napistu 0.1.0__py3-none-any.whl

napistu/constants.py

@@ -0,0 +1,500 @@
+"""Module to contain all constants for CPR"""
+
+from __future__ import annotations
+
+import libsbml
+
+from types import SimpleNamespace
+import pandas as pd
+
+PROTEINATLAS_SUBCELL_LOC_URL = (
+    "https://www.proteinatlas.org/download/tsv/subcellular_location.tsv.zip"
+)
+
+# GTEx
+GTEX_RNASEQ_EXPRESSION_URL = "https://storage.googleapis.com/adult-gtex/bulk-gex/v8/rna-seq/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_median_tpm.gct.gz"
+
+# Gencode
+GENCODE_URL = "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/gencode.v26.transcripts.fa.gz"
+
+FILE_EXT_ZIP = "zip"
+FILE_EXT_GZ = "gz"
+
+# SBML_dfs
+
+SBML_DFS = SimpleNamespace(
+    COMPARTMENTS="compartments",
+    SPECIES="species",
+    COMPARTMENTALIZED_SPECIES="compartmentalized_species",
+    REACTIONS="reactions",
+    REACTION_SPECIES="reaction_species",
+    SPECIES_DATA="species_data",
+    REACTIONS_DATA="reactions_data",
+    C_ID="c_id",
+    C_NAME="c_name",
+    C_IDENTIFIERS="c_Identifiers",
+    C_SOURCE="c_Source",
+    S_ID="s_id",
+    S_NAME="s_name",
+    S_IDENTIFIERS="s_Identifiers",
+    S_SOURCE="s_Source",
+    SC_ID="sc_id",
+    SC_NAME="sc_name",
+    SC_SOURCE="sc_Source",
+    R_ID="r_id",
+    R_NAME="r_name",
+    R_IDENTIFIERS="r_Identifiers",
+    R_SOURCE="r_Source",
+    R_ISREVERSIBLE="r_isreversible",
+    RSC_ID="rsc_id",
+    STOICHIOMETRY="stoichiometry",
+    SBO_TERM="sbo_term",
+)
+
+SBML_DFS_SCHEMA = SimpleNamespace(
+    SCHEMA={
+        SBML_DFS.COMPARTMENTS: {
+            "pk": SBML_DFS.C_ID,
+            "label": SBML_DFS.C_NAME,
+            "id": SBML_DFS.C_IDENTIFIERS,
+            "source": SBML_DFS.C_SOURCE,
+            "vars": [SBML_DFS.C_NAME, SBML_DFS.C_IDENTIFIERS, SBML_DFS.C_SOURCE],
+        },
+        SBML_DFS.SPECIES: {
+            "pk": SBML_DFS.S_ID,
+            "label": SBML_DFS.S_NAME,
+            "id": SBML_DFS.S_IDENTIFIERS,
+            "source": SBML_DFS.S_SOURCE,
+            "vars": [SBML_DFS.S_NAME, SBML_DFS.S_IDENTIFIERS, SBML_DFS.S_SOURCE],
+        },
+        SBML_DFS.COMPARTMENTALIZED_SPECIES: {
+            "pk": SBML_DFS.SC_ID,
+            "label": SBML_DFS.SC_NAME,
+            "fk": [SBML_DFS.S_ID, SBML_DFS.C_ID],
+            "source": SBML_DFS.SC_SOURCE,
+            "vars": [
+                SBML_DFS.SC_NAME,
+                SBML_DFS.S_ID,
+                SBML_DFS.C_ID,
+                SBML_DFS.SC_SOURCE,
+            ],
+        },
+        SBML_DFS.REACTIONS: {
+            "pk": SBML_DFS.R_ID,
+            "label": SBML_DFS.R_NAME,
+            "id": SBML_DFS.R_IDENTIFIERS,
