BTE problem parsing Automat-robokop, leads to TRAPI validation crashes (ARS can't use BTE's response)

[colleenXu]

Related to https://github.com/biothings/biothings_explorer/issues/865

Noticed in https://arax.ci.transltr.io/?r=c961069f-36da-4369-a141-3aad9234e5ca. There's a red X-mark for validation. But it only shows the basic TypeError message and nothing else. Consequently, the ARS doesn't ingest BTE's response. (TRAPI "orange" errors don't prevent ARS from using BTE's response. The "red" critical errors do.)

So I downloaded BTE's response bte-ci-pf2-validationProblem.json.zip and used a notebook to run TRAPI validation locally. I've confirmed that this is the only critical error in BTE's response (by mutating the response to force all-string qualifier values. Then no critical/unusual errors. You can see this in the notebook right now)

---

The problem is the KG edge qualifier value is an array, not a string.

It looks like a BTE-parsing-response issue or MetaKG issue (parsing Automat robokop's meta_knowledge_graph response).

Validation report right before crash

``` * Knowledge Graph Edge Qualifiers Qualifier: => Validation of qualifier in qualifiers threw an unexpected exception $ infores:text-mining-provider-targeted -> infores:automat-robokop -> infores:biothings-explorer # NCBIGene:6615[biolink:Gene]--biolink:affected_by->NCBIGene:2739[biolink:Gene] - qualifier_type_id | qualifier_value | reason: --------------------------------------------------------------------------- TypeError Traceback (most recent call last) Cell In[6], line 3 1 # validator.get_messages().keys() ----> 3 validator.dump() File ~/miniconda3/envs/2023_08_01_TRAPIvalidator/lib/python3.11/site-packages/reasoner_validator/report.py:845, in ValidationReporter.dump(self, title, id_rows, msg_rows, compact_format, file) 843 print(f"\t\t\t\t- {' | '.join(tags)}: ", file=file) 844 first_message = False --> 845 print(f"\t\t\t\t\t{' | '.join(parameters.values())}", file=file) 846 messages_per_row += 1 847 if msg_rows and messages_per_row >= msg_rows: TypeError: sequence item 1: expected str instance, list found ```

I found 4 almost-identical (?) KG edges matching this error message

