vgardner-renci
commented
3 years ago
{
"context": "https://raw.githubusercontent.com/biolink/biolink-model/master/context.jsonld",
"datetime": "2021-07-15 16:10:03",
"description": "Normal completion",
"id": "https://arax.ncats.io/api/arax/v1.1/response/16215",
"logs": [
{
"code": "",
"level": "INFO",
"message": "ARAX Query launching on incoming Query",
"timestamp": "2021-07-15T16:10:03.310534"
},
{
"code": "",
"level": "INFO",
"message": "Creating an empty template TRAPI Response",
"timestamp": "2021-07-15T16:10:03.310622"
},
{
"code": "",
"level": "INFO",
"message": "Examine input Query for needed information for dispatch",
"timestamp": "2021-07-15T16:10:03.312172"
},
{
"code": "",
"level": "INFO",
"message": "Validating the input query graph",
"timestamp": "2021-07-15T16:10:03.312245"
},
{
"code": "",
"level": "DEBUG",
"message": "Deserializing message",
"timestamp": "2021-07-15T16:10:03.312341"
},
{
"code": "",
"level": "INFO",
"message": "Found input query_graph. Interpreting it and generating ARAXi processing plan to answer it",
"timestamp": "2021-07-15T16:10:03.312905"
},
{
"code": "",
"level": "DEBUG",
"message": "Assessing the QueryGraph for basic information",
"timestamp": "2021-07-15T16:10:03.371783"
},
{
"code": "",
"level": "DEBUG",
"message": "Found 2 nodes and 1 edges",
"timestamp": "2021-07-15T16:10:03.372904"
},
{
"code": "",
"level": "DEBUG",
"message": "The QueryGraph reference template is: n00(ids)-e00()-n01(categories=biolink:Gene)",
"timestamp": "2021-07-15T16:10:03.373025"
},
{
"code": "",
"level": "INFO",
"message": "Found input processing plan. Sending to the ProcessingPlanExecutor",
"timestamp": "2021-07-15T16:10:03.373221"
},
{
"code": "",
"level": "DEBUG",
"message": "Entering execute_processing_plan",
"timestamp": "2021-07-15T16:10:03.373276"
},
{
"code": "",
"level": "DEBUG",
"message": "A single Message is ready and in hand",
"timestamp": "2021-07-15T16:10:03.420574"
},
{
"code": "",
"level": "DEBUG",
"message": "Found actions",
"timestamp": "2021-07-15T16:10:03.420684"
},
{
"code": "",
"level": "INFO",
"message": "Parsing input actions list",
"timestamp": "2021-07-15T16:10:03.420959"
},
{
"code": "",
"level": "DEBUG",
"message": "Parsing action: expand()",
"timestamp": "2021-07-15T16:10:03.420996"
},
{
"code": "",
"level": "DEBUG",
"message": "Parsing action: overlay(action=compute_ngd, virtual_relation_label=N1, subject_qnode_key=n0, object_qnode_key=n1)",
"timestamp": "2021-07-15T16:10:03.421064"
},
{
"code": "",
"level": "DEBUG",
"message": "Parsing action: resultify()",
"timestamp": "2021-07-15T16:10:03.421146"
},
{
"code": "",
"level": "DEBUG",
"message": "Parsing action: filter_results(action=limit_number_of_results, max_results=100)",
"timestamp": "2021-07-15T16:10:03.421190"
},
{
"code": "",
"level": "INFO",
"message": "Processing action 'expand' with parameters {'': 'true'}",
"timestamp": "2021-07-15T16:10:03.421402"
},
{
"code": "",
"level": "DEBUG",
"message": "Applying Expand to Message with parameters {'kp': None, 'edge_key': ['e01'], 'node_key': [], 'enforce_directionality': False, '': True}",
"timestamp": "2021-07-15T16:10:03.421645"
},
{
"code": "",
"level": "DEBUG",
"message": "Expand will consider qnode n0's category to be ['biolink:Gene', 'biolink:Protein']",
"timestamp": "2021-07-15T16:10:03.422116"
},
{
"code": "",
"level": "DEBUG",
"message": "Expand will consider qnode n1's category to be ['biolink:Gene', 'biolink:Protein']",
"timestamp": "2021-07-15T16:10:03.422159"
},
{
"code": "",
"level": "DEBUG",
