Datasets:
id string | task_type string | pipeline string | difficulty string | num_hops int64 | question string | context string | reasoning_chain dict | answer string | choices list | modalities list | modality_data list | evidence list | metadata unknown | path_confidence_score float64 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
co_path_00000 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from NOTCH1 to HAP1 through known protein interactions and pathway memberships? | NOTCH1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PSEN1 -> PSEN1 GENE_ANNOTATED_WITH_GO_TERM cerebellum development -> HAP1 GENE_ANNOTATED_WITH_GO_TERM cerebellum development | {
"steps": [
{
"hop": 1,
"source_node_id": "NOTCH1",
"source_node_type": "GENE",
"source_node_label": "NOTCH1",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.998,
"edge_source_db": "STRING",
... | NOTCH1 -> PSEN1 -> cerebellum development -> HAP1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NOTCH1",
"source_db": "UniProt",
"payload": {
"accession": "P46531",
"sequence": "MPPLLAPLLCLALLPALAARGPRCSQPGETCLNGGKCEAANGTEACVCGGAFVGPRCQDPNPCLSTPCKNAGTCHVVDRRGVADYACSCALGFSGPLCLTPLDNACLTNPCRNGGTCDLLTLTEYKCRCPPG... | [
{
"source_db": "STRING",
"source_id": "PSEN1",
"text": "NOTCH1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PSEN1",
"confidence": 0.998
},
{
"source_db": "GO",
"source_id": "GO:0021549",
"text": "PSEN1 GENE_ANNOTATED_WITH_GO_TERM cerebellum development",
"confidence": 0.6
},
{
"s... | {
"gene_a": "NOTCH1",
"gene_b": "HAP1",
"path_length": 3
} | 0.710904 |
co_path_00001 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from KRAS to GBA1 through known protein interactions and pathway memberships? | KRAS PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PIK3CA -> PIK3CA GENE_ANNOTATED_WITH_GO_TERM response to dexamethasone -> GBA1 GENE_ANNOTATED_WITH_GO_TERM response to dexamethasone | {
"steps": [
{
"hop": 1,
"source_node_id": "KRAS",
"source_node_type": "GENE",
"source_node_label": "KRAS",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.998,
"edge_source_db": "STRING",
"t... | KRAS -> PIK3CA -> response to dexamethasone -> GBA1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KRAS",
"source_db": "UniProt",
"payload": {
"accession": "P01116",
"sequence": "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLA... | [
{
"source_db": "STRING",
"source_id": "PIK3CA",
"text": "KRAS PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PIK3CA",
"confidence": 0.998
},
{
"source_db": "GO",
"source_id": "GO:0071548",
"text": "PIK3CA GENE_ANNOTATED_WITH_GO_TERM response to dexamethasone",
"confidence": 0.6
},
{
... | {
"gene_a": "KRAS",
"gene_b": "GBA1",
"path_length": 3
} | 0.710904 |
co_path_00002 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from POLE to MTA3 through known protein interactions and pathway memberships? | POLE GENE_ANNOTATED_WITH_GO_TERM zinc ion binding -> MTA3 GENE_ANNOTATED_WITH_GO_TERM zinc ion binding | {
"steps": [
{
"hop": 1,
"source_node_id": "POLE",
"source_node_type": "GENE",
"source_node_label": "POLE",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:UniProtKB-KW",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_i... | POLE -> zinc ion binding -> MTA3 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "POLE",
"source_db": "UniProt",
"payload": {
"accession": "Q07864",
"sequence": "MSLRSGGRRRADPGADGEASRDDGATSSVSALKRLERSQWTDKMDLRFGFERLKEPGEKTGWLINMHPTEILDEDKRLGSAVDYYFIQDDGSRFKVALPYKPYFYIATRKGCEREVSSFLSKKFQGKIAKVETV... | [
{
"source_db": "GO",
"source_id": "GO:0008270",
"text": "POLE GENE_ANNOTATED_WITH_GO_TERM zinc ion binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "MTA3",
