{ "cells": [ { "cell_type": "markdown", "id": "64bf0f0c", "metadata": { "lines_to_next_cell": 0 }, "source": [ "Biological Pathway Exchange (BioPAX) is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. It is an open and collaborative effort by the community of researchers, software developers, and institutions. BioPAX is defined in OWL DL and is represented in the RDF/XML format. For more details, see Demir E et al. 2010. The BioPAX community standard for pathway data sharing, Nature Biotechnology. 28(9)." ] }, { "cell_type": "markdown", "id": "62db559b", "metadata": { "lines_to_next_cell": 0 }, "source": [ "http://www.biopax.org/\n", "Specification: http://www.biopax.org/release/biopax-level3-documentation.pdf\n", "https://pypi.org/project/pybiopax/\n", "https://github.com/indralab/pybiopax" ] }, { "cell_type": "markdown", "id": "02e25b6b", "metadata": { "lines_to_next_cell": 0 }, "source": [ "For the reactions you need probably the `BiochemicalReaction` and `Degradation`.\n", "For the PhysicalEntities you would use `Protein` and `RNA`.\n", "For the inhibition you will probably use `Modulation`.\n", "Have a look at the specification and the introduction to BioPax." ] }, { "cell_type": "markdown", "id": "d5da4ce5", "metadata": {}, "source": [ "Example for fetching information\n", "https://github.com/indralab/pybiopax/blob/master/notebooks/tutorial.ipynb" ] }, { "cell_type": "code", "execution_count": 1, "id": "04e92d33", "metadata": { "execution": { "iopub.execute_input": "2023-04-17T14:01:44.724457Z", "iopub.status.busy": "2023-04-17T14:01:44.724104Z", "iopub.status.idle": "2023-04-17T14:01:44.955764Z", "shell.execute_reply": "2023-04-17T14:01:44.956193Z" } }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/usr/local/lib/python3.10/dist-packages/tqdm-4.64.1-py3.10.egg/tqdm/auto.py:22: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", " from .autonotebook import tqdm as notebook_tqdm\n" ] } ], "source": [ "\n", "import os\n", "from pathlib import Path\n", "\n", "import pybiopax\n", "from pybiopax.api import model_to_owl_str\n", "from pybiopax.biopax import (\n", " BioSource,\n", " CellularLocationVocabulary,\n", " Control,\n", " PhysicalEntity,\n", " Rna,\n", " UnificationXref,\n", ")\n", "from pybiopax.biopax.base import Protein\n", "from pybiopax.biopax.model import (\n", " BiochemicalReaction,\n", " BioPaxModel,\n", " Provenance,\n", " PublicationXref,\n", " Stoichiometry,\n", ")" ] }, { "cell_type": "code", "execution_count": 2, "id": "2a978ccc", "metadata": { "execution": { "iopub.execute_input": "2023-04-17T14:01:44.958940Z", "iopub.status.busy": "2023-04-17T14:01:44.957989Z", "iopub.status.idle": "2023-04-17T14:01:44.991215Z", "shell.execute_reply": "2023-04-17T14:01:44.991714Z" } }, "outputs": [], "source": [ "def create_repressilator(biopax_path: Path) -> BioPaxModel:\n", " \"\"\"Create repressilator using biopax.\"\"\"\n", " objects = []\n", "\n", " # \n", " # \n", " # LacI protein\n", " # \n", " # Protein(LacI protein)\n", " # {'_controller_of': set(), 'xref': [],\n", " # 'display_name': 'LacI protein', 'standard_name': None, '_name': [], 'evidence': [], 'uid': 'PX', 'comment': [], 'availability': None, 'data_source': [], '_participant_of': set(), 'feature': [], 'not_feature': [], 'member_physical_entity': [], 'cellular_location': None, '_component_of': set(), '_member_physical_entity_of': {PhysicalEntity(PX), PhysicalEntity(PX), PhysicalEntity(PX)}, 'entity_reference': None}\n", " #\n", " # \n", " # \n", " # PY\n", " # \n", " # \n", "\n", " p1 = PhysicalEntity(\n", " uid=\"RIGHT_0_conversion_Reaction5_PY\",\n", " display_name=\"PY\",\n", " cellular_location=\"cell\",\n", " member_physical_entity=\"PY\",\n", " )\n", " objects.append(p1)\n", "\n", " # \n", " # \n", " # 1.0\n", " # \n", " s1 = Stoichiometry(\n", " uid=\"LEFT_0_conversion_Reaction2_Y_STOICHIOMETRY\",\n", " physical_entity=\"LEFT_0_conversion_Reaction2_Y\",\n", " stoichiometric_coefficient=\"1\",\n", " )\n", " objects.append(s1)\n", "\n", " # '''\n", " # \n", " # \n", " # BioModels Database\n", " # \n", " # '''\n", " p3 = Provenance(\n", " uid=\"datasource_1\",\n", " xref=\"http://identifiers.org/biomodels.db/BIOMD0000000012\",\n", " display_name=\"BioModels Database\",\n", " )\n", " objects.append(p3)\n", " #\n", " p4 = PublicationXref(\n", " uid=\"http://identifiers.org/pubmed/10659856\", id=\"10659856\", db=\"PubMed\"\n", " )\n", " objects.append(p4)\n", "\n", " p5 = Provenance(\n", " uid=\"datasource_2\",\n", " xref=\"http://identifiers.org/biomodels.db/MODEL6615351360\",\n", " display_name=\"BioModels Database\",\n", " )\n", " objects.append(p5)\n", "\n", " u1 = UnificationXref(\n", " uid=\"http://identifiers.org/biomodels.db/BIOMD0000000012\",\n", " id=\"BIOMD0000000012\",\n", " db=\"BioModels Database\",\n", " )\n", " objects.append(u1)\n", "\n", " u2 = UnificationXref(\n", " uid=\"http://identifiers.org/obo.go/GO:0006402\",\n", " id=\"GO:0006402\",\n", " db=\"Gene Ontology\",\n", " )\n", " objects.append(u2)\n", "\n", " s2 = Stoichiometry(\n", " uid=\"LEFT_0_conversion_Reaction7_PX_STOICHIOMETRY\",\n", " physical_entity=\"LEFT_0_conversion_Reaction7_PX\",\n", " stoichiometric_coefficient=\"1\",\n", " )\n", " objects.append(s2)\n", "\n", " #\n", " # '''\n", " # \n", " # \n", " # INHIBITION\n", " # \n", " # \n", " # '''\n", " c1 = Control(\n", " uid=\"control_Reaction4_X_0\",\n", " controlled=\"conversion_Reaction4\",\n", " control_type=\"INHIBITION\",\n", " controller=\"PEP0_control_Reaction4X\",\n", " )\n", " objects.append(c1)\n", "\n", " s2 = Stoichiometry(\n", " uid=\"RIGHT_0_conversion_Reaction6_PZ_STOICHIOMETRY\",\n", " physical_entity=\"RIGHT_0_conversion_Reaction6_PZ\",\n", " stoichiometric_coefficient=\"1\",\n", " )\n", " objects.append(s2)\n", "\n", " c2 = PhysicalEntity(\n", " uid=\"PEP0_control_Reaction4X\",\n", " cellular_location=\"cell\",\n", " display_name=\"X\",\n", " member_physical_entity=\"X\",\n", " )\n", " objects.append(c2)\n", "\n", " u3 = UnificationXref(\n", " uid=\"http://identifiers.org/obo.go/GO:0030163\",\n", " id=\"GO:0030163\",\n", " db=\"Gene Ontology\",\n", " )\n", " objects.append(u3)\n", "\n", " s3 = Stoichiometry(\n", " uid=\"RIGHT_0_conversion_Reaction12_Z_STOICHIOMETRY\",\n", " physical_entity=\"RIGHT_0_conversion_Reaction12_Z\",\n", " stoichiometric_coefficient=\"1\",\n", " )\n", " objects.append(s3)\n", "\n", " c3 = PhysicalEntity(\n", " uid=\"LEFT_0_conversion_Reaction7_PX\",\n", " cellular_location=\"cell\",\n", " display_name=\"PX\",\n", " member_physical_entity=\"PX\",\n", " )\n", " objects.append(c3)\n", "\n", " s4 = Stoichiometry(\n", " uid=\"RIGHT_0_conversion_Reaction11_Y_STOICHIOMETRY\",\n", " physical_entity=\"RIGHT_0_conversion_Reaction11_Y\",\n", " stoichiometric_coefficient=\"1\",\n", " )\n", " objects.append(s4)\n", "\n", " c4 = CellularLocationVocabulary(\n", " uid=\"cell\", term=\"cell\", xref=\"http://identifiers.org/obo.go/GO:0005623\"\n", " )\n", " objects.append(c4)\n", "\n", " b1 = BiochemicalReaction(\n", " uid=\"conversion_Reaction12\",\n", " xref=\"http://identifiers.org/obo.go/GO:0006351\",\n", " participant_stoichiometry=\"RIGHT_0_conversion_Reaction12_Z_STOICHIOMETRY\",\n", " display_name=\"transcription of CI\",\n", " right=\"RIGHT_0_conversion_Reaction12_Z\",\n", " )\n", " objects.append(b1)\n", "\n", " b1 = BiochemicalReaction(\n", " uid=\"conversion_Reaction11\",\n", " xref=\"http://identifiers.org/obo.go/GO:0006351\",\n", " participant_stoichiometry=\"RIGHT_0_conversion_Reaction11_Y_STOICHIOMETRY\",\n", " display_name=\"transcription of TetR\",\n", " right=\"RIGHT_0_conversion_Reaction11_Y\",\n", " )\n", " objects.append(b1)\n", "\n", " b1 = BiochemicalReaction(\n", " uid=\"conversion_Reaction10\",\n", " xref=\"http://identifiers.org/obo.go/GO:0006351\",\n", " participant_stoichiometry=\"RIGHT_0_conversion_Reaction10_X_STOICHIOMETRY\",\n", " display_name=\"transcription of LacI\",\n", " right=\"RIGHT_0_conversion_Reaction10_X\",\n", " )\n", " objects.append(b1)\n", "\n", " p1 = PhysicalEntity(\n", " uid=\"LEFT_0_conversion_Reaction9_PZ\",\n", " cellular_location=\"cell\",\n", " display_name=\"PZ\",\n", " member_physical_entity=\"PZ\",\n", " )\n", " objects.append(p1)\n", "\n", " u1 = UnificationXref(\n", " uid=\"http://identifiers.org/kegg.compound/C00046\",\n", " id=\"C00046\",\n", " db=\"KEGG Compound\",\n", " )\n", " objects.append(u1)\n", "\n", " u1 = UnificationXref(\n", " uid=\"http://identifiers.org/obo.go/GO:0005623\",\n", " id=\"GO:0005623\",\n", " db=\"Gene Ontology\",\n", " )\n", " objects.append(u1)\n", "\n", " p1 = PhysicalEntity(\n", " uid=\"LEFT_0_conversion_Reaction8_PY\",\n", " cellular_location=\"cell\",\n", " display_name=\"PY\",\n", " member_physical_entity=\"PY\",\n", " )\n", " objects.append(p1)\n", "\n", " u1 = UnificationXref(\n", " uid=\"http://identifiers.org/chebi/CHEBI:33699\", id=\"CHEBI:33699\", db=\"ChEBI\"\n", " )\n", " objects.append(u1)\n", "\n", " p1 = Protein(\n", " uid=\"PX\",\n", " xref=\"http://identifiers.org/uniprot/P03023\",\n", " display_name=\"LacI protein\",\n", " )\n", " objects.append(p1)\n", "\n", " p1 = Protein(\n", " uid=\"PY\",\n", " xref=\"http://identifiers.org/uniprot/P04483\",\n", " display_name=\"TetR protein\",\n", " )\n", " objects.append(p1)\n", "\n", " s1 = Stoichiometry(\n", " uid=\"RIGHT_0_conversion_Reaction10_X_STOICHIOMETRY\",\n", " physical_entity=\"RIGHT_0_conversion_Reaction10_X\",\n", " stoichiometric_coefficient=\"1\",\n", " )\n", " objects.append(s1)\n", "\n", " p1 = Protein(\n", " uid=\"PZ\",\n", " xref=\"http://identifiers.org/uniprot/P03034\",\n", " display_name=\"cI protein\",\n", " )\n", " objects.append(p1)\n", "\n", " c1 = BiochemicalReaction(\n", " uid=\"conversion_Reaction2\",\n", " xref=\"http://identifiers.org/obo.go/GO:0006402\",\n", " participant_stoichiometry=\"LEFT_0_conversion_Reaction2_Y_STOICHIOMETRY\",\n", " left=\"LEFT_0_conversion_Reaction2_Y\",\n", " display_name=\"degradation of TetR transcripts\",\n", " )\n", " objects.append(c1)\n", "\n", " s1 = Stoichiometry(\n", " uid=\"RIGHT_0_conversion_Reaction4_PX_STOICHIOMETRY\",\n", " physical_entity=\"RIGHT_0_conversion_Reaction4_PX\",\n", " stoichiometric_coefficient=\"1\",\n", " )\n", " objects.append(s1)\n", "\n", " p1 = PhysicalEntity(\n", " uid=\"LEFT_0_conversion_Reaction3_Z\",\n", " cellular_location=\"cell\",\n", " display_name=\"Z\",\n", " member_physical_entity=\"Z\",\n", " )\n", " objects.append(p1)\n", "\n", " c1 = BiochemicalReaction(\n", " uid=\"conversion_Reaction3\",\n", " xref=\"http://identifiers.org/obo.go/GO:0006402\",\n", " participant_stoichiometry=\"LEFT_0_conversion_Reaction3_Z_STOICHIOMETRY\",\n", " left=\"LEFT_0_conversion_Reaction3_Z\",\n", " display_name=\"degradation