{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Example of using the IDR web API"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"OMERO.web uses a default session backend authentication scheme for authentication.\n",
"First create a HTTP session using the [`requests`](http://docs.python-requests.org/en/master/) library:"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"# initial data\n",
"IDR_BASE_URL = \"http://idr.openmicroscopy.org\"\n"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import requests\n",
"\n",
"INDEX_PAGE = \"%s/webclient/?experimenter=-1\" % IDR_BASE_URL\n",
"\n",
"# create http session\n",
"with requests.Session() as session:\n",
" request = requests.Request('GET', INDEX_PAGE)\n",
" prepped = session.prepare_request(request)\n",
" response = session.send(prepped)\n",
" if response.status_code != 200:\n",
" response.raise_for_status()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Studies:"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Get Study map annotation:"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"(u'Study Type', u'high content screen')\n",
"(u'Screen Type', u'primary screen')\n",
"(u'Screen Technology Type', u'RNAi screen')\n",
"(u'Imaging Method', u'fluorescence microscopy')\n",
"(u'Publication Title', u'Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation.')\n",
"(u'Publication Authors', u'Heriche JK, Lees JG, Morilla I, Walter T, Petrova B, Roberti MJ, Hossain MJ, Adler P, Fernandez JM, Krallinger M, Haering CH, Vilo J, Valencia A, Ranea JA, Orengo C, Ellenberg J.')\n",
"(u'PubMed ID', u'24943848 http://www.ncbi.nlm.nih.gov/pubmed/24943848')\n",
"(u'PMC ID', u'PMC4142622 http://europepmc.org/search?query=PMC4142622')\n",
"(u'Publication DOI', u'10.1091/mbc.E13-04-0221 http://dx.doi.org/10.1091/mbc.E13-04-0221')\n",
"(u'Annotation File', u'idr0002-screenA-annotation.csv https://github.com/IDR/idr-metadata/blob/master/idr0002-heriche-condensation/screenA/idr0002-screenA-annotation.csv')\n"
]
}
],
"source": [
"MAP_URL = \"{base}/webclient/api/annotations/?type=map&{type}={screen_id}\"\n",
"\n",
"SCREEN_ID = 102\n",
"\n",
"qs = {'base': IDR_BASE_URL, 'type': 'screen', 'screen_id': SCREEN_ID}\n",
"url = MAP_URL.format(**qs)\n",
"for a in session.get(url).json()['annotations']:\n",
" namespace = a['ns']\n",
" for v in a['values']:\n",
" key = v[0]\n",
" value = v[1]\n",
" print (key, value)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Get Plates in the given Screen:"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Plate: 422, Name: plate1_1_013, Children: 1\n",
"Plate: 492, Name: plate1_2_006, Children: 1\n",
"Plate: 559, Name: plate1_3_003, Children: 1\n",
"Plate: 620, Name: plate1_7_015, Children: 1\n",
"Plate: 680, Name: plate2_2_007, Children: 1\n",
"Plate: 728, Name: plate2_3_018, Children: 1\n",
"Plate: 800, Name: plate2_5_015, Children: 1\n",
"Plate: 869, Name: plate2_7_028, Children: 1\n",
"Plate: 944, Name: plate3_11_007, Children: 1\n",
"Plate: 1015, Name: plate3_4_034, Children: 1\n",
"Plate: 1072, Name: plate3_5_002, Children: 1\n",
"Plate: 4554, Name: plate3_8_010, Children: 1\n"
]
}
],
"source": [
"PLATES_URL = \"{base}/webclient/api/plates/?id={screen_id}\"\n",
"\n",
"SCREEN_ID = 102\n",
"\n",
"qs = {'base': IDR_BASE_URL, 'screen_id': SCREEN_ID}\n",
"url = PLATES_URL.format(**qs)\n",
"for p in session.get(url).json()['plates']:\n",
" plate_id = p['id']\n",
" print(\"Plate: {id}, Name: {name}, Children: {childCount}\".format(**p))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Get PlateGrid:"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Well: 1046859, Image: 1938559\n",
"Well: 1046944, Image: 1938650\n",
"Well: 1046877, Image: 1938583\n",
"Well: 1046904, Image: 1938610\n",
"Well: 1046910, Image: 1938616\n",
"Well: 1046869, Image: 1938575\n",
"Well: 1046864, Image: 1938570\n",
"Well: 1046940, Image: 1938646\n",
"Well: 1046930, Image: 1938636\n",
"Well: 1046853, Image: 1938560\n",
"Well: 1046920, Image: 1938626\n",
"Well: 1046863, Image: 1938569\n",
"Well: 1046890, Image: 1938596\n",
