napistu 0.4.1__tar.gz → 0.4.3__tar.gz

{napistu-0.4.1/src/napistu.egg-info → napistu-0.4.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napistu
-Version: 0.4.1
+Version: 0.4.3
 Summary: Connecting high-dimensional data to curated pathways
 Home-page: https://github.com/napistu/napistu-py
 Author: Sean Hackett

{napistu-0.4.1 → napistu-0.4.3}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = napistu
-version = 0.4.1
+version = 0.4.3
 description = Connecting high-dimensional data to curated pathways
 long_description = file: README.md
 long_description_content_type = text/markdown

{napistu-0.4.1 → napistu-0.4.3}/src/napistu/consensus.py

@@ -426,7 +426,7 @@ def post_consensus_species_ontology_check(sbml_dfs: sbml_dfs_core.SBML_dfs) -> s
 
     # get the sources of species in the consensus model
     consensus_sbmldf_tbl_var_sc = (
-        source.unnest_sources(sbml_dfs.species, SBML_DFS.S_SOURCE, verbose=False)
+        source.unnest_sources(sbml_dfs.species, verbose=False)
         .reset_index()
         .sort_values([SOURCE_SPEC.NAME])
     )
@@ -504,12 +504,11 @@ def post_consensus_source_check(
 ) -> pd.DataFrame:
     """Provide sources of tables in a consensus model; the output df will be used to determine whether models are merged."""
 
-    table_source = sbml_dfs.schema[table_name][SOURCE_SPEC.SOURCE]
-    table_pk = sbml_dfs.schema[table_name]["pk"]
+    table_pk = sbml_dfs.schema[table_name][SCHEMA_DEFS.PK]
 
     sbml_dfs_tbl = getattr(sbml_dfs, table_name)
     sbml_dfs_tbl_pathway_source = (
-        source.unnest_sources(sbml_dfs_tbl, table_source, verbose=False)
+        source.unnest_sources(sbml_dfs_tbl, verbose=False)
         .reset_index()
         .sort_values(["name"])
     )

{napistu-0.4.1 → napistu-0.4.3}/src/napistu/gcs/constants.py

@@ -7,7 +7,7 @@ GCS_SUBASSET_NAMES = SimpleNamespace(
     SBML_DFS="sbml_dfs",
     NAPISTU_GRAPH="napistu_graph",
     SPECIES_IDENTIFIERS="species_identifiers",
-    REGULATORY_DISTANCES="regulatory_distances",
+    PRECOMPUTED_DISTANCES="precomputed_distances",
 )
 
 
@@ -15,7 +15,7 @@ GCS_FILETYPES = SimpleNamespace(
     SBML_DFS="sbml_dfs.pkl",
     NAPISTU_GRAPH="napistu_graph.pkl",
     SPECIES_IDENTIFIERS="species_identifiers.tsv",
-    REGULATORY_DISTANCES="regulatory_distances.parquet",
+    PRECOMPUTED_DISTANCES="precomputed_distances.parquet",
 )
 
 
@@ -29,7 +29,7 @@ GCS_ASSETS = SimpleNamespace(
                 GCS_SUBASSET_NAMES.SBML_DFS: GCS_FILETYPES.SBML_DFS,
                 GCS_SUBASSET_NAMES.NAPISTU_GRAPH: GCS_FILETYPES.NAPISTU_GRAPH,
                 GCS_SUBASSET_NAMES.SPECIES_IDENTIFIERS: GCS_FILETYPES.SPECIES_IDENTIFIERS,
-                GCS_SUBASSET_NAMES.REGULATORY_DISTANCES: GCS_FILETYPES.REGULATORY_DISTANCES,
+                GCS_SUBASSET_NAMES.PRECOMPUTED_DISTANCES: GCS_FILETYPES.PRECOMPUTED_DISTANCES,
             },
             "public_url": "https://storage.googleapis.com/shackett-napistu-public/test_pathway.tar.gz",
         },
@@ -48,9 +48,9 @@ GCS_ASSETS = SimpleNamespace(
                 GCS_SUBASSET_NAMES.SBML_DFS: GCS_FILETYPES.SBML_DFS,
                 GCS_SUBASSET_NAMES.NAPISTU_GRAPH: GCS_FILETYPES.NAPISTU_GRAPH,
                 GCS_SUBASSET_NAMES.SPECIES_IDENTIFIERS: GCS_FILETYPES.SPECIES_IDENTIFIERS,
-                GCS_SUBASSET_NAMES.REGULATORY_DISTANCES: GCS_FILETYPES.REGULATORY_DISTANCES,
+                GCS_SUBASSET_NAMES.PRECOMPUTED_DISTANCES: GCS_FILETYPES.PRECOMPUTED_DISTANCES,
             },
-            "public_url": "https://storage.googleapis.com/calico-cpr-public/human_consensus_w_distances.tar.gz",
+            "public_url": "https://storage.googleapis.com/shackett-napistu-public/human_consensus_w_distances.tar.gz",
         },
         "reactome_members": {
             "file": "external_pathways/external_pathways_reactome_neo4j_members.csv",