"text": "MTA3 GENE_ANNOTATED_WITH_GO_TERM zinc ion binding",
"confidence": 0.6
}
] | {
"gene_a": "POLE",
"gene_b": "MTA3",
"path_length": 2
} | 0.6 |
co_path_00003 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from RAD51D to POLD1 through known protein interactions and pathway memberships? | RAD51D GENE_PARTICIPATES_IN_PATHWAY HDR through Homologous Recombination (HRR) -> POLD1 GENE_PARTICIPATES_IN_PATHWAY HDR through Homologous Recombination (HRR) | {
"steps": [
{
"hop": 1,
"source_node_id": "RAD51D",
"source_node_type": "GENE",
"source_node_label": "RAD51D",
"edge_relation": "GENE_PARTICIPATES_IN_PATHWAY",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "Reactome",
"target_node_i... | RAD51D -> HDR through Homologous Recombination (HRR) -> POLD1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "RAD51D",
"source_db": "UniProt",
"payload": {
"accession": "O75771",
"sequence": "MGVLRVGLCPGLTEEMIQLLRSHRIKTVVDLVSADLEEVAQKCGLSYKALVALRRVLLAQFSAFPVNGADLYEELKTSTAILSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCMAANVAHGLQQNV... | [
{
"source_db": "Reactome",
"source_id": "R-HSA-5685942",
"text": "RAD51D GENE_PARTICIPATES_IN_PATHWAY HDR through Homologous Recombination (HRR)",
"confidence": 1
},
{
"source_db": "Reactome",
"source_id": "POLD1",
"text": "POLD1 GENE_PARTICIPATES_IN_PATHWAY HDR through Homologous Re... | {
"gene_a": "RAD51D",
"gene_b": "POLD1",
"path_length": 2
} | 1 |
co_path_00004 | path_traversal | coding_variant | hard | 4 | What is the shortest molecular path from ATP6V1C1 to ADRA2A through known protein interactions and pathway memberships? | ATP6V1C1 GENE_ANNOTATED_WITH_GO_TERM regulation of macroautophagy -> ATP13A2 GENE_ANNOTATED_WITH_GO_TERM regulation of macroautophagy -> ATP13A2 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SLC6A3 -> ADRA2A PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SLC6A3 | {
"steps": [
{
"hop": 1,
"source_node_id": "ATP6V1C1",
"source_node_type": "GENE",
"source_node_label": "ATP6V1C1",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "NAS:ParkinsonsUK-UCL",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"t... | ATP6V1C1 -> regulation of macroautophagy -> ATP13A2 -> SLC6A3 -> ADRA2A | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATP6V1C1",
"source_db": "UniProt",
"payload": {
"accession": "P21283",
"sequence": "MTEFWLISAPGEKTCQQTWEKLHAATSKNNNLAVTSKFNIPDLKVGTLDVLVGLSDELAKLDAFVEGVVKKVAQYMADVLEDSKDKVQENLLANGVDLVTYITRFQWDMAKYPIKQSLKNISEIIAKGVT... | [
{
"source_db": "GO",
"source_id": "GO:0016241",
"text": "ATP6V1C1 GENE_ANNOTATED_WITH_GO_TERM regulation of macroautophagy",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "ATP13A2",
"text": "ATP13A2 GENE_ANNOTATED_WITH_GO_TERM regulation of macroautophagy",
"confidence":... | {
"gene_a": "ATP6V1C1",
"gene_b": "ADRA2A",
"path_length": 4
} | 0.703119 |
co_path_00005 | path_traversal | coding_variant | medium | 4 | What is the shortest molecular path from MLH1 to CD68 through known protein interactions and pathway memberships? | MLH1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BLM -> BLM GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity -> CD4 GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity -> CD68 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH CD4 | {
"steps": [
{
"hop": 1,
"source_node_id": "MLH1",
"source_node_type": "GENE",
"source_node_label": "MLH1",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
"t... | MLH1 -> BLM -> protein homodimerization activity -> CD4 -> CD68 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MLH1",
"source_db": "UniProt",
"payload": {
"accession": "P40692",