``` "241537d1a84d7a3a271291c63329c562": { "predicate": "biolink:affected_by", "subject": "NCBIGene:6615", "object": "NCBIGene:2739", "qualifiers": [ { "qualifier_type_id": "biolink:qualified_predicate", "qualifier_value": [ "biolink::caused_by" ] }, { "qualifier_type_id": "biolink:subject_aspect_qualifier", "qualifier_value": [ "degradation", "activity_or_abundance", "stability", "expression", "abundance", "activity" ] }, { "qualifier_type_id": "biolink:subject_direction_qualifier", "qualifier_value": [ "decreased", "increased" ] } ], "attributes": [ { "original_attribute_name": "agent_type", "value": "text_mining_agent", "attribute_type_id": "biolink:agent_type", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "knowledge_level", "value": "not_provided", "attribute_type_id": "biolink:knowledge_level", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "sentences", "value": "For example, downregulation of EMT driver genes (A375-GLO1-KO versus A375-GLO1-WT) [such as FN1 (3.2-fold), MELTF (2.5-fold), MMP2 (2.8-fold), MMP9 (5.2-fold), MYC (3.9-fold), PTGS2 (7.4-fold), SNAI2 (4.1-fold), TFRC (9.1-fold), VIM (2.7), ZEB2 (3.3-fold)] was reversed by GLO1 re-expression (A375-GLO1-R versus A375-GLO1-KO) [causing upregulation of FN1 (5.5-fold), MELTF (2.5-fold), MMP2 (2.9-fold), MMP9 (4.9-fold), MYC (3.4-fold), PTGS2 (5.8-fold), SNAI1 (2.5-fold), TFRC (13.9-fold),|NA|For example, downregulation of EMT driver genes (A375-GLO1-KO versus A375-GLO1-WT) [such as FN1 (3.2-fold), MELTF (2.5-fold), MMP2 (2.8-fold), MMP9 (5.2-fold), MYC (3.9-fold), PTGS2 (7.4-fold), SNAI2 (4.1-fold), TFRC (9.1-fold), VIM (2.7), ZEB2 (3.3-fold)] was reversed by GLO1 re-expression (A375-GLO1-R versus A375-GLO1-KO) [causing upregulation of FN1 (5.5-fold), MELTF (2.5-fold), MMP2 (2.9-fold), MMP9 (4.9-fold), MYC (3.4-fold), PTGS2 (5.8-fold), SNAI1 (2.5-fold), TFRC (13.9-fold),|NA|For example, downregulation of EMT driver genes (A375-GLO1-KO versus A375-GLO1-WT) [such as FN1 (3.2-fold), MELTF (2.5-fold), MMP2 (2.8-fold), MMP9 (5.2-fold), MYC (3.9-fold), PTGS2 (7.4-fold), SNAI2 (4.1-fold), TFRC (9.1-fold), VIM (2.7), ZEB2 (3.3-fold)] was reversed by GLO1 re-expression (A375-GLO1-R versus A375-GLO1-KO) [causing upregulation of FN1 (5.5-fold), MELTF (2.5-fold), MMP2 (2.9-fold), MMP9 (4.9-fold), MYC (3.4-fold), PTGS2 (5.8-fold), SNAI1 (2.5-fold), TFRC (13.9-fold),|NA", "attribute_type_id": "biolink:Attribute", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "tmkp_ids", "value": [ "tmkp:2f87dfb6ef4f3c0e03839c93f56d5d1eb03e29bcad9658e68be9eb06182b503c", "tmkp:50bac2d91922a1a3d8f223b8deea7751c6443cf47ef3c7cd40cb007356ffa71f", "tmkp:81bc9b8d85f1154cb047a1e1e87e4fe5fd860f4a293bdb3b83a4fc7f3fcf4f0c" ], "attribute_type_id": "biolink:Attribute", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "tmkp_confidence_score", "value": 