+            "source": SBML_DFS.R_SOURCE,
+            "vars": [
+                SBML_DFS.R_NAME,
+                SBML_DFS.R_IDENTIFIERS,
+                SBML_DFS.R_SOURCE,
+                SBML_DFS.R_ISREVERSIBLE,
+            ],
+        },
+        SBML_DFS.REACTION_SPECIES: {
+            "pk": SBML_DFS.RSC_ID,
+            "fk": [SBML_DFS.R_ID, SBML_DFS.SC_ID],
+            "vars": [
+                SBML_DFS.R_ID,
+                SBML_DFS.SC_ID,
+                SBML_DFS.STOICHIOMETRY,
+                SBML_DFS.SBO_TERM,
+            ],
+        },
+    },
+    REQUIRED_ENTITIES={
+        SBML_DFS.COMPARTMENTS,
+        SBML_DFS.SPECIES,
+        SBML_DFS.COMPARTMENTALIZED_SPECIES,
+        SBML_DFS.REACTIONS,
+        SBML_DFS.REACTION_SPECIES,
+    },
+    OPTIONAL_ENTITIES={
+        SBML_DFS.SPECIES_DATA,
+        SBML_DFS.REACTIONS_DATA,
+    },
+)
+
+ENTITIES_W_DATA = {SBML_DFS.SPECIES, SBML_DFS.REACTIONS}
+
+REQUIRED_REACTION_FROMEDGELIST_COLUMNS = [
+    "sc_id_up",
+    "sc_id_down",
+    "sbo_term",
+    "r_name",
+    "r_Identifiers",
+    "r_isreversible",
+]
+
+CPR_STANDARD_OUTPUTS = SimpleNamespace(
+    SPECIES_IDENTIFIERS="species_identifiers.tsv",
+    SPECIES="species.json",
+    REACTIONS="reactions.json",
+    REACTION_SPECIES="reaction_species.json",
+    COMPARTMENTS="compartments.json",
+    COMPARTMENTALIZED_SPECIES="compartmentalized_species.json",
+)
+
+INTERACTION_EDGELIST_EXPECTED_VARS = {
+    "upstream_name",
+    "downstream_name",
+    "upstream_compartment",
+    "downstream_compartment",
+    "r_name",
+    "sbo_term",
+    "r_Identifiers",
+    "r_isreversible",
+}
+
+BQB_PRIORITIES = pd.DataFrame(
+    [{"bqb": "BQB_IS", "bqb_rank": 1}, {"bqb": "BQB_HAS_PART", "bqb_rank": 2}]
+)
+
+ONTOLOGY_PRIORITIES = pd.DataFrame(
+    [
+        {"ontology": "reactome", "ontology_rank": 1},
+        {"ontology": "ensembl_gene", "ontology_rank": 2},
+        {"ontology": "chebi", "ontology_rank": 3},
+        {"ontology": "uniprot", "ontology_rank": 4},
+        {"ontology": "go", "ontology_rank": 5},
+    ]
+)
+
+# SBML
+# Biological qualifiers
+# Biomodels qualifiers
+BQB = SimpleNamespace(
+    IS="BQB_IS",
+    HAS_PART="BQB_HAS_PART",
+    IS_PART_OF="BQB_IS_PART_OF",
+    IS_VERSION_OF="BQB_IS_VERSION_OF",
+    HAS_VERSION="BQB_HAS_VERSION",
+    IS_HOMOLOG_TO="BQB_IS_HOMOLOG_TO",
+    IS_DESCRIBED_BY="BQB_IS_DESCRIBED_BY",
+    IS_ENCODED_BY="BQB_IS_ENCODED_BY",
+    ENCODES="BQB_ENCODES",
+    OCCURS_IN="BQB_OCCURS_IN",
+    HAS_PROPERTY="BQB_HAS_PROPERTY",
+    IS_PROPERTY_OF="BQB_IS_PROPERTY_OF",
+    HAS_TAXON="BQB_HAS_TAXON",
