From 2375e8162f22eb24f5af43544c06b1de81a83dc2 Mon Sep 17 00:00:00 2001 From: Rob Court Date: Tue, 19 Sep 2023 13:54:40 +0100 Subject: [PATCH] fixed run --- snippets/VFB_connect_Quick_Guide.ipynb | 1332 ++++++++++++++++++------ 1 file changed, 1010 insertions(+), 322 deletions(-) diff --git a/snippets/VFB_connect_Quick_Guide.ipynb b/snippets/VFB_connect_Quick_Guide.ipynb index 3e478164..cedb1a3a 100644 --- a/snippets/VFB_connect_Quick_Guide.ipynb +++ b/snippets/VFB_connect_Quick_Guide.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": 12, "metadata": {}, "outputs": [], "source": [ @@ -14,176 +14,251 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 13, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "[{'term': {'core': {'short_form': 'VFB_00010001',\n", - " 'label': 'fru-F-500075',\n", + "[{'term': {'core': {'symbol': '',\n", " 'iri': 'http://virtualflybrain.org/reports/VFB_00010001',\n", - " 'types': ['Individual',\n", - " 'VFB',\n", - " '_Individual',\n", - " 'NBLAST',\n", - " 'Neuron',\n", + " 'types': ['Entity',\n", + " 'Adult',\n", " 'Anatomy',\n", " 'Cell',\n", - " 'Entity']},\n", - " 'description': ['A(n) neuron expressing Scer\\\\GAL4[fru.P1.D] that is part of a female Scer\\\\GAL4[fru.P1.D] expression pattern.'],\n", + " 'Expression_pattern_fragment',\n", + " 'Individual',\n", + " 'Nervous_system',\n", + " 'Neuron',\n", + " 'VFB',\n", + " 'has_image',\n", + " 'FlyCircuit',\n", + " 'NBLAST'],\n", + " 'short_form': 'VFB_00010001',\n", + " 'unique_facets': ['Adult',\n", + " 'Expression_pattern_fragment',\n", + " 'Nervous_system',\n", + " 'Neuron'],\n", + " 'label': 'fru-F-500075'},\n", + " 'description': [],\n", " 'comment': ['OutAge: Adult 5~15 days']},\n", - " 'query': 'Get JSON for Individual:Anatomy',\n", - " 'version': '0f4d3af',\n", - " 'dataset_license': [{'dataset': {'link': 'http://flybase.org/reports/FBrf0210580.html',\n", - " 'core': {'short_form': 'Chiang2010',\n", - " 'label': 'FlyCircuit 1.0 - single neurons (Chiang2010)',\n", - " 'iri': 'http://virtualflybrain.org/reports/Chiang2010',\n", - " 'types': ['Individual', 'DataSet', 'Entity']}},\n", - " 'license': {'icon': '',\n", - " 'link': '',\n", - " 'core': {'short_form': 'VFBlicense_FlyCircuit_License',\n", - " 'label': 'FlyCircuit License',\n", + " 'query': 'Get JSON for Individual',\n", + " 'version': '3b19da3',\n", + " 'dataset_license': [{'license': {'core': {'symbol': '',\n", " 'iri': 'http://virtualflybrain.org/reports/VFBlicense_FlyCircuit_License',\n", - " 'types': ['Individual', 'License', 'Entity']}}}],\n", - " 'parents': [{'short_form': 'FBbt_00050031',\n", - " 'label': 'adult SMPpv1 lineage neuron',\n", + " 'types': ['Entity', 'Individual', 'License'],\n", + " 'short_form': 'VFBlicense_FlyCircuit_License',\n", + " 'unique_facets': ['License'],\n", + " 'label': 'FlyCircuit License'},\n", + " 'icon': '',\n", + " 'link': ''},\n", + " 'dataset': {'core': {'symbol': '',\n", + " 'iri': 'http://virtualflybrain.org/reports/Chiang2010',\n", + " 'types': ['Entity', 'DataSet', 'Individual', 'has_image', 'FlyCircuit'],\n", + " 'short_form': 'Chiang2010',\n", + " 'unique_facets': ['DataSet'],\n", + " 'label': 'FlyCircuit 1.0 - single neurons (Chiang2010)'},\n", + " 'link': 'http://flybase.org/reports/FBrf0210580.html'}}],\n", + " 'parents': [{'symbol': '',\n", " 'iri': 'http://purl.obolibrary.org/obo/FBbt_00050031',\n", - " 'types': ['Class',\n", - " 'VFB',\n", - " '_Class',\n", - " 'Neuron',\n", + " 'types': ['Entity',\n", + " 'Adult',\n", " 'Anatomy',\n", " 'Cell',\n", - " 'Entity',\n", - " 'Leaf_node']}],\n", - " 'relationships': [{'relation': {'label': 'member_of',\n", - " 'iri': 'http://purl.obolibrary.org/obo/RO_0002350',\n", - " 'type': 'member_of'},\n", - " 'object': {'short_form': 'VFB_00017636',\n", - " 'label': 'cluster 3.97',\n", - " 'iri': 'http://virtualflybrain.org/reports/VFB_00017636',\n", - " 'types': ['Individual', 'VFB', '_Individual', 'Entity', 'Cluster']}},\n", - " {'relation': {'label': 'expresses',\n", - " 'iri': 'http://purl.obolibrary.org/obo/RO_0002292',\n", + " 'Class',\n", + " 'Nervous_system',\n", + " 'Neuron'],\n", + " 'short_form': 'FBbt_00050031',\n", + " 'unique_facets': ['Adult', 'Nervous_system', 'Neuron'],\n", + " 'label': 'adult DPMpl1 lineage neuron'},\n", + " {'symbol': '',\n", + " 'iri': 'http://purl.obolibrary.org/obo/fbbt/vfb/VFBext_0000004',\n", + " 'types': ['Entity', 'Anatomy', 'Class', 'Expression_pattern_fragment'],\n", + " 'short_form': 'VFBext_0000004',\n", + " 'unique_facets': ['Anatomy'],\n", + " 'label': 'expression pattern fragment'}],\n", + " 'relationships': [{'relation': {'iri': 'http://purl.obolibrary.org/obo/RO_0002292',\n", + " 'label': 'expresses',\n", " 'type': 'expresses'},\n", - " 'object': {'short_form': 'FBal0276838',\n", - " 'label': 'Scer\\\\GAL4[fru.P1.D]',\n", + " 'object': {'symbol': '',\n", " 'iri': 'http://flybase.org/reports/FBal0276838',\n", - " 'types': ['Class', 'VFB', '_Class', 'Entity', 'Feature']}},\n", - " {'relation': {'label': 'part of',\n", - " 'iri': 'http://purl.obolibrary.org/obo/BFO_0000050',\n", - " 'type': 'part_of'},\n", - " 'object': {'short_form': 'VFBexp_FBal0276838',\n", - " 'label': 'Scer\\\\GAL4[fru.P1.D] expression pattern',\n", - " 'iri': 'http://virtualflybrain.org/reports/VFBexp_FBal0276838',\n", - " 'types': ['Class', 'VFB', '_Class', 'Expression_pattern', 'Entity']}},\n", - " {'relation': {'label': 'part of',\n", - " 'iri': 'http://purl.obolibrary.org/obo/BFO_0000050',\n", - " 'type': 'part_of'},\n", - " 'object': {'short_form': 'FBbt_00007011',\n", - " 'label': 'female organism',\n", - " 'iri': 'http://purl.obolibrary.org/obo/FBbt_00007011',\n", - " 'types': ['Class', 'VFB', '_Class', 'Anatomy', 'Entity']}},\n", - " {'relation': {'label': 'part of',\n", - " 'iri': 'http://purl.obolibrary.org/obo/BFO_0000050',\n", - " 'type': 'part_of'},\n", - " 'object': {'short_form': 'FBbt_00003624',\n", - " 'label': 'adult brain',\n", - " 'iri': 'http://purl.obolibrary.org/obo/FBbt_00003624',\n", - " 'types': ['Class', 'VFB', '_Class', 'Anatomy', 'Entity']}},\n", - " {'relation': {'label': 'overlaps',\n", - " 'iri': 'http://purl.obolibrary.org/obo/RO_0002131',\n", - " 'type': 'overlaps'},\n", - " 'object': {'short_form': 'FBbt_00007055',\n", - " 'label': 'superior medial protocerebrum',\n", - " 'iri': 'http://purl.obolibrary.org/obo/FBbt_00007055',\n", - " 'types': ['Class',\n", - " 'VFB',\n", - " '_Class',\n", - " 'Synaptic_neuropil',\n", - " 'Synaptic_neuropil_domain',\n", - " 'Anatomy',\n", - " 