0.99425588, "attribute_type_id": "biolink:Attribute", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "publications", "value": [ "PMC:7352620", "PMC:7352620", "PMC:7352620" ], "attribute_type_id": "biolink:publications", "value_type_id": "linkml:Uriorcurie" } ], "sources": [ { "resource_id": "infores:text-mining-provider-targeted", "resource_role": "primary_knowledge_source" }, { "resource_id": "infores:automat-robokop", "resource_role": "aggregator_knowledge_source", "upstream_resource_ids": [ "infores:text-mining-provider-targeted" ] }, { "resource_id": "infores:biothings-explorer", "resource_role": "aggregator_knowledge_source", "upstream_resource_ids": [ "infores:automat-robokop" ] } ] }, ``` ``` "92f8c15b2f0fb0588d793ede637f54b4": { "predicate": "biolink:affected_by", "subject": "NCBIGene:6615", "object": "NCBIGene:2739", "qualifiers": [ { "qualifier_type_id": "biolink:qualified_predicate", "qualifier_value": [ "biolink::caused_by" ] }, { "qualifier_type_id": "biolink:subject_aspect_qualifier", "qualifier_value": [ "transport", "degradation", "secretion", "activity_or_abundance", "molecular_interaction", "stability", "expression", "metabolic_processing", "abundance", "synthesis", "activity" ] }, { "qualifier_type_id": "biolink:subject_direction_qualifier", "qualifier_value": [ "decreased", "increased" ] } ], "attributes": [ { "original_attribute_name": "agent_type", "value": "text_mining_agent", "attribute_type_id": "biolink:agent_type", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "knowledge_level", "value": "not_provided", "attribute_type_id": "biolink:knowledge_level", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "sentences", "value": "For example, downregulation of EMT driver genes (A375-GLO1-KO versus A375-GLO1-WT) [such as FN1 (3.2-fold), MELTF (2.5-fold), MMP2 (2.8-fold), MMP9 (5.2-fold), MYC (3.9-fold), PTGS2 (7.4-fold), SNAI2 (4.1-fold), TFRC (9.1-fold), VIM (2.7), ZEB2 (3.3-fold)] was reversed by GLO1 re-expression (A375-GLO1-R versus A375-GLO1-KO) [causing upregulation of FN1 (5.5-fold), MELTF (2.5-fold), MMP2 (2.9-fold), MMP9 (4.9-fold), MYC (3.4-fold), PTGS2 (5.8-fold), SNAI1 (2.5-fold), TFRC (13.9-fold),|NA|For example, downregulation of EMT driver genes (A375-GLO1-KO versus A375-GLO1-WT) [such as FN1 (3.2-fold), MELTF (2.5-fold), MMP2 (2.8-fold), MMP9 (5.2-fold), MYC (3.9-fold), PTGS2 (7.4-fold), SNAI2 (4.1-fold), TFRC (9.1-fold), VIM (2.7), ZEB2 (3.3-fold)] was reversed by GLO1 re-expression (A375-GLO1-R versus A375-GLO1-KO) [causing upregulation of FN1 (5.5-fold), MELTF (2.5-fold), MMP2 (2.9-fold), MMP9 (4.9-fold), MYC (3.4-fold), PTGS2 (5.8-fold), SNAI1 (2.5-fold), TFRC (13.9-fold),|NA|For example, downregulation of EMT driver genes (A375-GLO1-KO versus A375-GLO1-WT) [such as FN1 (3.2-fold), MELTF (2.5-fold), MMP2 (2.8-fold), MMP9 (5.2-fold), MYC (3.9-fold), PTGS2 (7.4-fold), SNAI2 (4.1-fold), TFRC (9.1-fold), VIM (2.7), ZEB2 (3.3-fold)] was