"message": "Making sure QG only uses canonical predicates",
"timestamp": "2021-07-15T16:10:03.422182"
},
{
"code": "",
"level": "DEBUG",
"message": "Query graph for this Expand() call is: {'nodes': {'n1': {'ids': None, 'categories': ['biolink:Gene', 'biolink:Protein'], 'is_set': False, 'constraints': None, 'option_group_id': None}, 'n0': {'ids': ['NCBIGene:23221'], 'categories': ['biolink:Gene', 'biolink:Protein'], 'is_set': False, 'constraints': None, 'option_group_id': None}}, 'edges': {'e01': {'predicates': ['biolink:entity_negatively_regulates_entity', 'biolink:negatively_regulates_entity_to_entity'], 'relation': None, 'subject': 'n1', 'object': 'n0', 'constraints': None, 'exclude': None, 'option_group_id': None}}}",
"timestamp": "2021-07-15T16:10:03.422346"
},
{
"code": "",
"level": "DEBUG",
"message": "Modified QG for this qedge is (n0:['biolink:Gene', 'biolink:Protein'] ['NCBIGene:23221'])-['biolink:entity_negatively_regulates_entity', 'biolink:negatively_regulates_entity_to_entity']-(n1:['biolink:Gene', 'biolink:Protein'])",
"timestamp": "2021-07-15T16:10:03.422485"
},
{
"code": "",
"level": "DEBUG",
"message": "Loading meta map (already exists and isn't due for a refresh)",
"timestamp": "2021-07-15T16:10:03.422623"
},
{
"code": "",
"level": "DEBUG",
"message": "Loading category/predicate descendants map (Biolink model version 1.7.0)",
"timestamp": "2021-07-15T16:10:03.444973"
},
{
"code": "",
"level": "DEBUG",
"message": "Selecting KPs to use for qedge e01",
"timestamp": "2021-07-15T16:10:03.445456"
},
{
"code": "",
"level": "DEBUG",
"message": "Querying Biolink Model Lookup API for descendants of biolink:negatively_regulates_entity_to_entity",
"timestamp": "2021-07-15T16:10:03.445515"
},
{
"code": "",
"level": "WARNING",
"message": "Biolink Model Lookup API returned 404 response: No concept 'negativelyregulatesentitytoentity'\n",
"timestamp": "2021-07-15T16:10:03.766147"
},
{
"code": "",
"level": "INFO",
"message": "The KPs Expand decided to answer e01 with are: {'BTE', 'RTX-KG2'}",
"timestamp": "2021-07-15T16:10:03.766534"
},
{
"code": "",
"level": "DEBUG",
"message": "Loading meta map (already exists and isn't due for a refresh)",
"timestamp": "2021-07-15T16:10:03.766769"
},
{
"code": "",
"level": "DEBUG",
"message": "Loading category/predicate descendants map (Biolink model version 1.7.0)",
"timestamp": "2021-07-15T16:10:03.858522"
},
{
"code": "",
"level": "INFO",
"message": "Expanding qedge e01 using BTE",
"timestamp": "2021-07-15T16:10:04.083895"
},
{
"code": "",
"level": "DEBUG",
"message": "Converting curies in the QG to kinds that BTE can answer",
"timestamp": "2021-07-15T16:10:04.084462"
},
{
"code": "",
"level": "DEBUG",
"message": "Prefixes BTE supports for ['biolink:Gene', 'biolink:Protein'] are: {'OMIM', 'NAME', 'UMLS', 'ENSEMBL', 'NCBIGENE', 'UNIPROTKB', 'SYMBOL', 'MGI', 'HGNC'}",
"timestamp": "2021-07-15T16:10:04.084533"
},
{
"code": "",
"level": "DEBUG",
"message": "BTE: Converted n0's 1 curies to a list of 8 curies with prefixes BTE supports",
"timestamp": "2021-07-15T16:10:04.086492"
},
{
"code": "",
"level": "DEBUG",
"message": "BTE: Sending query to BTE API",
"timestamp": "2021-07-15T16:10:04.086657"
},
{
"code": "",
"level": "WARNING",
"message": "BTE: Query timed out (waited 15 seconds)",
"timestamp": "2021-07-15T16:10:19.119901"
},
{
"code": "",
"level": "INFO",
"message": "BTE: Query for edge e01 completed (no answers)",
"timestamp": "2021-07-15T16:10:19.119997"
},
{
"code": "",
"level": "DEBUG",
