diff --git a/src/pyBiodatafuse/graph/generator.py b/src/pyBiodatafuse/graph/generator.py index 09b8f06..4d78436 100644 --- a/src/pyBiodatafuse/graph/generator.py +++ b/src/pyBiodatafuse/graph/generator.py @@ -44,6 +44,7 @@ LITERATURE_DISEASE_NODE_ATTRS, LITERATURE_NODE_MAIN_LABEL, MINERVA, + MITOCARTA, MOLMEDB_COMPOUND_NODE_ATTRS, MOLMEDB_PROTEIN_COMPOUND_COL, MOLMEDB_PROTEIN_COMPOUND_EDGE_ATTRS, @@ -832,22 +833,24 @@ def add_mitocarta_gene_mito_subgraph(g, gene_node_label, annot_list): :returns: a NetworkX MultiDiGraph """ for annot in annot_list: - if pd.isna(annot["hpa_location"]): + if pd.isna(annot["mito_pathways"]): continue annot_node_label = annot["mito_pathways"] annot_node_attrs = {} annot_node_attrs["name"] = annot["mito_pathways"] - annot_node_attrs["datasource"] = "mitocarta" - annot_node_attrs["hpa_location"] = annot["hpa_location"] - annot_node_attrs["sub_mito_localization"] = annot["sub_mito_localization"] + annot_node_attrs["datasource"] = MITOCARTA + if not pd.isna(annot["hpa_location"]): + annot_node_attrs["hpa_location"] = annot["hpa_location"] + if not pd.isna(annot["sub_mito_localization"]): + annot_node_attrs["sub_mito_localization"] = annot["sub_mito_localization"] annot_node_attrs["evidence"] = annot["evidence"] - annot_node_attrs["labels"] = "mito_pathway" + annot_node_attrs["labels"] = "Mitochondrial_Pathway" g.add_node(annot_node_label, attr_dict=annot_node_attrs) edge_attrs = GENE_PATHWAY_EDGE_ATTRS.copy() - edge_attrs["datasource"] = "mitocarta" + edge_attrs["datasource"] = MITOCARTA edge_attrs["label"] = "encodes_mitochondrial_protein" edge_hash = hash(frozenset(edge_attrs.items())) @@ -1448,7 +1451,7 @@ def build_networkx_graph( PUBCHEM_COMPOUND_ASSAYS_COL: add_pubchem_assay_subgraph, f"{GPROFILER}_wp": add_gprofiler_gene_wikipathway_subgraph, f"{GPROFILER}_hp": add_gprofiler_gene_HP_subgraph, - f"{GPROFILER}_hpa": add_gprofiler_gene_HPA_subgraph, + # f"{GPROFILER}_hpa": add_gprofiler_gene_HPA_subgraph, f"{GPROFILER}_kegg": add_gprofiler_gene_KEGG_subgraph, f"{GPROFILER}_mirna": add_gprofiler_gene_MIRNA_subgraph, f"{GPROFILER}_reac": add_gprofiler_gene_REAC_subgraph, @@ -1456,7 +1459,7 @@ def build_networkx_graph( f"{GPROFILER}_go:bp": add_gprofiler_gene_GO_BP_subgraph, f"{GPROFILER}_go:cc": add_gprofiler_gene_GO_CC_subgraph, f"{GPROFILER}_go:mf": add_gprofiler_gene_GO_MF_subgraph, - "mitocarta": add_mitocarta_gene_mito_subgraph, + MITOCARTA: add_mitocarta_gene_mito_subgraph, } for _i, row in tqdm(combined_df.iterrows(), total=combined_df.shape[0], desc="Building graph"):