Duplicated edge-attributes #891

colleenXu · 2024-10-21T20:20:29Z

~~Related to #880?~~ Doesn't seem to be...

Noticing multiple cases in 10/20 automated test run, where edge-attributes were duplicated.

Example query

ARAX-UI link
BTE raw response from https://bte.ci.transltr.io/v1/asyncquery_response/RTZGUYSS16

"39b1bb8612f44069718af35dfb771c96" from MolePro

"UNII:RWM8CCW8GP" affects "NCBIGene:5294"
Has 4 copies of this set of edge-attributes

[
  {
    "attribute_source": "infores:dgidb",
    "attribute_type_id": "biolink:knowledge_level",
    "attributes": [],
    "original_attribute_name": "biolink:knowledge_level",
    "value": "unspecified",
    "value_type_id": "string"
  },
  {
    "attribute_source": "infores:dgidb",
    "attribute_type_id": "biolink:agent_type",
    "attributes": [],
    "original_attribute_name": "biolink:agent_type",
    "value": "unspecified",
    "value_type_id": "string"
  },
  {
    "attribute_type_id": "biolink:publications",
    "value": [
      "https://pubmed.ncbi.nlm.nih.gov/16452215",
      "PMID:16452215"
    ],
    "value_type_id": "linkml:Uriorcurie"
  },

"61028f688d7124cf8280bc1ef9abfcae" from Drug Approvals

"CHEBI:8378" applied_to_treat "MONDO:0015564"
Has 4 copies of this set of edge-attributes

[
  {
    "attribute_type_id": "biolink:clinical_approval_status",
    "value": "biolink:off_label_use",
    "value_type_id": "biolink:ClinicalApprovalStatusEnum"
  },
  {
    "attribute_source": "infores:multiomics-drugapprovals",
    "attribute_type_id": "biolink:knowledge_level",
    "value": "observation"
  },
  {
    "attribute_type_id": "N_cases",
    "value": 14
  },
  {
    "attribute_source": "infores:multiomics-drugapprovals",
    "attribute_type_id": "biolink:agent_type",
    "value": "manual_agent"
  },

Related TRAPI validation logs

Error: The 'knowledge_level' slot is duplicated for the given edge!
Error: The 'agent_type' slot is duplicated for the given edge!
Warning: Edge is missing its required 'knowledge_level' property
Warning: Edge is missing its required 'agent_type' property

The text was updated successfully, but these errors were encountered:

colleenXu · 2024-10-21T21:39:49Z

When I try replicating the subquery BTE would have sent MolePro, I don't get duplicated edge-attributes from the MolePro edge. But I do get different KL/AT values:

Saved response MolePro-direct-1.json

Query

curl --location 'https://molepro-trapi.ci.transltr.io/molepro/trapi/v1.5/query' \
--header 'Content-Type: application/json' \
--data '{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "ids": ["NCBIGene:5294"],
                    "categories": ["biolink:Gene"]
                },
                "n1": {
                    "categories": ["biolink:ChemicalEntity"]
                }
            },
            "edges": {
                "e0": {
                    "subject": "n0",
                    "object": "n1",
                    "predicates": ["biolink:affected_by"]
                }
            }
        }
    }
}'

Matching edge

PUBCHEM.COMPOUND:448601 has UNII:RWM8CCW8GP as xref

                "e612-C5vduVY5RT": {
                    "attributes": [
                        {
                            "attribute_source": "infores:dgidb",
                            "attribute_type_id": "biolink:knowledge_level",
                            "attributes": [],
                            "original_attribute_name": "biolink:knowledge_level",
                            "value": "not_provided",
                            "value_type_id": "string"
                        },
                        {
                            "attribute_source": "infores:dgidb",
                            "attribute_type_id": "biolink:agent_type",
                            "attributes": [],
                            "original_attribute_name": "biolink:agent_type",
                            "value": "not_provided",
                            "value_type_id": "string"
                        },
                        {
                            "attribute_type_id": "biolink:publications",
                            "value": [
                                "PMID:16452215",
                                "https://pubmed.ncbi.nlm.nih.gov/16452215"
                            ],
                            "value_type_id": "linkml:Uriorcurie"
                        }
                    ],
                    "object": "PUBCHEM.COMPOUND:448601",
                    "predicate": "biolink:affected_by",
                    "qualifiers": [],
                    "sources": [
                        {
                            "resource_id": "infores:dgidb",
                            "resource_role": "primary_knowledge_source",
                            "source_record_urls": [],
                            "upstream_resource_ids": []
                        },
                        {
                            "resource_id": "infores:molepro",
                            "resource_role": "aggregator_knowledge_source",
                            "source_record_urls": [],
                            "upstream_resource_ids": [
                                "infores:dgidb"
                            ]
                        }
                    ],
                    "subject": "NCBIGene:5294"
                }

colleenXu · 2024-10-21T21:46:01Z

When I try replicating the subquery BTE would have sent Drug Approvals, I don't get duplicated edge-attributes.