"Well: 1046889, Image: 1938595\n",
"Well: 1046942, Image: 1938648\n",
"Well: 1046915, Image: 1938621\n",
"Well: 1046934, Image: 1938640\n",
"Well: 1046880, Image: 1938586\n",
"Well: 1046881, Image: 1938587\n",
"Well: 1046919, Image: 1938625\n",
"Well: 1046870, Image: 1938576\n",
"Well: 1046947, Image: 1938653\n",
"Well: 1046892, Image: 1938598\n",
"Well: 1046856, Image: 1938563\n",
"Well: 1046900, Image: 1938606\n",
"Well: 1046901, Image: 1938607\n",
"Well: 1046945, Image: 1938651\n",
"Well: 1046873, Image: 1938579\n",
"Well: 1046936, Image: 1938642\n",
"Well: 1046908, Image: 1938614\n",
"Well: 1046897, Image: 1938603\n",
"Well: 1046867, Image: 1938573\n",
"Well: 1046865, Image: 1938571\n",
"Well: 1046921, Image: 1938627\n",
"Well: 1046922, Image: 1938628\n",
"Well: 1046855, Image: 1938562\n",
"Well: 1046887, Image: 1938593\n",
"Well: 1046906, Image: 1938612\n",
"Well: 1046931, Image: 1938637\n",
"Well: 1046875, Image: 1938581\n",
"Well: 1046866, Image: 1938572\n",
"Well: 1046854, Image: 1938561\n",
"Well: 1046860, Image: 1938566\n",
"Well: 1046911, Image: 1938617\n",
"Well: 1046907, Image: 1938613\n",
"Well: 1046876, Image: 1938582\n",
"Well: 1046857, Image: 1938564\n",
"Well: 1046926, Image: 1938632\n",
"Well: 1046932, Image: 1938638\n",
"Well: 1046891, Image: 1938597\n",
"Well: 1046874, Image: 1938580\n",
"Well: 1046903, Image: 1938609\n",
"Well: 1046935, Image: 1938641\n",
"Well: 1046898, Image: 1938604\n",
"Well: 1046899, Image: 1938605\n",
"Well: 1046939, Image: 1938645\n",
"Well: 1046858, Image: 1938565\n",
"Well: 1046923, Image: 1938629\n",
"Well: 1046896, Image: 1938602\n",
"Well: 1046912, Image: 1938618\n",
"Well: 1046884, Image: 1938590\n",
"Well: 1046924, Image: 1938630\n",
"Well: 1046937, Image: 1938643\n",
"Well: 1046938, Image: 1938644\n",
"Well: 1046941, Image: 1938647\n",
"Well: 1046893, Image: 1938599\n",
"Well: 1046861, Image: 1938567\n",
"Well: 1046928, Image: 1938634\n",
"Well: 1046927, Image: 1938633\n",
"Well: 1046948, Image: 1938654\n",
"Well: 1046933, Image: 1938639\n",
"Well: 1046862, Image: 1938568\n",
"Well: 1046929, Image: 1938635\n",
"Well: 1046888, Image: 1938594\n",
"Well: 1046917, Image: 1938623\n",
"Well: 1046902, Image: 1938608\n",
"Well: 1046918, Image: 1938624\n",
"Well: 1046882, Image: 1938588\n",
"Well: 1046943, Image: 1938649\n",
"Well: 1046885, Image: 1938591\n",
"Well: 1046879, Image: 1938585\n",
"Well: 1046916, Image: 1938622\n",
"Well: 1046871, Image: 1938577\n",
"Well: 1046946, Image: 1938652\n",
"Well: 1046914, Image: 1938620\n",
"Well: 1046905, Image: 1938611\n",
"Well: 1046886, Image: 1938592\n",
"Well: 1046909, Image: 1938615\n",
"Well: 1046868, Image: 1938574\n",
"Well: 1046895, Image: 1938601\n",
"Well: 1046925, Image: 1938631\n",
"Well: 1046883, Image: 1938589\n",
"Well: 1046913, Image: 1938619\n",
"Well: 1046894, Image: 1938600\n",
"Well: 1046878, Image: 1938584\n",
"Well: 1046872, Image: 1938578\n"
]
}
],
"source": [
"WELLS_IMAGES_URL = \"{base}/webgateway/plate/{plate_id}/{field}/\"\n",
"\n",
"qs = {'base': IDR_BASE_URL, 'plate_id': plate_id, 'field': 0}\n",
"url = WELLS_IMAGES_URL.format(**qs)\n",
"grid = session.get(url).json()\n",
"rowlabels = grid['rowlabels']\n",
"collabels = grid['collabels']\n",
"for row in grid['grid']:\n",
" for cell in row:\n",
" if cell is not None:\n",
" print(\"Well: {wellId}, Image: {id}\".format(**cell))\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Get Image Thumbnail:"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
""
],
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"from IPython.display import display, HTML\n",
"\n",
"WELLS_IMAGES_URL = \"{base}/webgateway/plate/{plate_id}/{field}/\"\n",
"PLATE_ID = 325\n",
"\n",
"qs = {'base': IDR_BASE_URL, 'plate_id': PLATE_ID, 'field': 0}\n",
"url = WELLS_IMAGES_URL.format(**qs)\n",
"grid = session.get(url).json()\n",
"\n",
"image_ids = [cell['id'] for row in grid['grid'] for cell in row if cell is not None]\n",
"\n",
"THUMBNAILS_URL = \"{base}/webgateway/get_thumbnails/\".format(**{'base': IDR_BASE_URL, })\n",
"\n",