{napistu-0.4.1 → napistu-0.4.3}/src/napistu/ingestion/constants.py

@@ -3,6 +3,7 @@ from __future__ import annotations
 
 from types import SimpleNamespace
 
+from napistu.constants import SBOTERM_NAMES
 
 SPECIES_FULL_NAME_HUMAN = "Homo sapiens"
 SPECIES_FULL_NAME_MOUSE = "Mus musculus"
@@ -90,6 +91,56 @@ REACTOME_PATHWAYS_URL = "https://reactome.org/download/current/ReactomePathways.
 REACTOME_PATHWAY_INDEX_COLUMNS = ["file", "source", "species", "pathway_id", "name"]
 REACTOME_PATHWAY_LIST_COLUMNS = ["pathway_id", "name", "species"]
 
+# REACTOME FI
+REACTOME_FI_URL = "http://cpws.reactome.org/caBigR3WebApp2025/FIsInGene_04142025_with_annotations.txt.zip"
+
+REACTOME_FI = SimpleNamespace(
+    GENE1="Gene1",
+    GENE2="Gene2",
+    ANNOTATION="Annotation",
+    DIRECTION="Direction",
+    SCORE="Score",
+)
+
+REACTOME_FI_DIRECTIONS = SimpleNamespace(
+    UNDIRECTED="-",
+    STIMULATED_BY="<-",
+    STIMULATES="->",
+    STIMULATES_AND_STIMULATED_BY="<->",
+    INHIBITED_BY="|-",
+    INHIBITS="-|",
+    INHIBITS_AND_INHIBITED_BY="|-|",
+    STIMULATES_AND_INHIBITED_BY="|->",
+    INHIBITS_AND_STIMULATED_BY="<-|",
+)
+
+VALID_REACTOME_FI_DIRECTIONS = REACTOME_FI_DIRECTIONS.__dict__.values()
+
+REACTOME_FI_RULES_REVERSE = SimpleNamespace(
+    NAME_RULES={"catalyzed by": SBOTERM_NAMES.CATALYST},
+    DIRECTION_RULES={
+        REACTOME_FI_DIRECTIONS.STIMULATED_BY: SBOTERM_NAMES.STIMULATOR,
+        REACTOME_FI_DIRECTIONS.STIMULATES_AND_STIMULATED_BY: SBOTERM_NAMES.STIMULATOR,
+        REACTOME_FI_DIRECTIONS.INHIBITED_BY: SBOTERM_NAMES.INHIBITOR,
+        REACTOME_FI_DIRECTIONS.INHIBITS_AND_INHIBITED_BY: SBOTERM_NAMES.INHIBITOR,
+        REACTOME_FI_DIRECTIONS.STIMULATES_AND_INHIBITED_BY: SBOTERM_NAMES.INHIBITOR,
+        REACTOME_FI_DIRECTIONS.UNDIRECTED: SBOTERM_NAMES.INTERACTOR,
+    },
+)
+
+REACTOME_FI_RULES_FORWARD = SimpleNamespace(
+    NAME_RULES={"catalyze(;$)": SBOTERM_NAMES.CATALYST},
+    DIRECTION_RULES={
+        REACTOME_FI_DIRECTIONS.STIMULATES: SBOTERM_NAMES.STIMULATOR,
+        REACTOME_FI_DIRECTIONS.STIMULATES_AND_STIMULATED_BY: SBOTERM_NAMES.STIMULATOR,
+        REACTOME_FI_DIRECTIONS.STIMULATES_AND_INHIBITED_BY: SBOTERM_NAMES.STIMULATOR,
+        REACTOME_FI_DIRECTIONS.INHIBITS: SBOTERM_NAMES.INHIBITOR,
+        REACTOME_FI_DIRECTIONS.INHIBITS_AND_INHIBITED_BY: SBOTERM_NAMES.INHIBITOR,
+        REACTOME_FI_DIRECTIONS.INHIBITS_AND_STIMULATED_BY: SBOTERM_NAMES.INHIBITOR,
+        REACTOME_FI_DIRECTIONS.UNDIRECTED: SBOTERM_NAMES.INTERACTOR,
+    },
+)
+
 # SBML
 SBML_DEFS = SimpleNamespace(
     ERROR_NUMBER="error_number",