Saved response DAKP-1.json

Query

curl --location 'https://multiomics.ci.transltr.io/dakp/query' \
--header 'Content-Type: application/json' \
--data '{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "ids": ["MONDO:0015564"],
                    "categories": ["biolink:Disease"]
                },
                "n1": {
                    "categories": ["biolink:ChemicalEntity"]
                }
            },
            "edges": {
                "e0": {
                    "subject": "n0",
                    "object": "n1"
                }
            }
        }
    }
}'

Matching Edge

                "f7fb9429-a916-36f7-beb8-9b35279c00ed": {
                    "attributes": [
                        {
                            "attribute_type_id": "biolink:clinical_approval_status",
                            "value": "biolink:off_label_use",
                            "value_type_id": "biolink:ClinicalApprovalStatusEnum"
                        },
                        {
                            "attribute_source": "infores:multiomics-drugapprovals",
                            "attribute_type_id": "biolink:knowledge_level",
                            "value": "observation"
                        },
                        {
                            "attribute_source": "infores:multiomics-drugapprovals",
                            "attribute_type_id": "biolink:agent_type",
                            "value": "manual_agent"
                        },
                        {
                            "attribute_type_id": "N_cases",
                            "value": 14
                        }
                    ],
                    "object": "MONDO:0015564",
                    "predicate": "biolink:applied_to_treat",
                    "sources": [
                        {
                            "resource_id": "infores:multiomics-drugapprovals",
                            "resource_role": "aggregator_knowledge_source",
                            "source_record_urls": [
                                "https://db.systemsbiology.net/gestalt/cgi-pub/KGinfo.pl?id=f7fb9429-a916-36f7-beb8-9b35279c00ed"
                            ],
                            "upstream_resource_ids": [
                                "infores:dailymed",
                                "infores:faers"
                            ]
                        },
                        {
                            "resource_id": "infores:faers",
                            "resource_role": "primary_knowledge_source"
                        },
                        {
                            "resource_id": "infores:dailymed",
                            "resource_role": "supporting_data_source"
                        }
                    ],
                    "subject": "CHEBI:8378"
                },

colleenXu · 2024-10-21T22:25:48Z

FYI: I'm seeing some duplicate/missing KL-AT validation issues occurring in Aragorn and Improving Agent as well. However, they appear to have had these issues before this weekend:

10/13 automated run ARAX-UI
10/2 automated run ARAX-UI
9/1 automated run ARAX-UI

It's hard to track down/review the edges in ARAX-UI. May need to recreate by querying those ARAs directly. But also maybe don't need to keep digging here.

colleenXu · 2024-10-21T22:40:00Z

Investigation so far

Mostly copied from Slack DMs with @tokebe

Jackson

Ok, confirmed, at the very least the main problem is that the attributes are being stored in a way that causes special handling, and that handling doesn't bother with deduplication. I'm surprised we're only seeing it now; I wonder if the new KPs are sending back nearly duplicate edges

It definitely looks like we could be getting handed some duplicate edges, but I haven't confirmed it. But we're definitely failing to avoid duplicates from multiple records after the fact, which might not be too difficult to handle, actually
We've had special handling for edge attributes that show up in the response mapping a specific way and at least part of that special handling could probably just be merged into the main handling and avoid the duplicate problem altogether

Me

Doesn't seem to be from biothings/bte_trapi_query_graph_handler#220. I locally reset module to 3a3c6de (before merging that PR), tested the MolePro query, and still had 4 sets of duplicate edge-attributes for that edge.

rjawesome · 2024-10-21T22:41:12Z

@colleenXu I believe I just fixed it, I'll get in a PR very soon.

colleenXu · 2024-10-22T05:54:36Z

I've confirmed Rohan's suspicion that this bug came from biothings/bte_trapi_query_graph_handler#219.

I locally reset to 6cefe98, before this PR was merged. Then I tested both queries and the "duplicate edge-attributes" seemed to be fixed for those example edges.

colleenXu · 2024-10-22T06:11:32Z

@tokebe

I confirmed that Rohan's PR fixes the example individual queries. I haven't tested a creative-mode query yet.

