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biothings / biothings_explorer

TRAPI service for BioThings Explorer
https://explorer.biothings.io
Apache License 2.0
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Duplicated edge-attributes #891

Closed colleenXu closed 1 month ago

colleenXu commented 1 month ago

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

colleenXu commented 1 month ago

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 commented 1 month ago

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 commented 1 month ago

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:

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 commented 1 month ago

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 https://github.com/biothings/bte_trapi_query_graph_handler/pull/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 commented 1 month ago

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

colleenXu commented 1 month ago

I've confirmed Rohan's suspicion that this bug came from https://github.com/biothings/bte_trapi_query_graph_handler/pull/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 commented 1 month ago

@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 https://github.com/biothings/bte_trapi_query_graph_handler/pull/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" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "126|129" } ], "value": "74783045" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "In contrast, Akt and GSK-3beta were little influenced by resveratrol." }, { "attribute_type_id": "biolink:publications", "value": "PMID:26054749" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "57|68" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "13|16" } ], "value": "169010331" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "This resveratrol analog activated the nuclear factor erythroid-2-related factor 2 (Nrf2) pathway through stimulating phosphorylation of Akt and inducing keap1 modification, thereby resulting in its nuclear translocation and subsequent transcriptional induction of phase II detoxifying enzymes." }, { "attribute_type_id": "biolink:publications", "value": "PMID:26314862" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "5|16" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "136|139" } ], "value": "162514069" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "Overall, we conclude that the antifibrotic effect of resveratrol is the result of blocking NF-kappaB activation and PI3K/Akt phosphorylation, which inhibits HSC activation to obstruct liver fibrosis." }, { "attribute_type_id": "biolink:publications", "value": "PMID:26613251" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "53|64" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "121|124" } ], "value": "138951064" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "Resveratrol Ameliorates Clonidine-Induced Endothelium-Dependent Relaxation Involving Akt and Endothelial Nitric Oxide Synthase Regulation in Type 2 Diabetic Mice." }, { "attribute_type_id": "biolink:publications", "value": "PMID:26632178" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "0|11" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "85|88" } ], "value": "135733593" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "MAIN METHODS: Phosphorylation of AMPK and Akt was assessed after C2C12 myotubes were exposed to chloroquine or resveratrol." }, { "attribute_type_id": "biolink:publications", "value": "PMID:27047993" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "111|122" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "42|45" } ], "value": "163123716" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "The ability of resveratrol to modulate AKT and p53, as well as reportedly many other antitumorigenic pathways, is attractive for therapy against a genetically heterogeneous tumor such as GBM." }, { "attribute_type_id": "biolink:publications", "value": "PMID:27419830" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "15|26" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "39|42" } ], "value": "136114582" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "RSV or MET alone did not have beneficial effects on glucose tolerance, although MET significantly improved insulin tolerance compared to HFD Glucose and insulin tolerance were significantly improved in COM compared to HFD and this was mirrored by enhanced insulin-stimulated AKT phosphorylation in triceps muscle and inguinal subcutaneous adipose tissue in COM compared to HFD mice." }, { "attribute_type_id": "biolink:publications", "value": "PMID:27482073" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "0|3" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "275|278" } ], "value": "143691545" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "Therefore, the effect of resveratrol on PKB/Akt signaling was tested in H295R cells and was found to be decreased under starvation growth conditions, but not under normal growth conditions." }, { "attribute_type_id": "biolink:publications", "value": "PMID:28323907" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "25|36" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "44|47" } ], "value": "141808250" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "In contrast, RSV was predicted to act primarily through modulation of the PI3K/AKT pathway." }, { "attribute_type_id": "biolink:publications", "value": "PMID:29432917" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "13|16" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "79|82" } ], "value": "164858917" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "Moreover, Res significantly induced higher HO-1 mRNA expression, upregulated HO-1 and Nrf-2 protein expression, and the phosphorylation of Akt in the lung tissue." }, { "attribute_type_id": "biolink:publications", "value": "PMID:29844304" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "10|13" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "139|142" } ], "value": "144722787" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "Conversely, trophic factors and protective signaling pathways, including sirtuin 1 (SIRT1), nuclear factor erythroid 2-related factor 2 (Nrf2), heme oxygenase-1 (HO-1), and phosphoinositide 3-kinase (PI3K)/Akt were positively modulated by resveratrol in both LPS-stimulated and unstimulated astrocytes, but adenosine receptor antagonism did not abrogate all effects of resveratrol." }, { "attribute_type_id": "biolink:publications", "value": "PMID:30611861" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "239|250" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "206|209" } ], "value": "178837123" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "Preliminary results indicate resveratrol affects proliferation and apoptosis of leukemia cells by regulating PTEN/PI3K/AKT pathway." }, { "attribute_type_id": "biolink:publications", "value": "PMID:31173300" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "29|40" }, { "attribute_type_id": 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effect of resveratrol." }, { "attribute_type_id": "biolink:publications", "value": "PMID:32581510" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "56|67" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "82|85" } ], "value": "187208190" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "[Retracted] Antitumor effect of resveratrol on chondrosarcoma cells via phosphoinositide 3-kinase/AKT and p38 mitogen-activated protein kinase pathways." }, { "attribute_type_id": "biolink:publications", "value": "PMID:34165165" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "32|43" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "98|101" } ], "value": "194561485" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "'Corrigendum to \"Resveratrol inhibits proliferation, migration and invasion via Akt and ERK1/2 signaling pathways in renal carcinoma cells\" [Biomed. Pharmacother. 