"def thumbnails_chunk(image_list, batch):\n",
" for b in xrange(0, len(image_list), batch):\n",
" yield image_list[b:b + batch]\n",
"batch_size = 20\n",
"\n",
"_thumbnails = {}\n",
"for batch in thumbnails_chunk(image_ids, batch_size):\n",
" payload = {'id': batch}\n",
" for iid, thumb in session.get(THUMBNAILS_URL, params=payload).json().iteritems():\n",
" _thumbnails[long(iid)] = thumb\n",
"\n",
"# Display plate\n",
"_tbody = []\n",
"for row in grid['grid']:\n",
" _tr = [\"\"]\n",
" for cell in row:\n",
" if cell is not None:\n",
" _tr.append('![](\"%s\"/) | ' % _thumbnails[cell['id']])\n",
" else:\n",
" _tr.append(' | ')\n",
" _tr.append(\"
\")\n",
" _tbody.append(\" \".join(_tr))\n",
"display(HTML(\"\" + \"\".join(_tbody) + \"
\"))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Get Image:"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{u'init_zoom': 0, u'tiles': False, u'perms': {u'canAnnotate': False, u'canEdit': False, u'canDelete': False, u'canLink': False}, u'split_channel': {u'c': {u'width': 1398, u'border': 2, u'gridy': 2, u'gridx': 2, u'height': 1046}, u'g': {u'width': 1398, u'border': 2, u'gridy': 2, u'gridx': 2, u'height': 1046}}, u'rdefs': {u'defaultT': 0, u'model': u'color', u'defaultZ': 0, u'invertAxis': False, u'projection': u'normal'}, u'pixel_range': [0, 65535], u'interpolate': True, u'channels': [{u'color': u'FF0000', u'active': True, u'window': {u'max': 4095.0, u'min': 250.0, u'end': 4095.0, u'start': 250.0}, u'emissionWave': None, u'label': u'DAPI'}, {u'color': u'00FF00', u'active': True, u'window': {u'max': 4095.0, u'min': 694.0, u'end': 4095.0, u'start': 694.0}, u'emissionWave': None, u'label': u'FITC-FilterWheel'}, {u'color': u'0000FF', u'active': True, u'window': {u'max': 4095.0, u'min': 237.0, u'end': 4095.0, u'start': 237.0}, u'emissionWave': None, u'label': u'TRITC-FilterWheel'}], u'meta': {u'projectDescription': u'', u'datasetName': u'Multiple', u'projectId': None, u'wellSampleId': 108953, u'projectName': u'Multiple', u'imageDescription': u'', u'imageId': 122770, u'imageAuthor': u'Demo User', u'imageName': u'Plate8_Actinome1 [Well O02 Field #1]', u'datasetDescription': u'', u'wellId': 45217, u'imageTimestamp': 1194540393.0, u'pixelsType': u'uint16', u'datasetId': None}, u'id': 122770, u'pixel_size': {u'y': 1.25195005, u'x': 1.25195005, u'z': None}, u'size': {u'width': 696, u'c': 3, u'z': 1, u't': 1, u'height': 520}}\n"
]
},
{
"data": {
"text/html": [
"
"
],
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"from IPython.display import display, HTML\n",
"\n",
"IMAGE_DETAILS_URL = \"{base}/webclient/imgData/{image_id}/\"\n",
"\n",
"IMAGE_ID = 122770\n",
"\n",
"qs = {'base': IDR_BASE_URL, 'image_id': IMAGE_ID}\n",
"url = IMAGE_DETAILS_URL.format(**qs)\n",
"r = session.get(url)\n",
"if r.status_code == 200:\n",
" print (r.json())\n",
"\n",
"RENDER_IMAGE = \"{base}/webgateway/render_image/{image_id}/0/0/\"\n",
"img_url = RENDER_IMAGE.format(**qs)\n",
"\n",
"display(HTML(\"
\" % img_url))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Get Image map annotation:"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"(u'Gene Identifier', u'NM_018098')\n",
"(u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_018098')\n",
"(u'Gene Symbol', u'ECT2')\n",
"(u'Analysis Gene Annotation Build', u'siRNA Pool Identifiers/Gene symbols from GRCh37, Ensembl release 56, Sept 2009')\n",
"(u'Gene Annotation Comments', u'Gene Symbol added using siRNA Pool Identifier name by IDR curator')\n",
"(u'Organism', u'Homo sapiens')\n",
"(u'Phenotype', u'increased cytoplasmic actin')\n",
"(u'Phenotype Term Name', u'increased actin localised to the cytoplasm')\n",
"(u'Phenotype Term Accession', u'CMPO_0000296')\n",
"(u'Phenotype Term Accession URL', u'http://www.ebi.ac.uk/cmpo/CMPO_0000296')\n",
"(u'Phenotype', u'misshapen DNA')\n",
"(u'Phenotype Term Name', u'misshapen DNA')\n",
"(u'Phenotype Term Accession', u'CMPO_0000177')\n",
"(u'Phenotype Term Accession URL', u'http://www.ebi.ac.uk/cmpo/CMPO_0000177')\n",
"(u'Phenotype 30 Term Name', u'misshapen DNA')\n",