napistu-0.4.3/src/napistu/ingestion/reactom_fi.py

@@ -0,0 +1,208 @@
+import logging
+import pandas as pd
+
+from napistu.identifiers import Identifiers
+from napistu import utils
+from napistu.ingestion.constants import (
+    REACTOME_FI,
+    REACTOME_FI_RULES_FORWARD,
+    REACTOME_FI_RULES_REVERSE,
+    REACTOME_FI_URL,
+    VALID_REACTOME_FI_DIRECTIONS,
+)
+
+
+logger = logging.getLogger(__name__)
+
+
+def download_reactome_fi(target_uri: str, url: str = REACTOME_FI_URL) -> None:
+    """
+    Download the Reactome Functional Interactions (FI) dataset as a TSV file.
+
+    Parameters
+    ----------
+    target_uri : str
+        The URI where the Reactome FI data should be saved. Should end with .tsv
+    url : str, optional
+        URL to download the zipped Reactome functional interactions TSV from.
+        Defaults to REACTOME_FI_URL.
+
+    Returns
+    -------
+    None
+
+    Raises
+    ------
+    ValueError
+        If target_uri does not end with .tsv
+    """
+
+    if not target_uri.endswith(".tsv"):
+        raise ValueError(f"Target URI must end with .tsv, got {target_uri}")
+
+    file_ext = url.split(".")[-1]
+    target_filename = url.split("/")[-1].split(f".{file_ext}")[0]
+    logger.info("Start downloading proteinatlas %s to %s", url, target_uri)
+    # target_filename is the name of the file in the zip file which will be renamed to target_uri
+    utils.download_wget(url, target_uri, target_filename=target_filename)
+
+    return None
+
+
+def format_reactome_fi_edgelist(interactions: pd.DataFrame):
+    """
+    Format the Reactome FI interactions DataFrame as an edgelist for network analysis.
+
+    Parameters
+    ----------
+    interactions : pd.DataFrame
+        DataFrame containing Reactome FI interactions.
+
+    Returns
+    -------
+    Dictonary of:
+
+    interaction_edgelist : pd.DataFrame
+        Table containing molecular interactions with columns:
+        - upstream_name : str, matches "s_name" from species_df
+        - downstream_name : str, matches "s_name" from species_df
+        - upstream_compartment : str, matches "c_name" from compartments_df
+        - downstream_compartment : str, matches "c_name" from compartments_df
+        - r_name : str, name for the interaction
+        - sbo_term : str, SBO term defining interaction type
+        - r_Identifiers : identifiers.Identifiers, supporting identifiers
+        - r_isreversible : bool, whether reaction is reversible
+    species_df : pd.DataFrame
+        Table defining molecular species with columns:
+        - s_name : str, name of molecular species
+        - s_Identifiers : identifiers.Identifiers, species identifiers
+    compartments_df : pd.DataFrame
+        Table defining compartments with columns:
+        - c_name : str, name of compartment
+        - c_Identifiers : identifiers.Identifiers, compartment identifiers
+
+    Notes
+    -----
+    This function is not yet implemented and will raise NotImplementedError.
+    """
+
+    raise NotImplementedError("TO DO - This function is incomplete")
+
+    formatted_annotations = _parse_reactome_fi_annotations(interactions)
+
+    # this join will expand some rows to 2 since the bidirectional relationships are captured as separate edges in Napistu
+    annotated_interactions = interactions.merge(
+        formatted_annotations,
+        on=[REACTOME_FI.ANNOTATION, REACTOME_FI.DIRECTION],
+        how="left",
+    )
+
+    # flip reverse entries so all relationships are forward or undirected
+    formatted_interactions = (
+        pd.concat(
+            [
+                annotated_interactions.query("polarity == 'forward'"),
+                (
+                    annotated_interactions.query("polarity == 'reverse'").rename(
+                        columns={
+                            REACTOME_FI.GENE1: REACTOME_FI.GENE2,