of CI transcripts\",\n", " )\n", " objects.append(c1)\n", "\n", " c1 = BiochemicalReaction(\n", " uid=\"conversion_Reaction4\",\n", " xref=\"http://identifiers.org/obo.go/GO:0006412\",\n", " participant_stoichiometry=\"RIGHT_0_conversion_Reaction4_PX_STOICHIOMETRY\",\n", " display_name=\"translation of LacI\",\n", " right=\"RIGHT_0_conversion_Reaction4_PX\",\n", " )\n", " objects.append(c1)\n", "\n", " c1 = BiochemicalReaction(\n", " uid=\"conversion_Reaction5\",\n", " xref=\"http://identifiers.org/obo.go/GO:0006412\",\n", " participant_stoichiometry=\"RIGHT_0_conversion_Reaction5_PY_STOICHIOMETRY\",\n", " display_name=\"translation of TetR\",\n", " right=\"RIGHT_0_conversion_Reaction5_PY\",\n", " )\n", " objects.append(c1)\n", "\n", " p1 = PhysicalEntity(\n", " uid=\"LEFT_0_conversion_Reaction2_Y\",\n", " cellular_location=\"cell\",\n", " display_name=\"Y\",\n", " member_physical_entity=\"Y\",\n", " )\n", " objects.append(p1)\n", "\n", " c1 = BiochemicalReaction(\n", " uid=\"conversion_Reaction6\",\n", " xref=\"http://identifiers.org/obo.go/GO:0006412\",\n", " participant_stoichiometry=\"RIGHT_0_conversion_Reaction6_PZ_STOICHIOMETRY\",\n", " display_name=\"translation of CI\",\n", " right=\"RIGHT_0_conversion_Reaction6_PZ\",\n", " )\n", " objects.append(c1)\n", "\n", " c1 = BiochemicalReaction(\n", " uid=\"conversion_Reaction7\",\n", " xref=\"http://identifiers.org/obo.go/GO:0030163\",\n", " participant_stoichiometry=\"LEFT_0_conversion_Reaction7_PX_STOICHIOMETRY\",\n", " display_name=\"degradation of LacI\",\n", " left=\"LEFT_0_conversion_Reaction7_PX\",\n", " )\n", " objects.append(c1)\n", "\n", " s1 = Stoichiometry(\n", " uid=\"LEFT_0_conversion_Reaction9_PZ_STOICHIOMETRY\",\n", " physical_entity=\"LEFT_0_conversion_Reaction9_PZ\",\n", " stoichiometric_coefficient=\"1\",\n", " )\n", " objects.append(s1)\n", "\n", " c1 = BiochemicalReaction(\n", " uid=\"conversion_Reaction8\",\n", " xref=\"http://identifiers.org/obo.go/GO:0030163\",\n", " participant_stoichiometry=\"LEFT_0_conversion_Reaction8_PY_STOICHIOMETRY\",\n", " display_name=\"degradation of TetR\",\n", " left=\"LEFT_0_conversion_Reaction8_PY\",\n", " )\n", " objects.append(c1)\n", "\n", " c1 = BiochemicalReaction(\n", " uid=\"conversion_Reaction9\",\n", " xref=\"http://identifiers.org/obo.go/GO:0030163\",\n", " participant_stoichiometry=\"LEFT_0_conversion_Reaction9_PZ_STOICHIOMETRY\",\n", " display_name=\"degradation of CI\",\n", " left=\"LEFT_0_conversion_Reaction9_PZ\",\n", " )\n", " objects.append(c1)\n", "\n", " u1 = UnificationXref(\n", " uid=\"http://identifiers.org/taxonomy/562\", id=\"562\", db=\"Taxonomy\"\n", " )\n", " objects.append(u1)\n", "\n", " s1 = Stoichiometry(\n", " uid=\"LEFT_0_conversion_Reaction1_X_STOICHIOMETRY\",\n", " physical_entity=\"LEFT_0_conversion_Reaction1_X\",\n", " stoichiometric_coefficient=\"1\",\n", " )\n", " objects.append(s1)\n", "\n", " p1 = PhysicalEntity(\n", " uid=\"RIGHT_0_conversion_Reaction4_PX\",\n", " cellular_location=\"cell\",\n", " display_name=\"PX\",\n", " member_physical_entity=\"PX\",\n", " )\n", " objects.append(p1)\n", "\n", " u1 = UnificationXref(\n", " uid=\"http://identifiers.org/uniprot/P03034\",\n", " id=\"P03034\",\n", " db=\"UniProt Knowledgebase\",\n", " )\n", " objects.append(u1)\n", "\n", " p1 = PhysicalEntity(\n", " uid=\"PEP0_control_Reaction10PZ\",\n", " cellular_location=\"cell\",\n", " display_name=\"PZ\",\n", " member_physical_entity=\"PZ\",\n", " )\n", " objects.append(p1)\n", "\n", " s1 = Stoichiometry(\n", " uid=\"LEFT_0_conversion_Reaction3_Z_STOICHIOMETRY\",\n", " physical_entity=\"LEFT_0_conversion_Reaction3_Z\",\n", " stoichiometric_coefficient=\"1\",\n", " )\n", " objects.append(s1)\n", "\n", " p1 = PhysicalEntity(\n", " uid=\"RIGHT_0_conversion_Reaction10_X\",\n", " cellular_location=\"cell\",\n", " display_name=\"X\",\n", " member_physical_entity=\"X\",\n", " )\n", " objects.append(p1)\n", "\n", " b1 = BioSource(uid=\"biosource_1\", xref=\"http://identifiers.org/taxonomy/562\")\n", " objects.append(b1)\n", "\n", " p1 = PhysicalEntity(\n", " uid=\"RIGHT_0_conversion_Reaction11_Y\",\n", " cellular_location=\"cell\",\n", " display_name=\"Y\",\n", " member_physical_entity=\"Y\",\n", " )\n", " objects.append(p1)\n", "\n", " p1 = PhysicalEntity(\n", " uid=\"RIGHT_0_conversion_Reaction12_Z\",\n", " cellular_location=\"cell\",\n", " display_name=\"Z\",\n", " member_physical_entity=\"Z\",\n", " )\n", " objects.append(p1)\n", "\n", " s1 = Stoichiometry(\n", " uid=\"LEFT_0_conversion_Reaction8_PY_STOICHIOMETRY\",\n", " physical_entity=\"LEFT_0_conversion_Reaction8_PY\",\n", " stoichiometric_coefficient=\"1\",\n", " )\n", " objects.append(s1)\n", "\n", " p1 = PhysicalEntity(\n", " uid=\"RIGHT_0_conversion_Reaction6_PZ\",\n", " cellular_location=\"cell\",\n", " display_name=\"PZ\",\n", " member_physical_entity=\"PZ\",\n", " )\n", " objects.append(p1)\n", "\n", " p1 = PhysicalEntity(\n", " uid=\"PEP0_control_Reaction6Z\",\n", " cellular_location=\"cell\",\n", " display_name=\"Z\",\n", " member_physical_entity=\"Z\",\n", " )\n", " objects.append(p1)\n", "\n", " p1 = PhysicalEntity(\n", " uid=\"PEP0_control_Reaction11PX\",\n", " cellular_location=\"cell\",\n", " display_name=\"PX\",\n", " member_physical_entity=\"PX\",\n", " )\n", " objects.append(p1)\n", "\n", " r1 = Rna(\n", " uid=\"Y\",\n", " xref=[\n", " \"http://identifiers.org/chebi/CHEBI:33699\",\n", " \"http://identifiers.org/kegg.compound/C00046\",\n", " \"http://identifiers.org/uniprot/P04483\",\n", " ],\n", " display_name=\"TetR mRNA\",\n", " )\n", " objects.append(r1)\n", "\n", " r1 = Rna(\n", " uid=\"X\",\n", " xref=[\n", " \"http://identifiers.org/chebi/CHEBI:33699\",\n", " \"http://identifiers.org/kegg.compound/C00046\",\n", " \"http://identifiers.org/uniprot/P03023\",\n", " ],\n", " display_name=\"LacI mRNA\",\n", " )\n", " objects.append(r1)\n", "\n", " s1 = Stoichiometry(\n", " uid=\"RIGHT_0_conversion_Reaction5_PY_STOICHIOMETRY\",\n", " physical_entity=\"RIGHT_0_conversion_Reaction5_PY\",\n", " stoichiometric_coefficient=\"1\",\n", " )\n", " objects.append(s1)\n", "\n", " r1 = Rna(\n", " uid=\"Z\",\n", " xref=[\n", " \"http://identifiers.org/chebi/CHEBI:33699\",\n", " \"http://identifiers.org/kegg.compound/C00046\",\n", " \"http://identifiers.org/uniprot/P03034\",\n", " ],\n", " display_name=\"cI mRNA\",\n", " )\n", " objects.append(r1)\n", "\n", " c1 = Control(\n", " uid=\"control_Reaction6_Z_0\",\n", " controlled=\"conversion_Reaction6\",\n", " control_type=\"INHIBITION\",\n", " controller=\"PEP0_control_Reaction6Z\",\n", " )\n", " objects.append(c1)\n", "\n", " c1 = Control(\n", " uid=\"control_Reaction12_PY_0\",\n", " controlled=\"conversion_Reaction12\",\n", " control_type=\"INHIBITION\",\n", " controller=\"PEP0_control_Reaction12PY\",\n", " )\n", " objects.append(c1)\n", "\n", " p1 = PhysicalEntity(\n", " uid=\"PEP0_control_Reaction12PY\",\n", " cellular_location=\"cell\",\n", " display_name=\"PY\",\n", " member_physical_entity=\"PY\",\n", " )\n", " objects.append(p1)\n", "\n", " u1 = UnificationXref(\n", " uid=\"http://identifiers.org/biomodels.db/MODEL6615351360\",\n", " id=\"MODEL6615351360\",\n", " db=\"BioModels Database\",\n", " )\n", " objects.append(u1)\n", "\n", " u1 = UnificationXref(\n", " uid=\"http://identifiers.org/uniprot/P03023\",\n", " id=\"P03023\",\n", " db=\"UniProt Knowledgebase\",\n", " )\n", " objects.append(u1)\n", "\n", " c1 = Control(\n", " uid=\"control_Reaction10_PZ_0\",\n", " controlled=\"conversion_Reaction10\",\n", " control_type=\"INHIBITION\",\n", " controller=\"PEP0_control_Reaction10PZ\",\n", " )\n", " objects.append(c1)\n", "\n", " u1 = UnificationXref(\n", " uid=\"http://identifiers.org/obo.go/GO:0006412\",\n", " id=\"GO:0006412\",\n", " db=\"Gene Ontology\",\n", " )\n", " objects.append(u1)\n", "\n", " u1 = UnificationXref(\n", " uid=\"http://identifiers.org/obo.go/GO:0040029\",\n", " id=\"GO:0040029\",\n", " db=\"Gene Ontology\",\n", " )\n", " objects.append(u1)\n", "\n", " u1 = UnificationXref(\n", " uid=\"http://identifiers.org/obo.go/GO:0006351\",\n", " id=\"GO:0006351\",\n", " db=\"Gene Ontology\",\n", " )\n", " objects.append(u1)\n", "\n", " c1 = Control(\n", " uid=\"control_Reaction5_Y_0\",\n", " controlled=\"conversion_Reaction5\",\n", " control_type=\"INHIBITION\",\n", " controller=\"PEP0_control_Reaction5Y\",\n", " )\n", " objects.append(c1)\n", "\n", " p1 = PhysicalEntity(\n", " uid=\"LEFT_0_conversion_Reaction1_X\",\n", " cellular_location=\"cell\",\n", " display_name=\"X\",\n", " member_physical_entity=\"X\",\n", " )\n", " objects.append(p1)\n", "\n", " p1 = PhysicalEntity(\n", " uid=\"PEP0_control_Reaction5Y\",\n", " cellular_location=\"cell\",\n", " display_name=\"Y\",\n", " member_physical_entity=\"Y\",\n", " )\n", " objects.append(p1)\n", "\n", " c1 = Control(\n", " uid=\"control_Reaction11_PX_0\",\n", " controlled=\"conversion_Reaction11\",\n", " control_type=\"INHIBITION\",\n", " controller=\"PEP0_control_Reaction11PX\",\n", " )\n", " objects.append(c1)\n", "\n", " c1 = BiochemicalReaction(\n", " uid=\"conversion_Reaction1\",\n", " xref=\"http://identifiers.org/obo.go/GO:0006402\",\n", " participant_stoichiometry=\"LEFT_0_conversion_Reaction1_X_STOICHIOMETRY\",\n", " display_name=\"degradation of LacI transcripts\",\n", " left=\"LEFT_0_conversion_Reaction1_X\",\n", " )\n", " objects.append(c1)\n", "\n", " u1 = UnificationXref(\n", " uid=\"http://identifiers.org/uniprot/P04483\",\n", " id=\"P04483\",\n", " db=\"UniProt Knowledgebase\",\n", " )\n", " objects.append(u1)\n", " # '''\n", " # \n", " # \n", " # \n", " # transcription of CI\n", " # \n", " # \n", " # '''\n", " # b1=BiochemicalReaction(uid=\"conversion_Reaction12\", displayName=\"transcription of CI\")\n", " # objects.append(b1)\n", "\n", " model = BioPaxModel(\n", " objects={o.uid: o for o in objects},\n", " xml_base=\"http://www.biopax.org/release/biopax-level3.owl#\",\n", " )\n", " owl_str: str = model_to_owl_str(model)\n", " os.makedirs(os.path.dirname(biopax_path), exist_ok=True)\n", "\n", " with open(biopax_path, \"w\") as f_biopax:\n", " f_biopax.write(owl_str)\n", "\n", " print(\"-\" * 80)\n", " print(owl_str)\n", " print(\"-\" * 80)\n", "\n", " return model" ] }, { "cell_type": "code", "execution_count": 3, "id": "44a9beae", "metadata": { "execution": { "iopub.execute_input": "2023-04-17T14:01:44.993993Z", "iopub.status.busy": "2023-04-17T14:01:44.993333Z", "iopub.status.idle": "2023-04-17T14:01:45.040300Z", "shell.execute_reply": "2023-04-17T14:01:45.040515Z" } }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "Serializing