I've also confirmed that the evidence_count fixes intended in biothings/bte_trapi_query_graph_handler#219 are still present. Examples from here

Example 1 edge has evidence_count 56

Edge c6225b095f6e79ba23394fe1bc8e9549

{
                    "predicate": "biolink:interacts_with",
                    "subject": "CHEBI:45713",
                    "object": "NCBIGene:207",
                    "attributes": [
                        {
                            "attribute_type_id": "biolink:knowledge_level",
                            "value": "not_provided"
                        },
                        {
                            "attribute_type_id": "biolink:agent_type",
                            "value": "text_mining_agent"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Akt phosphorylation in CFs was unaffected by treatment with either 100 nM ANG II or 25 microM RES."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:15498824"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "94|97"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "0|3"
                                }
                            ],
                            "value": "121483075"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Resveratrol phosphorylated both Akt and CREB that was blocked by MRS-1191, which also abolished cardioprotective abilities of resveratrol."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:15879002"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "0|11"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "32|35"
                                }
                            ],
                            "value": "119847019"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "These results indicate that resveratrol generates cardioprotection by preconditioning the heart by HO-1-mediated mechanisms, which are regulated by p38MAP kinase and Akt survival signaling, but non-dependent on NFkappaB activation."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:17015251"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "28|39"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "166|169"
                                }
                            ],
                            "value": "119762056"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Estrogen and resveratrol regulate Rac and Cdc42 signaling to the actin cytoskeleton of metastatic breast cancer cells."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:17356711"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "13|24"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "34|37"
                                }
                            ],
                            "value": "125418571"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Use of resveratrol or inhibition of Akt phosphorylation may represent an important therapeutic approach in combination with conventional therapies for the treatment of prostate cancer."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:17823925"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "7|18"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "36|39"
                                }
                            ],
                            "value": "166612130"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Finally, resveratrol generated a survival signal by phosphorylation of Akt and increase in induction of Bcl-2 expression, which was inhibited by cisplatin, but not by shRNA-Trx-1."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:18045550"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "9|20"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "71|74"
                                }
                            ],
                            "value": "122091210"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Because studies in cells other than cardiomyocytes revealed that AMP-activated protein kinase (AMPK) and Akt are affected by resveratrol, we hypothesized that resveratrol prevents cardiac myocyte hypertrophy via these two kinase systems."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:18562309"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "125|136"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "105|108"
                                }
                            ],
                            "value": "123747212"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "These inhibitory effects of resveratrol on Nox1 expression and MCP-1 production may target to the Akt and FoxO3a signaling pathways."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:19293636"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "28|39"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "98|101"
                                }
                            ],
                            "value": "131331101"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "In the current studies, the effect of resveratrol on phosphoinositide kinase-3 (PI3K)/protein kinase B (Akt)/mammalian target of rapamycin (mTOR) signaling pathway was examined in human U251 glioma cells."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:19827268"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "38|49"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "104|107"
                                }
                            ],
                            "value": "147376378"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Resveratrol regulates the PTEN/AKT pathway through androgen receptor-dependent and -independent mechanisms in prostate cancer cell lines."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:20729295"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "0|11"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "31|34"
                                }
                            ],
                            "value": "148990807"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Our findings demonstrate that resveratrol down-regulates the protein cyclin D1 and, in a concentration dependent manner, the phosphorylation levels of protein kinase B (Akt) and glycogen synthase kinase-3beta (GSK-3beta)."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:22234583"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "30|41"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "169|172"
                                }
                            ],