+                            REACTOME_FI.GENE2: REACTOME_FI.GENE1,
+                        }
+                    )
+                ),
+            ]
+        )[[REACTOME_FI.GENE1, REACTOME_FI.GENE2, "sbo_term_name", "Score"]]
+        # looks like they were already unique edges
+        .sort_values("Score", ascending=False)
+        .groupby([REACTOME_FI.GENE1, REACTOME_FI.GENE2])
+        .first()
+    )
+
+    fi_edgelist = (
+        formatted_interactions.reset_index()
+        .rename(
+            columns={
+                REACTOME_FI.GENE1: "upstream_name",
+                REACTOME_FI.GENE2: "downstream_name",
+            }
+        )
+        .assign(r_Identifiers=Identifiers([]))
+    )
+
+    return fi_edgelist
+
+
+def _parse_reactome_fi_annotations(interactions: pd.DataFrame) -> pd.DataFrame:
+    """
+    Parse and annotate Reactome FI interaction types and directions using regex-based rules.
+
+    Parameters
+    ----------
+    interactions : pd.DataFrame
+        DataFrame containing Reactome FI interactions, with annotation and direction columns.
+
+    Returns
+    -------
+    pd.DataFrame
+        DataFrame with annotation, direction, SBO term name, and polarity for each unique annotation/direction pair.
+
+    Raises
+    ------
+    ValueError
+        If an annotation/direction pair cannot be matched to a rule or if invalid directions are found.
+    """
+
+    distinct_annotations = (
+        interactions[[REACTOME_FI.ANNOTATION, REACTOME_FI.DIRECTION]]
+        .drop_duplicates()
+        .reset_index(drop=True)
+    )
+    invalid_directions = distinct_annotations.loc[
+        ~distinct_annotations[REACTOME_FI.DIRECTION].isin(VALID_REACTOME_FI_DIRECTIONS),
+        "Direction",
+    ]
+    if len(invalid_directions) > 0:
+        raise ValueError(f"Invalid directions: {invalid_directions}")
+
+    annotations = list()
+    for _, vals in distinct_annotations.iterrows():
+        annot, direction = vals
+
+        forward_match = utils.match_regex_dict(
+            annot, REACTOME_FI_RULES_FORWARD.NAME_RULES
+        )
+        if not forward_match:
+            if direction in REACTOME_FI_RULES_FORWARD.DIRECTION_RULES:
+                forward_match = REACTOME_FI_RULES_FORWARD.DIRECTION_RULES[direction]
+
+        reverse_match = utils.match_regex_dict(
+            annot, REACTOME_FI_RULES_REVERSE.NAME_RULES
+        )
+        if not reverse_match:
+            if direction in REACTOME_FI_RULES_REVERSE.DIRECTION_RULES:
+                reverse_match = REACTOME_FI_RULES_REVERSE.DIRECTION_RULES[direction]
+
+        if not (forward_match or reverse_match):
+            raise ValueError(f"No match found for {annot} with direction {direction}")
+
+        if forward_match:
+            annotations.append(
+                {
+                    REACTOME_FI.ANNOTATION: annot,
+                    REACTOME_FI.DIRECTION: direction,
+                    "sbo_term_name": forward_match,
+                    "polarity": "forward",
+                }
+            )
+
+        if reverse_match:
+            annotations.append(
+                {
+                    REACTOME_FI.ANNOTATION: annot,
+                    REACTOME_FI.DIRECTION: direction,
+                    "sbo_term_name": reverse_match,
+                    "polarity": "reverse",
+                }
+            )
+
+    return pd.DataFrame(annotations)

{napistu-0.4.1 → napistu-0.4.3}/src/napistu/network/constants.py

@@ -4,6 +4,7 @@ from __future__ import annotations
 
 from types import SimpleNamespace
 
+
 from napistu.constants import SBML_DFS
 from napistu.constants import SBOTERM_NAMES
 
@@ -13,7 +14,7 @@ NAPISTU_GRAPH_DIRECTEDNESS = SimpleNamespace(
     DIRECTED="directed", UNDIRECTED="undirected"
 )
 
-NAPISTU_GRAPH_NODES = SimpleNamespace(NAME="name")
+NAPISTU_GRAPH_VERTICES = SimpleNamespace(NAME="name")
 