'Entity']}},\n", - " {'relation': {'label': 'overlaps',\n", - " 'iri': 'http://purl.obolibrary.org/obo/RO_0002131',\n", + " 'types': ['Entity', 'Class', 'Feature'],\n", + " 'short_form': 'FBal0276838',\n", + " 'unique_facets': ['Allele'],\n", + " 'label': 'Scer\\\\GAL4[fru.P1.D]'}},\n", + " {'relation': {'iri': 'http://purl.obolibrary.org/obo/RO_0002131',\n", + " 'label': 'overlaps',\n", " 'type': 'overlaps'},\n", - " 'object': {'short_form': 'FBbt_00045050',\n", - " 'label': 'flange',\n", + " 'object': {'symbol': '',\n", " 'iri': 'http://purl.obolibrary.org/obo/FBbt_00045050',\n", - " 'types': ['Class',\n", - " 'VFB',\n", - " '_Class',\n", + " 'types': ['Entity',\n", + " 'Adult',\n", + " 'Anatomy',\n", + " 'Class',\n", + " 'Nervous_system',\n", " 'Synaptic_neuropil',\n", - " 'Synaptic_neuropil_domain',\n", + " 'Synaptic_neuropil_domain'],\n", + " 'short_form': 'FBbt_00045050',\n", + " 'unique_facets': ['Adult', 'Nervous_system', 'Synaptic_neuropil_domain'],\n", + " 'label': 'flange'}},\n", + " {'relation': {'iri': 'http://purl.obolibrary.org/obo/RO_0002131',\n", + " 'label': 'overlaps',\n", + " 'type': 'overlaps'},\n", + " 'object': {'symbol': '',\n", + " 'iri': 'http://purl.obolibrary.org/obo/FBbt_00007055',\n", + " 'types': ['Entity',\n", + " 'Adult',\n", " 'Anatomy',\n", - " 'Entity']}}],\n", + " 'Class',\n", + " 'Nervous_system',\n", + " 'Synaptic_neuropil',\n", + " 'Synaptic_neuropil_domain'],\n", + " 'short_form': 'FBbt_00007055',\n", + " 'unique_facets': ['Adult', 'Nervous_system', 'Synaptic_neuropil_domain'],\n", + " 'label': 'superior medial protocerebrum'}},\n", + " {'relation': {'iri': 'http://purl.obolibrary.org/obo/BFO_0000050',\n", + " 'label': 'is part of',\n", + " 'type': 'part_of'},\n", + " 'object': {'symbol': '',\n", + " 'iri': 'http://purl.obolibrary.org/obo/FBbt_00003624',\n", + " 'types': ['Entity', 'Adult', 'Anatomy', 'Class', 'Nervous_system'],\n", + " 'short_form': 'FBbt_00003624',\n", + " 'unique_facets': ['Adult', 'Nervous_system'],\n", + " 'label': 'adult brain'}},\n", + " {'relation': {'iri': 'http://purl.obolibrary.org/obo/BFO_0000050',\n", + " 'label': 'is part of',\n", + " 'type': 'part_of'},\n", + " 'object': {'symbol': '',\n", + " 'iri': 'http://virtualflybrain.org/reports/VFBexp_FBal0276838',\n", + " 'types': ['Entity', 'Anatomy', 'Class', 'Expression_pattern'],\n", + " 'short_form': 'VFBexp_FBal0276838',\n", + " 'unique_facets': ['Expression_pattern'],\n", + " 'label': 'Scer\\\\GAL4[fru.P1.D] expression pattern'}},\n", + " {'relation': {'iri': 'http://purl.obolibrary.org/obo/BFO_0000050',\n", + " 'label': 'is part of',\n", + " 'type': 'part_of'},\n", + " 'object': {'symbol': '',\n", + " 'iri': 'http://purl.obolibrary.org/obo/FBbt_00007011',\n", + " 'types': ['Entity', 'Anatomy', 'Class'],\n", + " 'short_form': 'FBbt_00007011',\n", + " 'unique_facets': ['Anatomy'],\n", + " 'label': 'female organism'}}],\n", " 'xrefs': [{'link_base': 'http://flycircuit.tw/modules.php?name=clearpage&op=detail_table&neuron=',\n", - " 'icon': '',\n", - " 'link_postfix': '',\n", - " 'site': {'short_form': 'FlyCircuit',\n", - " 'label': 'FlyCircuit',\n", + " 'site': {'symbol': '',\n", " 'iri': 'http://virtualflybrain.org/reports/FlyCircuit',\n", - " 'types': ['Individual', 'Site', 'Entity']},\n", + " 'types': ['Entity', 'Individual', 'Site'],\n", + " 'short_form': 'FlyCircuit',\n", + " 'unique_facets': ['Site'],\n", + " 'label': 'FlyCircuit 1.0'},\n", + " 'is_data_source': True,\n", + " 'link_postfix': '',\n", + " 'icon': '',\n", " 'accession': 'fru-F-500075',\n", - " 'link_text': 'fru-F-500075 on FlyCircuit',\n", + " 'link_text': 'fru-F-500075 on FlyCircuit 1.0',\n", " 'homepage': 'http://flycircuit.tw'}],\n", - " 'channel_image': [{'channel': {'short_form': 'VFBc_00010001',\n", - " 'label': 'fru-F-500075-c',\n", + " 'channel_image': [{'image': {'image_nrrd': 'http://www.virtualflybrain.org/data/VFB/i/0001/0001/VFB_00101567/volume.nrrd',\n", + " 'image_swc': 'http://www.virtualflybrain.org/data/VFB/i/0001/0001/VFB_00101567/volume.swc',\n", + " 'template_channel': {'symbol': '',\n", + " 'iri': 'http://virtualflybrain.org/reports/VFBc_00101567',\n", + " 'types': ['Entity', 'Individual', 'Template'],\n", + " 'short_form': 'VFBc_00101567',\n", + " 'unique_facets': [],\n", + " 'label': 'JRC2018Unisex_c'},\n", + " 'index': [],\n", + " 'template_anatomy': {'symbol': '',\n", + " 'iri': 'http://virtualflybrain.org/reports/VFB_00101567',\n", + " 'types': ['Entity',\n", + " 'Adult',\n", + " 'Anatomy',\n", + " 'Individual',\n", + " 'Nervous_system',\n", + " 'Template',\n", + " 'has_image'],\n", + " 'short_form': 'VFB_00101567',\n", + " 'unique_facets': ['Adult', 'Nervous_system'],\n", + " 'label': 'JRC2018Unisex'},\n", + " 'image_wlz': 'http://www.virtualflybrain.org/data/VFB/i/0001/0001/VFB_00101567/volume.wlz',\n", + " 'image_obj': 'http://www.virtualflybrain.org/data/VFB/i/0001/0001/VFB_00101567/volume.obj',\n", + " 'image_thumbnail': 'http://www.virtualflybrain.org/data/VFB/i/0001/0001/VFB_00101567/thumbnail.png',\n", + " 'image_folder': 'http://www.virtualflybrain.org/data/VFB/i/0001/0001/VFB_00101567/'},\n", + " 'channel': {'symbol': '',\n", " 'iri': 'http://virtualflybrain.org/reports/VFBc_00010001',\n", - " 'types': ['Individual', 'VFB', 'Entity']},\n", - " 'imaging_technique': {'short_form': 'FBbi_00000251',\n", - " 'label': 'confocal microscopy',\n", + " 'types': ['Entity', 'Individual', 'VFB'],\n", + " 'short_form': 'VFBc_00010001',\n", + " 'unique_facets': [],\n", + " 'label': 'fru-F-500075-c'},\n", + " 'imaging_technique': {'symbol': 'Confocal',\n", " 'iri': 'http://purl.obolibrary.org/obo/FBbi_00000251',\n", - " 'types': ['Class', '_Class', 'FBBI', 'Entity']},\n", - " 'image': {'template_channel': {'short_form': 'VFBc_00017894',\n", - " 'label': 'JFRC2_template_c',\n", + " 'types': ['Entity', 'Class'],\n", + " 'short_form': 'FBbi_00000251',\n", + " 'unique_facets': ['Class'],\n", + " 'label': 'confocal microscopy'}},\n", + " {'image': {'image_nrrd': 'http://www.virtualflybrain.org/data/VFB/i/0001/0001/VFB_00017894/volume.nrrd',\n", + " 'image_swc': 'http://www.virtualflybrain.org/data/VFB/i/0001/0001/VFB_00017894/volume.swc',\n", + " 'template_channel': {'symbol': '',\n", " 'iri': 'http://virtualflybrain.org/reports/VFBc_00017894',\n", - " 'types': ['Individual', 'VFB', 'Template', 'Entity']},\n", - " 'template_anatomy': {'short_form': 'VFB_00017894',\n", - " 'label': 'adult brain template JFRC2',\n", + " 'types': ['Entity', 'Individual', 