"(u'Phenotype', u'decreased cell number')\n",
"(u'Phenotype Term Name', u'decreased cell numbers')\n",
"(u'Phenotype Term Accession', u'CMPO_0000052')\n",
"(u'Phenotype Term Accession URL', u'http://www.ebi.ac.uk/cmpo/CMPO_0000052')\n",
"(u'Phenotype', u'increased cell size')\n",
"(u'Phenotype Term Name', u'increased cell size phenotype')\n",
"(u'Phenotype Term Accession', u'CMPO_0000128')\n",
"(u'Phenotype Term Accession URL', u'http://www.ebi.ac.uk/cmpo/CMPO_0000128')\n",
"(u'Phenotype', u'increased number of multinucleate cells')\n",
"(u'Phenotype Term Name', u'more multinucleate cells')\n",
"(u'Phenotype Term Accession', u'CMPO_0000300')\n",
"(u'Phenotype Term Accession URL', u'http://www.ebi.ac.uk/cmpo/CMPO_0000300')\n",
"(u'Phenotype', u'microtubules disorganised')\n",
"(u'Phenotype Term Name', u'disorganized microtubules phenotype')\n",
"(u'Phenotype Term Accession', u'CMPO_0000147')\n",
"(u'Phenotype Term Accession URL', u'http://www.ebi.ac.uk/cmpo/CMPO_0000147')\n",
"(u'Phenotype', u'loss of cell monolayer')\n",
"(u'Phenotype Term Name', u'loss of cell monolayer')\n",
"(u'Phenotype Term Accession', u'CMPO_0000293')\n",
"(u'Phenotype Term Accession URL', u'http://www.ebi.ac.uk/cmpo/CMPO_0000293')\n",
"(u'Phenotype', u'increased number of zigzag actin stress fibres')\n",
"(u'Phenotype Term Name', u'increased amount of zig-zag stress fibers')\n",
"(u'Phenotype Term Accession', u'CMPO_0000299')\n",
"(u'Phenotype Term Accession URL', u'http://www.ebi.ac.uk/cmpo/CMPO_0000299')\n",
"(u'Phenotype', u'increased actin over nucleus')\n",
"(u'Phenotype Term Name', u'increased actin localised to the nucleus')\n",
"(u'Phenotype Term Accession', u'CMPO_0000294')\n",
"(u'Phenotype Term Accession URL', u'http://www.ebi.ac.uk/cmpo/CMPO_0000294')\n",
"(u'Phenotype', u'increased width of lamellae')\n",
"(u'Phenotype Term Name', u'increased lamellipodia width phenotype')\n",
"(u'Phenotype Term Accession', u'CMPO_0000276')\n",
"(u'Phenotype Term Accession URL', u'http://www.ebi.ac.uk/cmpo/CMPO_0000276')\n",
"(u'Phenotype', u'increased number of actin puncta or dots')\n",
"(u'Phenotype Term Name', u'increased amount of punctate actin foci phenotype')\n",
"(u'Phenotype Term Accession', u'CMPO_0000291')\n",
"(u'Phenotype Term Accession URL', u'http://www.ebi.ac.uk/cmpo/CMPO_0000291')\n",
"(u'Phenotype', u'disorganised peripheral actin')\n",
"(u'Phenotype Term Name', u'disorganised cortical actin cytoskeleton phenotype')\n",
"(u'Phenotype Term Accession', u'CMPO_0000274')\n",
"(u'Phenotype Term Accession URL', u'http://www.ebi.ac.uk/cmpo/CMPO_0000274')\n",
"(u'Phenotype', u'increased DNA area')\n",
"(u'Phenotype Term Name', u'increased nucleus size phenotype')\n",
"(u'Phenotype Term Accession', u'CMPO_0000140')\n",
"(u'Phenotype Term Accession URL', u'http://www.ebi.ac.uk/cmpo/CMPO_0000140')\n",
"(u'siRNA Identifier', u'ECT2-02')\n",
"(u'siRNA Pool Identifier', u'ECT2')\n",
"(u'siRNA Catalog Number', u'D-006450-02')\n",
"(u'Sense Sequence', u'GCACUCACCUUGUAGUUGA')\n",
"(u'Cell Line', u'HeLa')\n",
"(u'Channels', u'DAPI:DNA;FITC-FilterWheel:alpha-tubulin;TIRTC-FilterWheel:phallodin/F-actin')\n",
"(u'Overall Hit Gene Consensus', u'yes')\n",
"(u'Has Phenotype', u'yes')\n",
"(u'Phenotype Annotation Level', u'gene')\n"
]
}
],
"source": [
"MAP_URL = \"{base}/webclient/api/annotations/?type=map&{type}={image_id}\"\n",
"\n",
"IMAGE_ID = 122770\n",
"\n",
"qs = {'base': IDR_BASE_URL, 'type': 'image', 'image_id': IMAGE_ID}\n",
"url = MAP_URL.format(**qs)\n",
"for a in session.get(url).json()['annotations']:\n",
" namespace = a['ns']\n",
" for v in a['values']:\n",
" key = v[0]\n",
" value = v[1]\n",
