From b8fdc147ad859d6e491657a6ad3fc8e8924c6b9e Mon Sep 17 00:00:00 2001 From: dvklopfenstein Date: Sun, 16 May 2021 10:52:39 -0400 Subject: [PATCH] v76 --- doc/md/README_download_hints.md | 46 +- ...8_molecules_in_interleukin_signaling.ipynb | 15 +- .../tutorial/fig4b_2018_ccr5_pathways.ipynb | 10 +- notebooks/tutorial/s1a_get_pathway.ipynb | 6 +- notebooks/tutorial/s1b_get_protein.ipynb | 2 +- .../tutorial/s2a_get_protein_fields.ipynb | 8 +- .../s2b_get_protein_fields_from_nodes.ipynb | 2 +- .../s3a_get_participants_complexes.ipynb | 636 +++++++++--------- .../tutorial/s4a_pathway_subpathways.ipynb | 8 +- .../tutorial/s4b_pathway_superpathways.ipynb | 4 +- .../tutorial/s5a_pathway_reactions.ipynb | 100 ++- .../tutorial/s6a_reaction_participants.ipynb | 8 +- .../tutorial/s6b_reaction_participants.ipynb | 2 +- .../tutorial/s7a_pathway_molecules.ipynb | 6 +- src/bin/compare_reactome_version.py | 7 +- 15 files changed, 451 insertions(+), 409 deletions(-) diff --git a/doc/md/README_download_hints.md b/doc/md/README_download_hints.md index 250d1d6..eb0bb81 100644 --- a/doc/md/README_download_hints.md +++ b/doc/md/README_download_hints.md @@ -41,7 +41,7 @@ Does the graph.db directory exist? No? Go to step 4. ``` -$ cd ~/neo4j/neo4j-community-3.4.7/data/databases/ +$ cd ~/neo4j/neo4j-community-4.1.9/data/databases/ $ ls graph.db ls: cannot access 'graph.db': No such file or directory ``` @@ -60,10 +60,10 @@ $ ls graph.db ### 4. Moved the Reactome database to the graph.db directory ``` -$ mv reactome.graphdb.v67 ~/neo4j/neo4j-community-3.4.7/data/databases/graph.db +$ mv reactome.graphdb.v67 ~/neo4j/neo4j-community-4.1.9/data/databases/graph.db # Confirm it is moved -$ cd ~/neo4j/neo4j-community-3.4.7/data/databases/graph.db +$ cd ~/neo4j/neo4j-community-4.1.9/data/databases/graph.db $ ls graph.db debug.log neostore.nodestore.db.labels neostore.relationshipgroupstore.db.id index neostore.nodestore.db.labels.id neostore.relationshipstore.db @@ -75,38 +75,46 @@ $ ls graph.db [Where to look if it does not work](#where-to-look-if-it-does-not-work) ``` -$ neo4j/neo4j-community-3.4.7/bin/neo4j start +$ neo4j/neo4j-community-4.1.9/bin/neo4j start Active database: graph.db Directories in use: - home: /home/neo4j/neo4j/neo4j-community-3.4.7 - config: /home/neo4j/neo4j/neo4j-community-3.4.7/conf/ - logs: /home/neo4j/neo4j/neo4j-community-3.4.7/logs - plugins: /home/neo4j/neo4j/neo4j-community-3.4.7/plugins - import: /home/neo4j/neo4j/neo4j-community-3.4.7/import - data: /home/neo4j/neo4j/neo4j-community-3.4.7/data - certificates: /home/neo4j/neo4j/neo4j-community-3.4.7/certificates - run: /home/neo4j/neo4j/neo4j-community-3.4.7/run + home: /home/neo4j/neo4j/neo4j-community-4.1.9 + config: /home/neo4j/neo4j/neo4j-community-4.1.9/conf/ + logs: /home/neo4j/neo4j/neo4j-community-4.1.9/logs + plugins: /home/neo4j/neo4j/neo4j-community-4.1.9/plugins + import: /home/neo4j/neo4j/neo4j-community-4.1.9/import + data: /home/neo4j/neo4j/neo4j-community-4.1.9/data + certificates: /home/neo4j/neo4j/neo4j-community-4.1.9/certificates + run: /home/neo4j/neo4j/neo4j-community-4.1.9/run Starting Neo4j. WARNING: Max 1024 open files allowed, minimum of 40000 recommended. See the Neo4j manual. Started neo4j (pid 545). It is available at http://localhost:7474/ There may be a short delay until the server is ready. - See /home/neo4j/neo4j/neo4j-community-3.4.7/logs/neo4j.log for current status. + See /home/neo4j/neo4j/neo4j-community-4.1.9/logs/neo4j.log for current status. ``` #### Where to look if it does not work -Look at the bottom of both the **debug.log** and the **neo4j.log** +Look at the bottom of both the **debug.log** and the **neo4j.log** ``` -$ find neo4j-community-3.4.7/logs -type f -neo4j-community-3.4.7/logs/debug.log -neo4j-community-3.4.7/logs/neo4j.log +$ find neo4j-community-4.1.9/logs -type f +neo4j-community-4.1.9/logs/debug.log +neo4j-community-4.1.9/logs/neo4j.log +``` + +Your neo4j config file is at `/home/neo4j/neo4j/neo4j-community-4.1.9/conf/neo4j.conf` if you see this in the `debug.log` file: +``` +Neo4j cannot be started because the database files require +upgrading and upgrades are disabled in the configuration. +Please set 'dbms.allow_upgrade' to 'true' in your +configuration file and try again. ``` ### 6. Connect to the server for the first time #### You will need to create a password -Setting both *Username* and *Password* to *neo4j* worked for us. Your results may vary. +Setting both *Username* and *Password* to *neo4j* worked for us when loading a new Reactome database version for the first time. ![Authentification1](/doc/md/images/neo4j_reactome_connect1.png) -#### Create your password +#### You will be asked to create a new password ![new password](/doc/md/images/neo4j_reactome_connect2.png) ### 7. View the Reactome database in the neo4j browser diff --git a/notebooks/tutorial/fig4a_2018_molecules_in_interleukin_signaling.ipynb b/notebooks/tutorial/fig4a_2018_molecules_in_interleukin_signaling.ipynb index 99d3205..9a145bb 100644 --- a/notebooks/tutorial/fig4a_2018_molecules_in_interleukin_signaling.ipynb +++ b/notebooks/tutorial/fig4a_2018_molecules_in_interleukin_signaling.ipynb @@ -14,7 +14,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ @@ -37,7 +37,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ @@ -56,7 +56,7 @@ "# Query and get the sub-pathways under R-HSA-983169\n", "def _get_data():\n", " with gdbdr.session() as session:\n", - " return [rec.data() for rec in session.run(query).records()]\n", + " return session.run(query).data()\n", "\n", "data = _get_data()" ] @@ -70,14 +70,14 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "223 molecules participate in \"Interleukin-4 and 13 