OWL elements: 100% 73.0/73.0 [00:00<00:00, 5.10kit/s]" ] }, { "name": "stdout", "output_type": "stream", "text": [ "--------------------------------------------------------------------------------\n", "\n", "\n", " \n", " \n", " \n", "\n", "\n", " cell\n", " PY\n", " PY\n", "\n", "\n", "\n", " LEFT_0_conversion_Reaction2_Y\n", " 1\n", "\n", "\n", "\n", " BioModels Database\n", " http://identifiers.org/biomodels.db/BIOMD0000000012\n", "\n", "\n", "\n", " PubMed\n", " 10659856\n", "\n", "\n", "\n", " BioModels Database\n", " http://identifiers.org/biomodels.db/MODEL6615351360\n", "\n", "\n", "\n", " BioModels Database\n", " BIOMD0000000012\n", "\n", "\n", "\n", " Gene Ontology\n", " GO:0006402\n", "\n", "\n", "\n", " LEFT_0_conversion_Reaction7_PX\n", " 1\n", "\n", "\n", "\n", " INHIBITION\n", " conversion_Reaction4\n", " PEP0_control_Reaction4X\n", "\n", "\n", "\n", " RIGHT_0_conversion_Reaction6_PZ\n", " 1\n", "\n", "\n", "\n", " cell\n", " X\n", " X\n", "\n", "\n", "\n", " Gene Ontology\n", " GO:0030163\n", "\n", "\n", "\n", " RIGHT_0_conversion_Reaction12_Z\n", " 1\n", "\n", "\n", "\n", " cell\n", " PX\n", " PX\n", "\n", "\n", "\n", " RIGHT_0_conversion_Reaction11_Y\n", " 1\n", "\n", "\n", "\n", " cell\n", " http://identifiers.org/obo.go/GO:0005623\n", "\n", "\n", "\n", " transcription of CI\n", " RIGHT_0_conversion_Reaction12_Z_STOICHIOMETRY\n", " RIGHT_0_conversion_Reaction12_Z\n", " http://identifiers.org/obo.go/GO:0006351\n", "\n", "\n", "\n", " transcription of TetR\n", " RIGHT_0_conversion_Reaction11_Y_STOICHIOMETRY\n", " RIGHT_0_conversion_Reaction11_Y\n", " http://identifiers.org/obo.go/GO:0006351\n", "\n", "\n", "\n", " transcription of LacI\n", " RIGHT_0_conversion_Reaction10_X_STOICHIOMETRY\n", " RIGHT_0_conversion_Reaction10_X\n", " http://identifiers.org/obo.go/GO:0006351\n", "\n", "\n", "\n", " cell\n", " PZ\n", " PZ\n", "\n", "\n", "\n", " KEGG Compound\n", " C00046\n", "\n", "\n", "\n", " Gene Ontology\n", " GO:0005623\n", "\n", "\n", "\n", " cell\n", " PY\n", " PY\n", "\n", "\n", "\n", " ChEBI\n", " CHEBI:33699\n", "\n", "\n", "\n", " LacI protein\n", " http://identifiers.org/uniprot/P03023\n", "\n", "\n", "\n", " TetR protein\n", " http://identifiers.org/uniprot/P04483\n", "\n", "\n", "\n", " RIGHT_0_conversion_Reaction10_X\n", " 1\n", "\n", "\n", "\n", " cI protein\n", " http://identifiers.org/uniprot/P03034\n", "\n", "\n", "\n", " degradation of TetR transcripts\n", " LEFT_0_conversion_Reaction2_Y\n", " LEFT_0_conversion_Reaction2_Y_STOICHIOMETRY\n", " http://identifiers.org/obo.go/GO:0006402\n", "\n", "\n", "\n", " RIGHT_0_conversion_Reaction4_PX\n", " 1\n", "\n", "\n", "\n", " cell\n", " Z\n", " Z\n", "\n", "\n", "\n", " degradation of CI transcripts\n", " LEFT_0_conversion_Reaction3_Z\n", " LEFT_0_conversion_Reaction3_Z_STOICHIOMETRY\n", " http://identifiers.org/obo.go/GO:0006402\n", "\n", "\n", "\n", " translation of LacI\n", " RIGHT_0_conversion_Reaction4_PX_STOICHIOMETRY\n", " RIGHT_0_conversion_Reaction4_PX\n", " http://identifiers.org/obo.go/GO:0006412\n", "\n", "\n", "\n", " translation of TetR\n", " RIGHT_0_conversion_Reaction5_PY_STOICHIOMETRY\n", " RIGHT_0_conversion_Reaction5_PY\n", " http://identifiers.org/obo.go/GO:0006412\n", "\n", "\n", "\n", " cell\n", " Y\n", " Y\n", "\n", "\n", "\n", " translation of CI\n", " RIGHT_0_conversion_Reaction6_PZ_STOICHIOMETRY\n", " RIGHT_0_conversion_Reaction6_PZ\n", " http://identifiers.org/obo.go/GO:0006412\n", "\n", "\n", "\n", " degradation of