 NAPISTU_GRAPH_EDGES = SimpleNamespace(
     DIRECTED="directed",
@@ -198,3 +199,24 @@ SCORE_CALIBRATION_POINTS_DICT = {
 }
 
 SOURCE_VARS_DICT = {"string_wt": 10}
+
+# network propagation
+NET_PROPAGATION_DEFS = SimpleNamespace(PERSONALIZED_PAGERANK="personalized_pagerank")
+
+# null distributions
+NULL_STRATEGIES = SimpleNamespace(
+    UNIFORM="uniform",
+    PARAMETRIC="parametric",
+    NODE_PERMUTATION="node_permutation",
+    EDGE_PERMUTATION="edge_permutation",
+)
+
+VALID_NULL_STRATEGIES = NULL_STRATEGIES.__dict__.values()
+
+PARAMETRIC_NULL_DEFAULT_DISTRIBUTION = "norm"
+
+# masks
+
+MASK_KEYWORDS = SimpleNamespace(
+    ATTR="attr",
+)

{napistu-0.4.1 → napistu-0.4.3}/src/napistu/network/ig_utils.py

@@ -9,7 +9,7 @@ from __future__ import annotations
 
 import logging
 import random
-from typing import Any, Optional, Sequence
+from typing import Any, Optional, Sequence, List, Dict, Union
 
 import igraph as ig
 import numpy as np
@@ -384,3 +384,163 @@ def _get_top_n_nodes(
     top_node_attrs = [graph.vs[idx].attributes() for idx in top_idxs]
     top_vals = [vals[idx] for idx in top_idxs]
     return [{val_name: val, **node} for val, node in zip(top_vals, top_node_attrs)]
+
+
+def _parse_mask_input(
+    mask_input: Optional[Union[str, np.ndarray, List, Dict]], attributes: List[str]
+) -> Dict[str, Union[str, np.ndarray, List, None]]:
+    """
+    Parse mask input and convert to attribute-specific mask specifications.
+
+    Parameters
+    ----------
+    mask_input : str, np.ndarray, List, Dict, or None
+        Mask specification that can be:
+        - None: use all nodes for all attributes
+        - "attr": use each attribute as its own mask
+        - np.ndarray/List: use same mask for all attributes
+        - Dict: attribute-specific mask specifications
+    attributes : List[str]
+        List of attribute names.
+
+    Returns
+    -------
+    Dict[str, Union[str, np.ndarray, List, None]]
+        Dictionary mapping each attribute to its mask specification.
+    """
+    if mask_input is None:
+        return {attr: None for attr in attributes}
+    elif isinstance(mask_input, str):
+        if mask_input == "attr":
+            return {attr: attr for attr in attributes}
+        else:
+            # Single attribute name used for all
+            return {attr: mask_input for attr in attributes}
+    elif isinstance(mask_input, (np.ndarray, list)):
+        # Same mask for all attributes
+        return {attr: mask_input for attr in attributes}
+    elif isinstance(mask_input, dict):
+        # Validate all attributes are present
+        for attr in attributes:
+            if attr not in mask_input:
+                raise ValueError(f"Attribute '{attr}' not found in mask dictionary")
+        return mask_input
+    else:
+        raise ValueError(f"Invalid mask input type: {type(mask_input)}")
+
+
+def _get_attribute_masks(
+    graph: ig.Graph,
+    mask_specs: Dict[str, Union[str, np.ndarray, List, None]],
+) -> Dict[str, np.ndarray]:
+    """
+    Generate boolean masks for each attribute based on specifications.
+
+    Parameters
+    ----------
+    graph : ig.Graph
+        Input graph.
+    attributes : List[str]
+        List of attribute names.
+    mask_specs : Dict[str, Union[str, np.ndarray, List, None]]
+        Dictionary mapping each attribute to its mask specification.
+
+    Returns
+    -------
+    Dict[str, np.ndarray]
+        Dictionary mapping each attribute to its boolean mask array.
+    """
+    n_nodes = graph.vcount()
+    masks = {}
+
+    invalid_attrs = set(mask_specs.keys()).difference(graph.vs.attributes())
+    if invalid_attrs:
+        raise ValueError(f"Attributes {invalid_attrs} not found in graph")
+
+    for attr in mask_specs.keys():
+
+        mask_spec = mask_specs[attr]
+
+        if mask_spec is None:
+            masks[attr] = np.ones(n_nodes, dtype=bool)
+        elif isinstance(mask_spec, str):
+            attr_values = np.array(graph.vs[mask_spec])
+            masks[attr] = attr_values > 0
+        elif isinstance(mask_spec, np.ndarray):
+            masks[attr] = mask_spec.astype(bool)
+        elif isinstance(mask_spec, list):
+            mask_array = np.zeros(n_nodes, dtype=bool)
+            if isinstance(mask_spec[0], str):
+                # Node names
+                node_names = (
+                    graph.vs["name"] if "name" in graph.vs.attributes() else None
+                )
+                if node_names is None:
+                    raise ValueError("Graph has no 'name' attribute for string mask")
+                for name in mask_spec:
+                    idx = node_names.index(name)
+                    mask_array[idx] = True
+            else:
+                # Node indices
+                mask_array[mask_spec] = True
+            masks[attr] = mask_array
+        else:
+            raise ValueError(
+                f"Invalid mask specification for attribute '{attr}': {type(mask_spec)}"
+            )
+
+    return masks
+
+
+def _ensure_valid_attribute(graph: ig.Graph, attribute: str, non_negative: bool = True):
+    """
+    Ensure a vertex attribute is present, numeric, and optionally non-negative for all vertices.
+
+    This utility checks that the specified vertex attribute exists, is numeric, and (optionally) non-negative
+    for all vertices in the graph. Missing or None values are treated as 0. Raises ValueError
+    if the attribute is missing for all vertices, if all values are zero, or if any value is negative (if non_negative=True).
+
+    Parameters
+    ----------
+    graph : NapistuGraph or ig.Graph
+        The input graph (NapistuGraph or igraph.Graph).
+    attribute : str
+        The name of the vertex attribute to check.
+    non_negative : bool, default True
+        Whether to require all values to be non-negative.
+
+    Returns
+    -------
+    np.ndarray
+        Array of attribute values (with missing/None replaced by 0).
+
+    Raises
+    ------
+    ValueError
+        If the attribute is missing for all vertices, all values are zero, or any value is negative (if non_negative=True).
+    """
+    all_missing = all(
+        (attribute not in v.attributes() or v[attribute] is None) for v in graph.vs
+    )
+    if all_missing:
+        raise ValueError(f"Vertex attribute '{attribute}' is missing for all vertices.")
+
+    values = [
+        (
+            v[attribute]
+            if (attribute in v.attributes() and v[attribute] is not None)
+            else 0.0
+        )
+        for v in graph.vs
+    ]
+
+    arr = np.array(values, dtype=float)
+
+    if np.all(arr == 0):
+        raise ValueError(
+            f"Vertex attribute '{attribute}' is zero for all vertices; cannot use as reset vector."
+        )
+    if non_negative and np.any(arr < 0):
+        raise ValueError(f"Attribute '{attribute}' contains negative values.")
+
+    return arr

