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Merge pull request #205 from WengLab-InformaticsResearch/kl_at
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Fix agent type from computatational_model to data_analysis_pipeline
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@CaseyTa
CaseyTa authored Aug 14, 2024
2 parents dfdcfc6 + 8756a38 commit bf7910d
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Showing 2 changed files with 19 additions and 17 deletions.
2 changes: 2 additions & 0 deletions cohd/cohd_trapi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -82,6 +82,8 @@ def operate(self):

_INFORES_ID = 'infores:cohd'
_SERVICE_NAME = 'COHD'
_KNOWLEDGE_LEVEL = 'statistical_association'
_AGENT_TYPE = 'data_analysis_pipeline'

def _get_kg_predicate(self) -> str:
""" Determines which predicate should be used to represent the COHD analysis
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34 changes: 17 additions & 17 deletions cohd/cohd_trapi_15.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ class CohdTrapi150(CohdTrapi):
edge_types_negative = ['biolink:negatively_correlated_with']
default_negative_predicate = edge_types_negative[0]

tool_version = f'{CohdTrapi._SERVICE_NAME} 6.5.1'
tool_version = f'{CohdTrapi._SERVICE_NAME} 6.5.2'
schema_version = '1.5.0'
biolink_version = bm_version

Expand Down Expand Up @@ -1557,13 +1557,13 @@ def _add_kg_edge(self, node_1, node_2, cohd_result):
# Knowledge Level
{
'attribute_type_id': 'biolink:knowledge_level',
'value': 'statistical_association',
'value': CohdTrapi._KNOWLEDGE_LEVEL,
'attribute_source': CohdTrapi._INFORES_ID
},
# Agent Type
{
'attribute_type_id': 'biolink:agent_type',
'value': 'computational_model',
'value': CohdTrapi._AGENT_TYPE,
'attribute_source': CohdTrapi._INFORES_ID
}
]
Expand Down Expand Up @@ -1606,13 +1606,13 @@ def _add_kg_edge(self, node_1, node_2, cohd_result):
# Knowledge Level
{
'attribute_type_id': 'biolink:knowledge_level',
'value': 'statistical_association',
'value': CohdTrapi._KNOWLEDGE_LEVEL,
'attribute_source': CohdTrapi._INFORES_ID
},
# Agent Type
{
'attribute_type_id': 'biolink:agent_type',
'value': 'computational_model',
'value': CohdTrapi._AGENT_TYPE,
'attribute_source': CohdTrapi._INFORES_ID
}
]
Expand Down Expand Up @@ -1662,13 +1662,13 @@ def _add_kg_edge(self, node_1, node_2, cohd_result):
# Knowledge Level
{
'attribute_type_id': 'biolink:knowledge_level',
'value': 'statistical_association',
'value': CohdTrapi._KNOWLEDGE_LEVEL,
'attribute_source': CohdTrapi._INFORES_ID
},
# Agent Type
{
'attribute_type_id': 'biolink:agent_type',
'value': 'computational_model',
'value': CohdTrapi._AGENT_TYPE,
'attribute_source': CohdTrapi._INFORES_ID
}
]
Expand Down Expand Up @@ -1725,13 +1725,13 @@ def _add_kg_edge(self, node_1, node_2, cohd_result):
# Knowledge Level
{
'attribute_type_id': 'biolink:knowledge_level',
'value': 'statistical_association',
'value': CohdTrapi._KNOWLEDGE_LEVEL,
'attribute_source': CohdTrapi._INFORES_ID
},
# Agent Type
{
'attribute_type_id': 'biolink:agent_type',
'value': 'computational_model',
'value': CohdTrapi._AGENT_TYPE,
'attribute_source': CohdTrapi._INFORES_ID
}
]
Expand Down Expand Up @@ -1780,27 +1780,27 @@ def _add_kg_edge(self, node_1, node_2, cohd_result):
# Knowledge Level
{
'attribute_type_id': 'biolink:knowledge_level',
'value': 'statistical_association',
'value': CohdTrapi._KNOWLEDGE_LEVEL,
'attribute_source': CohdTrapi._INFORES_ID
},
# Agent Type
{
'attribute_type_id': 'biolink:agent_type',
'value': 'computational_model',
'value': CohdTrapi._AGENT_TYPE,
'attribute_source': CohdTrapi._INFORES_ID
}
]
},
# Knowledge Level
{
'attribute_type_id': 'biolink:knowledge_level',
'value': 'statistical_association',
'value': CohdTrapi._KNOWLEDGE_LEVEL,
'attribute_source': CohdTrapi._INFORES_ID
},
# Agent Type
{
'attribute_type_id': 'biolink:agent_type',
'value': 'computational_model',
'value': CohdTrapi._AGENT_TYPE,
'attribute_source': CohdTrapi._INFORES_ID
}
]
Expand Down Expand Up @@ -1888,13 +1888,13 @@ def _add_kg_set_edge(self, node_2, is_subject, set_result):
# Knowledge Level
{
'attribute_type_id': 'biolink:knowledge_level',
'value': 'statistical_association',
'value': CohdTrapi._KNOWLEDGE_LEVEL,
'attribute_source': CohdTrapi._INFORES_ID
},
# Agent Type
{
'attribute_type_id': 'biolink:agent_type',
'value': 'computational_model',
'value': CohdTrapi._AGENT_TYPE,
'attribute_source': CohdTrapi._INFORES_ID
},
# Observed-expected frequency ratio analysis
Expand Down Expand Up @@ -1925,13 +1925,13 @@ def _add_kg_set_edge(self, node_2, is_subject, set_result):
# Knowledge Level
{
'attribute_type_id': 'biolink:knowledge_level',
'value': 'statistical_association',
'value': CohdTrapi._KNOWLEDGE_LEVEL,
'attribute_source': CohdTrapi._INFORES_ID
},
# Agent Type
{
'attribute_type_id': 'biolink:agent_type',
'value': 'computational_model',
'value': CohdTrapi._AGENT_TYPE,
'attribute_source': CohdTrapi._INFORES_ID
}
]
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