" print (key, value)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Get bulk annotation:"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{u'parentId': 206, u'addedBy': u'Demo User', u'parentType': u'Screen', u'annId': 6877055, u'owner': u'Demo User', u'data': {u'rows': [[340, u'338', 45217, u'Plate8_Actinome1_O2', u'Homo sapiens', u'NCBITaxon', u'NCBITaxon_9606', u'HeLa', u'EFO', u'EFO_0001185', u'ECT2-02', u'ECT2', u'D-006450-02', u'GCACUCACCUUGUAGUUGA', u'', u'NM_018098', u'ECT2', u'siRNA Pool Identifiers/Gene symbols from GRCh37, Ensembl release 56, Sept 2009', u'Gene Symbol added using siRNA Pool Identifier name by IDR curator', u'', u'', u'DAPI:DNA;FITC-FilterWheel:alpha-tubulin;TIRTC-FilterWheel:phallodin/F-actin', u'', u'yes', u'yes', u'yes', u'yes', u'gene', u'', u'', u'', u'', u'', u'', u'increased cytoplasmic actin', u'increased actin localised to the cytoplasm', u'CMPO_0000296', u'increased actin over nucleus', u'increased actin localised to the nucleus', u'CMPO_0000294', u'', u'', u'', u'increased width of lamellae', u'increased lamellipodia width phenotype', u'CMPO_0000276', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'increased number of actin puncta or dots', u'increased amount of punctate actin foci phenotype', u'CMPO_0000291', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'increased number of zigzag actin stress fibres', u'increased amount of zig-zag stress fibers', u'CMPO_0000299', u'disorganised peripheral actin', u'disorganised cortical actin cytoskeleton phenotype', u'CMPO_0000274', u'increased cell size', u'increased cell size phenotype', u'CMPO_0000128', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'decreased cell number', u'decreased cell numbers', u'CMPO_0000052', u'', u'', u'', u'increased number of multinucleate cells', u'more multinucleate cells', u'CMPO_0000300', u'increased DNA area', u'increased nucleus size phenotype', u'CMPO_0000140', u'', u'', u'', u'misshapen DNA', u'misshapen DNA', u'CMPO_0000177', u'', u'', u'', u'', u'', u'', u'microtubules disorganised', u'disorganized microtubules phenotype', u'CMPO_0000147', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'loss of cell monolayer', u'loss of cell monolayer', u'CMPO_0000293', u'', u'', u'', u'Plate8_Actinome1', u'o2']], u'descriptions': [u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u'', u''], u'columns': [u'Plate', u'Well Number', u'Well', u'Plate_Well', u'Characteristics [Organism]', u'Term Source 1 REF', u'Term Source 1 Accession', u'Characteristics [Cell Line]', u'Term Source 2 REF', u'Term Source 2 Accession', u'siRNA Identifier', u'siRNA Pool Identifier', u'siRNA Catalog Number', u'Sense Sequence', u'Reagent Design Gene Annotation Build', u'Gene Identifier', u'Gene Symbol', u'Analysis Gene Annotation Build', u'Gene Annotation Comments', u'Control Type', u'Control Comments', u'Channels', u'Comments', u'Final Well Hit Status Actinome 1', u'Final Well Hit status Actinome 2', u'Overall Hit Gene Consensus', u'Has Phenotype', u'Phenotype Annotation Level', u'Phenotype 1', u'Phenotype 1 Term Name', u'Phenotype 1 Term Accession', u'Phenotype 2', u'Phenotype 2 Term Name', u'Phenotype 2 Term Accession', u'Phenotype 3', u'Phenotype 3 Term Name', u'Phenotype 3 Term Accession', u'Phenotype 4', u'Phenotype 4 Term Name', u'Phenotype 4 Term Accession', u'Phenotype 5', u'Phenotype 5 Term Name', u'Phenotype 5 Term Accession', u'Phenotype 6', u'Phenotype 6 Term Name', u'Phenotype 6 Term Accession', u'Phenotype 7', u'Phenotype 7 Term Name', u'Phenotype 7 Term Accession', u'Phenotype 8', u'Phenotype 8 Term Name', u'Phenotype 8 Term Accession', u'Phenotype 9', u'Phenotype 9 Term Name', u'Phenotype 9 Term Accession', u'Phenotype 10', u'Phenotype 10 Term Name', u'Phenotype 10 Term Accession', u'Phenotype 11', u'Phenotype 11 Term Name', u'Phenotype 11 Term Accession', u'Phenotype 12', u'Phenotype 12 Term Name', u'Phenotype 12 Term Accession', u'Phenotype 13', u'Phenotype 13 Term Name', u'Phenotype 13 Term Accession', u'Phenotype 14', u'Phenotype 14 Term Name', u'Phenotype 14 Term Accession', u'Phenotype 15', u'Phenotype 15 Term Name', u'Phenotype 15 Term Accession', u'Phenotype 16', u'Phenotype 16 Term Name', u'Phenotype 16 Term Accession', u'Phenotype 17', u'Phenotype 17 Term Name', u'Phenotype 17 Term Accession', u'Phenotype 18', u'Phenotype 18 Term Name', u'Phenotype 18 Term Accession', u'Phenotype 19', u'Phenotype 19 Term Name', u'Phenotype 19 Term Accession', u'Phenotype 20', u'Phenotype 20 