{napistu-0.4.1 → napistu-0.4.3}/src/napistu/network/net_create.py

@@ -26,7 +26,7 @@ from napistu.constants import (
 )
 
 from napistu.network.constants import (
-    NAPISTU_GRAPH_NODES,
+    NAPISTU_GRAPH_VERTICES,
     NAPISTU_GRAPH_EDGES,
     NAPISTU_GRAPH_EDGE_DIRECTIONS,
     NAPISTU_GRAPH_NODE_TYPES,
@@ -152,7 +152,7 @@ def create_napistu_graph(
 
     # rename nodes to name since it is treated specially
     network_nodes_df = pd.concat(network_nodes).rename(
-        columns={"node_id": NAPISTU_GRAPH_NODES.NAME}
+        columns={"node_id": NAPISTU_GRAPH_VERTICES.NAME}
     )
 
     logger.info(f"Formatting edges as a {wiring_approach} graph")
@@ -234,7 +234,7 @@ def create_napistu_graph(
         vertices=network_nodes_df.to_dict("records"),
         edges=unique_edges.to_dict("records"),
         directed=directed,
-        vertex_name_attr=NAPISTU_GRAPH_NODES.NAME,
+        vertex_name_attr=NAPISTU_GRAPH_VERTICES.NAME,
         edge_foreign_keys=(NAPISTU_GRAPH_EDGES.FROM, NAPISTU_GRAPH_EDGES.TO),
     )