'Template', 'VFB'],\n", + " 'short_form': 'VFBc_00017894',\n", + " 'unique_facets': [],\n", + " 'label': 'JFRC2_template_c'},\n", + " 'index': [],\n", + " 'template_anatomy': {'symbol': '',\n", " 'iri': 'http://virtualflybrain.org/reports/VFB_00017894',\n", - " 'types': ['Individual',\n", - " 'VFB',\n", - " '_Individual',\n", - " 'Template',\n", + " 'types': ['Entity',\n", + " 'Adult',\n", " 'Anatomy',\n", - " 'Entity']},\n", - " 'image_folder': 'http://www.virtualflybrain.org/data/VFB/i/0001/0001/',\n", - " 'index': []}},\n", - " {'channel': {'short_form': 'VFBc_00010001',\n", - " 'label': 'fru-F-500075-c',\n", + " 'Individual',\n", + " 'Nervous_system',\n", + " 'Template',\n", + " 'VFB',\n", + " 'has_image'],\n", + " 'short_form': 'VFB_00017894',\n", + " 'unique_facets': ['Adult', 'Nervous_system'],\n", + " 'label': 'adult brain template JFRC2'},\n", + " 'image_wlz': 'http://www.virtualflybrain.org/data/VFB/i/0001/0001/VFB_00017894/volume.wlz',\n", + " 'image_obj': 'http://www.virtualflybrain.org/data/VFB/i/0001/0001/VFB_00017894/volume.obj',\n", + " 'image_thumbnail': 'http://www.virtualflybrain.org/data/VFB/i/0001/0001/VFB_00017894/thumbnail.png',\n", + " 'image_folder': 'http://www.virtualflybrain.org/data/VFB/i/0001/0001/VFB_00017894/'},\n", + " 'channel': {'symbol': '',\n", " 'iri': 'http://virtualflybrain.org/reports/VFBc_00010001',\n", - " 'types': ['Individual', 'VFB', 'Entity']},\n", - " 'imaging_technique': {'short_form': 'FBbi_00000251',\n", - " 'label': 'confocal microscopy',\n", + " 'types': ['Entity', 'Individual', 'VFB'],\n", + " 'short_form': 'VFBc_00010001',\n", + " 'unique_facets': [],\n", + " 'label': 'fru-F-500075-c'},\n", + " 'imaging_technique': {'symbol': 'Confocal',\n", " 'iri': 'http://purl.obolibrary.org/obo/FBbi_00000251',\n", - " 'types': ['Class', '_Class', 'FBBI', 'Entity']},\n", - " 'image': {'template_channel': {'short_form': 'VFBc_00101567',\n", - " 'label': 'JRC2018Unisex_c',\n", - " 'iri': 'http://virtualflybrain.org/reports/VFBc_00101567',\n", - " 'types': ['Individual', 'Template', 'Entity']},\n", - " 'template_anatomy': {'short_form': 'VFB_00101567',\n", - " 'label': 'JRC2018Unisex',\n", - " 'iri': 'http://virtualflybrain.org/reports/VFB_00101567',\n", - " 'types': ['Individual',\n", - " 'VFB',\n", - " '_Individual',\n", - " 'Template',\n", - " 'Anatomy',\n", - " 'Entity']},\n", - " 'image_folder': 'http://www.virtualflybrain.org/data/VFB/i/0001/0001/VFB_00101567/',\n", - " 'index': []}}],\n", - " 'related_individuals': [{'relation': {'label': 'member_of',\n", - " 'iri': 'http://purl.obolibrary.org/obo/RO_0002350',\n", - " 'type': 'member_of'},\n", - " 'object': {'short_form': 'VFB_00017636',\n", - " 'label': 'cluster 3.97',\n", - " 'iri': 'http://virtualflybrain.org/reports/VFB_00017636',\n", - " 'types': ['Individual', 'VFB', '_Individual', 'Entity', 'Cluster']}}]}]" + " 'types': ['Entity', 'Class'],\n", + " 'short_form': 'FBbi_00000251',\n", + " 'unique_facets': ['Class'],\n", + " 'label': 'confocal microscopy'}}],\n", + " 'pub_syn': [{'synonym': {'scope': 'has_exact_synonym',\n", + " 'label': 'FruMARCM-F000584_seg002',\n", + " 'type': ''},\n", + " 'pub': {'core': {'symbol': '',\n", + " 'iri': 'http://flybase.org/reports/Unattributed',\n", + " 'types': ['Entity', 'Individual', 'pub'],\n", + " 'short_form': 'Unattributed',\n", + " 'unique_facets': ['pub'],\n", + " 'label': ''},\n", + " 'FlyBase': '',\n", + " 'PubMed': '',\n", + " 'DOI': ''}},\n", + " {'synonym': {'scope': 'has_exact_synonym',\n", + " 'label': 'fru-F-500075',\n", + " 'type': ''},\n", + " 'pub': {'core': {'symbol': '',\n", + " 'iri': 'http://flybase.org/reports/Unattributed',\n", + " 'types': ['Entity', 'Individual', 'pub'],\n", + " 'short_form': 'Unattributed',\n", + " 'unique_facets': ['pub'],\n", + " 'label': ''},\n", + " 'FlyBase': '',\n", + " 'PubMed': '',\n", + " 'DOI': ''}}],\n", + " 'def_pubs': []}]" ] }, - "execution_count": 2, + "execution_count": 13, "metadata": {}, "output_type": "execute_result" } @@ -200,16 +275,16 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 14, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "dict_keys(['term', 'query', 'version', 'dataset_license', 'parents', 'relationships', 'xrefs', 'channel_image', 'related_individuals'])" + "dict_keys(['term', 'query', 'version', 'dataset_license', 'parents', 'relationships', 'xrefs', 'channel_image', 'pub_syn', 'def_pubs'])" ] }, - "execution_count": 3, + "execution_count": 14, "metadata": {}, "output_type": "execute_result" } @@ -220,25 +295,28 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 15, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "[{'link_base': 'http://flycircuit.tw/modules.php?name=clearpage&op=detail_table&neuron=',\n", - " 'icon': '',\n", - " 'link_postfix': '',\n", - " 'site': {'short_form': 'FlyCircuit',\n", - " 'label': 'FlyCircuit',\n", + " 'site': {'symbol': '',\n", " 'iri': 'http://virtualflybrain.org/reports/FlyCircuit',\n", - " 'types': ['Individual', 'Site', 'Entity']},\n", + " 'types': ['Entity', 'Individual', 'Site'],\n", + " 'short_form': 'FlyCircuit',\n", + " 'unique_facets': ['Site'],\n", + " 'label': 'FlyCircuit 1.0'},\n", + " 'is_data_source': True,\n", + " 'link_postfix': '',\n", + " 'icon': '',\n", " 'accession': 'fru-F-500075',\n", - " 'link_text': 'fru-F-500075 on FlyCircuit',\n", + " 'link_text': 'fru-F-500075 on FlyCircuit 1.0',\n", " 'homepage': 'http://flycircuit.tw'}]" ] }, - "execution_count": 4, + "execution_count": 15, "metadata": {}, "output_type": "execute_result" } @@ -249,39 +327,550 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 16, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "[{'term': {'link': 'http://flybase.org/reports/FBrf0221438.html',\n", - " 'core': {'short_form': 'Ito2013',\n", - " 'label': 'Ito lab adult brain lineage clone image set',\n", + "[{'term': {'core': {'symbol': '',\n", " 'iri': 'http://virtualflybrain.org/reports/Ito2013',\n", - " 'types': ['Individual', 'DataSet', 'Entity']},\n", - " 'description': [\"An exhaustive set of lineage clones covering the adult brain from Kei Ito\\\\'s lab.\"],\n", + " 'types': ['Entity', 'DataSet', 'Individual', 'has_image'],\n", + " 'short_form': 'Ito2013',\n", + " 'unique_facets': ['DataSet'],\n", + " 'label': 'Ito lab adult brain lineage clone image set'},\n", + " 'link': 'http://flybase.org/reports/FBrf0221438.html',\n", + " 'description': [\"An exhaustive set of lineage clones covering the adult brain from Kei Ito's lab.