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Datasets:
AmelieSchreiber
/
toricblm_fot

Tasks:
Text Generation
Graph Machine Learning
Feature Extraction
Languages:
English
License:
Dataset card Data Studio Files
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record_id
string
dataset
string
task_family
string
uniprot_accession
string
entry_name
string
protein_name
string
sequence
string
function
string
text
string
graph_json
string
forest_json
string
metadata_json
string
structure_coordinates
list
ca_coordinates
list
backbone_coordinates
list
coordinate_mask
list
plddt
list
residue_names
list
residue_indices
list
chain_ids
list
structure_source
string
structure_file
string
structure_file_cached
bool
structure_cif_url
string
foldseek_3di_sequence
string
foldseek_3di_available
bool
foldseek_3di_status
string
mean_plddt
float64
residue_count
int64
coordinate_residue_count
int64
source_residue_count
int64
coordinate_truncated
bool
split_cluster
string
split
string
afdb_structure_fot_E9Q8I9_4a8967ed3df7add7
toricblm_afdb_structure_fot
structure_function_fot_coordinate_training
E9Q8I9
FRY_MOUSE
Protein furry homolog
"MASQQDSGFFEISIKYLLKSWSNASPVGNGYIKPPVPPASGTHREKGPPAMLPINVDPDSKPGEYVLKSLFVNFTTQAERKIRIIMAEPLEKPLTKSLQ(...TRUNCATED)
"Plays a crucial role in the structural integrity of mitotic centrosomes and in the maintenance of s(...TRUNCATED)
"UniProt E9Q8I9 structure-function record. Protein: Protein furry homolog. Function: Plays a crucial(...TRUNCATED)
"{\"edges\": [{\"id\": \"protein_has_sequence\", \"source\": \"protein\", \"target\": \"sequence\", (...TRUNCATED)
"{\"edges\": [{\"source\": \"root\", \"target\": \"geometry\", \"type\": \"branch\"}, {\"source\": \(...TRUNCATED)
"{\"bcif_url\": \"https://alphafold.ebi.ac.uk/files/AF-E9Q8I9-3-F1-model_v6.bcif\", \"cif_url\": \"h(...TRUNCATED)
[[-10.564000129699707,-30.22599983215332,-30.966999053955078],[-9.005999565124512,-26.97999954223632(...TRUNCATED)
[[-10.564000129699707,-30.22599983215332,-30.966999053955078],[-9.005999565124512,-26.97999954223632(...TRUNCATED)
[[[-9.798999786376953,-30.958999633789062,-29.93899917602539],[-10.564000129699707,-30.2259998321533(...TRUNCATED)
[true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true(...TRUNCATED)
[32.78,30.91,31.19,32.69,32.91,33.75,35.59,33.41,41.41,39.62,46.88,47.94,51.0,48.09,45.19,54.72,40.4(...TRUNCATED)
["MET","GLU","ILE","THR","THR","ALA","CYS","TRP","ARG","ARG","SER","CYS","VAL","ILE","SER","LEU","IL(...TRUNCATED)
[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,(...TRUNCATED)
["A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A"(...TRUNCATED)
AFDB
false
https://alphafold.ebi.ac.uk/files/AF-E9Q8I9-3-F1-model_v6.cif
"ddppddpddpvvvvvvvvvvdddddddddddddddddddddddddddddqpdqpppddplvsvvvvlvsvlvvvlvvllvvqlvddlldacccrffppn(...TRUNCATED)
true
foldseek_3di_extracted
85.346719
512
512
814
true
4a8967ed3df7
train
afdb_structure_fot_E9Q8Q8_15b5d79978d89e2d
toricblm_afdb_structure_fot
structure_function_fot_coordinate_training
E9Q8Q8
SACA6_MOUSE
Sperm acrosome membrane-associated protein 6
"MTSQRSLSSPQTRRPSVMGLISLVGSIVLLFLLIFRASTWACLFCFTTYEERLRVCQLFVGREETKINLCRNELEGAFEDLKDMKINYDERSYLHDEFT(...TRUNCATED)
Sperm protein required for fusion of sperm with the egg membrane during fertilization.