signaling\":\n", + "228 molecules participate in \"Interleukin-4 and 13 signaling\":\n", "\n", "Database| ID | Name\n", "--------|-----------------|--------------------------\n", @@ -181,6 +181,11 @@ "ENSEMBL | ENSG00000112715 | VEGFA gene [nucleoplasm]\n", "ENSEMBL | ENSG00000026025 | VIM gene [nucleoplasm]\n", "ENSEMBL | ENSG00000148516 | ZEB1 gene [nucleoplasm]\n", + "Guide to Pharmacology| 8912 | acalabrutinib [cytosol]\n", + "Guide to Pharmacology| 7792 | baricitinib [cytosol]\n", + "Guide to Pharmacology| 6912 | ibrutinib [cytosol]\n", + "Guide to Pharmacology| 5688 | ruxolitinib [cytosol]\n", + "Guide to Pharmacology| 5677 | tofacitinib [cytosol]\n", "UniProt | P16671 | 4xPalmC-CD36 [plasma membrane]\n", "UniProt | P31749 | AKT1 [cytosol]\n", "UniProt | P16050 | ALOX15 [cytosol]\n", diff --git a/notebooks/tutorial/fig4b_2018_ccr5_pathways.ipynb b/notebooks/tutorial/fig4b_2018_ccr5_pathways.ipynb index 2d9f544..6d1a3f0 100644 --- a/notebooks/tutorial/fig4b_2018_ccr5_pathways.ipynb +++ b/notebooks/tutorial/fig4b_2018_ccr5_pathways.ipynb @@ -14,7 +14,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ @@ -37,7 +37,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ @@ -53,7 +53,7 @@ "# Query and get the sub-pathways under R-HSA-983169\n", "def _get_data():\n", " with gdbdr.session() as session:\n", - " return [rec.data() for rec in session.run(query).records()]\n", + " return session.run(query).data()\n", "\n", "data = _get_data()" ] @@ -67,14 +67,14 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "18 sub-pathways found\n", + "18 sub-pathways found:\n", "\n", " ID | Pathway Name\n", "--------------|----------------------\n", diff --git a/notebooks/tutorial/s1a_get_pathway.ipynb b/notebooks/tutorial/s1a_get_pathway.ipynb index 8ebac68..c3447a2 100644 --- a/notebooks/tutorial/s1a_get_pathway.ipynb +++ b/notebooks/tutorial/s1a_get_pathway.ipynb @@ -45,15 +45,15 @@ "output_type": "stream", "text": [ " schemaClass Pathway\n", - " speciesName Homo sapiens\n", " oldStId REACT_111119\n", " isInDisease False\n", " releaseDate 2011-09-20\n", " displayName Antigen processing-Cross presentation\n", + " stId R-HSA-1236975\n", + " speciesName Homo sapiens\n", " stIdVersion R-HSA-1236975.1\n", " dbId 1236975\n", " name ['Antigen processing-Cross presentation']\n", - " stId R-HSA-1236975\n", " hasDiagram False\n", " isInferred False\n" ] @@ -63,7 +63,7 @@ "query = 'MATCH (pathway:Pathway{stId:\"R-HSA-1236975\"}) RETURN pathway'\n", "\n", "with gdbdr.session() as session:\n", - " for rec in session.run(query).records():\n", + " for rec in session.run(query).data():\n", " for key, val in rec['pathway'].items():\n", " print(\" {KEY:11} {VAL}\".format(KEY=key, VAL=val))" ] diff --git a/notebooks/tutorial/s1b_get_protein.ipynb b/notebooks/tutorial/s1b_get_protein.ipynb index 47dfd4b..6cfc186 100644 --- a/notebooks/tutorial/s1b_get_protein.ipynb +++ b/notebooks/tutorial/s1b_get_protein.ipynb @@ -64,7 +64,7 @@ "query = 'MATCH (ewas:EntityWithAccessionedSequence{stId:\"R-HSA-199420\"}) RETURN ewas'\n", "\n", "with gdbdr.session() as session:\n", - " for rec in session.run(query).records():\n", + " for rec in session.run(query).data():\n", " for key, val in rec['ewas'].items():\n", " print(\" {KEY:11} {VAL}\".format(KEY=key, VAL=val))" ] diff --git a/notebooks/tutorial/s2a_get_protein_fields.ipynb b/notebooks/tutorial/s2a_get_protein_fields.ipynb index b9b36f9..9a151f7 100644 --- a/notebooks/tutorial/s2a_get_protein_fields.ipynb +++ b/notebooks/tutorial/s2a_get_protein_fields.ipynb @@ -14,7 +14,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -38,7 +38,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 2, "metadata": {}, "outputs": [ { @@ -55,7 +55,7 @@ " 'RETURN ewas.displayName AS Name, re.identifier AS ID')\n", "\n", "with gdbdr.session() as session:\n", - " for rec in session.run(query).records():\n", + " for rec in session.run(query).data():\n", " print(\" {ID:11} {Name}\".format(**rec))" ] }, @@ -63,7 +63,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Copyright (C) 2018-2021, DV Klopfenstein. All rights reserved." + "Copyright (C) 2018-present, DV Klopfenstein. All rights reserved." ] } ], diff --git a/notebooks/tutorial/s2b_get_protein_fields_from_nodes.ipynb b/notebooks/tutorial/s2b_get_protein_fields_from_nodes.ipynb index 7ad8828..8d69a59 100644 --- a/notebooks/tutorial/s2b_get_protein_fields_from_nodes.ipynb +++ b/notebooks/tutorial/s2b_get_protein_fields_from_nodes.ipynb @@ -58,7 +58,7 @@ " 'rd.displayName AS Database')\n", "\n", "with gdbdr.session() as session:\n", - " for rec in session.run(query).records():\n", + " for rec in session.run(query).data():\n", " print(\" {ID} {Database} {Name}\".format(**rec))" ] }, diff --git a/notebooks/tutorial/s3a_get_participants_complexes.ipynb b/notebooks/tutorial/s3a_get_participants_complexes.ipynb index 95ba74a..b7b4bba 100644 --- a/notebooks/tutorial/s3a_get_participants_complexes.ipynb +++ b/notebooks/tutorial/s3a_get_participants_complexes.ipynb @@ -13,7 +13,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ @@ -36,7 +36,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 5, "metadata": {}, "outputs": [ { @@ -55,8 +55,8 @@ " 'pe.stId AS ID, pe.displayName AS Name, pe.schemaClass as schemaClass')\n", "\n", "with gdbdr.session() as session:\n", - " for rec in session.run(query).records():\n", - " print(\" {ID} {schemaClass} {Name}\".format(**rec))" + " for dct in session.run(query).data():\n", + " print(\" {ID} {schemaClass} {Name}\".format(**dct))" ] }, { @@ -77,321 +77,315 @@ "name": "stdout", "output_type": "stream", "text": [ - " R-HSA-141412 EntityWithAccessionedSequence CDC20 [cytosol]\n", - " R-HSA-174242 EntityWithAccessionedSequence ANAPC7 [cytosol]\n", - " R-HSA-174211 EntityWithAccessionedSequence ANAPC5 [cytosol]\n", - " R-HSA-174052 EntityWithAccessionedSequence CDC26 [cytosol]\n", - " R-HSA-174244 EntityWithAccessionedSequence UBE2C [cytosol]\n", - " R-HSA-174126 EntityWithAccessionedSequence ANAPC11 [cytosol]\n", - " R-HSA-174156 EntityWithAccessionedSequence CDC16 [cytosol]\n", - " R-HSA-174189 EntityWithAccessionedSequence ANAPC1 [cytosol]\n", - " R-HSA-174100 EntityWithAccessionedSequence UBE2E1 [cytosol]\n", - " R-HSA-174229 EntityWithAccessionedSequence ANAPC2 [cytosol]\n", - " R-HSA-174168 EntityWithAccessionedSequence ANAPC4 [cytosol]\n", - " R-HSA-174073 EntityWithAccessionedSequence CDC27 [cytosol]\n", - " R-HSA-174137 EntityWithAccessionedSequence CDC23 [cytosol]\n", - " R-HSA-174142 EntityWithAccessionedSequence ANAPC10 [cytosol]\n", - " R-HSA-174236 EntityWithAccessionedSequence UBE2D1 [cytosol]\n", - " R-HSA-113595 DefinedSet Ub [cytosol]\n", - " R-HSA-939214 EntityWithAccessionedSequence UBB(1-76) [cytosol]\n", - " R-HSA-939213 EntityWithAccessionedSequence UBB(77-152) [cytosol]\n", - " R-HSA-939239 EntityWithAccessionedSequence UBC(533-608) [cytosol]\n", - " R-HSA-939205 EntityWithAccessionedSequence RPS27A(1-76) [cytosol]\n", - " R-HSA-939203 EntityWithAccessionedSequence UBA52(1-76) [cytosol]\n", - " R-HSA-939232 EntityWithAccessionedSequence UBC(305-380) [cytosol]\n", - " R-HSA-939230 EntityWithAccessionedSequence UBB(153-228) [cytosol]\n", - " R-HSA-939164 EntityWithAccessionedSequence UBC(77-152) [cytosol]\n", - " R-HSA-939165 EntityWithAccessionedSequence UBC(609-684) [cytosol]\n", - " R-HSA-939258 EntityWithAccessionedSequence UBC(153-228) [cytosol]\n", - " R-HSA-939192 EntityWithAccessionedSequence UBC(229-304) [cytosol]\n", - " R-HSA-939191 EntityWithAccessionedSequence UBC(381-456) [cytosol]\n", - " R-HSA-939188 EntityWithAccessionedSequence UBC(1-76) [cytosol]\n", - " R-HSA-939184 EntityWithAccessionedSequence UBC(457-532) [cytosol]\n", - " R-HSA-174150 EntityWithAccessionedSequence SKP1 [cytosol]\n", - " R-HSA-174150 EntityWithAccessionedSequence SKP1 [cytosol]\n", - " R-HSA-174230 EntityWithAccessionedSequence CUL1 [cytosol]\n", - " R-HSA-174230 EntityWithAccessionedSequence CUL1 [cytosol]\n", - " R-HSA-976035 EntityWithAccessionedSequence FBXW11 [cytosol]\n", - " R-HSA-174237 EntityWithAccessionedSequence BTRC [cytosol]\n", - " R-HSA-205753 EntityWithAccessionedSequence UBE2V1 [cytosol]\n", - " R-HSA-206072 EntityWithAccessionedSequence UBE2N [cytosol]\n", - " R-HSA-204910 EntityWithAccessionedSequence SOCS1 [cytosol]\n", - " R-HSA-975995 EntityWithAccessionedSequence ITCH [cytosol]\n", - " R-HSA-174249 EntityWithAccessionedSequence FZR1 [cytosol]\n", - " R-HSA-1472879 EntityWithAccessionedSequence MIB2 [cytosol]\n", - " R-HSA-180582 EntityWithAccessionedSequence RBX1 [cytosol]\n", - " R-HSA-180582 EntityWithAccessionedSequence RBX1 [cytosol]\n", - " R-HSA-180582 EntityWithAccessionedSequence RBX1 [cytosol]\n", - " R-HSA-180582 EntityWithAccessionedSequence RBX1 [cytosol]\n", - " R-HSA-180582 EntityWithAccessionedSequence RBX1 [cytosol]\n", - " R-HSA-180582 EntityWithAccessionedSequence RBX1 [cytosol]\n", - " R-HSA-8854063 EntityWithAccessionedSequence FBXL18 [cytosol]\n", - " R-HSA-8854032 EntityWithAccessionedSequence FBXL7 [cytosol]\n", - " R-HSA-975992 EntityWithAccessionedSequence NEDD4 [cytosol]\n", - " R-HSA-975970 EntityWithAccessionedSequence STUB1 [cytosol]\n", - " R-HSA-976042 EntityWithAccessionedSequence MKRN1 [cytosol]\n", - " R-HSA-180528 EntityWithAccessionedSequence CUL5 [cytosol]\n", - " R-HSA-180528 EntityWithAccessionedSequence CUL5 [cytosol]\n", - " R-HSA-180528 EntityWithAccessionedSequence CUL5 [cytosol]\n", - " R-HSA-975977 EntityWithAccessionedSequence RNF41 [cytosol]\n", - " R-HSA-873794 EntityWithAccessionedSequence SOCS3 [cytosol]\n", - " R-HSA-173537 EntityWithAccessionedSequence SMURF2 [cytosol]\n", - " R-HSA-975972 EntityWithAccessionedSequence SMURF1 [cytosol]\n", - " R-HSA-975979 EntityWithAccessionedSequence CUL3 [cytosol]\n", - " R-HSA-5658415 EntityWithAccessionedSequence KBTBD7 [cytosol]\n", - " R-HSA-947621 EntityWithAccessionedSequence CDC34 [cytosol]\n", - " R-HSA-934628 EntityWithAccessionedSequence UBE2D2 [cytosol]\n", - " R-HSA-976093 Complex RBX1-CUL2-EloB,C-VHL [cytosol]\n", - " R-HSA-416982 EntityWithAccessionedSequence CUL2 [cytosol]\n", - " R-HSA-390483 Complex VBC complex [cytosol]\n", - " R-HSA-180535 EntityWithAccessionedSequence ELOC [cytosol]\n", - " R-HSA-180535 EntityWithAccessionedSequence ELOC [cytosol]\n", - " R-HSA-180535 EntityWithAccessionedSequence ELOC [cytosol]\n", - " R-HSA-180535 EntityWithAccessionedSequence ELOC [cytosol]\n", - " R-HSA-180551 EntityWithAccessionedSequence ELOB [cytosol]\n", - " R-HSA-180551 EntityWithAccessionedSequence ELOB [cytosol]\n", - " R-HSA-180551 EntityWithAccessionedSequence ELOB [cytosol]\n", - " R-HSA-180551 EntityWithAccessionedSequence ELOB [cytosol]\n", - " R-HSA-391423 EntityWithAccessionedSequence VHL [cytosol]\n", - " R-HSA-934630 EntityWithAccessionedSequence UBE2D3 [cytosol]\n", - " R-HSA-877267 DefinedSet SOCS-1 and SOCS-3 [cytosol]\n", - " R-HSA-976003 EntityWithAccessionedSequence NEDD4L [cytosol]\n", - " R-HSA-936014 EntityWithAccessionedSequence UBE2L6 [cytosol]\n", - " R-HSA-936550 EntityWithAccessionedSequence UBA7 [cytosol]\n", - " R-HSA-936553 EntityWithAccessionedSequence HERC5 [cytosol]\n", - " R-HSA-391295 EntityWithAccessionedSequence FBXL5 [cytosol]\n", - " R-HSA-976018 EntityWithAccessionedSequence RBCK1 [cytosol]\n", - " R-HSA-976037 EntityWithAccessionedSequence WWP1 [cytosol]\n", - " R-HSA-976051 EntityWithAccessionedSequence TRIM21 [cytosol]\n", - " R-HSA-976030 EntityWithAccessionedSequence