                            "value": "128683166"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "The expression of hTERT is regulated by the PI3-K/Akt pathway; therefore, we examined the effect of resveratrol on Akt activity in EPCs."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:22340406"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "100|111"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "50|53"
                                }
                            ],
                            "value": "173747471"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "4'-O-methylresveratrol was more effective than  resveratrol in inhibiting Akt phosphorylation, which is related to AR  signaling, in LNCaP cells."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:22700762"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "11|22"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "74|77"
                                }
                            ],
                            "value": "127504048"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Additionally, the activity of the migration/invasion regulator Rac, which we have previously shown to be regulated by resveratrol in vitro, was measured in tumors from resveratrol treated mice."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:23298290"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "118|129"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "63|66"
                                }
                            ],
                            "value": "175773461"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Piceatannol attenuated the H-ras-induced phosphorylation of Akt in a time- and dose-dependent manner, whereas resveratrol, at the same concentrations, did not exert an inhibitory effect."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:23877152"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "110|121"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "60|63"
                                }
                            ],
                            "value": "78751153"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Interestingly, in all of the experiments involving a low concentration of resveratrol (1 MUM), the observed effects on Akt, p70S6K, and NFAT were independent from AMP-activated protein kinase (AMPK) activation while these effects at higher concentrations of resveratrol (50 MUM) were potentiated by AMPK activation."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:25394677"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "74|85"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "119|122"
                                }
                            ],
                            "value": "161946148"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Resveratrol regulates PTEN/Akt pathway through inhibition of MTA1/HDAC unit of the NuRD complex in prostate cancer."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:25447541"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "0|11"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "27|30"
                                }
                            ],
                            "value": "76850932"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "In this study, we aimed to investigate the effects of resveratrol on the phosphatidylinositol-3-kinase/protein kinase B (PI3K/Akt)/FoxO3a pathway in mediating high glucose (HG)-induced injuries in neuronal PC12 cells."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:25471227"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "54|65"
                                },
                                {
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                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "BACKGROUND: We observed the effects of resveratrol on the expression of molecules involved in the mTOR signaling pathway in pathological scar fibroblasts, including PI3K, Akt and mTOR."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:28195449"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "171|174"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "39|50"
                                }
                            ],
                            "value": "155403287"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Western blot analysis of the effects of resveratrol on upstream cyclin D1 transcriptional signaling, extracellular signal-related kinase (ERK), p90RSK, Akt, and p70S6K revealed inhibition of Akt but not the ERK signaling pathway."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:28385009"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "152|155"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "40|51"
                                }
                            ],
                            "value": "141037678"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "METHODS AND MATERIALS: To investigate whether phosphatidylinositol 3-kinase/Akt (PI3K/Akt) pathway was involved in RSV anti-inflammatory and neuroprotective properties."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:30156477"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "76|79"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "115|118"
                                }
                            ],
                            "value": "165439824"
                        },
                        {
                            "attribute_type_id": "biolink:evidence_count",
                            "value": 56
                        }
                    ],
                    "sources": [
                        {
                            "resource_id": "infores:semmeddb",
                            "resource_role": "primary_knowledge_source"
                        },
                        {
                            "resource_id": "infores:biothings-semmeddb",
                            "resource_role": "aggregator_knowledge_source",
                            "upstream_resource_ids": [
                                "infores:semmeddb"
                            ]
                        },
                        {
                            "resource_id": "infores:service-provider-trapi",
                            "resource_role": "aggregator_knowledge_source",
                            "upstream_resource_ids": [
                                "infores:biothings-semmeddb"
                            ]
                        }
                    ]
                }

