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CaseyTaCaseyTa
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Merge pull request #205 from WengLab-InformaticsResearch/kl_at
Fix agent type from computatational_model to data_analysis_pipeline
2 parents dfdcfc6 + 8756a38 commit bf7910d

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+19
-17
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-17
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‎cohd/cohd_trapi.py‎

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Original file line numberDiff line numberDiff line change
@@ -82,6 +82,8 @@ def operate(self):
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_INFORES_ID = 'infores:cohd'
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_SERVICE_NAME = 'COHD'
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_KNOWLEDGE_LEVEL = 'statistical_association'
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_AGENT_TYPE = 'data_analysis_pipeline'
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def _get_kg_predicate(self) -> str:
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""" Determines which predicate should be used to represent the COHD analysis

‎cohd/cohd_trapi_15.py‎

Lines changed: 17 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -42,7 +42,7 @@ class CohdTrapi150(CohdTrapi):
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edge_types_negative = ['biolink:negatively_correlated_with']
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default_negative_predicate = edge_types_negative[0]
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45-
tool_version = f'{CohdTrapi._SERVICE_NAME} 6.5.1'
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tool_version = f'{CohdTrapi._SERVICE_NAME} 6.5.2'
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schema_version = '1.5.0'
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biolink_version = bm_version
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@@ -1557,13 +1557,13 @@ def _add_kg_edge(self, node_1, node_2, cohd_result):
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# Knowledge Level
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{
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'attribute_type_id': 'biolink:knowledge_level',
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'value': 'statistical_association',
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'value': CohdTrapi._KNOWLEDGE_LEVEL,
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'attribute_source': CohdTrapi._INFORES_ID
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},
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# Agent Type
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{
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'attribute_type_id': 'biolink:agent_type',
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'value': 'computational_model',
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'value': CohdTrapi._AGENT_TYPE,
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'attribute_source': CohdTrapi._INFORES_ID
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}
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]
@@ -1606,13 +1606,13 @@ def _add_kg_edge(self, node_1, node_2, cohd_result):
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# Knowledge Level
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{
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'attribute_type_id': 'biolink:knowledge_level',
1609-
'value': 'statistical_association',
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'value': CohdTrapi._KNOWLEDGE_LEVEL,
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'attribute_source': CohdTrapi._INFORES_ID
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},
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# Agent Type
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{
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'attribute_type_id': 'biolink:agent_type',
1615-
'value': 'computational_model',
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'value': CohdTrapi._AGENT_TYPE,
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'attribute_source': CohdTrapi._INFORES_ID
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}
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]
@@ -1662,13 +1662,13 @@ def _add_kg_edge(self, node_1, node_2, cohd_result):
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# Knowledge Level
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{
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'attribute_type_id': 'biolink:knowledge_level',
1665-
'value': 'statistical_association',
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'value': CohdTrapi._KNOWLEDGE_LEVEL,
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'attribute_source': CohdTrapi._INFORES_ID
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},
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# Agent Type
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{
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'attribute_type_id': 'biolink:agent_type',
1671-
'value': 'computational_model',
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'value': CohdTrapi._AGENT_TYPE,
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'attribute_source': CohdTrapi._INFORES_ID
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}
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]
@@ -1725,13 +1725,13 @@ def _add_kg_edge(self, node_1, node_2, cohd_result):
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# Knowledge Level
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{
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'attribute_type_id': 'biolink:knowledge_level',
1728-
'value': 'statistical_association',
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'value': CohdTrapi._KNOWLEDGE_LEVEL,
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'attribute_source': CohdTrapi._INFORES_ID
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},
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# Agent Type
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{
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'attribute_type_id': 'biolink:agent_type',
1734-
'value': 'computational_model',
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'value': CohdTrapi._AGENT_TYPE,
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'attribute_source': CohdTrapi._INFORES_ID
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}
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]
@@ -1780,27 +1780,27 @@ def _add_kg_edge(self, node_1, node_2, cohd_result):
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# Knowledge Level
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{
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'attribute_type_id': 'biolink:knowledge_level',
1783-
'value': 'statistical_association',
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'value': CohdTrapi._KNOWLEDGE_LEVEL,
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'attribute_source': CohdTrapi._INFORES_ID
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},
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# Agent Type
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{
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'attribute_type_id': 'biolink:agent_type',
1789-
'value': 'computational_model',
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'value': CohdTrapi._AGENT_TYPE,
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'attribute_source': CohdTrapi._INFORES_ID
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}
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]
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},
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# Knowledge Level
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{
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'attribute_type_id': 'biolink:knowledge_level',
1797-
'value': 'statistical_association',
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'value': CohdTrapi._KNOWLEDGE_LEVEL,
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'attribute_source': CohdTrapi._INFORES_ID
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},
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# Agent Type
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{
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'attribute_type_id': 'biolink:agent_type',
1803-
'value': 'computational_model',
1803+
'value': CohdTrapi._AGENT_TYPE,
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'attribute_source': CohdTrapi._INFORES_ID
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}
18061806
]
@@ -1888,13 +1888,13 @@ def _add_kg_set_edge(self, node_2, is_subject, set_result):
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# Knowledge Level
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{
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'attribute_type_id': 'biolink:knowledge_level',
1891-
'value': 'statistical_association',
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'value': CohdTrapi._KNOWLEDGE_LEVEL,
18921892
'attribute_source': CohdTrapi._INFORES_ID
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},
18941894
# Agent Type
18951895
{
18961896
'attribute_type_id': 'biolink:agent_type',
1897-
'value': 'computational_model',
1897+
'value': CohdTrapi._AGENT_TYPE,
18981898
'attribute_source': CohdTrapi._INFORES_ID
18991899
},
19001900
# Observed-expected frequency ratio analysis
@@ -1925,13 +1925,13 @@ def _add_kg_set_edge(self, node_2, is_subject, set_result):
19251925
# Knowledge Level
19261926
{
19271927
'attribute_type_id': 'biolink:knowledge_level',
1928-
'value': 'statistical_association',
1928+
'value': CohdTrapi._KNOWLEDGE_LEVEL,
19291929
'attribute_source': CohdTrapi._INFORES_ID
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},
19311931
# Agent Type
19321932
{
19331933
'attribute_type_id': 'biolink:agent_type',
1934-
'value': 'computational_model',
1934+
'value': CohdTrapi._AGENT_TYPE,
19351935
'attribute_source': CohdTrapi._INFORES_ID
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}
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]

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