microMolar)\",\n",
" \"Concentration (microMolar)\",\n",
" \"Dose\",\n",
" \"Compound MoA\",\n",
" \"Compound Action\")\n",
"}"
"COMPOUND_NAME = \"Compound Name\""
]
},
{
Expand All @@ -168,43 +155,34 @@
},
"outputs": [],
"source": [
"def parse_annotation(writer, json_data, name, data_type):\n",
" plate_name = \"-\"\n",
" screen_name = name\n",
" for p in json_data[data_type]:\n",
" parent_id = p['id']\n",
" plate_name = p['name']\n",
" qs3 = {'key': TYPE, 'value': compound,\n",
" 'parent_type': data_type[:-1], 'parent_id': parent_id}\n",
" url3 = IMAGES_URL.format(**qs3)\n",
"def parse_annotation(writer, json_data, compound):\n",
" for p in json_data:\n",
" plate_name = p['plate_name']\n",
" screen_name = p['screen_name']\n",
" c = compound.lower()\n",
" if c.startswith(\"ml\"):\n",
" c = 'ml9'\n",
" for i in session.get(url3).json()['images']:\n",
" image_id = i['id']\n",
" url4 = ATTRIBUTES_URL.format(**{'image_id': image_id})\n",
" row = {}\n",
" inchikey = \"unknown\"\n",
" concentration = \"unknown\"\n",
" moa = \"unknown\"\n",
" for a in session.get(url4).json()['annotations']:\n",
" for v in a['values']:\n",
" key = str(v[0])\n",
" if key in KEYS[TYPE]:\n",
" if key in ['InChIKey', 'PubChem InChIKey']:\n",
" inchikey = v[1]\n",
" elif key in ['Dose', 'Compound Concentration (microMolar)', 'Concentration (microMolar)']:\n",
" concentration = float(v[1].replace(' micromolar', ''))\n",
" elif key in ['Compound MoA', 'Compound Action']:\n",
" moa = v[1]\n",
" row.update({'Compound': c,\n",
" 'Screen': screen_name,\n",
" 'Plate': plate_name,\n",
" 'Image': image_id,\n",
" 'InChIKey': inchikey,\n",
" 'Concentration (microMolar)': concentration,\n",
" 'MoA': moa})\n",
" writer.writerow(row)"
" image_id = p['id']\n",
" inchikey = \"unknown\"\n",
" concentration = \"unknown\"\n",
" moa = \"unknown\"\n",
" for v in p['key_values']:\n",
" key = v[\"name\"]\n",
" value = v[\"value\"]\n",
" if key in ['InChIKey', 'PubChem InChIKey']:\n",
" inchikey = value\n",
" elif key in ['Dose', 'Compound Concentration (microMolar)', 'Concentration (microMolar)']:\n",
" concentration = float(value.replace(' micromolar', ''))\n",
" elif key in ['Compound MoA', 'Compound Action']:\n",
" moa = value\n",
" row = {'Compound': c,\n",
" 'Screen': screen_name,\n",
" 'Plate': plate_name,\n",
" 'Image': image_id,\n",
" 'InChIKey': inchikey,\n",
" 'Concentration (microMolar)': concentration,\n",
" 'MoA': moa}\n",
" writer.writerow(row)"
]
},
{
Expand Down Expand Up @@ -236,19 +214,10 @@
" 'InChIKey', 'Concentration (microMolar)', 'MoA']\n",
" writer = csv.DictWriter(csvfile, fieldnames=fieldnames)\n",
" writer.writeheader()\n",
" for compound in compounds:\n",
" qs1 = {'key': TYPE, 'value': compound}\n",
" url1 = URL.format(**qs1)\n",
" json_data = session.get(url1).json()\n",
" for m in json_data['maps']:\n",
" qs2 = {'key': TYPE, 'value': compound, 'compound_id': m['id']}\n",
" url2 = SCREENS_PROJECTS_URL.format(**qs2)\n",
" json_data = session.get(url2).json()\n",
" for s in json_data['screens']:\n",
" compound = s['extra']['value']\n",
" qs3 = {'key': TYPE, 'value': compound, 'screen_id': s['id']}\n",
" url3 = PLATES_URL.format(**qs3)\n",
" parse_annotation(writer, session.get(url3).json(), s['name'], 'plates')\n",
" for compound in compounds[:2]:\n",
" url = SEARCH_URL.format(**{'key': COMPOUND_NAME, 'value': compound})\n",
" json_data = session.get(url).json()\n",
" parse_annotation(writer, json_data['results']['results'], compound)\n",
"finally:\n",
" csvfile.close()"
]
Expand Down

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