98 (2018) 36-44]'." }, { "attribute_type_id": "biolink:publications", "value": "PMID:35760645" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "17|28" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "80|83" } ], "value": "201641761" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "Our results suggests that the effect of RSV is non-insulin dependent and triggers some of the similar intracellular insulin signalling components in myocardium such as eNOS, Akt through AMPK pathway and also by regulating the caveolin-1 and caveolin-3 status that might play an essential role in Glut-4 translocation and glucose uptake in STZ- induced type-1 diabetic myocardium." }, { "attribute_type_id": "biolink:publications", "value": "PMID:18266981" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "174|177" }, { "attribute_type_id": 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AMPK, AKT and survivin, suggesting its potential therapeutic application in the treatment or prevention of obesity and related metabolic symptoms." }, { "attribute_type_id": "biolink:publications", "value": "PMID:22137261" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "134|137" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "48|59" } ], "value": "128993252" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "It has been known that resveratrol is a sirtuin 1 (SIRT1) activator and protective effects of resveratrol are mediated by Akt and mitogen-activated protein kinases." }, { "attribute_type_id": "biolink:publications", "value": "PMID:22878646" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "122|125" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "23|34" } ], "value": "134109187" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "In this study, the effect of resveratrol on mitochondrial dysfunction, PI3K-Akt signaling and inositol polyphosphate 4 phosphatase was studied in murine model of allergic airway inflammation." }, { "attribute_type_id": "biolink:publications", "value": "PMID:22986054" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "76|79" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "29|40" } ], "value": "128971632" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "Similar anti-tumor effects of resveratrol were observed in DU145 and LNCaP prostate cancer cells which were associated with suppression of Akt and PDCD4, but independent of miR-21." }, { "attribute_type_id": "biolink:publications", "value": "PMID:23272133" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "139|142" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "30|41" } ], "value": "72237606" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "An early resveratrol effect was the inhibition of AKT and mitogen-activated protein kinase signaling, accompanied by down regulation of cyclin D1 expression, abrogation of retinoblastoma protein hyperphosphorylation, and subsequent inhibition of cell cycle reentry and clonal expansion, as indicated by cyclin A2 repression." }, { "attribute_type_id": "biolink:publications", "value": "PMID:23525482" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "50|53" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "9|20" } ], "value": "79144098" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "Thus, our findings strongly suggest that the anti-proliferative effects of Res in human colon cancer cells may be mediated by regulating separately the PTEN/PI3K/Akt and Wnt/beta-catenin signaling." }, { "attribute_type_id": "biolink:publications", "value": "PMID:24756222" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "162|165" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "75|78" } ], "value": "73215641" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "To obtain information on interplay between resveratrol and AKT, resveratrol affinity chromatography was performed." }, { "attribute_type_id": "biolink:publications", "value": "PMID:24968355" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "59|62" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "43|54" } ], "value": "161639912" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "The resveratrol effect on AMPAR protein expression is independent of sirtuin 1 (SIRT1), the conventional downstream target of resveratrol, but rather is mediated by AMP-activated protein kinase (AMPK) and subsequent downstream phosphoinositide 3-kinase (PI3K)/Akt signaling." }, { "attribute_type_id": "biolink:publications", "value": "PMID:25791529" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "260|263" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "4|15" } ], "value": "138366438" }, { "attribute_type_id": "biolink:has_supporting_study_result", "attributes": [ { "attribute_type_id": "biolink:supporting_text", "value": "The RSV-mediated inhibition of Akt in the presence of 2-DG was not prevented by the selective inhibition of SIRT1, a known target of RSV, indicating that the effects of RSV on this pathway are independent of SIRT1." }, { "attribute_type_id": "biolink:publications", "value": "PMID:26891914" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "31|34" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "4|7" } ], "value": "143557025" }, { "attribute_type_id": "biolink:has_supporting_study_result", "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." }, { 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}, { "attribute_type_id": "biolink:subject_location_in_text", "value": "47|58" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "27|32" } ], "value": "172009844" }, { "attribute_type_id": "biolink:has_supporting_study_result", "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" }, { "attribute_type_id": "biolink:subject_location_in_text", "value": "24|35" }, { "attribute_type_id": "biolink:object_location_in_text", "value": "107|112" } ], "value": "140406721" }, { "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 commented 1 month ago

Noticed problems with other TRAPI edge-attributes sigh. Going to revert this issue's PR and semmeddb-text-snippet PRs, see https://github.com/biothings/biothings_explorer/issues/833#issuecomment-2430017074

colleenXu commented 1 month ago

Messy notes:

colleenXu commented 1 month ago

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 commented 1 month ago

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