Example 2 edge has evidence_count 80

edge 5fc3251c17fac62783ca703aefc76f8a

{
                    "predicate": "biolink:interacts_with",
                    "subject": "CHEBI:45713",
                    "object": "NCBIGene:23411",
                    "attributes": [
                        {
                            "attribute_type_id": "biolink:knowledge_level",
                            "value": "not_provided"
                        },
                        {
                            "attribute_type_id": "biolink:agent_type",
                            "value": "text_mining_agent"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Resveratrol-mediated SIRT1 activation attenuates ovalbumin-induced allergic rhinitis in mice."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:32361418"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "0|11"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "21|26"
                                }
                            ],
                            "value": "186134764"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Resveratrol mimics this neurovascular protection, at least in part, via SIRT1."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:33010255"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "0|11"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "72|77"
                                }
                            ],
                            "value": "189559448"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "In the elderly, the SIRT1 remains antioxidant and RSV ceases its operation via SIRT1."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:33444643"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "50|53"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "20|25"
                                }
                            ],
                            "value": "191401035"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Moreover, many of the physiologic improvements observed with resveratrol and NAD precursors are consistent with modulation of known SIRT1 targets."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:33462707"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "61|72"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "132|137"
                                }
                            ],
                            "value": "194213170"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "As expected, resveratrol reduced cognitive damage and promoted neurogenesis in Pb-induced injury by regulation of SIRT1 pathway."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:33978298"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "13|24"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "114|119"
                                }
                            ],
                            "value": "193727480"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Totally six studies evaluated the effects of resveratrol on SIRT1 gene expression, and six articles investigate protein expression."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:34403949"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "45|56"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "60|70"
                                }
                            ],
                            "value": "195737417"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Furthermore, RSV targets Sirtuin1 (Sirt1), a histone deacetylase."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:34870752"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "13|16"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "25|33"
                                }
                            ],
                            "value": "197632356"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "End-point activity assays have shown that resveratrol can have different effects on SIRT1 activity depending on the acetylated peptide substrate used, including an increase, decrease, or no change in deacetylation activity."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:35555597"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "42|53"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "84|89"
                                }
                            ],
                            "value": "200721352"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Resveratrol can interact with several molecular targets (Nf-kB, SIRT1, mTOR, HIF-1alpha, miRNAs, and TNF-alpha) and effectively prevent/ alleviate IBD symptoms with promising results."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:35777588"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "0|11"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "64|69"
                                }
                            ],
                            "value": "201708733"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "However, the possible therapeutic roles of RSV-mediated SIRT1 enhancement on the regulation of hippocampal neurogenesis and reversal of memory loss through the Wnt signaling pathway have not been addressed yet."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:36463442"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "43|46"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "56|61"
                                }
                            ],
                            "value": "204762024"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Although resveratrol has poor pharmacokinetics, it can bind to Sirt1 and activate it allosterically-as can so-called sirtuin-activating compound drugs."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:36522127"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "9|20"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "63|68"
                                }
                            ],
                            "value": "205067898"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Moreover, the critical role of SIRT1-UCP2 axis was further supported by the results that SIRT1 activator SRT1720 reversed ethanol-induced impairment of glucose-stimulated insulin secretion by decreasing UCP2, while SIRT1 inhibitor Ex527 abolished the beneficial effects of resveratrol."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:32087266"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "31|36"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "273|284"
                                }
                            ],
                            "value": "183689694"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Importantly, the addition of EX527, which is a selective inhibitor of Sirt1, reversed the protective effect of Res pretreatment, indicating that Sirt1 may be an important mediator of the protective effect of Res."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:32446930"
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                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "70|75"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "111|114"
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                            "value": "186521091"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "We investigated the role of SIRT1 in the effect of RSV using two genetic mouse models."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:32777783"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "28|33"
                                },
                                {
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                                    "value": "51|54"
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                            "value": "188245333"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "The results showed that the effect of resveratrol may be closely associated with targets such as AKT serine/threonine kinase 1 (AKT1), mitogen-activated protein kinase 3 (MAPK3), Sirtuin-1 (SIRT1) and proto-oncogene tyrosine-protein kinase Src (SRC), as well as biological processes such as cell proliferation, inflammatory response, and redox balance."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:32798507"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "179|188"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "38|49"
                                }
                            ],
                            "value": "189380155"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Upregulation of sirtuin-1 was an examined mechanism proposed for some observed effects of resveratrol."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:34312768"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "16|25"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "90|101"
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                            ],
                            "value": "195250334"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Then, inhibition of AMPK and Sirt1 pathways has significantly reversed protective effect of resveratrol on miR-155 expression."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:34739715"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "29|34"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "92|103"
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                            ],
                            "value": "197028955"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "RELA/SIRT1 may be the potential target of resveratrol for premature senescence."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:35166167"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "5|10"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "42|53"
                                }
                            ],
                            "value": "198966436"
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                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Moreover, neonatal rat ventricular myocytes (NRVMs) and H9c2 cells with knockdown the expression of AMPK, SIRT1 or FOXO1 were used to uncover the underlying molecular mechanism for the cardio-protection of RSV."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:35791579"
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                                {
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                                    "value": "106|111"
                                },
                                {
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                                    "value": "206|209"
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                            ],
                            "value": "201761177"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Furthermore, using resveratrol and Ex 527, SIRT1 expression was found to be negatively associated with autophagy induced by N. caninum infection in caprine EECs, and the intracellular propagation of N. caninum tachyzoites in caprine EECs was negatively affected by SIRT1 expression."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:35915458"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "43|48"
                                },
                                {
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                                    "value": "19|30"
                                }
                            ],
                            "value": "202328663"
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                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Substrate competition studies indicated that the fluorophore decreased the binding affinity of the peptide, and, in the presence of resveratrol, fluorophore-containing substrates bound more tightly to SIRT1."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:15749705"
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                                {
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                            "value": "119984374"
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                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Resveratrol induces longevity in C. elegans through the action of SIR2."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:16271528"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "0|11"
                                },
                                {
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                                }
                            ],
                            "value": "148238430"
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                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "(3) Studies of resveratrol, which was identified in a screen for compounds that affect the activity of the Sir2 protein that influences lifespan."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:16872777"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "15|26"
                                },
                                {
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                                    "value": "107|111"
                                }
                            ],
                            "value": "125233850"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Protection from oxidative stress appears to be a common feature of resveratrol that may be mediated through SirT1, though more specific molecular mechanisms by which resveratrol mediates its effects remain unclear."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:17064666"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "67|78"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "108|113"
                                }
                            ],
                            "value": "124634738"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "This mechanism is consistent with RSV being a known activator of the protein deacetylase, SIRT1, and by the lack of effect of RSV in SIRT1(-/-) MEFs."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:17112576"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "34|37"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "90|95"
                                }
                            ],
                            "value": "120430891"
                        },
                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Modulation of Sirt1 by resveratrol and nicotinamide alters proliferation and differentiation of pig preadipocytes."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:17851734"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "23|34"
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                                {
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                            "attributes": [
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                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Resveratrol appears to mediate these effects partly by activating SIRT1, a deacetylase enzyme that regulates the activity of several transcriptional factors and enzymes responsive to nutrient availability."
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                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "We postulate that these effects by resveratrol are mediated via Sirt1 but further studies are needed to confirm or refute this theory."
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                                {
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                                {
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                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Although it is thought that resveratrol targets Sirt1, this is controversial because resveratrol also activates 5' AMP-activated protein kinase (AMPK), which also regulates insulin sensitivity and mitochondrial biogenesis."
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                                {
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                            "attributes": [
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                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "This study was undertaken to investigate whether resveratrol can regulate SIRT1, FOXO1, adiponectin, PPAR?1-3, and PPAR?/?"
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                        {
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                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "In order to investigate the dependence of resveratrol on SIRT1, the effects of resveratrol on cells treated by SIRT1 siRNA were also examined."
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                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "The role of SIRT1 in cell-cycle effects mediated by resveratrol was studied through changes in the expression of SIRT1 using western blot."
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                                {
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                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Resveratrol-mediated SIRT1 activation decreased the acetylation of p53 and p65 induced by prion protein and SIRT1 inhibitor."
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                                {
                                    "attribute_type_id": "biolink:publications",
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                                {
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                            "attributes": [
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                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Our studies using mammalian cell lines are revealing effects of Sirt1 on DNA methylation, and indicate that Sirt1 and resveratrol affect the expression of different sets of genes."
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                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "OBJECTIVES: The primary aims of the study were to examine the effect of resveratrol on skeletal muscle SIRT1 expression and energy expenditure in subjects with Type 2 diabetes mellitus (T2DM)."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:23918588"
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                                {
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                                    "value": "72|83"
                                },
                                {
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                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "The antimycin A-induced increase in ROS levels and apoptosis was enhanced by SIRT1 inhibitors nicotinamide and splitomicin, whereas it was suppressed by a SIRT1 activator, resveratrol, and a SIRT1 cofactor, NAD+."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:24040102"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "172|183"
                                },
                                {
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                                    "value": "77|82"
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                            "value": "79691301"
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                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Resveratrol differentially regulates NAMPT and SIRT1 in Hepatocarcinoma cells and primary human hepatocytes."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:24603648"
                                },
                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
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                        {
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                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "The present study was designed to explore the radioprotective and antioxidant effect of resveratrol on Sirt1 expression and activity induced by radiation and to provide a new target for the development of radiation protection drugs."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
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                                {
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                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "To address this question, we investigated whether miRNAs and resveratrol regulate the SIRT1 and the functional changes of mice microglia cell lines pre-treated with or without lipopolysaccharide (LPS)."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
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                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
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                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Resveratrol-mediated SIRT1 stimuli did not induce lipogenesis and reduced the retinol-mediated fat-storing capacity in GRX."
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                                {
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                        {
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                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "The two NTD-bound resveratrol molecules are principally responsible for promoting tighter binding between SIRT1 and the peptide and the stimulation of SIRT1 activity."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
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                                },
                                {
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                        {
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                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "A dietary polyphenol resveratrol acts to provide neuroprotection in recurrent stroke models by regulating AMPK and SIRT1 signaling, thereby reducing energy requirements during ischemia."
                                },
                                {
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                                {
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                            ],
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                        {
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                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Pb exposure decreased SIRT1 and CREB phosphorylation in a dose-dependent manner in the rat hippocampus at both PNW3 and 52, and resveratrol reversed those losses."
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                                {
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                                {
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                        {
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                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "MiR-34a overexpression significantly reduced the effect of RV on restoring Sirt1 expression in ARI."
                                },
                                {
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                        {
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                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "Then, silencing Tsc2 in MIN6 or in MEF Tsc2-/- cells, the effects of SIRT1 modulation by NAM or RESV on mTORC1 signaling were abolished."
                                },
                                {
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                                },
                                {
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                                    "value": "96|100"
                                },
                                {
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                        {
                            "attribute_type_id": "biolink:has_supporting_study_result",
                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "In the present study, we used a hippocampal injection model in rats to investigate the effects of resveratrol on Abeta1-42-induced impairment of spatial learning, memory and synaptic plasticity as well as on alterations of SIRT1 expression and CREB phosphorylation."
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                        {
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                            "attributes": [
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                                    "attribute_type_id": "biolink:supporting_text",
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                        {
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                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "This new mechanism highlights the importance of the N-terminal domain in substrate recognition, explains the activity restoration role of resveratrol toward some \"loose-binding\" substrates of SIRT1, and has significant implications for the rational design of new substrate-specific SIRT1 modulators."
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                            "attributes": [
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                                    "value": "RESULTS: Overexpression of SIRT1-WT as well as Resveratrol-mediated SIRT1 activation antagonized the invasion of OC cells by suppressing EMT."
                                },
                                {
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                                {
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                        {
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                            "attributes": [
                                {
                                    "attribute_type_id": "biolink:supporting_text",
                                    "value": "The effect of exercise, resveratrol or their combination on Sarcopenia in aged rats via regulation of AMPK/Sirt1 pathway."
                                },
                                {
                                    "attribute_type_id": "biolink:publications",
                                    "value": "PMID:28847722"
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                                {
                                    "attribute_type_id": "biolink:subject_location_in_text",
                                    "value": "24|35"
                                },
                                {
                                    "attribute_type_id": "biolink:object_location_in_text",
                                    "value": "107|112"
                                }
                            ],
                            "value": "140406721"
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                        {
                            "attribute_type_id": "biolink:evidence_count",
                            "value": 80
                        }
                    ],
                    "sources": [
                        {
                            "resource_id": "infores:semmeddb",
                            "resource_role": "primary_knowledge_source"
                        },
                        {
                            "resource_id": "infores:biothings-semmeddb",
                            "resource_role": "aggregator_knowledge_source",
                            "upstream_resource_ids": [
                                "infores:semmeddb"
                            ]
                        },
                        {
                            "resource_id": "infores:service-provider-trapi",
                            "resource_role": "aggregator_knowledge_source",
                            "upstream_resource_ids": [
                                "infores:biothings-semmeddb"
                            ]
                        }
                    ]
                }