"sequence": "MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGK... | [
{
"source_db": "STRING",
"source_id": "BLM",
"text": "MLH1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BLM",
"confidence": 0.999
},
{
"source_db": "GO",
"source_id": "GO:0042803",
"text": "BLM GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity",
"confidence": 0.6
},
{
... | {
"gene_a": "MLH1",
"gene_b": "CD68",
"path_length": 4
} | 0.753852 |
co_path_00006 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from MAPT to EGFR through known protein interactions and pathway memberships? | MAPT GENE_ANNOTATED_WITH_GO_TERM double-stranded DNA binding -> EGFR GENE_ANNOTATED_WITH_GO_TERM double-stranded DNA binding | {
"steps": [
{
"hop": 1,
"source_node_id": "MAPT",
"source_node_type": "GENE",
"source_node_label": "MAPT",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "TAS:ARUK-UCL",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": ... | MAPT -> double-stranded DNA binding -> EGFR | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MAPT",
"source_db": "UniProt",
"payload": {
"accession": "P10636",
"sequence": "MAEPRQEFEVMEDHAGTYGLGDRKDQGGYTMHQDQEGDTDAGLKESPLQTPTEDGSEEPGSETSDAKSTPTAEDVTAPLVDEGAPGKQAAAQPHTEIPEGTTAEEAGIGDTPSLEDEAAGHVTQEPESGKVVQE... | [
{
"source_db": "GO",
"source_id": "GO:0003690",
"text": "MAPT GENE_ANNOTATED_WITH_GO_TERM double-stranded DNA binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "EGFR",
"text": "EGFR GENE_ANNOTATED_WITH_GO_TERM double-stranded DNA binding",
"confidence": 0.6
}
] | {
"gene_a": "MAPT",
"gene_b": "EGFR",
"path_length": 2
} | 0.6 |
co_path_00007 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from BIN1 to BRAF through known protein interactions and pathway memberships? | BIN1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH MYC -> MYC GENE_ANNOTATED_WITH_GO_TERM MAPK cascade -> BRAF GENE_ANNOTATED_WITH_GO_TERM MAPK cascade | {
"steps": [
{
"hop": 1,
"source_node_id": "BIN1",
"source_node_type": "GENE",
"source_node_label": "BIN1",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
"t... | BIN1 -> MYC -> MAPK cascade -> BRAF | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BIN1",
"source_db": "UniProt",
"payload": {
"accession": "O00499",
"sequence": "MAEMGSKGVTAGKIASNVQKKLTRAQEKVLQKLGKADETKDEQFEQCVQNFNKQLTEGTRLQKDLRTYLASVKAMHEASKKLNECLQEVYEPDWPGRDEANKIAENNDLLWMDYHQKLVDQALLTMDTYLGQFP... | [
{
"source_db": "STRING",
"source_id": "MYC",
"text": "BIN1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH MYC",
"confidence": 0.999
},
{
"source_db": "GO",
"source_id": "GO:0000165",
"text": "MYC GENE_ANNOTATED_WITH_GO_TERM MAPK cascade",
"confidence": 0.6
},
{
"source_db": "GO",
... | {
"gene_a": "BIN1",
"gene_b": "BRAF",
"path_length": 3
} | 0.711141 |
co_path_00008 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from ADRA2A to FOXA1 through known protein interactions and pathway memberships? | ADRA2A GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell population proliferation -> AR GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell population proliferation -> AR PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH FOXA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "ADRA2A",
"source_node_type": "GENE",
"source_node_label": "ADRA2A",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "TAS:ProtInc",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id... | ADRA2A -> positive regulation of cell population proliferation -> AR -> FOXA1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ADRA2A",
"source_db": "UniProt",
"payload": {
"accession": "P08913",