reversed by GLO1 re-expression (A375-GLO1-R versus A375-GLO1-KO) [causing upregulation of FN1 (5.5-fold), MELTF (2.5-fold), MMP2 (2.9-fold), MMP9 (4.9-fold), MYC (3.4-fold), PTGS2 (5.8-fold), SNAI1 (2.5-fold), TFRC (13.9-fold),|NA", "attribute_type_id": "biolink:Attribute", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "tmkp_ids", "value": [ "tmkp:2f87dfb6ef4f3c0e03839c93f56d5d1eb03e29bcad9658e68be9eb06182b503c", "tmkp:50bac2d91922a1a3d8f223b8deea7751c6443cf47ef3c7cd40cb007356ffa71f", "tmkp:81bc9b8d85f1154cb047a1e1e87e4fe5fd860f4a293bdb3b83a4fc7f3fcf4f0c" ], "attribute_type_id": "biolink:Attribute", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "tmkp_confidence_score", "value": 0.99425588, "attribute_type_id": "biolink:Attribute", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "publications", "value": [ "PMC:7352620", "PMC:7352620", "PMC:7352620" ], "attribute_type_id": "biolink:publications", "value_type_id": "linkml:Uriorcurie" } ], "sources": [ { "resource_id": "infores:text-mining-provider-targeted", "resource_role": "primary_knowledge_source" }, { "resource_id": "infores:automat-robokop", "resource_role": "aggregator_knowledge_source", "upstream_resource_ids": [ "infores:text-mining-provider-targeted" ] }, { "resource_id": "infores:biothings-explorer", "resource_role": "aggregator_knowledge_source", "upstream_resource_ids": [ "infores:automat-robokop" ] } ] }, ``` ``` "3a5cf5eb8b1c26de585da3377f340266": { "predicate": "biolink:affected_by", "subject": "NCBIGene:6615", "object": "NCBIGene:2739", "qualifiers": [ { "qualifier_type_id": "biolink:qualified_predicate", "qualifier_value": [ "biolink::caused_by" ] }, { "qualifier_type_id": "biolink:subject_aspect_qualifier", "qualifier_value": [ "degradation", "secretion", "uptake", "activity_or_abundance", "molecular_interaction", "stability", "expression", "abundance", "activity" ] }, { "qualifier_type_id": "biolink:subject_direction_qualifier", "qualifier_value": [ "decreased", "increased" ] } ], "attributes": [ { "original_attribute_name": "agent_type", "value": "text_mining_agent", "attribute_type_id": "biolink:agent_type", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "knowledge_level", "value": "not_provided", "attribute_type_id": "biolink:knowledge_level", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "sentences", "value": "For example, downregulation of EMT driver genes (A375-GLO1-KO versus A375-GLO1-WT) [such as FN1 (3.2-fold), MELTF (2.5-fold), MMP2 (2.8-fold), MMP9 (5.2-fold), MYC (3.9-fold), PTGS2 (7.4-fold), SNAI2 (4.1-fold), TFRC (9.1-fold), VIM (2.7), ZEB2 (3.3-fold)] was reversed by GLO1 re-expression (A375-GLO1-R versus A375-GLO1-KO) [causing upregulation of FN1 (5.5-fold), MELTF (2.5-fold), MMP2 (2.9-fold), MMP9 (4.9-fold), MYC (3.4-fold), PTGS2 (5.8-fold), SNAI1 (2.5-fold), TFRC (13.9-fold),|NA|For example, downregulation of EMT driver