Merge pull request #108 from Knowledge-Graph-Hub/uniprot_sourcename_i…

…ssue

Uniprot sourcename fix

kg_microbe/transform_utils/constants.py

@@ -236,6 +236,7 @@
 ORGANISM_TO_ENZYME_EDGE = "biolink:expresses"
 ENZYME_CATEGORY = "biolink:Enzyme"
 CHEMICAL_TO_ENZYME_EDGE = "biolink:binds_to"
+UNIPROT_GENOME_FEATURES = "uniprot_genome_features"
 UNIPROT_BASE_URL = "https://rest.uniprot.org/uniprotkb/"
 UNIPROT_FIELDS = ["organism_id", "id", "accession", "protein_name", "ec", "ft_binding"]
 UNIPROT_KEYWORDS = ["Reference+proteome"]

kg_microbe/transform_utils/uniprot/uniprot.py

@@ -15,6 +15,7 @@
     ENZYME_CATEGORY,
     NCBITAXON_PREFIX,
     ORGANISM_TO_ENZYME_EDGE,
+    UNIPROT_GENOME_FEATURES,
     UNIPROT_ORG_ID_COLUMN_NAME,
     UNIPROT_PREFIX,
 )
@@ -43,7 +44,7 @@ def __init__(self, input_dir: Optional[Path] = None, output_dir: Optional[Path]
         """
         self.__enz_data = {}
 
-        source_name = "uniprot_genome_features"
+        source_name = UNIPROT_GENOME_FEATURES
         super().__init__(source_name, input_dir, output_dir)
 
     def run(self, data_file: Union[Optional[Path], Optional[str]] = None):
@@ -70,7 +71,6 @@ def run(self, data_file: Union[Optional[Path], Optional[str]] = None):
                 input_dir, ncbi_organisms, self.source_name, node_writer, edge_writer
             )
 
-
         drop_duplicates(self.output_node_file)
         drop_duplicates(self.output_edge_file)
 
@@ -152,6 +152,25 @@ def write_to_df(self, uniprot_values, edge_writer, node_writer):
                 else None
             )
 
+            # Use primary accession number as it's ID does not change, as opposed to Entry Name
+            if "Entry" in entry.keys():
+                self.__enz_data["id"] = entry["Entry"]
+
+            # example response with  multiple protein names:
+            # {
+            #     "Organism (ID)": "100",
+            #     "Entry Name": "A0A4R1H4N5_ANCAQ",
+            #     "Entry": "A0A4R1H4N5",
+            #     "Protein names": "Ubiquinone biosynthesis O-methyltransferase
+            #                       (2-polyprenyl-6-hydroxyphenol methylase) (EC 2.1.1.222)
+            #                       (3-demethylubiquinone 3-O-methyltransferase) (EC 2.1.1.64)",
+            #     "EC number": "2.1.1.222; 2.1.1.64",
+            # }
+            if "Protein names" in entry:
+                self.__enz_data["name"] = entry["Protein names"].split("(EC")[0]
+
+            organism_id = entry["Organism (ID)"] if "Organism (ID)" in entry.keys() else None
+
             # Use primary accession number as it's ID does not change, as opposed to Entry Name
             if "Entry" in entry.keys():
                 self.__enz_data["id"] = entry["Entry"]

merge.yaml

@@ -63,13 +63,13 @@ merged_graph:
         filename:
           - data/transformed/traits/nodes.tsv
           - data/transformed/traits/edges.tsv
-    uniprot:
+    uniprot_genome_features:
       input:
-        name: "uniprot"
+        name: "uniprot_genome_features"
         format: tsv
         filename:
-          - data/transformed/uniprot/nodes.tsv
-          - data/transformed/uniprot/edges.tsv
+          - data/transformed/uniprot_genome_features/nodes.tsv
+          - data/transformed/uniprot_genome_features/edges.tsv
   operations:
     - name: kgx.graph_operations.summarize_graph.generate_graph_stats
       args: