Merge 0d7f9b4 into b8b829b

Knowledge-Graph-Hub · May 1, 2020 · 15a93df · 15a93df
2 parents b8b829b + 0d7f9b4
commit 15a93df
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Showing 10 changed files with 30 additions and 14 deletions.
diff --git a/kg_covid_19/transform_utils/drug_central/drug_central.py b/kg_covid_19/transform_utils/drug_central/drug_central.py
@@ -42,7 +42,8 @@ def run(self, data_file: Optional[str] = None, species: str = "Homo sapiens") ->
         gene_node_type = "biolink:Gene"
         drug_gene_edge_label = "biolink:interacts_with"
         drug_gene_edge_relation = "RO:0002436"  # molecularly interacts with
-        self.edge_header = ['subject', 'edge_label', 'object', 'relation', 'comment']
+        self.edge_header = ['subject', 'edge_label', 'object', 'relation',
+                            'provided_by', 'comment']
 
         with open(self.output_node_file, 'w') as node, \
                 open(self.output_edge_file, 'w') as edge, \
@@ -89,13 +90,15 @@ def run(self, data_file: Optional[str] = None, species: str = "Homo sapiens") ->
                                                gene_node_type])
 
                     # WRITE EDGES
-                    # ['subject', 'edge_label', 'object', 'relation', 'comment']
+                    # ['subject', 'edge_label', 'object', 'relation', 'provided_by',
+                    # 'comment']
                     write_node_edge_item(fh=edge,
                                          header=self.edge_header,
                                          data=[drug_id,
                                                drug_gene_edge_label,
                                                gene_id,
                                                drug_gene_edge_relation,
+                                               self.source_name,
                                                items_dict['ACT_COMMENT']])
 
         return None

diff --git a/kg_covid_19/transform_utils/intact/intact.py b/kg_covid_19/transform_utils/intact/intact.py
@@ -51,7 +51,7 @@ def __init__(self, input_dir: str = None, output_dir: str = None) -> None:
         self.pubmed_curie_prefix = 'PMID:'
         self.ppi_edge_label = 'biolink:interacts_with'
         self.ppi_ro_relation = 'RO:0002437'
-        self.edge_header = ['subject', 'edge_label', 'object', 'relation',
+        self.edge_header = ['subject', 'edge_label', 'object', 'relation', 'provided_by',
                             'publication', 'num_participants', 'association_type',
                             'detection_method',  'subj_exp_role', 'obj_exp_role']
 
@@ -181,8 +181,9 @@ def interaction_to_edge(self, interaction: object, nodes_dict: dict,
                 if None not in [node1, node2]:
                     edges.append(
                         [node1, self.ppi_edge_label, node2, self.ppi_ro_relation,
-                        publication, str(len(participants)), interaction_type_str,
-                        detection_method, p1_exp_role, p2_exp_role])
+                         self.source_name, publication, str(len(participants)),
+                         interaction_type_str, detection_method, p1_exp_role,
+                         p2_exp_role])
 
         return edges
 

diff --git a/kg_covid_19/transform_utils/pharmgkb/pharmgkb.py b/kg_covid_19/transform_utils/pharmgkb/pharmgkb.py
@@ -24,7 +24,8 @@ class PharmGKB(Transform):
     def __init__(self, input_dir: str = None, output_dir: str = None):
         source_name = "pharmgkb"
         super().__init__(source_name, input_dir, output_dir)
-        self.edge_header = ['subject', 'edge_label', 'object', 'relation', 'evidence']
+        self.edge_header = ['subject', 'edge_label', 'object', 'relation',
+                            'provided_by', 'evidence']
         self.node_header = ['id', 'name', 'category']
         self.edge_of_interest = ['Gene',
                                  'Chemical']  # logic also matches 'Chemical'-'Gene'
@@ -140,6 +141,7 @@ def make_pharmgkb_edge(self,
                                    self.drug_gene_edge_label,
                                    gene_id,
                                    self.drug_gene_edge_relation,
+                                   self.source_name,
                                    evidence])
 
     def make_pharmgkb_gene_node(self,

diff --git a/kg_covid_19/transform_utils/sars_cov_2_gene_annot/sars_cov_2_gene_annot.py b/kg_covid_19/transform_utils/sars_cov_2_gene_annot/sars_cov_2_gene_annot.py
@@ -23,7 +23,8 @@ def __init__(self, input_dir: Optional[str] = None, output_dir: str = None):
 
         self.node_header = ['id', 'name', 'category', 'synonym', 'taxon']
         self.edge_header = ['subject', 'edge_label', 'object', 'relation',
-                            'DB_References', 'ECO_code', 'With', 'Interacting_taxon_ID',
+                            'provided_by', 'DB_References', 'ECO_code', 'With',
+                            'Interacting_taxon_ID',
                             'Date', 'Assigned_by', 'Annotation_Extension',
                             'Annotation_Properties']
 
@@ -77,7 +78,8 @@ def gpa_to_edge_data(self, rec: dict) -> list:
         except KeyError:
             relation = ''
 
-        edge_data = [subj, self.edge_label_prefix + edge_label, obj, relation]
+        edge_data = [subj, self.edge_label_prefix + edge_label, obj, relation,
+                     self.source_name]
         # all the others
         for key in ['DB:Reference', 'ECO_Evidence_code', 'With', 'Interacting_taxon_ID',
                     'Date', 'Assigned_by', 'Annotation_Extension',

diff --git a/kg_covid_19/transform_utils/transform.py b/kg_covid_19/transform_utils/transform.py
@@ -14,7 +14,7 @@ def __init__(self, source_name, input_dir: str = None, output_dir: str = None):
         self.source_name = source_name
         self.node_header = ['id', 'name', 'category']
         self.edge_header = ['subject', 'edge_label', 'object', 'relation',
-                            'publications']
+                            'provided_by']
 
         # default dirs
         self.input_base_dir = input_dir if input_dir else self.DEFAULT_INPUT_DIR

diff --git a/kg_covid_19/transform_utils/ttd/ttd.py b/kg_covid_19/transform_utils/ttd/ttd.py
@@ -41,7 +41,8 @@ def run(self, data_file: Optional[str] = None):
         drug_gene_edge_relation = "RO:0002436"  # molecularly interacts with
         uniprot_curie_prefix = "UniProtKB:"
 
-        self.edge_header = ['subject', 'edge_label', 'object', 'relation', 'target_type']
+        self.edge_header = ['subject', 'edge_label', 'object', 'relation',
+                            'provided_by', 'target_type']
 
         # make name to id map for uniprot names of human proteins
         dat_gz_id_file = os.path.join(self.input_base_dir,
@@ -108,6 +109,7 @@ def run(self, data_file: Optional[str] = None):
                                                    drug_gene_edge_label,
                                                    this_id,
                                                    drug_gene_edge_relation,
+                                                   self.source_name,
                                                    targ_type])
 
     def get_uniproids(self, data: dict, name_2_id_map: dict,

diff --git a/kg_covid_19/transform_utils/zhou_host_proteins/zhou_transform.py b/kg_covid_19/transform_utils/zhou_host_proteins/zhou_transform.py
@@ -34,6 +34,9 @@ class ZhouTransform(Transform):
     def __init__(self, input_dir: str = None, output_dir: str = None) -> None:
         source_name = "zhou_host_proteins"
         super().__init__(source_name, input_dir, output_dir)
+        self.node_header = ['id', 'name', 'category']
+        self.edge_header = ['subject', 'edge_label', 'object', 'relation',
+                            'provided_by', 'publication']
 
     def run(self, data_file: Optional[str] = None):
         """Method is called and performs needed transformations to process the zhou host protein data, additional
@@ -110,6 +113,7 @@ def run(self, data_file: Optional[str] = None):
                                          host_gene_vgene_edge_label,
                                          corona_curie,
                                          host_gene_vgene_relation,
+                                         self.source_name,
                                          pubmed_curie_prefix + row['PubMed ID']
                                      ])
 

diff --git a/tests/test_intact.py b/tests/test_intact.py
@@ -15,7 +15,7 @@ def test_intact_instance(self):
         self.assertEqual(self.intact.node_header,
                          ['id', 'name', 'category'])
         self.assertEqual(self.intact.edge_header,
-                        ['subject', 'edge_label', 'object', 'relation',
+                        ['subject', 'edge_label', 'object', 'relation', 'provided_by',
                          'publication', 'num_participants', 'association_type',
                          'detection_method', 'subj_exp_role', 'obj_exp_role'])
 
@@ -34,7 +34,7 @@ def test_struct_parse_xml_to_nodes_edges(self):
          {'nodes': [['UniProtKB:P20290', 'btf3_human', 'biolink:Protein'],
                     ['UniProtKB:P0C6X7-PRO_0000037317', 'nsp10_cvhsa', 'biolink:RNA']],
           'edges': [['UniProtKB:P20290', 'biolink:interacts_with',
-                     'UniProtKB:P0C6X7-PRO_0000037317', 'RO:0002437',
+                     'UniProtKB:P0C6X7-PRO_0000037317', 'RO:0002437', 'intact',
                      'PMID:16157265', '2', 'physical association', '2 hybrid', 'prey',
                      'bait']]
          }),
@@ -45,6 +45,7 @@ def test_struct_parse_xml_to_nodes_edges(self):
                 'biolink:interacts_with',
                 'UniProtKB:P41811',
                 'RO:0002437',
+                'intact',
                 'PMID:23481256',
                 '3',
                 'physical association',

diff --git a/tests/test_sars_cov_2_gene_annot.py b/tests/test_sars_cov_2_gene_annot.py
@@ -53,7 +53,8 @@ def test_gpa_to_edge_data(self):
 
         self.assertEqual(len(self.sc2ga.edge_header), len(edge1))
         self.assertEqual(edge1,
-                         ['UniProtKB:P0DTC1', 'biolink:enables', 'GO:0003723', 'RO:0002327',
+                         ['UniProtKB:P0DTC1', 'biolink:enables', 'GO:0003723',
+                          'RO:0002327', 'sars_cov_2_gene_annot',
                           'GO_REF:0000043', 'ECO:0000322', 'UniProtKB-KW:KW-0694', '',
                           '20200321', 'UniProt', '', 'go_evidence=IEA'])
 

diff --git a/tests/test_transform_class.py b/tests/test_transform_class.py
@@ -17,7 +17,7 @@ def test_reality(self):
         ('source_name', 'test_transform'),
         ('node_header', ['id', 'name', 'category']),
         ('edge_header',
-         ['subject', 'edge_label', 'object', 'relation', 'publications']),
+         ['subject', 'edge_label', 'object', 'relation', 'provided_by']),
         ('output_base_dir', os.path.join("data", "transformed")),
         ('input_base_dir', os.path.join("data", "raw")),
         ('output_dir', os.path.join("data", "transformed", "test_transform")),