genes (A375-GLO1-KO versus A375-GLO1-WT) [such as FN1 (3.2-fold), MELTF (2.5-fold), MMP2 (2.8-fold), MMP9 (5.2-fold), MYC (3.9-fold), PTGS2 (7.4-fold), SNAI2 (4.1-fold), TFRC (9.1-fold), VIM (2.7), ZEB2 (3.3-fold)] was reversed by GLO1 re-expression (A375-GLO1-R versus A375-GLO1-KO) [causing upregulation of FN1 (5.5-fold), MELTF (2.5-fold), MMP2 (2.9-fold), MMP9 (4.9-fold), MYC (3.4-fold), PTGS2 (5.8-fold), SNAI1 (2.5-fold), TFRC (13.9-fold),|NA|For example, downregulation of EMT driver genes (A375-GLO1-KO versus A375-GLO1-WT) [such as FN1 (3.2-fold), MELTF (2.5-fold), MMP2 (2.8-fold), MMP9 (5.2-fold), MYC (3.9-fold), PTGS2 (7.4-fold), SNAI2 (4.1-fold), TFRC (9.1-fold), VIM (2.7), ZEB2 (3.3-fold)] was reversed by GLO1 re-expression (A375-GLO1-R versus A375-GLO1-KO) [causing upregulation of FN1 (5.5-fold), MELTF (2.5-fold), MMP2 (2.9-fold), MMP9 (4.9-fold), MYC (3.4-fold), PTGS2 (5.8-fold), SNAI1 (2.5-fold), TFRC (13.9-fold),|NA", "attribute_type_id": "biolink:Attribute", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "tmkp_ids", "value": [ "tmkp:2f87dfb6ef4f3c0e03839c93f56d5d1eb03e29bcad9658e68be9eb06182b503c", "tmkp:50bac2d91922a1a3d8f223b8deea7751c6443cf47ef3c7cd40cb007356ffa71f", "tmkp:81bc9b8d85f1154cb047a1e1e87e4fe5fd860f4a293bdb3b83a4fc7f3fcf4f0c" ], "attribute_type_id": "biolink:Attribute", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "tmkp_confidence_score", "value": 0.99425588, "attribute_type_id": "biolink:Attribute", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "publications", "value": [ "PMC:7352620", "PMC:7352620", "PMC:7352620" ], "attribute_type_id": "biolink:publications", "value_type_id": "linkml:Uriorcurie" } ], "sources": [ { "resource_id": "infores:text-mining-provider-targeted", "resource_role": "primary_knowledge_source" }, { "resource_id": "infores:automat-robokop", "resource_role": "aggregator_knowledge_source", "upstream_resource_ids": [ "infores:text-mining-provider-targeted" ] }, { "resource_id": "infores:biothings-explorer", "resource_role": "aggregator_knowledge_source", "upstream_resource_ids": [ "infores:automat-robokop" ] } ] }, ``` ``` "4d589f7402f498079be5c89750f6fe98": { "predicate": "biolink:affected_by", "subject": "NCBIGene:6615", "object": "NCBIGene:2739", "qualifiers": [ { "qualifier_type_id": "biolink:qualified_predicate", "qualifier_value": [ "biolink::caused_by" ] }, { "qualifier_type_id": "biolink:subject_aspect_qualifier", "qualifier_value": [ "transport", "degradation", "secretion", "uptake", "activity_or_abundance", "molecular_interaction", "stability", "expression", "metabolic_processing", "abundance", "synthesis", "activity" ] }, { "qualifier_type_id": "biolink:subject_direction_qualifier", "qualifier_value": [ "decreased", "increased" ] } ], "attributes": [ { "original_attribute_name": "agent_type", "value": "text_mining_agent", "attribute_type_id": "biolink:agent_type", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "knowledge_level", "value": "not_provided", "attribute_type_id": "biolink:knowledge_level", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "sentences", "value": "For example, downregulation of EMT driver genes (A375-GLO1-KO versus A375-GLO1-WT) [such as FN1 (3.2-fold), MELTF (2.5-fold), MMP2 (2.8-fold), MMP9 (5.2-fold), MYC (3.9-fold), PTGS2 (7.4-fold), SNAI2 (4.1-fold), TFRC (9.1-fold), VIM (2.7), ZEB2 (3.3-fold)] was reversed by GLO1 re-expression (A375-GLO1-R versus A375-GLO1-KO) [causing upregulation of FN1 (5.5-fold), MELTF (2.5-fold), MMP2 (2.9-fold), MMP9 (4.9-fold), MYC (3.4-fold), PTGS2 (5.8-fold), SNAI1 (2.5-fold), TFRC (13.9-fold),|NA|For example, downregulation of EMT driver genes (A375-GLO1-KO versus A375-GLO1-WT) [such as FN1 (3.2-fold), MELTF (2.5-fold), MMP2 (2.8-fold), MMP9 (5.2-fold), MYC (3.9-fold), PTGS2 (7.4-fold), SNAI2 (4.1-fold), TFRC (9.1-fold), VIM (2.7), ZEB2 (3.3-fold)] was reversed by GLO1 re-expression (A375-GLO1-R versus A375-GLO1-KO) [causing upregulation of FN1 (5.5-fold), MELTF (2.5-fold), MMP2 (2.9-fold), MMP9 (4.9-fold), MYC (3.4-fold), PTGS2 (5.8-fold), SNAI1 (2.5-fold), TFRC (13.9-fold),|NA|For example, downregulation of EMT driver genes (A375-GLO1-KO versus A375-GLO1-WT) [such as FN1 (3.2-fold), MELTF (2.5-fold), MMP2 (2.8-fold), MMP9 (5.2-fold), MYC (3.9-fold), PTGS2 (7.4-fold), SNAI2 (4.1-fold), TFRC (9.1-fold), VIM (2.7), ZEB2 (3.3-fold)] was reversed by GLO1 re-expression (A375-GLO1-R versus A375-GLO1-KO) [causing upregulation of FN1 (5.5-fold), MELTF (2.5-fold), MMP2 (2.9-fold), MMP9 (4.9-fold), MYC (3.4-fold), PTGS2 (5.8-fold), SNAI1 (2.5-fold), TFRC (13.9-fold),|NA", "attribute_type_id": "biolink:Attribute", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "tmkp_ids", "value": [ "tmkp:2f87dfb6ef4f3c0e03839c93f56d5d1eb03e29bcad9658e68be9eb06182b503c", "tmkp:50bac2d91922a1a3d8f223b8deea7751c6443cf47ef3c7cd40cb007356ffa71f", "tmkp:81bc9b8d85f1154cb047a1e1e87e4fe5fd860f4a293bdb3b83a4fc7f3fcf4f0c" ], "attribute_type_id": "biolink:Attribute", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "tmkp_confidence_score", "value": 0.99425588, "attribute_type_id": "biolink:Attribute", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "publications", "value": [ "PMC:7352620", "PMC:7352620", "PMC:7352620" ], "attribute_type_id": "biolink:publications", "value_type_id": "linkml:Uriorcurie" } ], "sources": [ { "resource_id": "infores:text-mining-provider-targeted", "resource_role": "primary_knowledge_source" }, { "resource_id": "infores:automat-robokop", "resource_role": "aggregator_knowledge_source", "upstream_resource_ids": [ "infores:text-mining-provider-targeted" ] }, { "resource_id": "infores:biothings-explorer", "resource_role": "aggregator_knowledge_source", "upstream_resource_ids": [ "infores:automat-robokop" ] } ] }, ```

Easier way to test: quick non-creative-mode query to retrieve these problematic edges

POST query to local instance ARA-mode: http://localhost:3000/v1/query ``` { "message": { "query_graph": { "nodes": { "n0": { "categories": ["biolink:Gene"] }, "n1": { "ids": ["NCBIGene:2739"], "categories": ["biolink:Gene"] } }, "edges": { "e01": { "subject": "n0", "object": "n1", "predicates": ["biolink:affected_by"] } } } } } ```

Querying Automat robokop directly: no qualifier issues + only 1 corresponding edge

POST to `https://automat.ci.transltr.io/robokopkg/query`. Will get some other edges too: this KP seems to have query-directionality issues. It also returns edges in the canonical direction (not what was asked for). ``` { "message": { "query_graph": { "nodes": { "n0": { "categories": ["biolink:Gene"] }, "n1": { "ids": ["NCBIGene:2739"], "categories": ["biolink:Gene"] } }, "edges": { "e01": { "subject": "n0", "object": "n1", "predicates": ["biolink:affected_by"] } } } } } ``` Only found 1 edge that matches the 4 BTE edges and its qualifier set is fine... ``` "5:4bbbd080-7349-4312-bad6-e2c56677957a:136870644": { "subject": "NCBIGene:2739", "predicate": "biolink:affects", "object": "NCBIGene:6615", "sources": [ { "resource_id": "infores:text-mining-provider-targeted", "resource_role": "primary_knowledge_source" }, { "resource_id": "infores:automat-robokop", "resource_role": "aggregator_knowledge_source", "upstream_resource_ids": [ "infores:text-mining-provider-targeted" ] } ], "attributes": [ { "original_attribute_name": "agent_type", "value": "text_mining_agent", "attribute_type_id": "biolink:agent_type", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "knowledge_level", "value": "not_provided", "attribute_type_id": "biolink:knowledge_level", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "sentences", "value": "For example, downregulation of EMT driver genes (A375-GLO1-KO versus A375-GLO1-WT) [such as FN1 (3.2-fold), MELTF (2.5-fold), MMP2 (2.8-fold), MMP9 (5.2-fold), MYC (3.9-fold), PTGS2 (7.4-fold), SNAI2 (4.1-fold), TFRC (9.1-fold), VIM (2.7), ZEB2 (3.3-fold)] was reversed by GLO1 re-expression (A375-GLO1-R versus A375-GLO1-KO) [causing upregulation of FN1 (5.5-fold), MELTF (2.5-fold), MMP2 (2.9-fold), MMP9 (4.9-fold), MYC (3.4-fold), PTGS2 (5.8-fold), SNAI1 (2.5-fold), TFRC (13.9-fold),|NA|For example, downregulation of EMT driver genes (A375-GLO1-KO versus A375-GLO1-WT) [such as FN1 (3.2-fold), MELTF (2.5-fold), MMP2 (2.8-fold), MMP9 (5.2-fold), MYC (3.9-fold), PTGS2 (7.4-fold), SNAI2 (4.1-fold), TFRC (9.1-fold), VIM (2.7), ZEB2 (3.3-fold)] was reversed by GLO1 re-expression (A375-GLO1-R versus A375-GLO1-KO) [causing upregulation of FN1 (5.5-fold), MELTF (2.5-fold), MMP2 (2.9-fold), MMP9 (4.9-fold), MYC (3.4-fold), PTGS2 (5.8-fold), SNAI1 (2.5-fold), TFRC (13.9-fold),|NA|For example, downregulation of EMT driver genes (A375-GLO1-KO versus A375-GLO1-WT) [such as FN1 (3.2-fold), MELTF (2.5-fold), MMP2 (2.8-fold), MMP9 (5.2-fold), MYC (3.9-fold), PTGS2 (7.4-fold), SNAI2 (4.1-fold), TFRC (9.1-fold), VIM (2.7), ZEB2 (3.3-fold)] was reversed by GLO1 re-expression (A375-GLO1-R versus A375-GLO1-KO) [causing upregulation of FN1 (5.5-fold), MELTF (2.5-fold), MMP2 (2.9-fold), MMP9 (4.9-fold), MYC (3.4-fold), PTGS2 (5.8-fold), SNAI1 (2.5-fold), TFRC (13.9-fold),|NA", "attribute_type_id": "biolink:Attribute", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "tmkp_ids", "value": [ "tmkp:2f87dfb6ef4f3c0e03839c93f56d5d1eb03e29bcad9658e68be9eb06182b503c", "tmkp:50bac2d91922a1a3d8f223b8deea7751c6443cf47ef3c7cd40cb007356ffa71f", "tmkp:81bc9b8d85f1154cb047a1e1e87e4fe5fd860f4a293bdb3b83a4fc7f3fcf4f0c" ], "attribute_type_id": "biolink:Attribute", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "tmkp_confidence_score", "value": 0.99425588, "attribute_type_id": "biolink:Attribute", "value_type_id": "EDAM:data_0006" }, { "original_attribute_name": "publications", "value": [ "PMC:7352620", "PMC:7352620", "PMC:7352620" ], "attribute_type_id": "biolink:publications", "value_type_id": "linkml:Uriorcurie" } ], "qualifiers": [ { "qualifier_type_id": "biolink:object_direction_qualifier", "qualifier_value": "decreased" }, { "qualifier_type_id": "biolink:qualified_predicate", "qualifier_value": "biolink:causes" }, { "qualifier_type_id": "biolink:object_aspect_qualifier", "qualifier_value": "activity_or_abundance" } ] }, ```

[colleenXu]

Probably want to fix ASAP @andrewsu @tokebe @rjawesome @NeuralFlux

[NeuralFlux]

Going through it now. I will discuss with @rjawesome later.

[NeuralFlux]

@colleenXu do we have a query which returns a vaild TRAPI response, i.e., qualifier_value is a string? I couldn't find any edges in the given test query's response where it is a string. (randomly sampled 10 of them)

[RichardBruskiewich]

@colleenXu , the reasoner-validator reporting bug you identified is resolved in release 4.2.7

As you noted, a real validation error was triggered by the use of array values for qualifiers. This is actually a TRAPI compliance error. The patch to reasoner-validator just now ensures that the report succeeds in dumping its results without crashing. I guess this Biothings issue can be closed?

[tokebe]

@RichardBruskiewich This issue is still tracking what BTE is doing wrong to produce the legitimate validation error, so it'll remain open until a fix is made on BTE's side and said fix makes its way up to Prod.

[RichardBruskiewich]

Ok... the BTE TRAPI non-compliance error should now be properly reported and simply relates to the face that Edge qualifiers cannot be arrays of values, only a single string scalar value