TRIM32 [cytosol]\n", - " R-HSA-947623 EntityWithAccessionedSequence UBE2D4 [cytosol]\n", - " R-HSA-934631 EntityWithAccessionedSequence UBE2K [cytosol]\n", - " R-HSA-8863321 EntityWithAccessionedSequence KCTD6 [cytosol]\n", - " R-HSA-177320 DefinedSet Cdc20/Cdh1 [cytosol]\n", - " R-HSA-975495 EntityWithAccessionedSequence SKP2 [cytosol]\n", - " R-HSA-374563 EntityWithAccessionedSequence SIAH1 [cytosol]\n", - " R-HSA-374566 EntityWithAccessionedSequence SIAH2 [cytosol]\n", - " R-HSA-976020 EntityWithAccessionedSequence TRIM63 [cytosol]\n", - " R-HSA-264453 EntityWithAccessionedSequence FBXO32 [cytosol]\n", - " R-HSA-180596 Complex Cul5-SCF complex [cytosol]\n", - " R-HSA-180596 Complex Cul5-SCF complex [cytosol]\n", - " R-HSA-8850908 EntityWithAccessionedSequence MYLIP [cytosol]\n", - " R-HSA-976075 CandidateSet E3 ligases in proteasomal degradation [cytosol]\n", - " R-HSA-976014 EntityWithAccessionedSequence GAN [cytosol]\n", - " R-HSA-976014 EntityWithAccessionedSequence GAN [cytosol]\n", - " R-HSA-976015 EntityWithAccessionedSequence LRRC41 [cytosol]\n", - " R-HSA-976015 EntityWithAccessionedSequence LRRC41 [cytosol]\n", - " R-HSA-976012 EntityWithAccessionedSequence UBE3C [cytosol]\n", - " R-HSA-976013 EntityWithAccessionedSequence RCHY1 [cytosol]\n", - " R-HSA-976010 EntityWithAccessionedSequence RNF182 [cytosol]\n", - " R-HSA-976008 EntityWithAccessionedSequence RNF138 [cytosol]\n", - " R-HSA-976009 EntityWithAccessionedSequence CBLB [cytosol]\n", - " R-HSA-976007 EntityWithAccessionedSequence DET1 [cytosol]\n", - " R-HSA-976004 EntityWithAccessionedSequence LRSAM1 [cytosol]\n", - " R-HSA-976002 EntityWithAccessionedSequence DZIP3 [cytosol]\n", - " R-HSA-976031 EntityWithAccessionedSequence FBXO44 [cytosol]\n", - " R-HSA-976031 EntityWithAccessionedSequence FBXO44 [cytosol]\n", - " R-HSA-976028 EntityWithAccessionedSequence UBE3A [cytosol]\n", - " R-HSA-976022 EntityWithAccessionedSequence UBE4A [cytosol]\n", - " R-HSA-976023 EntityWithAccessionedSequence SPSB4 [cytosol]\n", - " R-HSA-976147 Complex RBX1-CUL5-EloB/C-SOCS [cytosol]\n", - " R-HSA-976019 EntityWithAccessionedSequence LRR1 [cytosol]\n", - " R-HSA-976045 EntityWithAccessionedSequence UBR4 [cytosol]\n", - " R-HSA-976043 EntityWithAccessionedSequence UBE3B [cytosol]\n", - " R-HSA-976040 EntityWithAccessionedSequence UBR1 [cytosol]\n", - " R-HSA-976039 EntityWithAccessionedSequence FBXO27 [cytosol]\n", - " R-HSA-976039 EntityWithAccessionedSequence FBXO27 [cytosol]\n", - " R-HSA-976036 EntityWithAccessionedSequence FBXO17 [cytosol]\n", - " R-HSA-976036 EntityWithAccessionedSequence FBXO17 [cytosol]\n", - " R-HSA-976034 EntityWithAccessionedSequence UBOX5 [cytosol]\n", - " R-HSA-976033 EntityWithAccessionedSequence TRIM11 [cytosol]\n", - " R-HSA-976054 EntityWithAccessionedSequence TRIM9 [cytosol]\n", - " R-HSA-8851647 EntityWithAccessionedSequence UBE3D [cytosol]\n", - " R-HSA-8851646 EntityWithAccessionedSequence ZNF645 [cytosol]\n", - " R-HSA-8851645 EntityWithAccessionedSequence HERC4 [cytosol]\n", - " R-HSA-8851644 EntityWithAccessionedSequence UBAC1 [cytosol]\n", - " R-HSA-8851643 EntityWithAccessionedSequence RNF130 [cytosol]\n", - " R-HSA-8851642 EntityWithAccessionedSequence RNF126 [cytosol]\n", - " R-HSA-976048 EntityWithAccessionedSequence SPSB2 [cytosol]\n", - " R-HSA-8851641 EntityWithAccessionedSequence LNX1 [cytosol]\n", - " R-HSA-976049 EntityWithAccessionedSequence TRIM37 [cytosol]\n", - " R-HSA-8851640 EntityWithAccessionedSequence MEX3C [cytosol]\n", - " R-HSA-8851655 EntityWithAccessionedSequence HERC1 [cytosol]\n", - " R-HSA-976079 Complex RBX1:CUL5:EloB/C:LRRC41 [cytosol]\n", - " R-HSA-8851654 EntityWithAccessionedSequence HACE1 [cytosol]\n", - " R-HSA-8851653 EntityWithAccessionedSequence KLHL11 [cytosol]\n", - " R-HSA-8851653 EntityWithAccessionedSequence KLHL11 [cytosol]\n", - " R-HSA-8851652 EntityWithAccessionedSequence TRAIP [cytosol]\n", - " R-HSA-976074 Complex RBX1:CUL7:SKP1:FBXW8:GLMN [cytosol]\n", - " R-HSA-535534 EntityWithAccessionedSequence CUL7 [cytosol]\n", - " R-HSA-8951779 EntityWithAccessionedSequence GLMN [cytosol]\n", - " R-HSA-976017 EntityWithAccessionedSequence FBXW8 [cytosol]\n", - " R-HSA-976017 EntityWithAccessionedSequence FBXW8 [cytosol]\n", - " R-HSA-8851651 EntityWithAccessionedSequence HERC3 [cytosol]\n", - " R-HSA-8851650 EntityWithAccessionedSequence BTBD1 [cytosol]\n", - " R-HSA-8851650 EntityWithAccessionedSequence BTBD1 [cytosol]\n", - " R-HSA-5688976 EntityWithAccessionedSequence TRIM50 [cytosol]\n", - " R-HSA-8851648 EntityWithAccessionedSequence AREL1 [cytosol]\n", - " R-HSA-8851657 EntityWithAccessionedSequence TRIM4 [cytosol]\n", - " R-HSA-8851656 EntityWithAccessionedSequence HECW2 [cytosol]\n", - " R-HSA-5688966 EntityWithAccessionedSequence HECTD1 [cytosol]\n", - " R-HSA-5688967 EntityWithAccessionedSequence LTN1 [cytosol]\n", - " R-HSA-5688974 EntityWithAccessionedSequence RNF14 [cytosol]\n", - " R-HSA-5688975 EntityWithAccessionedSequence TRIM41 [cytosol]\n", - " R-HSA-5688972 EntityWithAccessionedSequence TRIM71 [cytosol]\n", - " R-HSA-5688973 EntityWithAccessionedSequence TRAF7 [cytosol]\n", - " R-HSA-5688970 EntityWithAccessionedSequence UFL1 [cytosol]\n", - " R-HSA-5688971 EntityWithAccessionedSequence TRIM39 [cytosol]\n", - " R-HSA-5688968 EntityWithAccessionedSequence SH3RF1 [cytosol]\n", - " R-HSA-976109 Complex RNF7 (RBX2):CUL5:EloB/C:ASB [cytosol]\n", - " R-HSA-975431 DefinedSet ASB family [cytosol]\n", - " R-HSA-975428 EntityWithAccessionedSequence ASB1 [cytosol]\n", - " R-HSA-975426 EntityWithAccessionedSequence ASB15 [cytosol]\n", - " R-HSA-975427 EntityWithAccessionedSequence ASB13 [cytosol]\n", - " R-HSA-975424 EntityWithAccessionedSequence ASB9 [cytosol]\n", - " R-HSA-975425 EntityWithAccessionedSequence ASB7 [cytosol]\n", - " R-HSA-975422 EntityWithAccessionedSequence ASB8 [cytosol]\n", - " R-HSA-975423 EntityWithAccessionedSequence ASB2 [cytosol]\n", - " R-HSA-975420 EntityWithAccessionedSequence ASB5 [cytosol]\n", - " R-HSA-975421 EntityWithAccessionedSequence ASB14 [cytosol]\n", - " R-HSA-975418 EntityWithAccessionedSequence ASB18 [cytosol]\n", - " R-HSA-975419 EntityWithAccessionedSequence ASB4 [cytosol]\n", - " R-HSA-975416 EntityWithAccessionedSequence ASB16 [cytosol]\n", - " R-HSA-975417 EntityWithAccessionedSequence ASB10 [cytosol]\n", - " R-HSA-975414 EntityWithAccessionedSequence ASB12 [cytosol]\n", - " R-HSA-975415 EntityWithAccessionedSequence ASB11 [cytosol]\n", - " R-HSA-975412 EntityWithAccessionedSequence ASB6 [cytosol]\n", - " R-HSA-975413 EntityWithAccessionedSequence ASB17 [cytosol]\n", - " R-HSA-975411 EntityWithAccessionedSequence ASB3 [cytosol]\n", - " R-HSA-8863132 EntityWithAccessionedSequence RNF7 (RBX2) [cytosol]\n", - " R-HSA-975981 EntityWithAccessionedSequence RNF111 [cytosol]\n", - " R-HSA-975978 EntityWithAccessionedSequence RNF220 [cytosol]\n", - " R-HSA-975976 EntityWithAccessionedSequence RNF25 [cytosol]\n", - " R-HSA-201579 EntityWithAccessionedSequence PARK2 [cytosol]\n", - " R-HSA-975974 EntityWithAccessionedSequence RNF4 [cytosol]\n", - " R-HSA-975975 EntityWithAccessionedSequence HERC2 [cytosol]\n", - " R-HSA-976101 Complex RBX1:CUL3:BTB [cytosol]\n", - " R-HSA-976145 DefinedSet BTB proteins [cytosol]\n", - " R-HSA-976047 EntityWithAccessionedSequence ZBTB16 [cytosol]\n", - " R-HSA-8863204 EntityWithAccessionedSequence KLHL42 [cytosol]\n", - " R-HSA-8863202 EntityWithAccessionedSequence KBTBD13 [cytosol]\n", - " R-HSA-976041 EntityWithAccessionedSequence KLHL13 [cytosol]\n", - " R-HSA-976038 EntityWithAccessionedSequence KEAP1 [cytosol]\n", - " R-HSA-8863210 EntityWithAccessionedSequence KLHL22 [cytosol]\n", - " R-HSA-976032 EntityWithAccessionedSequence KLHL20 [cytosol]\n", - " R-HSA-8863208 EntityWithAccessionedSequence BTBD6 [cytosol]\n", - " R-HSA-8863223 EntityWithAccessionedSequence KLHL5 [cytosol]\n", - " R-HSA-8863222 EntityWithAccessionedSequence KLHL41 [cytosol]\n", - " R-HSA-8863189 EntityWithAccessionedSequence KLHL25 [cytosol]\n", - " R-HSA-8863221 EntityWithAccessionedSequence KBTBD6 [cytosol]\n", - " R-HSA-976026 EntityWithAccessionedSequence KLHL21 [cytosol]\n", - " R-HSA-976056 EntityWithAccessionedSequence KLHL9 [cytosol]\n", - " R-HSA-8863217 EntityWithAccessionedSequence KLHL2 [cytosol]\n", - " R-HSA-8863184 EntityWithAccessionedSequence KCTD7 [cytosol]\n", - " R-HSA-8863198 EntityWithAccessionedSequence KLHL3 [cytosol]\n", - " R-HSA-8863192 EntityWithAccessionedSequence KBTBD8 [cytosol]\n", - " R-HSA-975971 EntityWithAccessionedSequence MGRN1 [cytosol]\n", - " R-HSA-975998 EntityWithAccessionedSequence RNF34 [cytosol]\n", - " R-HSA-975996 EntityWithAccessionedSequence RNF123 [cytosol]\n", - " R-HSA-975997 EntityWithAccessionedSequence RNF6 [cytosol]\n", - " R-HSA-976123 Complex APC/C E3 ligase complex [cytosol]\n", - " R-HSA-975982 EntityWithAccessionedSequence ANAPC13 [cytosol]\n", - " R-HSA-975993 EntityWithAccessionedSequence PJA2 [cytosol]\n", - " R-HSA-975991 EntityWithAccessionedSequence HECTD3 [cytosol]\n", - " R-HSA-975989 EntityWithAccessionedSequence PJA1 [cytosol]\n", - " R-HSA-975987 EntityWithAccessionedSequence ARIH2 [cytosol]\n", - " R-HSA-975984 EntityWithAccessionedSequence VPRBP [cytosol]\n", - " R-HSA-5688977 EntityWithAccessionedSequence TRIM69 [cytosol]\n", - " R-HSA-8850895 EntityWithAccessionedSequence RBBP6 [cytosol]\n", - " R-HSA-8850894 EntityWithAccessionedSequence RNF114 [cytosol]\n", - " R-HSA-8850903 EntityWithAccessionedSequence ZNRF1 [cytosol]\n", - " R-HSA-8850901 EntityWithAccessionedSequence ZNRF2 [cytosol]\n", - " R-HSA-976029 EntityWithAccessionedSequence TRIM36 [cytosol]\n", - " R-HSA-8850900 EntityWithAccessionedSequence UNKL [cytosol]\n", - " R-HSA-8850899 EntityWithAccessionedSequence FBXL4 [cytosol]\n", - " R-HSA-8850899 EntityWithAccessionedSequence FBXL4 [cytosol]\n", - " R-HSA-8850898 EntityWithAccessionedSequence RLIM [cytosol]\n", - " R-HSA-976024 EntityWithAccessionedSequence SPSB1 [cytosol]\n", - " R-HSA-8850897 EntityWithAccessionedSequence RNF213 [cytosol]\n", - " R-HSA-8850896 EntityWithAccessionedSequence RNF217 [cytosol]\n", - " R-HSA-8850909 EntityWithAccessionedSequence RNF19A [cytosol]\n", - " R-HSA-8850907 EntityWithAccessionedSequence HECTD2 [cytosol]\n", - " R-HSA-8850906 EntityWithAccessionedSequence HERC6 [cytosol]\n", - " R-HSA-976016 EntityWithAccessionedSequence WSB1 [cytosol]\n", - " R-HSA-8850905 EntityWithAccessionedSequence LONRF1 [cytosol]\n", - " R-HSA-8850904 EntityWithAccessionedSequence RNF115 [cytosol]\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - " R-HSA-976046 EntityWithAccessionedSequence TRIP12 [cytosol]\n", - " R-HSA-976110 Complex SCF E3 ubiquitin ligase [cytosol]\n", - " R-HSA-976085 DefinedSet F-box protein [cytosol]\n", - " R-HSA-391300 EntityWithAccessionedSequence FBXW2 [cytosol]\n", - " R-HSA-8862597 EntityWithAccessionedSequence FBXL22 [cytosol]\n", - " R-HSA-391296 EntityWithAccessionedSequence FBXO6 [cytosol]\n", - " R-HSA-391298 EntityWithAccessionedSequence FBXO4 [cytosol]\n", - " R-HSA-8862592 EntityWithAccessionedSequence FBXO21 [cytosol]\n", - " R-HSA-8862607 EntityWithAccessionedSequence FBXL19 [cytosol]\n", - " R-HSA-8862606 EntityWithAccessionedSequence FBXL21 [cytosol]\n", - " R-HSA-8862603 EntityWithAccessionedSequence FBXL14 [cytosol]\n", - " R-HSA-391305 EntityWithAccessionedSequence FBXW4 [cytosol]\n", - " R-HSA-8862602 EntityWithAccessionedSequence CCNF [cytosol]\n", - " R-HSA-391304 EntityWithAccessionedSequence FBXW7 [cytosol]\n", - " R-HSA-391307 EntityWithAccessionedSequence FBXW10 [cytosol]\n", - " R-HSA-8862600 EntityWithAccessionedSequence FBXO22 [cytosol]\n", - " R-HSA-8862614 EntityWithAccessionedSequence FBXW12 [cytosol]\n", - " R-HSA-8862612 EntityWithAccessionedSequence FBXO40 [cytosol]\n", - " R-HSA-8862611 EntityWithAccessionedSequence FBXL12 [cytosol]\n", - " R-HSA-8862609 EntityWithAccessionedSequence FBXL16 [cytosol]\n", - " R-HSA-8862608 EntityWithAccessionedSequence FBXO9 [cytosol]\n", - " R-HSA-8850911 EntityWithAccessionedSequence FBXO31 [cytosol]\n", - " R-HSA-8862623 EntityWithAccessionedSequence FBXO41 [cytosol]\n", - " R-HSA-8862622 EntityWithAccessionedSequence FBXO15 [cytosol]\n", - " R-HSA-8955092 EntityWithAccessionedSequence FBXO11 [cytosol]\n", - " R-HSA-8862619 EntityWithAccessionedSequence FBXO30 [cytosol]\n", - " R-HSA-8862618 EntityWithAccessionedSequence FBXO10 [cytosol]\n", - " R-HSA-8862616 EntityWithAccessionedSequence FBXL13 [cytosol]\n", - " R-HSA-976044 EntityWithAccessionedSequence FBXO2 [cytosol]\n", - " R-HSA-8862627 EntityWithAccessionedSequence FBXO7 [cytosol]\n", - " R-HSA-8862625 EntityWithAccessionedSequence FBXL15 [cytosol]\n", - " R-HSA-8850912 EntityWithAccessionedSequence FBXL8 [cytosol]\n", - " R-HSA-391286 EntityWithAccessionedSequence FBXW5 [cytosol]\n", - " R-HSA-8862591 EntityWithAccessionedSequence FBXL20 [cytosol]\n", - " R-HSA-8862589 EntityWithAccessionedSequence LMO7 [cytosol]\n", - " R-HSA-391289 EntityWithAccessionedSequence FBXL3 [cytosol]\n", - " R-HSA-391290 EntityWithAccessionedSequence FBXW9 [cytosol]\n", - " R-HSA-975983 EntityWithAccessionedSequence HUWE1 [cytosol]\n", - " R-HSA-975969 EntityWithAccessionedSequence RNF19B [cytosol]\n", - " R-HSA-975994 EntityWithAccessionedSequence DTX3L [cytosol]\n", - " R-HSA-976055 EntityWithAccessionedSequence UBR2 [cytosol]\n", - " R-HSA-975988 EntityWithAccessionedSequence RNF144B [cytosol]\n", - " R-ALL-983035 OtherEntity antigenic substrate [cytosol]\n", - " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", - " R-HSA-947628 CandidateSet E2 Ubiquitin-conjugating enzyme [cytosol]\n", - " R-HSA-947630 EntityWithAccessionedSequence UBE2R2 [cytosol]\n", - " R-HSA-947631 EntityWithAccessionedSequence UBE2L3 [cytosol]\n", - " R-HSA-947629 EntityWithAccessionedSequence UBE2Q1 [cytosol]\n", - " R-HSA-947626 EntityWithAccessionedSequence UBE2E2 [cytosol]\n", - " R-HSA-947627 EntityWithAccessionedSequence UBE2G1 [cytosol]\n", - " R-HSA-947624 EntityWithAccessionedSequence UBE2V2 [cytosol]\n", - " R-HSA-947625 EntityWithAccessionedSequence UBE2J1 [cytosol]\n", - " R-HSA-947622 EntityWithAccessionedSequence UBE2S [cytosol]\n", - " R-HSA-947618 EntityWithAccessionedSequence UBE2Q2 [cytosol]\n", - " R-HSA-947619 EntityWithAccessionedSequence UBE2M [cytosol]\n", - " R-HSA-947616 EntityWithAccessionedSequence UBE2Z [cytosol]\n", - " R-HSA-947640 EntityWithAccessionedSequence UBE2G2 [cytosol]\n", - " R-HSA-947641 EntityWithAccessionedSequence UBE2O [cytosol]\n", - " R-HSA-947638 EntityWithAccessionedSequence UBE2H [cytosol]\n", - " R-HSA-947639 EntityWithAccessionedSequence UBE2W [cytosol]\n", - " R-HSA-947636 EntityWithAccessionedSequence UBE2B [cytosol]\n", - " R-HSA-947637 EntityWithAccessionedSequence UBE2J2 [cytosol]\n", - " R-HSA-947634 EntityWithAccessionedSequence UBE2U [cytosol]\n", - " R-HSA-947635 EntityWithAccessionedSequence UBE2F [cytosol]\n", - " R-HSA-947633 EntityWithAccessionedSequence UBE2E3 [cytosol]\n", - " R-HSA-947617 EntityWithAccessionedSequence UBE2A [cytosol]\n" + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex 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Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n", + " R-HSA-976165 Complex Ubiquitin:E2 conjugating enzymes [cytosol]\n" ] } ], @@ -400,8 +394,8 @@ " 'RETURN pe.stId AS ID, pe.displayName AS Name, pe.schemaClass as schemaClass')\n", "\n", "with gdbdr.session() as session:\n", - " for rec in session.run(query).records():\n", - " print(\" {ID:13} {schemaClass:29} {Name}\".format(**rec))" + " for dct in session.run(query).data():\n", + " print(\" {ID:13} {schemaClass:29} {Name}\".format(**dct))" ] }, { diff --git a/notebooks/tutorial/s4a_pathway_subpathways.ipynb b/notebooks/tutorial/s4a_pathway_subpathways.ipynb index 2911b1b..e20d0a9 100644 --- a/notebooks/tutorial/s4a_pathway_subpathways.ipynb +++ b/notebooks/tutorial/s4a_pathway_subpathways.ipynb @@ -37,7 +37,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -50,7 +50,7 @@ "# Query and get the sub-pathways under R-HSA-983169\n", "def _get_data():\n", " with gdbdr.session() as session:\n", - " return [rec.data() for rec in session.run(query).records()]" + " return session.run(query).data()" ] }, { @@ -69,8 +69,8 @@ "# Print sub-pathways under R-HSA-983169\n", "print(' Pathway | SubPathway ID | SubPathway Name')\n", "print('-----------------|---------------|----------------')\n", - "for record in _get_data():\n", - " print(\" {Pathway} | {SubPathway_ID:13} | {SubPathway_Name}\".format(**record))\n" + "for dct in _get_data():\n", + " print(\" {Pathway} | {SubPathway_ID:13} | {SubPathway_Name}\".format(**dct))\n" ] }, { diff --git a/notebooks/tutorial/s4b_pathway_superpathways.ipynb b/notebooks/tutorial/s4b_pathway_superpathways.ipynb index 09c49a5..121810a 100644 --- a/notebooks/tutorial/s4b_pathway_superpathways.ipynb +++ b/notebooks/tutorial/s4b_pathway_superpathways.ipynb @@ -50,7 +50,7 @@ "# Query and get the sub-pathways under R-HSA-983169\n", "def _get_data():\n", " with gdbdr.session() as session:\n", - " return [rec.data() for rec in session.run(query).records()]" + " return session.run(query).data()" ] }, { @@ -106,7 +106,7 @@ "# Query and get the sub-pathways under R-HSA-983169\n", "def _get_data():\n", " with gdbdr.session() as session:\n", - " return [rec.data() for rec in session.run(query).records()]" + " return session.run(query).data()" ] }, { diff --git a/notebooks/tutorial/s5a_pathway_reactions.ipynb b/notebooks/tutorial/s5a_pathway_reactions.ipynb index e0548ea..ed2db0f 100644 --- a/notebooks/tutorial/s5a_pathway_reactions.ipynb +++ b/notebooks/tutorial/s5a_pathway_reactions.ipynb @@ -16,33 +16,7 @@ "cell_type": "code", "execution_count": 1, "metadata": {}, - "outputs": [ - { - "ename": "AuthError", - "evalue": "The client is unauthorized due to authentication failure.", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mAuthError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0mneo4j_password\u001b[0m \u001b[0;34m=\u001b[0m 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to resolve addresses for %s\"\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0maddress\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 971\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 972\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mlast_error\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", - "\u001b[0;32m~/anaconda3/lib/python3.6/site-packages/neobolt/direct.py\u001b[0m in \u001b[0;36mconnect\u001b[0;34m(address, **config)\u001b[0m\n\u001b[1;32m 962\u001b[0m \u001b[0ms\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_connect\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mresolved_address\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 963\u001b[0m \u001b[0ms\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mder_encoded_server_certificate\u001b[0m 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metadata)\u001b[0m\n\u001b[1;32m 772\u001b[0m \u001b[0mmessage\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmetadata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"message\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"Connection initialisation failed\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 773\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mcode\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m\"Neo.ClientError.Security.Unauthorized\"\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 774\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mAuthError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmessage\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 775\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 776\u001b[0m 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Name\n", + "-------------|---------------|----------------\n", + "R-HSA-983169 | R-HSA-1236935 | Proteasomal cleavage of substrate\n", + "R-HSA-983169 | R-HSA-1236938 | Partial proteolysis of antigen in phagolysosomes\n", + "R-HSA-983169 | R-HSA-1236939 | Interaction of exogenous soluble antigen with its corresponding receptor\n", + "R-HSA-983169 | R-HSA-1236940 | Exogenous soluble antigen targeted to more stable early endosome\n", + "R-HSA-983169 | R-HSA-1236941 | Internalization of receptor bound antigen into clathrin coted vesicles\n", + "R-HSA-983169 | R-HSA-1236943 | Loading of antigen peptide onto MHC class I molecule\n", + "R-HSA-983169 | R-HSA-1236947 | Egress of internalized antigen to the cytosol via sec61\n", + "R-HSA-983169 | R-HSA-1236948 | Antigen processing by cathepsin S in endosoytic vesicle\n", + "R-HSA-983169 | R-HSA-1236949 | Translocation of antigenic peptides back to phagosomes via TAP\n", + "R-HSA-983169 | R-HSA-1236954 | Trimming of peptides by IRAP in endocytic vesicles\n", + "R-HSA-983169 | R-HSA-1236955 | Movement of clathrin coated vesicles into early endosome\n", + "R-HSA-983169 | R-HSA-1236956 | Engulfment of particulate antigen into phagocytic vesicle\n", + "R-HSA-983169 | R-HSA-1236958 | Interaction of particulate antigens with dendritic cell receptors\n", + "R-HSA-983169 | R-HSA-1236963 | Maturation of phagosome into phagolysosome\n", + "R-HSA-983169 | R-HSA-1236964 | Translocation of peptide bound MHC class I complex to cell surface\n", + "R-HSA-983169 | R-HSA-1236965 | Export of peptide loaded MHC class I complex to PM\n", + "R-HSA-983169 | R-HSA-1236967 | Alkalization of the phagosomal lumen by NOX2\n", + "R-HSA-983169 | R-HSA-1236968 | Egress of internalized antigen into cytosol from early endosome\n", + "R-HSA-983169 | R-HSA-1236970 | Proteasomal clevage of exogenous antigen\n", + "R-HSA-983169 | R-HSA-1236971 | Peptide loading on MHC class I in phagosome\n", + "R-HSA-983169 | R-HSA-1236972 | Escape of antigens from phagosome to cytosol\n", + "R-HSA-983169 | R-HSA-203979 | Coat Assembly\n", + "R-HSA-983169 | R-HSA-8863858 | SEC22B, CALR, STX4, TAP and TAPBP bind\n", + "R-HSA-983169 | R-HSA-8863895 | IKKB phosphorylates SNAP23\n", + "R-HSA-983169 | R-HSA-8863914 | Transport of SEC22B, TAP and PLC from ER to ERGIC\n", + "R-HSA-983169 | R-HSA-8863973 | Fusion of ERC and phagosome\n", + "R-HSA-983169 | R-HSA-8940641 | THOP1 cleaves oligopeptide fragment (8-16aa)\n", + "R-HSA-983169 | R-HSA-8951499 | Loading of antigenic peptides on to class I MHC\n", + "R-HSA-983169 | R-HSA-8951595 | CALR, TAP, TAPBP dissociate from SEC22B:STX4\n", + "R-HSA-983169 | R-HSA-983138 | Transport of MHC heterotrimer to ER exit site\n", + "R-HSA-983169 | R-HSA-983140 | Transfer of Ub from E2 to substrate and release of E2\n", + "R-HSA-983169 | R-HSA-983142 | Formation of peptide loading complex (PLC)\n", + "R-HSA-983169 | R-HSA-983144 | Transport of Antigen peptide in to ER\n", + "R-HSA-983169 | R-HSA-983145 | Binding of newly synthesized MHC class I heavy chain (HC) with calnexin\n", + "R-HSA-983169 | R-HSA-983146 | Interaction