colleenXu · 2024-10-22T18:58:51Z

Noticed problems with other TRAPI edge-attributes sigh. Going to revert this issue's PR and semmeddb-text-snippet PRs, see #833 (comment)

colleenXu · 2024-10-22T19:10:34Z

Example of TRAPI edge-attribute problem:

Query

{
    "message": {
        "query_graph": {
            "nodes": {
                "n0": {
                    "ids":["CHEBI:6427"],
                    "categories":["biolink:SmallMolecule"]
                },
                "n1": {
                    "categories":["biolink:PhenotypicFeature"]
                }
            },
            "edges": {
                "e0": {
                    "subject": "n0",
                    "object": "n1"
                }
            }
        }
    }
}

If you send this query to Automat-robokop, you get this edge. It has 3 diff edge-attributes that have the SAME attribute_type_id...for sentences, tmkp_confidence_score, tmkp_ids. (yes it's weird but that's what automat does)

                "e_137": {
                    "subject": "CHEBI:6427",
                    "predicate": "biolink:treats_or_applied_or_studied_to_treat",
                    "object": "HP:0034750",
                    "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": "publications",
                            "value": [
                                "PMC:3615993",
                                "PMC:4991634"
                            ],
                            "attribute_type_id": "biolink:publications",
                            "value_type_id": "linkml:Uriorcurie"
                        },
                        {
                            "original_attribute_name": "knowledge_level",
                            "value": "not_provided",
                            "attribute_type_id": "biolink:knowledge_level",
                            "value_type_id": "EDAM:data_0006"
                        },
                        {
                            "original_attribute_name": "agent_type",
                            "value": "text_mining_agent",
                            "attribute_type_id": "biolink:agent_type",
                            "value_type_id": "EDAM:data_0006"
                        },
                        {
                            "original_attribute_name": "sentences",
                            "value": "Ahamed et al. reported a case of prostate cancer with metastatic supraclavicular lymphadenopathy, wherein the patient experienced a dramatic improvement in symptoms and a significant drop in PSA level from 586.0 ng/ml to 251.5 ng/ml within 7 months of treatment with cyproterone acetate and leuprorelin acetate.|NA|Ahamed et al reported a case of prostate cancer with metastatic supraclavicular lymphadenopathy wherein the patient experienced a dramatic improvement in symptoms and a significant reduction in PSA level from 586.0 ng/mL to 251.5 ng/mL within 7 months of treatment with cyproterone acetate and leuprorelin acetate.|NA",
                            "attribute_type_id": "biolink:Attribute",
                            "value_type_id": "EDAM:data_0006"
                        },
                        {
                            "original_attribute_name": "tmkp_confidence_score",
                            "value": 0.9986806699999999,
                            "attribute_type_id": "biolink:Attribute",
                            "value_type_id": "EDAM:data_0006"
                        },
                        {
                            "original_attribute_name": "tmkp_ids",
                            "value": [
                                "tmkp:eaecfea6f0a904fe4d0abcabdbe0059bc6d2b758ee4778f3bcb8cc75dddd3724",
                                "tmkp:1b6f3e387e2c195138e78414c740f6d5f83a9876c205a186625a78941a811247"
                            ],
                            "attribute_type_id": "biolink:Attribute",
                            "value_type_id": "EDAM:data_0006"
                        }
                    ]
                },

But the equivalent edge in BTE CI is missing the tmkp_confidence_score and tmkp_ids edge-attributes

                "0249e23e4500bc316c83dac8e9a3a2eb": {
                    "predicate": "biolink:treats_or_applied_or_studied_to_treat",
                    "subject": "CHEBI:6427",
                    "object": "HP:0034750",
                    "attributes": [
                        {
                            "original_attribute_name": "publications",
                            "value": [
                                "PMC:3615993",
                                "PMC:4991634"
                            ],
                            "attribute_type_id": "biolink:publications",
                            "value_type_id": "linkml:Uriorcurie"
                        },
                        {
                            "original_attribute_name": "knowledge_level",
                            "value": "not_provided",
                            "attribute_type_id": "biolink:knowledge_level",
                            "value_type_id": "EDAM:data_0006"
                        },
                        {
                            "original_attribute_name": "agent_type",
                            "value": "text_mining_agent",
                            "attribute_type_id": "biolink:agent_type",
                            "value_type_id": "EDAM:data_0006"
                        },
                        {
                            "original_attribute_name": "sentences",
                            "value": "Ahamed et al. reported a case of prostate cancer with metastatic supraclavicular lymphadenopathy, wherein the patient experienced a dramatic improvement in symptoms and a significant drop in PSA level from 586.0 ng/ml to 251.5 ng/ml within 7 months of treatment with cyproterone acetate and leuprorelin acetate.|NA|Ahamed et al reported a case of prostate cancer with metastatic supraclavicular lymphadenopathy wherein the patient experienced a dramatic improvement in symptoms and a significant reduction in PSA level from 586.0 ng/mL to 251.5 ng/mL within 7 months of treatment with cyproterone acetate and leuprorelin acetate.|NA",
                            "attribute_type_id": "biolink:Attribute",
                            "value_type_id": "EDAM:data_0006"
                        }
                    ],
                    "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"
                            ]
                        }
                    ]
                },

Note: Text-mined-targeted (through x-bte annotation) is fine. See same-info edge e2a8c871443a2a9609278d7daa9e6970 when sending that query to BTE-CI, vs sending it to Text-Mined-Targeted-only (http://localhost:3000/v1/smartapi/978fe380a147a8641caf72320862697b/query). All edge-attributes are kept correctly.

colleenXu · 2024-10-23T18:55:23Z

Closing this issue: addressed by reverting semmeddb text-snippet PRs. Also ended up reverting this issue's PR...

colleenXu added the bug Something isn't working label Oct 21, 2024

colleenXu assigned tokebe Oct 21, 2024

rjawesome mentioned this issue Oct 21, 2024

do not allow edge attribtues with same type id for trapi biothings/bte_trapi_query_graph_handler#222

Merged

This was referenced Oct 22, 2024

Run all creative mode templates simultaneously / fix and adjust record-counting for queries and template execution #824

Open

refactor semmeddb SmartAPI annotation to better represent text snippets #833

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Duplicated edge-attributes #891

Duplicated edge-attributes #891

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Duplicated edge-attributes #891

Duplicated edge-attributes #891

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Example query

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Investigation so far

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