Term Name', u'Phenotype 20 Term Accession', u'Phenotype 21', u'Phenotype 21 Term Name', u'Phenotype 21 Term Accession', u'Phenotype 22', u'Phenotype 22 Term Name', u'Phenotype 22 Term Accession', u'Phenotype 23', u'Phenotype 23 Term Name', u'Phenotype 23 Term Accession', u'Phenotype 24', u'Phenotype 24 Term Name', u'Phenotype 24 Term Accession', u'Phenotype 25', u'Phenotype 25 Term Name', u'Phenotype 25 Term Accession', u'Phenotype 26', u'Phenotype 26 Term Name', u'Phenotype 26 Term Accession', u'Phenotype 27', u'Phenotype 27 Term Name', u'Phenotype 27 Term Accession', u'Phenotype 28', u'Phenotype 28 Term Name', u'Phenotype 28 Term Accession', u'Phenotype 29', u'Phenotype 29 Term Name', u'Phenotype 29 Term Accession', u'Phenotype 30', u'Phenotype 30 Term Name', u'Phenotype 30 Term Accession', u'Phenotype 31', u'Phenotype 31 Term Name', u'Phenotype 31 Term Accession', u'Phenotype 32', u'Phenotype 32 Term Name', u'Phenotype 32 Term Accession', u'Phenotype 33', u'Phenotype 33 Term Name', u'Phenotype 33 Term Accession', u'Phenotype 34', u'Phenotype 34 Term Name', u'Phenotype 34 Term Accession', u'Phenotype 35', u'Phenotype 35 Term Name', u'Phenotype 35 Term Accession', u'Phenotype 36', u'Phenotype 36 Term Name', u'Phenotype 36 Term Accession', u'Phenotype 37', u'Phenotype 37 Term Name', u'Phenotype 37 Term Accession', u'Phenotype 38', u'Phenotype 38 Term Name', u'Phenotype 38 Term Accession', u'Phenotype 39', u'Phenotype 39 Term Name', u'Phenotype 39 Term Accession', u'Phenotype 40', u'Phenotype 40 Term Name', u'Phenotype 40 Term Accession', u'Plate Name', u'Well Name']}, u'id': 14209180, u'addedOn': 1481675335684}\n",
"('Download URL:', 'http://idr.openmicroscopy.org/webclient/annotation/6877055')\n",
"('Download URL:', 'http://idr.openmicroscopy.org/webclient/annotation/2891867')\n"
]
}
],
"source": [
"BULK_URL = \"{base}/webgateway/table/Screen.plateLinks.child.wells/{well_id}/query/?query=Well-{well_id}\"\n",
"\n",
"WELL_ID = 45217\n",
"qs = {'base': IDR_BASE_URL, 'well_id': WELL_ID}\n",
"url = BULK_URL.format(**qs)\n",
"r = session.get(url)\n",
"print (r.json())\n",
"\n",
"\n",
"# or download entire bulk_annotation file:\n",
"\n",
"FILEANNOTATION_URL = \"{base}/webclient/api/annotations/?type=file&screen={screen_id}\"\n",
"DOWNLOAD_URL = \"{base}/webclient/annotation/{ann_id}\"\n",
"\n",
"SCREEN_ID = 206\n",
"\n",
"qs = {'base': IDR_BASE_URL, 'screen_id': SCREEN_ID}\n",
"url = FILEANNOTATION_URL.format(**qs)\n",
"for a in session.get(url).json()['annotations']:\n",
" namespace = a['ns']\n",
" ann_id = a['id']\n",
" qs2 = {'base': IDR_BASE_URL, 'ann_id': a['id']}\n",
" url2 = DOWNLOAD_URL.format(**qs2)\n",
" print (\"Download URL:\", url2)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Attributes (e.g. Gene, Phenotype...)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Get Screens that are annotated with gene:"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"(102, u'idr0002-heriche-condensation/screenA (24)')\n",
"(51, u'idr0003-breker-plasticity/screenA (15)')\n",
"(253, u'idr0006-fong-nuclearbodies/screenA (48)')\n",
"(201, u'idr0007-srikumar-sumo/screenA (9)')\n",
"(251, u'idr0009-simpson-secretion/screenA (12)')\n",
"(1351, u'idr0010-doil-dnadamage/screenA (4)')\n",
"(1551, u'idr0011-ledesmafernandez-dad4/screenB (13)')\n",
"(1602, u'idr0011-ledesmafernandez-dad4/screenD (21)')\n",
"(1202, u'idr0012-fuchs-cellmorph/screenA (2)')\n",
"(1101, u'idr0013-neumann-mitocheck/screenA (6)')\n",
"(1302, u'idr0013-neumann-mitocheck/screenB (8)')\n",
"(1204, u'idr0020-barr-chtog/screenA (120)')\n"
]
}
],
"source": [
"SCREENS_PROJECTS_URL = \"{base}/mapr/api/{key}/?value={value}\"\n",
"\n",
"qs = {'base': IDR_BASE_URL, 'key': 'gene', 'value': 'CDC20'}\n",
"url = SCREENS_PROJECTS_URL.format(**qs)\n",
"for s in session.get(url).json()['screens']:\n",
" screen_id = s['id']\n",
" print (s['id'], s['name'])"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Get Plates in Screen that are annotated with gene:"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"(4357, u'200972429 TOG[2702]')\n",
