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Fix agent type from computatational_model to data_analysis_pipeline
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2 files changed

+19
-17
lines changed

2 files changed

+19
-17
lines changed

‎cohd/cohd_trapi.py‎

Lines changed: 2 additions & 0 deletions
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'
85+
_KNOWLEDGE_LEVEL = 'statistical_association'
86+
_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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{
15591559
'attribute_type_id': 'biolink:knowledge_level',
1560-
'value': 'statistical_association',
1560+
'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',
1566-
'value': 'computational_model',
1566+
'value': CohdTrapi._AGENT_TYPE,
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'attribute_source': CohdTrapi._INFORES_ID
15681568
}
15691569
]
@@ -1606,13 +1606,13 @@ def _add_kg_edge(self, node_1, node_2, cohd_result):
16061606
# Knowledge Level
16071607
{
16081608
'attribute_type_id': 'biolink:knowledge_level',
1609-
'value': 'statistical_association',
1609+
'value': CohdTrapi._KNOWLEDGE_LEVEL,
16101610
'attribute_source': CohdTrapi._INFORES_ID
16111611
},
16121612
# Agent Type
16131613
{
16141614
'attribute_type_id': 'biolink:agent_type',
1615-
'value': 'computational_model',
1615+
'value': CohdTrapi._AGENT_TYPE,
16161616
'attribute_source': CohdTrapi._INFORES_ID
16171617
}
16181618
]
@@ -1662,13 +1662,13 @@ def _add_kg_edge(self, node_1, node_2, cohd_result):
16621662
# Knowledge Level
16631663
{
16641664
'attribute_type_id': 'biolink:knowledge_level',
1665-
'value': 'statistical_association',
1665+
'value': CohdTrapi._KNOWLEDGE_LEVEL,
16661666
'attribute_source': CohdTrapi._INFORES_ID
16671667
},
16681668
# Agent Type
16691669
{
16701670
'attribute_type_id': 'biolink:agent_type',
1671-
'value': 'computational_model',
1671+
'value': CohdTrapi._AGENT_TYPE,
16721672
'attribute_source': CohdTrapi._INFORES_ID
16731673
}
16741674
]
@@ -1725,13 +1725,13 @@ def _add_kg_edge(self, node_1, node_2, cohd_result):
17251725
# Knowledge Level
17261726
{
17271727
'attribute_type_id': 'biolink:knowledge_level',
1728-
'value': 'statistical_association',
1728+
'value': CohdTrapi._KNOWLEDGE_LEVEL,
17291729
'attribute_source': CohdTrapi._INFORES_ID
17301730
},
17311731
# Agent Type
17321732
{
17331733
'attribute_type_id': 'biolink:agent_type',
1734-
'value': 'computational_model',
1734+
'value': CohdTrapi._AGENT_TYPE,
17351735
'attribute_source': CohdTrapi._INFORES_ID
17361736
}
17371737
]
@@ -1780,27 +1780,27 @@ def _add_kg_edge(self, node_1, node_2, cohd_result):
17801780
# Knowledge Level
17811781
{
17821782
'attribute_type_id': 'biolink:knowledge_level',
1783-
'value': 'statistical_association',
1783+
'value': CohdTrapi._KNOWLEDGE_LEVEL,
17841784
'attribute_source': CohdTrapi._INFORES_ID
17851785
},
17861786
# Agent Type
17871787
{
17881788
'attribute_type_id': 'biolink:agent_type',
1789-
'value': 'computational_model',
1789+
'value': CohdTrapi._AGENT_TYPE,
17901790
'attribute_source': CohdTrapi._INFORES_ID
17911791
}
17921792
]
17931793
},
17941794
# Knowledge Level
17951795
{
17961796
'attribute_type_id': 'biolink:knowledge_level',
1797-
'value': 'statistical_association',
1797+
'value': CohdTrapi._KNOWLEDGE_LEVEL,
17981798
'attribute_source': CohdTrapi._INFORES_ID
17991799
},
18001800
# Agent Type
18011801
{
18021802
'attribute_type_id': 'biolink:agent_type',
1803-
'value': 'computational_model',
1803+
'value': CohdTrapi._AGENT_TYPE,
18041804
'attribute_source': CohdTrapi._INFORES_ID
18051805
}
18061806
]
@@ -1888,13 +1888,13 @@ def _add_kg_set_edge(self, node_2, is_subject, set_result):
18881888
# Knowledge Level
18891889
{
18901890
'attribute_type_id': 'biolink:knowledge_level',
1891-
'value': 'statistical_association',
1891+
'value': CohdTrapi._KNOWLEDGE_LEVEL,
18921892
'attribute_source': CohdTrapi._INFORES_ID
18931893
},
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
19301930
},
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
19361936
}
19371937
]

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