"message": "BTE: Deduplicating nodes",
"timestamp": "2021-07-15T16:10:19.120034"
},
{
"code": "",
"level": "DEBUG",
"message": "BTE: After deduplication, answer KG counts are: no answers",
"timestamp": "2021-07-15T16:10:19.120075"
},
{
"code": "",
"level": "DEBUG",
"message": "Merging answer into Message.KnowledgeGraph",
"timestamp": "2021-07-15T16:10:19.150583"
},
{
"code": "",
"level": "DEBUG",
"message": "Sending NodeSynonymizer.get_canonical_curies() a list of 1 curies",
"timestamp": "2021-07-15T16:10:19.151295"
},
{
"code": "",
"level": "DEBUG",
"message": "Got response back from NodeSynonymizer",
"timestamp": "2021-07-15T16:10:19.151922"
},
{
"code": "",
"level": "DEBUG",
"message": "Loading meta map (already exists and isn't due for a refresh)",
"timestamp": "2021-07-15T16:10:03.766769"
},
{
"code": "",
"level": "DEBUG",
"message": "Loading category/predicate descendants map (Biolink model version 1.7.0)",
"timestamp": "2021-07-15T16:10:03.858522"
},
{
"code": "",
"level": "INFO",
"message": "Expanding qedge e01 using RTX-KG2",
"timestamp": "2021-07-15T16:10:04.106066"
},
{
"code": "",
"level": "DEBUG",
"message": "RTX-KG2: Sending query to RTX-KG2 API",
"timestamp": "2021-07-15T16:10:04.106771"
},
{
"code": "",
"level": "DEBUG",
"message": "RTX-KG2: No 'results' were returned.",
"timestamp": "2021-07-15T16:10:05.523344"
},
{
"code": "",
"level": "INFO",
"message": "RTX-KG2: Query for edge e01 completed (no answers)",
"timestamp": "2021-07-15T16:10:05.523530"
},
{
"code": "",
"level": "DEBUG",
"message": "Merging answer into Message.KnowledgeGraph",
"timestamp": "2021-07-15T16:10:19.152030"
},
{
"code": "",
"level": "DEBUG",
"message": "Sending NodeSynonymizer.get_canonical_curies() a list of 1 curies",
"timestamp": "2021-07-15T16:10:19.152458"
},
{
"code": "",
"level": "DEBUG",
"message": "Got response back from NodeSynonymizer",
"timestamp": "2021-07-15T16:10:19.152836"
},
{
"code": "",
"level": "DEBUG",
"message": "Pruning any paths that are now dead ends",
"timestamp": "2021-07-15T16:10:19.152929"
},
{
"code": "",
"level": "DEBUG",
"message": "After pruning, KG counts are: no answers",
"timestamp": "2021-07-15T16:10:19.153028"
},
{
"code": "",
"level": "WARNING",
"message": "No paths were found in {'BTE', 'RTX-KG2'} satisfying qedge e01",
"timestamp": "2021-07-15T16:10:19.153068"
},
{
"code": "",
"level": "INFO",
"message": "Processing action 'overlay' with parameters {'action': 'compute_ngd', 'virtual_relation_label': 'N1', 'subject_qnode_key': 'n0', 'object_qnode_key': 'n1'}",
"timestamp": "2021-07-15T16:10:19.156172"
},
{
"code": "",
"level": "DEBUG",
"message": "Applying Overlay to Message with parameters {'action': 'compute_ngd', 'virtual_relation_label': 'N1', 'subject_qnode_key': 'n0', 'object_qnode_key': 'n1'}",
"timestamp": "2021-07-15T16:10:19.156272"
},
{
"code": "",
"level": "DEBUG",
"message": "Nothing to overlay (KG is empty)",
"timestamp": "2021-07-15T16:10:19.156311"
},
{
"code": "",
"level": "INFO",
"message": "Processing action 'resultify' with parameters {'': 'true'}",
"timestamp": "2021-07-15T16:10:19.156337"
},
{
"code": "",
"level": "DEBUG",
"message": "Applying Resultifier to Message with parameters {'': 'true'}",
"timestamp": "2021-07-15T16:10:19.156386"
},
{
"code": "",
"level": "WARNING",
"message": "no results returned; empty knowledge graph",
"timestamp": "2021-07-15T16:10:19.156503"
},
{
"code": "",
"level": "DEBUG",
"message": "Cleaning up the KG to remove nodes not used in the results",
"timestamp": "2021-07-15T16:10:19.156535"
},
{
"code": "",
"level": "INFO",
"message": "After cleaning, the KG contains 0 nodes and 0 edges",
"timestamp": "2021-07-15T16:10:19.156582"
},
{
"code": "",
"level": "INFO",
"message": "Running experimental reranker on results",
"timestamp": "2021-07-15T16:10:19.156607"
},
{
"code": "",
"level": "DEBUG",
"message": "Starting to rank results",
"timestamp": "2021-07-15T16:10:19.156655"
},
{
"code": "",
"level": "WARNING",
"message": "No non-infinite value was encountered in any edge attribute in the knowledge graph.",
"timestamp": "2021-07-15T16:10:19.156824"
},
{
"code": "",
"level": "INFO",
"message": "Summary of available edge metrics: {}",
"timestamp": "2021-07-15T16:10:19.156846"
},
{
"code": "",
"level": "DEBUG",
"message": "Results have been ranked and sorted",
"timestamp": "2021-07-15T16:10:19.157465"
},
{
"code": "",
"level": "INFO",
"message": "Processing action 'filter_results' with parameters {'action': 'limit_number_of_results', 'max_results': '100'}",
"timestamp": "2021-07-15T16:10:19.157511"
},
{
"code": "",
"level": "DEBUG",
"message": "Before filtering, there are 0 results",
"timestamp": "2021-07-15T16:10:19.157540"
},
{
"code": "",
"level": "WARNING",
"message": "filter_results called with no results.",
"timestamp": "2021-07-15T16:10:19.157584"
},
{
"code": "",
"level": "DEBUG",
"message": "Applying Overlay to Message with parameters {'action': 'limit_number_of_results', 'max_results': '100'}",
"timestamp": "2021-07-15T16:10:19.157611"
},
{
"code": "",
"level": "DEBUG",
"message": "Query graph is {'edges': {'e01': {'constraints': None,\n 'exclude': None,\n 'object': 'n0',\n 'option_group_id': None,\n 'predicates': ['biolink:entity_negatively_regulates_entity',\n 'biolink:negatively_regulates_entity_to_entity'],\n 'relation': None,\n 'subject': 'n1'}},\n 'nodes': {'n0': {'categories': ['biolink:Gene'],\n 'constraints': None,\n 'ids': ['NCBIGene:23221'],\n 'is_set': False,\n 'option_group_id': None},\n 'n1': {'categories': ['biolink:Gene'],\n 'constraints': None,\n 'ids': None,\n 'is_set': False,\n 'option_group_id': None}}}",
"timestamp": "2021-07-15T16:10:19.158323"
},
{
"code": "",
"level": "DEBUG",
"message": "Storing resulting Message",
"timestamp": "2021-07-15T16:10:19.158371"
},
{
"code": "",
"level": "INFO",
"message": "Processing is complete. Transmitting resulting Message back to client.",
"timestamp": "2021-07-15T16:10:19.166785"
}
],
"message": {
"knowledge_graph": {
"edges": {},
"nodes": {}
},
"query_graph": {
"edges": {
"e01": {
"object": "n0",
"predicates": [
"biolink:entity_negatively_regulates_entity",
"biolink:negatively_regulates_entity_to_entity"
],
"subject": "n1"
}
},
"nodes": {
"n0": {
"categories": [
"biolink:Gene"
],
"ids": [
"NCBIGene:23221"
],
"is_set": false
},
"n1": {
"categories": [
"biolink:Gene"
],
"is_set": false
}
}
},
"results": []
},
"operations": {
"actions": [
"expand()",
"overlay(action=compute_ngd, virtual_relation_label=N1, subject_qnode_key=n0, object_qnode_key=n1)",
"resultify()",
"filter_results(action=limit_number_of_results, max_results=100)"
]
},
"reasoner_id": "ARAX",
"schema_version": "1.1.0",
"status": "OK",
"table_column_names": [
"score",
"essence",
"essence_category"
],
"tool_version": "ARAX 0.8.0",
"type": "translator_reasoner_response",
"validation_result": {
"message": "",
"n_edges": 0,
"n_nodes": 0,
"size": "19 kB",
"status": "PASS",
"version": "1.1.1"
}
}
dkoslicki
https://arax.ncats.io/?source=ARS&id=84fc74fb-03d9-4fec-a2f4-6293955bb2b0
ROHBTB2-neg_reg_entity_to_entity-Gene