"sequence": "MFRQEQPLAEGSFAPMGSLQPDAGNASWNGTEAPGGGARATPYSLQVTLTLVCLAGLLMLLTVFGNVLVIIAVFTSRALKAPQNLFLVSLASADILVATLVIPFSLANEVMGYWYFGKAWCEIYLALDVLFC... | [
{
"source_db": "GO",
"source_id": "GO:0008284",
"text": "ADRA2A GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell population proliferation",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "AR",
"text": "AR GENE_ANNOTATED_WITH_GO_TERM positive regulation of cell populati... | {
"gene_a": "ADRA2A",
"gene_b": "FOXA1",
"path_length": 3
} | 0.710429 |
co_path_00009 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from PARK7 to MTA3 through known protein interactions and pathway memberships? | PARK7 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PRKN -> PRKN GENE_ANNOTATED_WITH_GO_TERM histone deacetylase binding -> MTA3 GENE_ANNOTATED_WITH_GO_TERM histone deacetylase binding | {
"steps": [
{
"hop": 1,
"source_node_id": "PARK7",
"source_node_type": "GENE",
"source_node_label": "PARK7",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.999,
"edge_source_db": "STRING",
... | PARK7 -> PRKN -> histone deacetylase binding -> MTA3 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PARK7",
"source_db": "UniProt",
"payload": {
"accession": "Q99497",
"sequence": "MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAKKEGPYDVVVLPGGNLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGFGSKVTTHPLAKDKM... | [
{
"source_db": "STRING",
"source_id": "PRKN",
"text": "PARK7 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PRKN",
"confidence": 0.999
},
{
"source_db": "GO",
"source_id": "GO:0042826",
"text": "PRKN GENE_ANNOTATED_WITH_GO_TERM histone deacetylase binding",
"confidence": 0.6
},
{
"... | {
"gene_a": "PARK7",
"gene_b": "MTA3",
"path_length": 3
} | 0.711141 |
co_path_00010 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from BRAF to ATP6V1B2 through known protein interactions and pathway memberships? | BRAF GENE_ANNOTATED_WITH_GO_TERM ATP binding -> ATP6V1B2 GENE_ANNOTATED_WITH_GO_TERM ATP binding | {
"steps": [
{
"hop": 1,
"source_node_id": "BRAF",
"source_node_type": "GENE",
"source_node_label": "BRAF",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:UniProtKB-KW",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_i... | BRAF -> ATP binding -> ATP6V1B2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRAF",
"source_db": "UniProt",
"payload": {
"accession": "P15056",
"sequence": "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEHIEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTVTSSSSSSLSVLPSS... | [
{
"source_db": "GO",
"source_id": "GO:0005524",
"text": "BRAF GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "ATP6V1B2",
"text": "ATP6V1B2 GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
}
] | {
"gene_a": "BRAF",
"gene_b": "ATP6V1B2",
"path_length": 2
} | 0.6 |
co_path_00011 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from ACTB to CDK12 through known protein interactions and pathway memberships? | ACTB GENE_ANNOTATED_WITH_GO_TERM ATP binding -> CDK12 GENE_ANNOTATED_WITH_GO_TERM ATP binding | {
"steps": [
{
"hop": 1,
"source_node_id": "ACTB",
"source_node_type": "GENE",
"source_node_label": "ACTB",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IEA:UniProtKB-KW",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_i... | ACTB -> ATP binding -> CDK12 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACTB",
"source_db": "UniProt",
"payload": {
"accession": "P60709",
"sequence": "MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYV... | [
{
"source_db": "GO",
"source_id": "GO:0005524",
"text": "ACTB GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "CDK12",
"text": "CDK12 GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
}
] | {