\"],\n", " 'comment': []},\n", " 'query': 'Get JSON for DataSet',\n", - " 'version': '0f4d3af',\n", + " 'version': '3b19da3',\n", + " 'anatomy_channel_image': [{'anatomy': {'symbol': '',\n", + " 'iri': 'http://virtualflybrain.org/reports/VFB_00020206',\n", + " 'types': ['Entity',\n", + " 'Adult',\n", + " 'Anatomy',\n", + " 'Clone',\n", + " 'Individual',\n", + " 'Nervous_system',\n", + " 'VFB',\n", + " 'has_image'],\n", + " 'short_form': 'VFB_00020206',\n", + " 'unique_facets': ['Adult', 'Clone', 'Nervous_system'],\n", + " 'label': 'PSa1 clone of Ito 2013'},\n", + " 'channel_image': {'image': {'image_nrrd': 'http://www.virtualflybrain.org/data/VFB/i/0002/0206/VFB_00017894/volume.nrrd',\n", + " 'image_swc': '',\n", + " 'template_channel': {'symbol': '',\n", + " 'iri': 'http://virtualflybrain.org/reports/VFBc_00017894',\n", + " 'types': ['Entity', 'Individual', 'Template', 'VFB'],\n", + " 'short_form': 'VFBc_00017894',\n", + " 'unique_facets': [],\n", + " 'label': 'JFRC2_template_c'},\n", + " 'index': [],\n", + " 'template_anatomy': {'symbol': '',\n", + " 'iri': 'http://virtualflybrain.org/reports/VFB_00017894',\n", + " 'types': ['Entity',\n", + " 'Adult',\n", + " 'Anatomy',\n", + " 'Individual',\n", + " 'Nervous_system',\n", + " 'Template',\n", + " 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JFRC2'},\n", + " 'image_wlz': 'http://www.virtualflybrain.org/data/VFB/i/0002/0201/VFB_00017894/volume.wlz',\n", + " 'image_obj': 'http://www.virtualflybrain.org/data/VFB/i/0002/0201/VFB_00017894/volume.obj',\n", + " 'image_thumbnail': 'http://www.virtualflybrain.org/data/VFB/i/0002/0201/VFB_00017894/thumbnail.png',\n", + " 'image_folder': 'http://www.virtualflybrain.org/data/VFB/i/0002/0201/VFB_00017894/'},\n", + " 'channel': {'symbol': '',\n", + " 'iri': 'http://virtualflybrain.org/reports/VFBc_00020201',\n", + " 'types': ['Entity', 'Individual', 'VFB'],\n", + " 'short_form': 'VFBc_00020201',\n", + " 'unique_facets': [],\n", + " 'label': 'DM3_01_c'},\n", + " 'imaging_technique': {'symbol': 'Confocal',\n", + " 'iri': 'http://purl.obolibrary.org/obo/FBbi_00000251',\n", + " 'types': ['Entity', 'Class'],\n", + " 'short_form': 'FBbi_00000251',\n", + " 'unique_facets': ['Class'],\n", + " 'label': 'confocal microscopy'}}},\n", + " {'anatomy': {'symbol': '',\n", + " 'iri': 'http://virtualflybrain.org/reports/VFB_00020201',\n", + " 'types': ['Entity',\n", + " 'Adult',\n", + " 'Anatomy',\n", + " 'Clone',\n", + " 'Individual',\n", + " 'Nervous_system',\n", + " 'VFB',\n", + " 'has_image'],\n", + " 'short_form': 'VFB_00020201',\n", + " 'unique_facets': ['Adult', 'Clone', 'Nervous_system'],\n", + " 'label': 'DM3 clone of Ito 2013'},\n", + " 'channel_image': {'image': {'image_nrrd': 'http://www.virtualflybrain.org/data/VFB/i/0002/0201/VFB_00101567/volume.nrrd',\n", + " 'image_swc': '',\n", + " 'template_channel': {'symbol': '',\n", + " 'iri': 'http://virtualflybrain.org/reports/VFBc_00101567',\n", + " 'types': ['Entity', 'Individual', 'Template'],\n", + " 'short_form': 'VFBc_00101567',\n", + " 'unique_facets': [],\n", + " 'label': 'JRC2018Unisex_c'},\n", + " 'index': [],\n", + " 'template_anatomy': {'symbol': '',\n", + " 'iri': 'http://virtualflybrain.org/reports/VFB_00101567',\n", + " 'types': ['Entity',\n", + " 'Adult',\n", + " 'Anatomy',\n", + " 'Individual',\n", + " 'Nervous_system',\n", + " 'Template',\n", + " 'has_image'],\n", + " 'short_form': 'VFB_00101567',\n", + " 'unique_facets': ['Adult', 'Nervous_system'],\n", + " 'label': 'JRC2018Unisex'},\n", + " 'image_wlz': 'http://www.virtualflybrain.org/data/VFB/i/0002/0201/VFB_00101567/volume.wlz',\n", + " 'image_obj': 'http://www.virtualflybrain.org/data/VFB/i/0002/0201/VFB_00101567/volume.obj',\n", + " 'image_thumbnail': 'http://www.virtualflybrain.org/data/VFB/i/0002/0201/VFB_00101567/thumbnail.png',\n", + " 'image_folder': 'http://www.virtualflybrain.org/data/VFB/i/0002/0201/VFB_00101567/'},\n", + " 'channel': {'symbol': '',\n", + " 'iri': 'http://virtualflybrain.org/reports/VFBc_00020201',\n", + " 'types': ['Entity', 'Individual', 'VFB'],\n", + " 'short_form': 'VFBc_00020201',\n", + " 'unique_facets': [],\n", + " 'label': 'DM3_01_c'},\n", + " 'imaging_technique': {'symbol': 'Confocal',\n", + " 'iri': 'http://purl.obolibrary.org/obo/FBbi_00000251',\n", + " 'types': ['Entity', 'Class'],\n", + " 'short_form': 'FBbi_00000251',\n", + " 'unique_facets': ['Class'],\n", + " 'label': 'confocal microscopy'}}}],\n", " 'xrefs': [],\n", - " 'license': [{'icon': 'http://mirrors.creativecommons.org/presskit/buttons/88x31/png/by-nc-sa.png',\n", - " 'link': 'https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode',\n", - " 'core': {'short_form': 'VFBlicense_CC_BY_NC_SA_4_0',\n", - " 'label': 'CC-BY-NC-SA_4.0',\n", + " 'license': [{'core': {'symbol': '',\n", " 'iri': 'http://virtualflybrain.org/reports/VFBlicense_CC_BY_NC_SA_4_0',\n", - " 'types': ['Individual', 'License', 'Entity']}}],\n", - " 'pubs': [{'core': {'short_form': 'FBrf0221438',\n", - " 'label': 'Ito et al., 2013, Curr. Biol. 23(8): 644--655',\n", + " 'types': ['Entity', 'Individual', 'License'],\n", + " 'short_form': 'VFBlicense_CC_BY_NC_SA_4_0',\n", + " 'unique_facets': ['License'],\n", + " 'label': 'CC-BY-NC-SA_4.0'},\n", + " 'icon': 'http://mirrors.creativecommons.org/presskit/buttons/88x31/png/by-nc-sa.png',\n", + " 'link': 'https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode'}],\n", + " 'pubs': [{'core': {'symbol': '',\n", " 'iri': 'http://flybase.org/reports/FBrf0221438',\n", - " 'types': ['Individual', 'pub', 'Entity']},\n", - " 'PubMed': '23541729',\n", + " 'types': ['Entity', 'Individual', 'pub'],\n", + " 'short_form': 'FBrf0221438',\n", + " 'unique_facets': ['pub'],\n", + " 'label': 'Ito et al., 2013, Curr. Biol. 23(8): 644--655'},\n", " 'FlyBase': 'FBrf0221438',\n", + " 'PubMed': '23541729',\n", " 'DOI': '10.1016/j.cub.2013.03.015'}],\n", " 'dataset_counts': {'images': 96, 'types': 96}}]" ] }, - "execution_count": 5, + "execution_count": 16, "metadata": {}, "output_type": "execute_result" } @@ -294,37 +883,51 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 17, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "['catmaid_l1em',\n", - " 'FlyLightSplit',\n", - " 'FlyPNS',\n", - " 'FlyBase',\n", - " 'larvalbrain_axon_tract',\n", - " 'larvalbrain_neuropil',\n", + "['vnc1_catmaid_api',\n", + " 'vnc_harvard_catmaid_api',\n", + " 'l1em_catmaid_api',\n", + " 'fafb_catmaid_api',\n", + " 'jrc_slide_code_api',\n", + " 'InsectBrainDB',\n", + " 'FlyBrain_NDB',\n", " 