+    UNKNOWN="BQB_UNKNOWN",
+)
+
+# molecules are distinctly defined by these BQB terms
+BQB_DEFINING_ATTRS = ["BQB_IS", "IS_HOMOLOG_TO"]
+
+# a looser convention which will aggregate genes, transcripts, and proteins
+# if they are linked with the appropriate bioqualifiers
+BQB_DEFINING_ATTRS_LOOSE = [
+    "BQB_IS",
+    "IS_HOMOLOG_TO",
+    "BQB_IS_ENCODED_BY",
+    "BQB_ENCODES",
+]
+
+# identifiers
+IDENTIFIERS = SimpleNamespace(
+    ONTOLOGY="ontology", IDENTIFIER="identifier", BQB="bqb", URL="url"
+)
+
+SPECIES_IDENTIFIERS_REQUIRED_VARS = {
+    SBML_DFS.S_ID,
+    IDENTIFIERS.ONTOLOGY,
+    IDENTIFIERS.IDENTIFIER,
+    IDENTIFIERS.BQB,
+    SBML_DFS.S_NAME,
+}
+
+BIOLOGICAL_QUALIFIERS = [
+    "BQB_IS",
+    "BQB_HAS_PART",
+    "BQB_IS_PART_OF",
+    "BQB_IS_VERSION_OF",
+    "BQB_HAS_VERSION",
+    "BQB_IS_HOMOLOG_TO",
+    "BQB_IS_DESCRIBED_BY",
+    "BQB_IS_ENCODED_BY",
+    "BQB_ENCODES",
+    "BQB_OCCURS_IN",
+    "BQB_HAS_PROPERTY",
+    "BQB_IS_PROPERTY_OF",
+    "BQB_HAS_TAXON",
+    "BQB_UNKNOWN",
+]
+
+
+def get_biological_qualifier_codes():
+    bio_qualifier_codes = {getattr(libsbml, bqb): bqb for bqb in BIOLOGICAL_QUALIFIERS}
+
+    return bio_qualifier_codes
+
+
+BIOLOGICAL_QUALIFIER_CODES = get_biological_qualifier_codes()
+
+# Systems biology ontology
+SBOTERM_NAMES = SimpleNamespace(
+    REACTANT="reactant",
+    PRODUCT="product",
+    CATALYST="catalyst",
+    INHIBITOR="inhibitor",
+    STIMULATOR="stimulator",
+    MODIFIER="modifier",
+    INTERACTOR="interactor",
+)
+
+MINI_SBO_TO_NAME = {
+    "SBO:0000010": SBOTERM_NAMES.REACTANT,
+    "SBO:0000011": SBOTERM_NAMES.PRODUCT,
+    "SBO:0000013": SBOTERM_NAMES.CATALYST,
+    "SBO:0000020": SBOTERM_NAMES.INHIBITOR,
+    "SBO:0000459": SBOTERM_NAMES.STIMULATOR,
+    "SBO:0000019": SBOTERM_NAMES.MODIFIER,
+    "SBO:0000336": SBOTERM_NAMES.INTERACTOR,
+}
+
+MINI_SBO_FROM_NAME = {
+    SBOTERM_NAMES.REACTANT: "SBO:0000010",
+    SBOTERM_NAMES.PRODUCT: "SBO:0000011",
+    SBOTERM_NAMES.CATALYST: "SBO:0000013",
+    SBOTERM_NAMES.INHIBITOR: "SBO:0000020",
+    SBOTERM_NAMES.STIMULATOR: "SBO:0000459",
+    SBOTERM_NAMES.MODIFIER: "SBO:0000019",  # parent category of inhibitor and stimulator (i.e., activator)
+    SBOTERM_NAMES.INTERACTOR: "SBO:0000336",  # entity participating in a physical or functional interaction
+}
+
+SBO_MODIFIER_NAMES = {
+    SBOTERM_NAMES.INHIBITOR,
+    SBOTERM_NAMES.STIMULATOR,
+    SBOTERM_NAMES.MODIFIER,
+}
+
+MINI_SBO_NAME_TO_POLARITY = {
+    SBOTERM_NAMES.REACTANT: "activation",
+    SBOTERM_NAMES.PRODUCT: "activation",
+    SBOTERM_NAMES.CATALYST: "activation",
+    SBOTERM_NAMES.INHIBITOR: "inhibition",