"gene_a": "ACTB",
"gene_b": "CDK12",
"path_length": 2
} | 0.6 |
co_path_00012 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from MAPT to ACVR1B through known protein interactions and pathway memberships? | MAPT PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TUBA4A -> TUBA4A GENE_ANNOTATED_WITH_GO_TERM metal ion binding -> ACVR1B GENE_ANNOTATED_WITH_GO_TERM metal ion binding | {
"steps": [
{
"hop": 1,
"source_node_id": "MAPT",
"source_node_type": "GENE",
"source_node_label": "MAPT",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.981,
"edge_source_db": "STRING",
"t... | MAPT -> TUBA4A -> metal ion binding -> ACVR1B | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MAPT",
"source_db": "UniProt",
"payload": {
"accession": "P10636",
"sequence": "MAEPRQEFEVMEDHAGTYGLGDRKDQGGYTMHQDQEGDTDAGLKESPLQTPTEDGSEEPGSETSDAKSTPTAEDVTAPLVDEGAPGKQAAAQPHTEIPEGTTAEEAGIGDTPSLEDEAAGHVTQEPESGKVVQE... | [
{
"source_db": "STRING",
"source_id": "TUBA4A",
"text": "MAPT PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH TUBA4A",
"confidence": 0.981
},
{
"source_db": "GO",
"source_id": "GO:0046872",
"text": "TUBA4A GENE_ANNOTATED_WITH_GO_TERM metal ion binding",
"confidence": 0.6
},
{
"sourc... | {
"gene_a": "MAPT",
"gene_b": "ACVR1B",
"path_length": 3
} | 0.706844 |
co_path_00013 | path_traversal | coding_variant | easy | 2 | What is the shortest molecular path from TP53 to BCHE through known protein interactions and pathway memberships? | TP53 GENE_ANNOTATED_WITH_GO_TERM negative regulation of cell population proliferation -> BCHE GENE_ANNOTATED_WITH_GO_TERM negative regulation of cell population proliferation | {
"steps": [
{
"hop": 1,
"source_node_id": "TP53",
"source_node_type": "GENE",
"source_node_label": "TP53",
"edge_relation": "GENE_ANNOTATED_WITH_GO_TERM",
"edge_evidence_type": "IDA:CACAO",
"edge_confidence": 0.6,
"edge_source_db": "GO",
"target_node_id": "GO... | TP53 -> negative regulation of cell population proliferation -> BCHE | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TP53",
"source_db": "UniProt",
"payload": {
"accession": "P04637",
"sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMF... | [
{
"source_db": "GO",
"source_id": "GO:0008285",
"text": "TP53 GENE_ANNOTATED_WITH_GO_TERM negative regulation of cell population proliferation",
"confidence": 0.6
},
{
"source_db": "GO",
"source_id": "BCHE",
"text": "BCHE GENE_ANNOTATED_WITH_GO_TERM negative regulation of cell popula... | {
"gene_a": "TP53",
"gene_b": "BCHE",
"path_length": 2
} | 0.6 |
co_path_00014 | path_traversal | coding_variant | easy | 3 | What is the shortest molecular path from ACHE to NOTCH1 through known protein interactions and pathway memberships? | ACHE PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH APP -> APP PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PSEN1 -> PSEN1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH NOTCH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "ACHE",
"source_node_type": "GENE",
"source_node_label": "ACHE",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.937,
"edge_source_db": "STRING",
"t... | ACHE -> APP -> PSEN1 -> NOTCH1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACHE",
"source_db": "UniProt",
"payload": {
"accession": "P22303",
"sequence": "MRPPQCLLHTPSLASPLLLLLLWLLGGGVGAEGREDAELLVTVRGGRLRGIRLKTPGGPVSAFLGIPFAEPPMGPRRFLPPEPKQPWSGVVDATTFQSVCYQYVDTLYPGFEGTEMWNPNRELSEDCLYLNVWT... | [
{
"source_db": "STRING",
"source_id": "APP",
"text": "ACHE PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH APP",
"confidence": 0.937
},
{
"source_db": "STRING",
"source_id": "PSEN1",
"text": "APP PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH PSEN1",