'catmaid_fafb',\n", + " 'catmaid_fanc',\n", + " 'scExpressionAtlas',\n", " 'Konstantinides_et_al_2018_OpticLobe',\n", - " 'neuprint_JRC_Hemibrain_1point0point1',\n", - " 'fafb_catmaid_api',\n", " 'FlyCircuit',\n", - " 'FlyLight',\n", + " 'QuickGO',\n", + " 'catmaid_l1em',\n", + " 'FlyLightSplit',\n", + " 'AmiGO',\n", + " 'VDRC',\n", + " 'FlyBase',\n", + " 'catmaid_leg40',\n", + " 'larvalbrain_neuropil',\n", " 'BrainTrap',\n", - " 'FlyBrain_NDB',\n", + " 'catmaid_fanc_JRC2018VF',\n", + " 'FlyBase_vocabularies',\n", + " 'FlyLightSplitSlideCode',\n", + " 'FlyLightGen1MCFO',\n", + " 'FlyCircuit1v2',\n", + " 'neuronbridge',\n", + " 'FlyPNS',\n", + " 'larvalbrain_axon_tract',\n", + " 'FlyLightGen1MCFOSlideCode',\n", + " 'FlyLight',\n", " 'DoOR',\n", + " 'neuprint_JRC_Hemibrain_1point0point1',\n", " 'lmb_cluster_pages_v3',\n", " 'lmb_cluster_pages_v2',\n", - " 'VDRC',\n", - " 'l1em_catmaid_api',\n", - " 'neuronbridge',\n", - " 'neuprint_JRC_Hemibrain_1point1',\n", - " 'vnc1_catmaid_api']" + " 'neuprint_JRC_Hemibrain_1point1']" ] }, - "execution_count": 6, + "execution_count": 17, "metadata": {}, "output_type": "execute_result" } @@ -338,86 +941,139 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 18, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "[{'term': {'core': {'short_form': 'VFB_00100184',\n", - " 'label': 'L1 CNS neuron cypress left',\n", - " 'iri': 'http://virtualflybrain.org/reports/VFB_00100184',\n", - " 'types': ['Individual',\n", - " 'VFB',\n", - " '_Individual',\n", - " 'Neuron',\n", + "[{'term': {'core': {'iri': 'http://virtualflybrain.org/reports/VFB_00100184',\n", + " 'symbol': '',\n", + " 'types': ['Entity',\n", " 'Anatomy',\n", " 'Cell',\n", - " 'Entity']},\n", - " 'description': ['A(n) larval subesophageal zone cypress neuron.'],\n", + " 'Individual',\n", + " 'Larva',\n", + " 'Nervous_system',\n", + " 'Neuron',\n", + " 'has_image',\n", + " 'has_neuron_connectivity',\n", + " 'L1EM',\n", + " 'NBLAST'],\n", + " 'short_form': 'VFB_00100184',\n", + " 'unique_facets': ['Larva', 'Nervous_system', 'Neuron'],\n", + " 'label': 'mPN (L1EM:17545695)'},\n", + " 'description': [],\n", " 'comment': []},\n", - " 'query': 'Get JSON for Individual:Anatomy',\n", - " 'version': '0f4d3af',\n", - " 'dataset_license': [{'dataset': {'link': 'https://l1em.catmaid.virtualflybrain.org',\n", - " 'core': {'short_form': 'Berck2016',\n", - " 'label': 'Larval olfactory system neurons - EM (Berk2016)',\n", - " 'iri': 'http://virtualflybrain.org/reports/Berck2016',\n", - " 'types': ['Individual', 'DataSet', 'Entity']}},\n", - " 'license': {'icon': 'https://mirrors.creativecommons.org/presskit/buttons/88x31/png/by-sa.png',\n", - " 'link': 'https://creativecommons.org/licenses/by-sa/4.0/legalcode',\n", - " 'core': {'short_form': 'VFBlicense_CC_BY_SA_4_0',\n", - " 'label': 'CC-BY-SA_4.0',\n", - " 'iri': 'http://virtualflybrain.org/reports/VFBlicense_CC_BY_SA_4_0',\n", - " 'types': ['Individual', 'License', 'Entity']}}}],\n", - " 'parents': [{'short_form': 'FBbt_00111724',\n", - " 'label': 'larval subesophageal zone cypress neuron',\n", + " 'query': 'Get JSON for Individual',\n", + " 'version': '3b19da3',\n", + " 'dataset_license': [{'license': {'core': {'iri': 'http://virtualflybrain.org/reports/VFBlicense_CC_BY_SA_4_0',\n", + " 'symbol': '',\n", + " 'types': ['Entity', 'Individual', 'License'],\n", + " 'short_form': 'VFBlicense_CC_BY_SA_4_0',\n", + " 'unique_facets': ['License'],\n", + " 'label': 'CC-BY-SA_4.0'},\n", + " 'icon': 'https://mirrors.creativecommons.org/presskit/buttons/88x31/png/by-sa.png',\n", + " 'link': 'https://creativecommons.org/licenses/by-sa/4.0/legalcode'},\n", + " 'dataset': {'core': {'iri': 'http://virtualflybrain.org/reports/Berck2016',\n", + " 'symbol': '',\n", + " 'types': ['Entity', 'DataSet', 'Individual', 'has_image'],\n", + " 'short_form': 'Berck2016',\n", + " 'unique_facets': ['DataSet'],\n", + " 'label': 'Larval olfactory system neurons - EM (Berk2016)'},\n", + " 'link': 'https://l1em.catmaid.virtualflybrain.org'}}],\n", + " 'parents': [{'symbol': '',\n", " 'iri': 'http://purl.obolibrary.org/obo/FBbt_00111724',\n", - " 'types': ['Class',\n", - " 'VFB',\n", - " '_Class',\n", - " 'Neuron',\n", + " 'types': ['Entity',\n", " 'Anatomy',\n", " 'Cell',\n", - " 'Entity',\n", - " 'Leaf_node']}],\n", + " 'Class',\n", + " 'Larva',\n", + " 'Nervous_system',\n", + " 'Neuron'],\n", + " 'short_form': 'FBbt_00111724',\n", + " 'unique_facets': ['Larva', 'Nervous_system', 'Neuron'],\n", + " 'label': 'larval subesophageal zone cypress neuron'}],\n", " 'relationships': [],\n", " 'xrefs': [{'link_base': 'https://l1em.catmaid.virtualflybrain.org/?pid=1&tool=tracingtool&sid0=1&s0=2&active_skeleton_id=',\n", - " 'icon': '',\n", - " 'link_postfix': '',\n", - " 'site': {'short_form': 'catmaid_l1em',\n", - " 'label': 'VFB CATMAID L1 CNS',\n", + " 'site': {'symbol': '',\n", " 'iri': 'http://virtualflybrain.org/reports/catmaid_l1em',\n", - " 'types': ['Individual', 'Site', 'Entity']},\n", + " 'types': ['Entity', 'Individual', 'Site'],\n", + " 'short_form': 'catmaid_l1em',\n", + " 'unique_facets': ['Site'],\n", + " 'label': 'VFB CATMAID L1 CNS'},\n", + " 'is_data_source': True,\n", + " 'link_postfix': '',\n", + " 'icon': '',\n", " 'accession': '17545695',\n", - " 'link_text': 'L1 CNS neuron cypress left on VFB CATMAID L1 CNS',\n", - " 'homepage': 'https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=56100&yp=32927.1&xp=27265&tool=tracingtool&sid0=1&s0=2'}],\n", - " 'channel_image': [{'channel': {'short_form': 'VFBc_00100184',\n", - " 'label': 'L1 CNS neuron cypress left_c',\n", - " 'iri': 'http://virtualflybrain.org/reports/VFBc_00100184',\n", - " 'types': ['Individual', 'Entity']},\n", - " 'imaging_technique': {'short_form': 'FBbi_00000258',\n", - " 'label': 'transmission electron microscopy (TEM)',\n", - " 'iri': 'http://purl.obolibrary.org/obo/FBbi_00000258',\n", - " 'types': ['Class', '_Class', 'FBBI', 'Entity']},\n", - " 'image': {'template_channel': {'short_form': 'VFBc_00050000',\n", - " 'label': 'L1 larval CNS ssTEM - Cardona/Janelia_c',\n", + " 'link_text': 'mPN (L1EM:17545695) on VFB CATMAID L1 CNS',\n", + " 'homepage': 'https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=108250&yp=82961.59999999999&xp=54210.799999999996&tool=tracingtool&sid0=1&s0=2.4999999999999996&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22papers%22%7D%7D,%200.6)'}],\n", + " 'channel_image': [{'image': {'image_nrrd': 'http://www.virtualflybrain.org/data/VFB/i/0010/0184/VFB_00050000/volume.nrrd',\n", + " 