+    SBOTERM_NAMES.STIMULATOR: "activation",
+    SBOTERM_NAMES.MODIFIER: "ambiguous",
+    SBOTERM_NAMES.INTERACTOR: "ambiguous",
+}
+
+# how does changing a reactions' membership
+# affect whether a reaction can occur
+# for example, if I remove any substrate a reaction won't occur
+# but I would have to remove all catalysts for it to not occur
+SBO_NAME_TO_ROLE = {
+    SBOTERM_NAMES.REACTANT: "DEFINING",
+    SBOTERM_NAMES.PRODUCT: "DEFINING",
+    SBOTERM_NAMES.INTERACTOR: "DEFINING",
+    SBOTERM_NAMES.CATALYST: "REQUIRED",
+    SBOTERM_NAMES.INHIBITOR: "OPTIONAL",
+    SBOTERM_NAMES.STIMULATOR: "OPTIONAL",
+    SBOTERM_NAMES.MODIFIER: "OPTIONAL",
+}
+
+# see also https://github.com/calico/netcontextr/blob/main/R/reactionTrimmingFunctions.R
+VALID_SBO_ROLES = (
+    # there is a direct correspondence between the set of defining entries and the identity of a reaction
+    # e.g., the stoichiometery of a metabolic reaction or the members of a protein-protein interaction
+    "DEFINING",
+    # 1+ entries are needed if entries were initially defined. i.e., reactions which require a catalyst
+    # would no longer exist if the catalyst was removed, but many reactions do not require a catalyst.
+    "REQUIRED",
+    # 0+ entries. optional species can be added or removed to a reaction without changing its identity
+    "OPTIONAL",
+)
+
+# required variables for the edgelist formats used by mechanism_matching
+CPR_EDGELIST = SimpleNamespace(
+    S_ID_UPSTREAM="s_id_upstream",
+    S_ID_DOWNSTREAM="s_id_downstream",
+    SC_ID_UPSTREAM="sc_id_upstream",
+    SC_ID_DOWNSTREAM="sc_id_downstream",
+    IDENTIFIER_UPSTREAM="identifier_upstream",
+    IDENTIFIER_DOWNSTREAM="identifier_downstream",
+    S_NAME_UPSTREAM="s_name_upstream",
+    S_NAME_DOWNSTREAM="s_name_downstream",
+    SC_ID_ORIGIN="sc_id_origin",
+    SC_ID_DEST="sc_id_dest",
+)
+
+IDENTIFIER_EDGELIST_REQ_VARS = {
+    CPR_EDGELIST.IDENTIFIER_UPSTREAM,
+    CPR_EDGELIST.IDENTIFIER_DOWNSTREAM,
+}
+
+CPR_EDGELIST_REQ_VARS = {
+    CPR_EDGELIST.S_ID_UPSTREAM,
+    CPR_EDGELIST.S_ID_DOWNSTREAM,
+    CPR_EDGELIST.SC_ID_UPSTREAM,
+    CPR_EDGELIST.SC_ID_DOWNSTREAM,
+}
+
+CPR_PATH_REQ_VARS = {CPR_EDGELIST.SC_ID_ORIGIN, CPR_EDGELIST.SC_ID_DEST}
+
+# specifying weighting schemes schema
+
+DEFAULT_WT_TRANS = "identity"
+
+DEFINED_WEIGHT_TRANSFORMATION = {
+    DEFAULT_WT_TRANS: "_wt_transformation_identity",
+    "string": "_wt_transformation_string",
+    "string_inv": "_wt_transformation_string_inv",
+}
+
+SCORE_CALIBRATION_POINTS_DICT = {
+    "weights": {"strong": 3, "good": 7, "okay": 20, "weak": 40},
+    "string_wt": {"strong": 950, "good": 400, "okay": 230, "weak": 150},