"(4401, u'200972430 TOG[2703]')\n",
"(4451, u'200972431 NS[2667]')\n",
"(4453, u'200972432 NS[2668]')\n"
]
}
],
"source": [
"PLATES_URL = \"{base}/mapr/api/{key}/plates/?value={value}&id={screen_id}\"\n",
"\n",
"qs = {'base': IDR_BASE_URL, 'key': 'gene', 'value': 'CDC20', 'screen_id': screen_id}\n",
"url = PLATES_URL.format(**qs)\n",
"for p in session.get(url).json()['plates']:\n",
" plate_id = p['id']\n",
" print (p['id'], p['name'])"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Get Images in Plate that are annotated with gene:"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915895\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915895/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915895/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915879\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915879/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915879/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915899\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915899/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915899/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915893\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915893/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915893/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915894\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915894/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915894/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915903\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915903/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915903/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915904\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915904/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915904/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915887\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915887/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915887/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915883\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915883/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915883/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915890\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915890/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915890/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915882\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915882/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915882/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915897\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915897/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915897/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915906\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915906/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915906/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915880\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915880/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915880/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915884\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915884/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915884/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915891\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915891/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915891/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915896\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915896/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915896/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915907\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915907/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915907/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915881\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915881/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915881/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915886\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915886/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915886/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915888\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915888/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915888/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915878\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915878/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915878/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915900\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915900/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915900/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915905\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915905/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915905/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915898\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915898/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915898/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915885\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915885/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915885/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915889\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915889/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915889/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915901\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915901/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915901/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915892\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915892/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915892/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n",
"Image link: http://idr.openmicroscopy.org/webclient/?show=image-1915902\n",
"Image viewer link: http://idr.openmicroscopy.org/webclient/img_detail/1915902/\n",
"Thumbnail URL: http://idr.openmicroscopy.org/webclient/render_thumbnail/1915902/\n",
"Annotations:\n",
"\t[[u'Gene Identifier', u'991'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/991'], [u'Gene Symbol', u'CDC20'], [u'Gene Identifier URL', u'http://www.ncbi.nlm.nih.gov/gene/?term=991']]\n",
"\t[[u'RefSeq Accession', u'NM_001255'], [u'RefSeq Accession URL', u'http://www.ncbi.nlm.nih.gov/nuccore/NM_001255'], [u'RefSeq GI Number', u'4557436']]\n",
"\t[[u'Organism', u'Homo sapiens']]\n",
"\t[[u'siRNA Pool Identifier', u'L-003225-00'], [u'siRNA Identifier', u'']]\n",
"\t[[u'siRNA Sequences', u'CGGAAGACCUGCCGUUACA;GGGCCGAACUCCUGGCAAA;GAUCAAAGAGGGCAACUAC;CAGAACAGACUGAAAGUAC']]\n",
"\t[[u'Cell Line', u'HeLa'], [u'shRNA', u'non-silencing shRNA'], [u'Channels', u'Hoescht: nuclei;Anti-Ser10 PhosphoHistone H3: mitotic nuclei;Anti-alpha-tubulin: microtubules;RFP: whole cell']]\n"
]
}
],
"source": [
"IMAGES_URL = \"{base}/mapr/api/{key}/images/?value={value}&node={parent_type}&id={parent_id}\"\n",
"\n",
"IMAGE_URL = \"{base}/webclient/?show=image-{image_id}\"\n",
"IMAGE_VIEWER = \"{base}/webclient/img_detail/{image_id}/\"\n",
"THUMBNAIL_URL = \"{base}/webclient/render_thumbnail/{image_id}/\"\n",
"ATTRIBUTES_URL = \"{base}/webclient/api/annotations/?type=map&image={image_id}\"\n",
"\n",
"qs = {'base': IDR_BASE_URL, 'key': 'gene', 'value': 'CDC20', 'parent_type': 'plate', 'parent_id': plate_id}\n",
"url = IMAGES_URL.format(**qs)\n",
"for i in session.get(url).json()['images']:\n",
" image_id = i['id']\n",
" print 'Image link:', IMAGE_URL.format(**{'base': IDR_BASE_URL, 'image_id': image_id})\n",
" print 'Image viewer link:', IMAGE_VIEWER.format(**{'base': IDR_BASE_URL, 'image_id': image_id})\n",
" print 'Thumbnail URL:', THUMBNAIL_URL.format(**{'base': IDR_BASE_URL, 'image_id': image_id})\n",
" url = ATTRIBUTES_URL.format(**{'base': IDR_BASE_URL, 'image_id': image_id})\n",
" print 'Annotations:'\n",
" for a in session.get(url).json()['annotations']:\n",
" print '\\t%s' % a['values']"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
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