'image_swc': 'http://www.virtualflybrain.org/data/VFB/i/0010/0184/VFB_00050000/volume.swc',\n", + " 'template_channel': {'symbol': '',\n", " 'iri': 'http://virtualflybrain.org/reports/VFBc_00050000',\n", - " 'types': ['Individual', 'Template', 'Entity']},\n", - " 'template_anatomy': {'short_form': 'VFB_00050000',\n", - " 'label': 'L1 larval CNS ssTEM - Cardona/Janelia',\n", + " 'types': ['Entity', 'Individual', 'Template'],\n", + " 'short_form': 'VFBc_00050000',\n", + " 'unique_facets': [],\n", + " 'label': 'L1 larval CNS ssTEM - Cardona/Janelia_c'},\n", + " 'index': [],\n", + " 'template_anatomy': {'symbol': '',\n", " 'iri': 'http://virtualflybrain.org/reports/VFB_00050000',\n", - " 'types': ['Individual',\n", - " 'VFB',\n", - " '_Individual',\n", - " 'Template',\n", + " 'types': ['Entity',\n", " 'Anatomy',\n", - " 'Entity']},\n", - " 'image_folder': 'http://www.virtualflybrain.org/data/VFB/i/0010/0184/',\n", - " 'index': []}}],\n", - " 'related_individuals': []}]" + " 'Individual',\n", + " 'Larva',\n", + " 'Nervous_system',\n", + " 'Template',\n", + " 'has_image',\n", + " 'L1EM'],\n", + " 'short_form': 'VFB_00050000',\n", + " 'unique_facets': ['Larva', 'Nervous_system'],\n", + " 'label': 'L1 larval CNS ssTEM - Cardona/Janelia'},\n", + " 'image_wlz': 'http://www.virtualflybrain.org/data/VFB/i/0010/0184/VFB_00050000/volume.wlz',\n", + " 'image_obj': 'http://www.virtualflybrain.org/data/VFB/i/0010/0184/VFB_00050000/volume.obj',\n", + " 'image_thumbnail': 'http://www.virtualflybrain.org/data/VFB/i/0010/0184/VFB_00050000/thumbnail.png',\n", + " 'image_folder': 'http://www.virtualflybrain.org/data/VFB/i/0010/0184/VFB_00050000/'},\n", + " 'channel': {'symbol': '',\n", + " 'iri': 'http://virtualflybrain.org/reports/VFBc_00100184',\n", + " 'types': ['Entity', 'Individual'],\n", + " 'short_form': 'VFBc_00100184',\n", + " 'unique_facets': [],\n", + " 'label': 'L1 CNS neuron cypress left_c'},\n", + " 'imaging_technique': {'symbol': 'TEM',\n", + " 'iri': 'http://purl.obolibrary.org/obo/FBbi_00000258',\n", + " 'types': ['Entity', 'Class'],\n", + " 'short_form': 'FBbi_00000258',\n", + " 'unique_facets': ['Class'],\n", + " 'label': 'transmission electron microscopy (TEM)'}}],\n", + " 'pub_syn': [{'synonym': {'scope': 'has_exact_synonym',\n", + " 'label': 'cypress left',\n", + " 'type': ''},\n", + " 'pub': {'core': {'symbol': '',\n", + " 'iri': 'http://flybase.org/reports/Unattributed',\n", + " 'types': ['Entity', 'Individual', 'pub'],\n", + " 'short_form': 'Unattributed',\n", + " 'unique_facets': ['pub'],\n", + " 'label': ''},\n", + " 'FlyBase': '',\n", + " 'PubMed': '',\n", + " 'DOI': ''}},\n", + " {'synonym': {'scope': 'has_exact_synonym',\n", + " 'label': 'skid:17545695',\n", + " 'type': ''},\n", + " 'pub': {'core': {'symbol': '',\n", + " 'iri': 'http://flybase.org/reports/Unattributed',\n", + " 'types': ['Entity', 'Individual', 'pub'],\n", + " 'short_form': 'Unattributed',\n", + " 'unique_facets': ['pub'],\n", + " 'label': ''},\n", + " 'FlyBase': '',\n", + " 'PubMed': '',\n", + " 'DOI': ''}}],\n", + " 'def_pubs': []}]" ] }, - "execution_count": 7, + "execution_count": 18, "metadata": {}, "output_type": "execute_result" } @@ -429,25 +1085,25 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 19, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "[('10958111', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_001001bs'}]),\n", - " ('9362069', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_001000sr'}]),\n", - " ('9896992', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_001000y4'}]),\n", - " ('4355299', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_00101346'}]),\n", - " ('8336193', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_001000n4'}]),\n", - " ('10883867', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_001001ae'}]),\n", - " ('3445525', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_00101273'}]),\n", - " ('17194', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_001000cc'}]),\n", - " ('57414', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_00101174'}]),\n", - " ('62434', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_00101244'}])]" + "[('8715730', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_001014lj'}]),\n", + " ('10604732', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_0010018d'}]),\n", + " ('36108', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_00101209'}]),\n", + " ('9672619', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_001000w0'}]),\n", + " ('2766186', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_0010123z'}]),\n", + " ('30891', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_00101219'}]),\n", + " ('10483848', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_001029b4'}]),\n", + " ('4081200', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_001011ln'}]),\n", + " ('9874011', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_001000xq'}]),\n", + " ('8242', [{'db': 'catmaid_fafb', 'vfb_id': 'VFB_0010005d'}])]" ] }, - "execution_count": 15, + "execution_count": 19, "metadata": {}, "output_type": "execute_result" } @@ -460,7 +1116,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 20, "metadata": {}, "outputs": [ { @@ -469,16 +1125,16 @@ "text": [ "Running query: RO:0002131 some FBbt:00003679\n", "Query URL: http://owl.virtualflybrain.org/kbs/vfb/subclasses?object=RO%3A0002131+some+FBbt%3A00003679&prefixes=%7B%22FBbt%22%3A+%22http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FFBbt_%22%2C+%22RO%22%3A+%22http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_%22%2C+%22BFO%22%3A+%22http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_%22%7D&direct=False\n", - "Query results: 183\n" + "Query results: 233\n" ] }, { "data": { "text/plain": [ - "183" + "233" ] }, - "execution_count": 8, + "execution_count": 20, "metadata": {}, "output_type": "execute_result" } @@ -495,7 +1151,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 21, "metadata": {}, "outputs": [ { @@ -504,27 +1160,25 @@ "text": [ "Running query: RO:0002131 some FBbt:00003679\n", "Query URL: http://owl.virtualflybrain.org/kbs/vfb/subclasses?object=RO%3A0002131+some+FBbt%3A00003679&prefixes=%7B%22FBbt%22%3A+%22http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FFBbt_%22%2C+%22RO%22%3A+%22http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_%22%2C+%22BFO%22%3A+%22http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_%22%7D&direct=False\n", - "Query