+}
+
+SOURCE_VARS_DICT = {"string_wt": 10}
+
+# source
+SOURCE_SPEC = SimpleNamespace(
+    PATHWAY_ID="pathway_id",
+    MODEL="model",
+    SOURCE="source",
+    SPECIES="species",
+    NAME="name",
+    ENTRY="entry",
+    N_COLLAPSED_PATHWAYS="n_collapsed_pathways",
+    INDEX_NAME="entry",
+    FILE="file",
+    DATE="date",
+)
+
+EXPECTED_PW_INDEX_COLUMNS = {
+    SOURCE_SPEC.FILE,
+    SOURCE_SPEC.PATHWAY_ID,
+    SOURCE_SPEC.SOURCE,
+    SOURCE_SPEC.SPECIES,
+    SOURCE_SPEC.NAME,
+    SOURCE_SPEC.DATE,
+}
+
+# rules for specific ontologies
+
+ONTOLOGIES = SimpleNamespace(
+    CHEBI="chebi",
+    ENSEMBL_GENE="ensembl_gene",
+    ENSEMBL_TRANSCRIPT="ensembl_transcript",
+    ENSEMBL_PROTEIN="ensembl_protein",
+    GENE_NAME="gene_name",
+    GO="go",
+    MIRBASE="mirbase",
+    NCBI_ENTREZ_GENE="ncbi_entrez_gene",
+    PHAROS="pharos",
+    REACTOME="reactome",
+    SYMBOL="symbol",
+    UNIPROT="uniprot",
+)
+
+CHARACTERISTIC_COMPLEX_ONTOLOGIES = [
+    ONTOLOGIES.ENSEMBL_GENE,
+    ONTOLOGIES.NCBI_ENTREZ_GENE,
+    ONTOLOGIES.MIRBASE,
+]
+
+ONTOLOGY_ALIASES = SimpleNamespace(NCBI_ENTREZ_GENE={"ncbigene", "ncbi_gene"})
+
+ENSEMBL_MOLECULE_TYPES_TO_ONTOLOGY = {
+    "G": ONTOLOGIES.ENSEMBL_GENE,
+    "T": ONTOLOGIES.ENSEMBL_TRANSCRIPT,
+    "P": ONTOLOGIES.ENSEMBL_PROTEIN,
+}
+
+ENSEMBL_MOLECULE_TYPES_FROM_ONTOLOGY = {
+    ONTOLOGIES.ENSEMBL_GENE: "G",
+    ONTOLOGIES.ENSEMBL_TRANSCRIPT: "T",
+    ONTOLOGIES.ENSEMBL_PROTEIN: "P",
+}
+
+ENSEMBL_SPECIES_FROM_CODE = {"MUS": "Mus musculus"}
+
+ENSEMBL_SPECIES_TO_CODE = {"Mus musculus": "MUS"}
+
+ENSEMBL_PREFIX_TO_ONTOLOGY = {
+    "ENSG": ONTOLOGIES.ENSEMBL_GENE,
+    "ENST": ONTOLOGIES.ENSEMBL_TRANSCRIPT,
+    "ENSP": ONTOLOGIES.ENSEMBL_PROTEIN,
+}
+
+COMPARTMENTS = {
+    "NUCLEOPLASM": "nucleoplasm",
+    "CYTOPLASM": "cytoplasm",
+    "CELLULAR_COMPONENT": "cellular_component",
+    "CYTOSOL": "cytosol",
+    "MITOCHONDRIA": "mitochondria",
+    "MITOMEMBRANE": "mitochondrial membrane",
+    "INNERMITOCHONDRIA": "inner mitochondria",
+    "MITOMATRIX": "mitochondrial matrix",
+    "ENDOPLASMICRETICULUM": "endoplasmic reticulum",
+    "ERMEMBRANE": "endoplasmic reticulum membrane",
+    "ERLUMEN": "endoplasmic reticulum lumen",
+    "GOLGIAPPARATUS": "golgi apparatus",
+    "GOLGIMEMBRANE": "golgi membrane",
+    "NUCLEUS": "nucleus",
+    "NUCLEARLUMEN": "nuclear lumen",
+    "NUCLEOLUS": "nucleolus",
+    "LYSOSOME": "lysosome",
+    "PEROXISOME": "peroxisome",
+    "EXTRACELLULAR": "extracellular",
+}
+
+COMPARTMENT_ALIASES = {
+    "NUCLEOPLASM": ["nucleoplasm", "Nucleoplasm"],
+    "CYTOPLASM": ["cytoplasm", "Cytoplasm"],