LacI\n", " LEFT_0_conversion_Reaction7_PX\n", " LEFT_0_conversion_Reaction7_PX_STOICHIOMETRY\n", " http://identifiers.org/obo.go/GO:0030163\n", "\n", "\n", "\n", " LEFT_0_conversion_Reaction9_PZ\n", " 1\n", "\n", "\n", "\n", " degradation of TetR\n", " LEFT_0_conversion_Reaction8_PY\n", " LEFT_0_conversion_Reaction8_PY_STOICHIOMETRY\n", " http://identifiers.org/obo.go/GO:0030163\n", "\n", "\n", "\n", " degradation of CI\n", " LEFT_0_conversion_Reaction9_PZ\n", " LEFT_0_conversion_Reaction9_PZ_STOICHIOMETRY\n", " http://identifiers.org/obo.go/GO:0030163\n", "\n", "\n", "\n", " Taxonomy\n", " 562\n", "\n", "\n", "\n", " LEFT_0_conversion_Reaction1_X\n", " 1\n", "\n", "\n", "\n", " cell\n", " PX\n", " PX\n", "\n", "\n", "\n", " UniProt Knowledgebase\n", " P03034\n", "\n", "\n", "\n", " cell\n", " PZ\n", " PZ\n", "\n", "\n", "\n", " LEFT_0_conversion_Reaction3_Z\n", " 1\n", "\n", "\n", "\n", " cell\n", " X\n", " X\n", "\n", "\n", "\n", " http://identifiers.org/taxonomy/562\n", "\n", "\n", "\n", " cell\n", " Y\n", " Y\n", "\n", "\n", "\n", " cell\n", " Z\n", " Z\n", "\n", "\n", "\n", " LEFT_0_conversion_Reaction8_PY\n", " 1\n", "\n", "\n", "\n", " cell\n", " PZ\n", " PZ\n", "\n", "\n", "\n", " cell\n", " Z\n", " Z\n", "\n", "\n", "\n", " cell\n", " PX\n", " PX\n", "\n", "\n", "\n", " TetR mRNA\n", " http://identifiers.org/chebi/CHEBI:33699\n", " http://identifiers.org/kegg.compound/C00046\n", " http://identifiers.org/uniprot/P04483\n", "\n", "\n", "\n", " LacI mRNA\n", " http://identifiers.org/chebi/CHEBI:33699\n", " http://identifiers.org/kegg.compound/C00046\n", " http://identifiers.org/uniprot/P03023\n", "\n", "\n", "\n", " RIGHT_0_conversion_Reaction5_PY\n", " 1\n", "\n", "\n", "\n", " cI mRNA\n", " http://identifiers.org/chebi/CHEBI:33699\n", " http://identifiers.org/kegg.compound/C00046\n", " http://identifiers.org/uniprot/P03034\n", "\n", "\n", "\n", " INHIBITION\n", " conversion_Reaction6\n", " PEP0_control_Reaction6Z\n", "\n", "\n", "\n", " INHIBITION\n", " conversion_Reaction12\n", " PEP0_control_Reaction12PY\n", "\n", "\n", "\n", " cell\n", " PY\n", " PY\n", "\n", "\n", "\n", " BioModels Database\n", " MODEL6615351360\n", "\n", "\n", "\n", " UniProt Knowledgebase\n", " P03023\n", "\n", "\n", "\n", " INHIBITION\n", " conversion_Reaction10\n", " PEP0_control_Reaction10PZ\n", "\n", "\n", "\n", " Gene Ontology\n", " GO:0006412\n", "\n", "\n", "\n", " Gene Ontology\n", " GO:0040029\n", "\n", "\n", "\n", " Gene Ontology\n", " GO:0006351\n", "\n", "\n", "\n", " INHIBITION\n", " conversion_Reaction5\n", " PEP0_control_Reaction5Y\n", "\n", "\n", "\n", " cell\n", " X\n", " X\n", "\n", "\n", "\n", " cell\n", " Y\n", " Y\n", "\n", "\n", "\n", " INHIBITION\n", " conversion_Reaction11\n", " PEP0_control_Reaction11PX\n", "\n", "\n", "\n", " degradation of LacI transcripts\n", " LEFT_0_conversion_Reaction1_X\n", " LEFT_0_conversion_Reaction1_X_STOICHIOMETRY\n", " http://identifiers.org/obo.go/GO:0006402\n", "\n", "\n", "\n", " UniProt Knowledgebase\n", " P04483\n", "\n", "\n", "\n", "--------------------------------------------------------------------------------\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "\n" ] } ], "source": [ "if __name__ == \"__main__\":\n", " from combine_notebooks import RESULTS_DIR\n", "\n", " create_repressilator(biopax_path=RESULTS_DIR / \"repressilator_biopax.owl\")" ] } ], "metadata": { "jupytext": { "cell_metadata_filter": "-all", "main_language": "python", "notebook_metadata_filter": "-all" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.10.6" } }, "nbformat": 4, "nbformat_minor": 5 }