results: 183\n" + "Query results: 233\n" ] }, { "data": { "text/plain": [ - "[('adult SIPp1 lineage clone', 'FBbt_00050078'),\n", - " ('PB 1 glomerulus-FB layers 1 to 4-bilateral IDFP HB-medial neuron',\n", - " 'FBbt_00111451'),\n", - " ('PB slice 7-FB layers 3 and 6-ventral gall ipsilateral neuron',\n", - " 'FBbt_00111463'),\n", - " ('horizontal fiber system neuron pb3', 'FBbt_00007572'),\n", - " ('pb-fb neuron', 'FBbt_00111050'),\n", - " ('PB slice 6-FB layers 3-5-IDFP RB neuron', 'FBbt_00111430'),\n", - " ('fan-shaped body slice 4', 'FBbt_00110645'),\n", - " ('extrinsic ring neuron ExR1', 'FBbt_00003655'),\n", - " ('vertical fiber system neuron pb7', 'FBbt_00007560'),\n", - " ('PB slice 3-FB-NO3 anterior domain neuron', 'FBbt_00111397')]" + "[('fan-shaped body layer 4', 'FBbt_00007491'),\n", + " ('fan-shaped body layer 5', 'FBbt_00007492'),\n", + " ('fan-shaped body layer 3', 'FBbt_00007490'),\n", + " ('octopaminergic VPM3 neuron', 'FBbt_00110151'),\n", + " ('fan-shaped body segment pair Z', 'FBbt_00007497'),\n", + " ('fan-shaped body segment pair X', 'FBbt_00007495'),\n", + " ('fan-shaped body segment pair Y', 'FBbt_00007496'),\n", + " ('fan-shaped body layer 6', 'FBbt_00007493'),\n", + " ('fan-shaped body segment pair W', 'FBbt_00007494'),\n", + " ('fan-shaped body layer 9', 'FBbt_00047032')]" ] }, - "execution_count": 9, + "execution_count": 21, "metadata": {}, "output_type": "execute_result" } @@ -536,53 +1190,34 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 22, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Running query: FBbt:00111724\n" - ] - }, - { - "ename": "KeyboardInterrupt", - "evalue": "", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mcyp_neuron_images\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_images\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'larval subesophageal zone cypress neuron'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", - "\u001b[0;32m/usr/local/lib/python3.8/site-packages/vfb_connect/cross_server_tools.py\u001b[0m in \u001b[0;36mget_images\u001b[0;34m(self, class_expression, query_by_label, direct)\u001b[0m\n\u001b[1;32m 62\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mre\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msearch\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"'\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mclass_expression\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 63\u001b[0m \u001b[0mclass_expression\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"'\"\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mclass_expression\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m\"'\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 64\u001b[0;31m \u001b[0mterms\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_instances\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"%s\"\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mclass_expression\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mquery_by_label\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mquery_by_label\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 65\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mneo_query_wrapper\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_anatomical_individual_TermInfo\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmap\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mgen_short_form\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mterms\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 66\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/usr/local/lib/python3.8/site-packages/vfb_connect/owl/owlery_query_tools.py\u001b[0m in \u001b[0;36mget_instances\u001b[0;34m(self, query, query_by_label, direct)\u001b[0m\n\u001b[1;32m 80\u001b[0m \"\"\"Get instances satisfying query, where query is an OWL DL query\n\u001b[1;32m 81\u001b[0m \"\"\"\n\u001b[0;32m---> 82\u001b[0;31m return self.query(query_type='instances', return_type='hasInstance',\n\u001b[0m\u001b[1;32m 83\u001b[0m \u001b[0mquery\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mquery\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mquery_by_label\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mquery_by_label\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 84\u001b[0m direct=direct)\n", - "\u001b[0;32m/usr/local/lib/python3.8/site-packages/vfb_connect/owl/owlery_query_tools.py\u001b[0m in \u001b[0;36mquery\u001b[0;34m(self, query_type, return_type, query, query_by_label, direct, verbose)\u001b[0m\n\u001b[1;32m 61\u001b[0m 'direct': direct}\n\u001b[1;32m 62\u001b[0m \u001b[0;31m# print(payload)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 63\u001b[0;31m \u001b[0mr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrequests\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0murl\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mowl_endpoint\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mparams\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mpayload\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 64\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Query URL: \"\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0murl\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 65\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstatus_code\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;36m200\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/usr/local/lib/python3.8/site-packages/requests/api.py\u001b[0m in \u001b[0;36mget\u001b[0;34m(url, params, **kwargs)\u001b[0m\n\u001b[1;32m 74\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 75\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msetdefault\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'allow_redirects'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 76\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mrequest\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'get'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0murl\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mparams\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mparams\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 77\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 78\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/usr/local/lib/python3.8/site-packages/requests/api.py\u001b[0m in \u001b[0;36mrequest\u001b[0;34m(method, url, **kwargs)\u001b[0m\n\u001b[1;32m 59\u001b[0m \u001b[0;31m# cases, and look like a memory leak in others.