"confidence": 0.999
},
{
"source_db": "STR... | {
"gene_a": "ACHE",
"gene_b": "NOTCH1",
"path_length": 3
} | 0.977564 |
co_path_00015 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from PTEN to ATP6V1B2 through known protein interactions and pathway memberships? | PTEN PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AKT1 -> AKT1 GENE_ANNOTATED_WITH_GO_TERM ATP binding -> ATP6V1B2 GENE_ANNOTATED_WITH_GO_TERM ATP binding | {
"steps": [
{
"hop": 1,
"source_node_id": "PTEN",
"source_node_type": "GENE",
"source_node_label": "PTEN",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.988,
"edge_source_db": "STRING",
"t... | PTEN -> AKT1 -> ATP binding -> ATP6V1B2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PTEN",
"source_db": "UniProt",
"payload": {
"accession": "P60484",
"sequence": "MTAIIKEIVSRNKRRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLCAERHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVM... | [
{
"source_db": "STRING",
"source_id": "AKT1",
"text": "PTEN PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH AKT1",
"confidence": 0.988
},
{
"source_db": "GO",
"source_id": "GO:0005524",
"text": "AKT1 GENE_ANNOTATED_WITH_GO_TERM ATP binding",
"confidence": 0.6
},
{
"source_db": "GO",... | {
"gene_a": "PTEN",
"gene_b": "ATP6V1B2",
"path_length": 3
} | 0.708522 |
co_path_00016 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from ATXN2 to BIRC5 through known protein interactions and pathway memberships? | TIA1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ATXN2 -> TIA1 GENE_ANNOTATED_WITH_GO_TERM apoptotic process -> BIRC5 GENE_ANNOTATED_WITH_GO_TERM apoptotic process | {
"steps": [
{
"hop": 1,
"source_node_id": "ATXN2",
"source_node_type": "GENE",
"source_node_label": "ATXN2",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.895,
"edge_source_db": "STRING",
... | ATXN2 -> TIA1 -> apoptotic process -> BIRC5 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATXN2",
"source_db": "UniProt",
"payload": {
"accession": "Q99700",
"sequence": "MRSAAAAPRSPAVATESRRFAAARWPGWRSLQRPARRSGRGGGGAAPGPYPSAAPPPPGPGPPPSRQSSPPSASDCFGSNGNGGGAFRPGSRRLLGLGGPPRPFVVLLLPLASPGAPPAAPTRASPLGARASP... | [
{
"source_db": "STRING",
"source_id": "TIA1",
"text": "TIA1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH ATXN2",
"confidence": 0.895
},
{
"source_db": "GO",
"source_id": "GO:0006915",
"text": "TIA1 GENE_ANNOTATED_WITH_GO_TERM apoptotic process",
"confidence": 0.6
},
{
"source_db"... | {
"gene_a": "ATXN2",
"gene_b": "BIRC5",
"path_length": 3
} | 0.685554 |
co_path_00017 | path_traversal | coding_variant | medium | 4 | What is the shortest molecular path from MTA3 to BST1 through known protein interactions and pathway memberships? | MTA3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH RBBP4 -> RBBP4 PROTEIN_MEMBER_OF_COMPLEX ASF1A / ASF1B / BRCA1 / CDKN3... -> SIRT6 PROTEIN_MEMBER_OF_COMPLEX ASF1A / ASF1B / BRCA1 / CDKN3... -> BST1 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH SIRT6 | {
"steps": [
{
"hop": 1,
"source_node_id": "MTA3",
"source_node_type": "GENE",
"source_node_label": "MTA3",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.998,
"edge_source_db": "STRING",
"t... | MTA3 -> RBBP4 -> ASF1A / ASF1B / BRCA1 / CDKN3... -> SIRT6 -> BST1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MTA3",
"source_db": "UniProt",
"payload": {
"accession": "Q9BTC8",
"sequence": "MAANMYRVGDYVYFENSSSNPYLIRRIEELNKTASGNVEAKVVCFYRRRDISNTLIMLADKHAKEIEEESETTVEADLTDKQKHQLKHRELFLSRQYESLPATHIRGKCSVALLNETESVLSYLDKEDTFFYSL... | [
{
"source_db": "STRING",
"source_id": "RBBP4",
"text": "MTA3 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH RBBP4",