+    "CELLULAR_COMPONENT": ["cellular_component", "Cellular_component"],
+    "CYTOSOL": ["cytosol", "Cytosol"],
+    "MITOCHONDRIA": ["mitochondria", "Mitochondria"],
+    "MITOMEMBRANE": ["mitochondrial membrane", "Mitochondrial membrane"],
+    "INNERMITOCHONDRIA": [
+        "inner mitochondria",
+        "Inner mitochondria",
+        "inner mitochondrial compartment",
+    ],
+    "MITOMATRIX": [
+        "mitochondrial matrix",
+        "Mitochondrial matrix",
+        "mitochondrial lumen",
+        "Mitochondrial lumen",
+    ],
+    "ENDOPLASMICRETICULUM": ["endoplasmic reticulum", "Endoplasmic reticulum"],
+    "ERMEMBRANE": ["endoplasmic reticulum membrane", "Endoplasmic reticulum membrane"],
+    "ERLUMEN": ["endoplasmic reticulum lumen", "Endoplasmic reticulum lumen"],
+    "GOLGIAPPARATUS": ["golgi apparatus", "Golgi apparatus"],
+    "GOLGIMEMBRANE": ["Golgi membrane", "golgi membrane"],
+    "NUCLEUS": ["nucleus", "Nucleus"],
+    "NUCLEARLUMEN": ["nuclear lumen", "Nuclear lumen"],
+    "NUCLEOLUS": ["nucleolus", "Nucleolus"],
+    "LYSOSOME": ["lysosome", "Lysosome"],
+    "PEROXISOME": ["peroxisome", "Peroxisome", "peroxisome/glyoxysome"],
+    "EXTRACELLULAR": [
+        "extracellular",
+        "Extracellular",
+        "extracellular space",
+        "Extracellular space",
+    ],
+}
+
+COMPARTMENTS_GO_TERMS = {
+    "NUCLEOPLASM": "GO:0005654",
+    "CELLULAR_COMPONENT": "GO:0005575",
+    "CYTOPLASM": "GO:0005737",
+    "CYTOSOL": "GO:0005829",
+    "MITOCHONDRIA": "GO:0005739",
+    "MITOMEMBRANE": "GO:0031966",
+    "INNERMITOCHONDRIA": "GO:0005743",
+    "MITOMATRIX": "GO:0005759",
+    "ENDOPLASMICRETICULUM": "GO:0005783",
+    "ERMEMBRANE": "GO:0005789",
+    "ERLUMEN": "GO:0005788",
+    "GOLGIAPPARATUS": "GO:0005794",
+    "GOLGIMEMBRANE": "GO:0000139",
+    "NUCLEUS": "GO:0005634",
+    "NUCLEARLUMEN": "GO:0031981",
+    "NUCLEOLUS": "GO:0005730",
+    "LYSOSOME": "GO:0005764",
+    "PEROXISOME": "GO:0005777",
+    "EXTRACELLULAR": "GO:0005615",
+}

napistu/gcs/__init__.py

@@ -0,0 +1,10 @@
+from __future__ import annotations
+
+from importlib.metadata import PackageNotFoundError
+from importlib.metadata import version
+
+try:
+    __version__ = version("calicolabs-cpr")
+except PackageNotFoundError:
+    # package is not installed
+    pass

napistu/gcs/constants.py

@@ -0,0 +1,69 @@
+# GCS constants
+from __future__ import annotations
+
+from types import SimpleNamespace
+
+GCS_SUBASSET_NAMES = SimpleNamespace(
+    SBML_DFS="sbml_dfs",
+    IDENTIFIERS="identifiers",
+    REGULATORY_GRAPH="regulatory_graph",
+    REGULATORY_DISTANCES="regulatory_distances",
+)
+
+
+GCS_FILETYPES = SimpleNamespace(
+    SBML_DFS="sbml_dfs.pkl",
+    IDENTIFIERS="identifiers.tsv",
+    REGULATORY_GRAPH="regulatory_graph.pkl",
+    REGULATORY_DISTANCES="regulatory_distances.json",
+)
+
+
+GCS_ASSETS = SimpleNamespace(
+    PROJECT="calico-public-data",
+    BUCKET="calico-cpr-public",
+    ASSETS={
+        "test_pathway": {
+            "file": "test_pathway.tar.gz",
+            "subassets": {
+                GCS_SUBASSET_NAMES.SBML_DFS: GCS_FILETYPES.SBML_DFS,
+                GCS_SUBASSET_NAMES.IDENTIFIERS: GCS_FILETYPES.IDENTIFIERS,
+                GCS_SUBASSET_NAMES.REGULATORY_GRAPH: GCS_FILETYPES.REGULATORY_GRAPH,
+                GCS_SUBASSET_NAMES.REGULATORY_DISTANCES: GCS_FILETYPES.REGULATORY_DISTANCES,
+            },
+            "public_url": "https://storage.googleapis.com/calico-cpr-public/test_pathway.tar.gz",
+        },
+        "human_consensus": {
+            "file": "human_consensus.tar.gz",
+            "subassets": {
+                GCS_SUBASSET_NAMES.SBML_DFS: GCS_FILETYPES.SBML_DFS,
+                GCS_SUBASSET_NAMES.IDENTIFIERS: GCS_FILETYPES.IDENTIFIERS,
+                GCS_SUBASSET_NAMES.REGULATORY_GRAPH: GCS_FILETYPES.REGULATORY_GRAPH,
+            },
+            "public_url": "https://storage.googleapis.com/calico-cpr-public/human_consensus.tar.gz",
+        },
+        "human_consensus_w_distances": {
+            "file": "human_consensus_w_distances.tar.gz",
+            "subassets": {
+                GCS_SUBASSET_NAMES.SBML_DFS: GCS_FILETYPES.SBML_DFS,
+                GCS_SUBASSET_NAMES.IDENTIFIERS: GCS_FILETYPES.IDENTIFIERS,
+                GCS_SUBASSET_NAMES.REGULATORY_GRAPH: GCS_FILETYPES.REGULATORY_GRAPH,
+                GCS_SUBASSET_NAMES.REGULATORY_DISTANCES: GCS_FILETYPES.REGULATORY_DISTANCES,
+            },
+            "public_url": "https://storage.googleapis.com/calico-cpr-public/human_consensus_w_distances.tar.gz",
+        },
+        "reactome_members": {
+            "file": "external_pathways/external_pathways_reactome_neo4j_members.csv",
+            "subassets": None,
+            "public_url": "https://storage.googleapis.com/calico-cpr-public/external_pathways/external_pathways_reactome_neo4j_members.csv",
+        },
+        "reactome_xrefs": {
+            "file": "external_pathways/external_pathways_reactome_neo4j_crossref.csv",
+            "subassets": None,
+            "public_url": "https://storage.googleapis.com/calico-cpr-public/external_pathways/external_pathways_reactome_neo4j_crossref.csv",
+        },
+    },
+)
+
+
+INIT_DATA_DIR_MSG = "The `data_dir` {data_dir} does not exist."