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 60\u001b[0m \u001b[0;32mwith\u001b[0m \u001b[0msessions\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mSession\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0msession\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 61\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0msession\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrequest\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmethod\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmethod\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0murl\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0murl\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 62\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 63\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m/usr/local/lib/python3.8/site-packages/requests/sessions.py\u001b[0m in \u001b[0;36mrequest\u001b[0;34m(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json)\u001b[0m\n\u001b[1;32m 528\u001b[0m }\n\u001b[1;32m 529\u001b[0m \u001b[0msend_kwargs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mupdate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msettings\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 530\u001b[0;31m \u001b[0mresp\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mprep\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0msend_kwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 531\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 532\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mresp\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - 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"\u001b[0;32m/usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/lib/python3.8/socket.py\u001b[0m in \u001b[0;36mreadinto\u001b[0;34m(self, b)\u001b[0m\n\u001b[1;32m 667\u001b[0m \u001b[0;32mwhile\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 668\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 669\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_sock\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrecv_into\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mb\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 670\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mtimeout\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 671\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_timeout_occurred\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mKeyboardInterrupt\u001b[0m: " - ] - } - ], + "outputs": [], "source": [ "cyp_neuron_images = vc.get_instances('larval subesophageal zone cypress neuron')" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 23, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "[('mPN (L1EM:17545695)',\n", + " [{'image_folder': 'http://www.virtualflybrain.org/data/VFB/i/0010/0184/VFB_00050000/',\n", + " 'template': 'L1 larval CNS ssTEM - Cardona/Janelia'}]),\n", + " ('mPN (L1EM:14154154)',\n", + " [{'image_folder': 'http://www.virtualflybrain.org/data/VFB/i/0010/0173/VFB_00050000/',\n", + " 'template': 'L1 larval CNS ssTEM - Cardona/Janelia'}])]" + ] + }, + "execution_count": 23, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "# Returned JSON includes direct links to image folders for each template the image is registered to:\n", "\n", @@ -593,9 +1228,32 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 24, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "[('fan-shaped body on adult brain template JFRC2',\n", + " [{'image_folder': 'http://www.virtualflybrain.org/data/VFB/i/0003/0633/VFB_00017894/',\n", + " 'template': 'adult brain template JFRC2'}]),\n", + " ('FB on JRC_FlyEM_Hemibrain',\n", + " [{'image_folder': 'http://www.virtualflybrain.org/data/VFB/i/0010/1398/VFB_00101384/',\n", + " 'template': 'JRC_FlyEM_Hemibrain'}]),\n", + " ('FB on JRC2018Unisex adult brain',\n", + " [{'image_folder': 'http://www.virtualflybrain.org/data/VFB/i/0010/2134/VFB_00101567/',\n", + " 'template': 'JRC2018Unisex'}]),\n", + " ('fan-shaped body on adult brain template Ito2014',\n", + " [{'image_folder': 'http://www.virtualflybrain.org/data/VFB/i/0003/0811/VFB_00030786/',\n", + " 'template': 'adult brain template Ito2014'}]),\n", + " ('FB-column3 on JRC_FlyEM_Hemibrain', [])]" + ] + }, + "execution_count": 24, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "[(i['term']['core']['label'],\n", " [{ 'image_folder': x['image']['image_folder'], 'template': x['image']['template_anatomy']['label']}\n", @@ -604,9 +1262,39 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 25, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "[('CREa1A_H22(b2)_0_2018U',\n", + " ['adult CREa1 lineage neuron', 'dopaminergic PAM neuron'],\n", + " [{'image_folder': 'http://www.virtualflybrain.org/data/VFB/i/0010/2734/VFB_00101567/',\n", + " 'template': 'JRC2018Unisex'}]),\n", + " ('CREa1A_H17(r4_r2)_0_2018U',\n", + " ['adult CREa1 lineage neuron', 'dopaminergic PAM neuron'],\n", + " [{'image_folder': 'http://www.virtualflybrain.org/data/VFB/i/0010/2729/VFB_00101567/',\n", + " 'template': 'JRC2018Unisex'}]),\n", + " ('CREa2A_H17(r4_r2)_0_2018U',\n", + " ['adult DALcm1 lineage neuron', 'dopaminergic PAM neuron'],\n", + " [{'image_folder': 'http://www.virtualflybrain.org/data/VFB/i/0010/2457/VFB_00101567/',\n", + " 'template': 'JRC2018Unisex'}]),\n", + " (\"CREa2A_H07(b\\\\'2r5)_0_2018U\",\n", + " ['adult DALcm1 lineage neuron', 'dopaminergic PAM neuron'],\n", + " [{'image_folder': 'http://www.virtualflybrain.org/data/VFB/i/0010/2447/VFB_00101567/',\n", + " 'template': 'JRC2018Unisex'}]),\n", + " ('CREa2A_H19(r4_5)_0_2018U',\n", + " ['dopaminergic PAM neuron', 'adult DALcm1 lineage neuron'],\n", + " [{'image_folder': 'http://www.virtualflybrain.org/data/VFB/i/0010/2459/VFB_00101567/',\n", + " 'template': 'JRC2018Unisex'}])]" + ] + }, + "execution_count": 25, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "# Image queries range across multiple types\n", "[(i['term']['core']['label'],\n", @@ -617,7 +1305,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 26, "metadata": {}, "outputs": [ { @@ -662,7 +1350,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 27, "metadata": {}, "outputs": [ { @@ -681,7 +1369,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 28, "metadata": {}, "outputs": [ { @@ -748,7 +1436,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9" + "version": "3.7.5" } }, "nbformat": 4,