"confidence": 0.998
},
{
"source_db": "OmniPath",
"source_id": "Compleat:HC6117",
"text": "RBBP4 PROTEIN_MEMBER_OF_COMPLEX ASF1A / ASF1B / BRCA1 / CDKN3...",
"confidence": 1
... | {
"gene_a": "MTA3",
"gene_b": "BST1",
"path_length": 4
} | 0.981001 |
co_path_00018 | path_traversal | coding_variant | medium | 3 | What is the shortest molecular path from BUB1B to APOE through known protein interactions and pathway memberships? | BIRC5 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BUB1B -> BIRC5 GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity -> APOE GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity | {
"steps": [
{
"hop": 1,
"source_node_id": "BUB1B",
"source_node_type": "GENE",
"source_node_label": "BUB1B",
"edge_relation": "PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH",
"edge_evidence_type": "multi-channel",
"edge_confidence": 0.987,
"edge_source_db": "STRING",
... | BUB1B -> BIRC5 -> protein homodimerization activity -> APOE | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BUB1B",
"source_db": "UniProt",
"payload": {
"accession": "O60566",
"sequence": "MAAVKKEGGALSEAMSLEGDEWELSKENVQPLRQGRIMSTLQGALAQESACNNTLQQQKRAFEYEIRFYTGNDPLDVWDRYISWTEQNYPQGGKESNMSTLLERAVEALQGEKRYYSDPRFLNLWLKLGRLCN... | [
{
"source_db": "STRING",
"source_id": "BIRC5",
"text": "BIRC5 PROTEIN_FUNCTIONALLY_ASSOCIATED_WITH BUB1B",
"confidence": 0.987
},
{
"source_db": "GO",
"source_id": "GO:0042803",
"text": "BIRC5 GENE_ANNOTATED_WITH_GO_TERM protein homodimerization activity",
"confidence": 0.6
},
... | {
"gene_a": "BUB1B",
"gene_b": "APOE",
"path_length": 3
} | 0.708283 |
End of preview. Expand in Data Studio
GenBench CoCG QA Dataset
Multi-hop genetic reasoning QA items generated from GenBench's knowledge graph (Ensembl, ClinVar, VEP, BioGRID, STRING, Reactome, UniProt, GO, SIGNOR, OmniPath, KEGG, DisGeNET, OpenTargets, PubTator3, GTEx, and more), built for CoCG (Co-Evolving Confidence Graph) agent training.
2513 items across 11 task types.
Task types
| task_type | count |
|---|---|
coding_variant |
53 |
conservation_reasoning |
246 |
counterfactual |
246 |
disease_reasoning |
246 |
evidence_attribution |
246 |
hallucination_detection |
246 |
interaction_propagation |
246 |
mechanistic_explanation |
246 |
path_traversal |
246 |
structural_effect |
246 |
tissue_specific |
246 |
Schema
Each item has:
id,task_type,pipeline(coding_variant/noncoding_regulatory),difficultyquestion,answer,choices(MCQ options, when applicable)context-- either a templated chain narration, or (ifllm_rewritewas applied) an LLM-rewritten fluent Step/Evidence/Interpretation/Conclusion narrativereasoning_chain-- the grounded, machine-checkable multi-hop path (steps: each withsource_node_id/target_node_id/edge_relation/edge_confidence/edge_source_db), never touched by any LLM stepmodality_data-- raw modality payloads (sequence, structural, transcriptomic, post_translational, signaling_role, etc.) attached to the chain's anchor nodesevidence-- supporting evidence entries with source database/PMIDpath_confidence_score-- continuous, confidence-derived difficulty score
Companion graph
graph.json (if included in this repo) is the exact knowledge graph these
items' reasoning_chain node IDs refer to -- load it with
GenBench's GraphBuilder.load() to
resolve full node/edge attributes beyond what's inlined in each item.
Source
Generated from data\curated\qa_dataset.jsonl in GenBench,
the substrate for CoCG (Co-Evolving Confidence Graph) agent training --
per-edge, per-modality KG confidence that co-adapts with an RL policy
during training rather than treating the KG as a frozen oracle.
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