of beta-2-microglobulin (B2M) chain with class I HC\n", + "R-HSA-983169 | R-HSA-983147 | Release of E3 from polyubiquitinated substrate\n", + "R-HSA-983169 | R-HSA-983148 | Interaction of Erp57 with MHC class I HC\n", + "R-HSA-983169 | R-HSA-983150 | Proteasomal cleavage of substrate\n", + "R-HSA-983169 | R-HSA-983152 | Transfer of ubiquitin from E1 to E2\n", + "R-HSA-983169 | R-HSA-983153 | E1 mediated ubiquitin activation\n", + "R-HSA-983169 | R-HSA-983156 | Polyubiquitination of substrate\n", + "R-HSA-983169 | R-HSA-983157 | Interaction of E3 with substrate and E2-Ub complex\n", + "R-HSA-983169 | R-HSA-983158 | Trimming of peptides in ER\n", + "R-HSA-983169 | R-HSA-983161 | Dissociation of the Antigenic peptide:MHC:B2M peptide loading complex\n", + "R-HSA-983169 | R-HSA-983162 | Trimming of N-ter extended precursor fragments by cytosolic aminopeptidases\n", + "R-HSA-983169 | R-HSA-983421 | Journey of cargo through Golgi complex\n", + "R-HSA-983169 | R-HSA-983422 | Disassembly of COPII coated vesicle\n", + "R-HSA-983169 | R-HSA-983424 | Budding of COPII coated vesicle\n", + "R-HSA-983169 | R-HSA-983425 | Recruitment of Sec31p:Sec13p to prebudding complex and formation of COPII vesicle\n", + "R-HSA-983169 | R-HSA-983426 | Capturing cargo and formation of prebudding complex\n", + "R-HSA-983169 | R-HSA-983427 | Expression of peptide bound class I MHC on cell surface\n" + ] + } + ], "source": [ "# Print sub-pathways under R-HSA-983169\n", "print(' Pathway | Reaction ID | Reaction Name')\n", "print('-------------|---------------|----------------')\n", - "for record in sorted(_get_data(), key=lambda d:d['Reaction_ID']):\n", - " print(\"{Pathway} | {Reaction_ID:13} | {Reaction_Name}\".format(**record))" + "for dct in sorted(_get_data(), key=lambda d:d['Reaction_ID']):\n", + " print(\"{Pathway} | {Reaction_ID:13} | {Reaction_Name}\".format(**dct))" ] }, { diff --git a/notebooks/tutorial/s6a_reaction_participants.ipynb b/notebooks/tutorial/s6a_reaction_participants.ipynb index c4731e5..b6aa880 100644 --- a/notebooks/tutorial/s6a_reaction_participants.ipynb +++ b/notebooks/tutorial/s6a_reaction_participants.ipynb @@ -38,7 +38,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -50,7 +50,7 @@ "# Query the first level participants in the reaction, R-HSA-8863895, IKKB phosphorylates SNAP23\n", "def _get_data():\n", " with gdbdr.session() as session:\n", - " return [rec.data() for rec in session.run(query).records()]" + " return session.run(query).data()" ] }, { @@ -84,8 +84,8 @@ "# Print the first level participants in the reaction, R-HSA-8863895, IKKB phosphorylates SNAP23\n", "print(' Reaction | Participant | Participant Name')\n", "print('--------------|---------------|----------------')\n", - "for record in sorted(_get_data(), key=lambda r: r['Participant']):\n", - " print(\"{Reaction} | {Participant:13} | {DisplayName}\".format(**record))" + "for dct in sorted(_get_data(), key=lambda r: r['Participant']):\n", + " print(\"{Reaction} | {Participant:13} | {DisplayName}\".format(**dct))" ] }, { diff --git a/notebooks/tutorial/s6b_reaction_participants.ipynb b/notebooks/tutorial/s6b_reaction_participants.ipynb index 200f511..4f5ab56 100644 --- a/notebooks/tutorial/s6b_reaction_participants.ipynb +++ b/notebooks/tutorial/s6b_reaction_participants.ipynb @@ -51,7 +51,7 @@ "# Query all the participants in the reaction, R-HSA-8863895, IKKB phosphorylates SNAP23?\n", "def _get_data():\n", " with gdbdr.session() as session:\n", - " return [rec.data() for rec in session.run(query).records()]" + " return session.run(query).data()" ] }, { diff --git a/notebooks/tutorial/s7a_pathway_molecules.ipynb b/notebooks/tutorial/s7a_pathway_molecules.ipynb index e488e28..2244fa5 100644 --- a/notebooks/tutorial/s7a_pathway_molecules.ipynb +++ b/notebooks/tutorial/s7a_pathway_molecules.ipynb @@ -56,7 +56,7 @@ "# Query and get the sub-pathways under R-HSA-983169\n", "def _get_data():\n", " with gdbdr.session() as session:\n", - " return [rec.data() for rec in session.run(query).records()]\n", + " return session.run(query).data()\n", "\n", "data = _get_data()" ] @@ -1071,8 +1071,8 @@ "# Print all the molecules in the pathway, R-HSA-983169, Class I MHC mediated antigen processing & presentation\n", "print('Database| ID | Name')\n", "print('--------|--------|------')\n", - "for record in sorted(data, key=lambda r:[r['Database'], r['Name']]):\n", - " print(\"{Database:8}| {Identifier:6} | {Name}\".format(**record))" + "for data in sorted(data, key=lambda r:[r['Database'], r['Name']]):\n", + " print(\"{Database:8}| {Identifier:6} | {Name}\".format(**data))" ] }, { diff --git a/src/bin/compare_reactome_version.py b/src/bin/compare_reactome_version.py index da1da1b..b9b1731 100755 --- a/src/bin/compare_reactome_version.py +++ b/src/bin/compare_reactome_version.py @@ -23,12 +23,13 @@ def main(): # Reactome version from Content Service obj = ContentService() ver_curr = obj.get_version() - # Reactome version from locally loaded Reactome DAG - ver_local = get_version(get_gdbdr()) print('\n Current Reactome Knowledgebase Version:') print(' {VER:3} <- Latest version from Content Service'.format(VER=ver_curr)) + # Reactome version from locally loaded Reactome DAG + ver_local = get_version(get_gdbdr()) print(' {VER:3} <- version from locally loaded DAG'.format(VER=ver_local)) - print(' {VER:3} <- Version in this repo\n\n'.format(VER=VERSION)) + print(' {VER:3} <- Version in this repo: src/reactomepy/data/reactome_version.py\n\n'.format( + VER=VERSION)) assert ver_local == ver_curr, 'VERSION: LOCAL DAG({A}) != CONTENT SERVICE({E})'.format( E=ver_curr, A=ver_local) assert VERSION == ver_curr, 'PLEASE DOWNLOAD THE MOST RECENT REACTOME KNOWLEDGEBASE'