"UniProt E9Q8Q8 structure-function record. Protein: Sperm acrosome membrane-associated protein 6. Fu(...TRUNCATED)
"{\"edges\": [{\"id\": \"protein_has_sequence\", \"source\": \"protein\", \"target\": \"sequence\", (...TRUNCATED)
"{\"edges\": [{\"source\": \"root\", \"target\": \"geometry\", \"type\": \"branch\"}, {\"source\": \(...TRUNCATED)
"{\"bcif_url\": \"\", \"cif_url\": \"https://alphafold.ebi.ac.uk/files/AF-E9Q8Q8-F1-model_v6.cif\", (...TRUNCATED)
[[-38.5099983215332,-20.98200035095215,-81.90399932861328],[-38.356998443603516,-19.516000747680664,(...TRUNCATED)
[[-38.5099983215332,-20.98200035095215,-81.90399932861328],[-38.356998443603516,-19.516000747680664,(...TRUNCATED)
[[[-39.40999984741211,-20.358999252319336,-82.89700317382812],[-38.5099983215332,-20.98200035095215,(...TRUNCATED)
[true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true(...TRUNCATED)
[45.94,43.59,51.91,47.72,50.5,50.59,47.84,45.78,43.66,46.84,46.41,43.66,49.69,50.53,52.0,53.56,60.34(...TRUNCATED)
["MET","THR","SER","GLN","ARG","SER","LEU","SER","SER","PRO","GLN","THR","ARG","ARG","PRO","SER","VA(...TRUNCATED)
[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,(...TRUNCATED)
["A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A"(...TRUNCATED)
AFDB
false
https://alphafold.ebi.ac.uk/files/AF-E9Q8Q8-F1-model_v6.cif
"dddddddddddpddddpvvvvvvvvvvvvvvvvvvvpaqffllplqdppvlllllqclqpnpdpvssvvlsvllcvlrvvrsfdkafpvcsvvlsvlsv(...TRUNCATED)
true
foldseek_3di_extracted
85.193953
339
339
339
false
15b5d79978d8
train
afdb_structure_fot_E9Q8T2_a995efdb93ec453e
toricblm_afdb_structure_fot
structure_function_fot_coordinate_training
E9Q8T2
PRD15_MOUSE
PR domain zinc finger protein 15 (EC 2.1.1.-) (PR domain-containing protein 15)
"MCPPTIWEKGGQVGARWSLRAPEVSAMAEDGSEEIMFIWCEDCSQYHDSECPELGPVVMVKDSFVLSRARSSLPSNLEIRRLDDGAEGVFAVTQLVKRT(...TRUNCATED)
"Sequence-specific DNA-binding transcriptional regulator. Plays a role as a molecular node in a tran(...TRUNCATED)
"UniProt E9Q8T2 structure-function record. Protein: PR domain zinc finger protein 15 (EC 2.1.1.-) (P(...TRUNCATED)
"{\"edges\": [{\"id\": \"protein_has_sequence\", \"source\": \"protein\", \"target\": \"sequence\", (...TRUNCATED)
"{\"edges\": [{\"source\": \"root\", \"target\": \"geometry\", \"type\": \"branch\"}, {\"source\": \(...TRUNCATED)
"{\"bcif_url\": \"\", \"cif_url\": \"https://alphafold.ebi.ac.uk/files/AF-E9Q8T2-F1-model_v6.cif\", (...TRUNCATED)
[[-2.7920000553131104,-3.563999891281128,4.436999797821045],[-5.9120001792907715,-3.86899995803833,2(...TRUNCATED)
[[-2.7920000553131104,-3.563999891281128,4.436999797821045],[-5.9120001792907715,-3.86899995803833,2(...TRUNCATED)
[[[-2.364000082015991,-2.3499999046325684,5.176000118255615],[-2.7920000553131104,-3.563999891281128(...TRUNCATED)
[true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true(...TRUNCATED)
[29.14,31.45,36.28,31.3,37.72,32.94,31.72,30.42,32.0,31.8,30.89,38.66,33.16,36.38,36.44,32.81,34.09,(...TRUNCATED)
["MET","CYS","PRO","PRO","THR","ILE","TRP","GLU","LYS","GLY","GLY","GLN","VAL","GLY","ALA","ARG","TR(...TRUNCATED)
[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,(...TRUNCATED)
["A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A"(...TRUNCATED)
AFDB
false
https://alphafold.ebi.ac.uk/files/AF-E9Q8T2-F1-model_v6.cif
"ddafdfdddddddddddddddppddddddddddpqdwdadpvvrdtdspddpvpdddddddddpdqfqavvqddpqwdwdqdpvraififgqakdaffd(...TRUNCATED)
true
foldseek_3di_extracted
56.523809
512
512
1,174
true
a995efdb93ec
train
afdb_structure_fot_E9Q956_df42818a0d49d1be
toricblm_afdb_structure_fot
structure_function_fot_coordinate_training
E9Q956
MCMD2_MOUSE
Minichromosome maintenance domain-containing protein 2 (MCM domain-containing protein 2)
"METLQMKEAALVYLDRSGGLQKFIDDCKSYNDSKQSYAVYRFSILIDPCDVVELDADLGNHILHHPLKAARVFQSVCFVAVKTLSLIGQLQTETQINIV(...TRUNCATED)
Plays an important role in meiotic recombination and associated DNA double-strand break repair.
"UniProt E9Q956 structure-function record. Protein: Minichromosome maintenance domain-containing pro(...TRUNCATED)
"{\"edges\": [{\"id\": \"protein_has_sequence\", \"source\": \"protein\", \"target\": \"sequence\", (...TRUNCATED)
"{\"edges\": [{\"source\": \"root\", \"target\": \"geometry\", \"type\": \"branch\"}, {\"source\": \(...TRUNCATED)
"{\"bcif_url\": \"\", \"cif_url\": \"https://alphafold.ebi.ac.uk/files/AF-E9Q956-F1-model_v6.cif\", (...TRUNCATED)
[[20.042999267578125,17.801000595092773,-41.92599868774414],[17.58300018310547,15.911999702453613,-3(...TRUNCATED)
[[20.042999267578125,17.801000595092773,-41.92599868774414],[17.58300018310547,15.911999702453613,-3(...TRUNCATED)
[[[21.025999069213867,16.711999893188477,-42.108001708984375],[20.042999267578125,17.801000595092773(...TRUNCATED)
[true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true(...TRUNCATED)
[51.5,61.66,79.62,87.69,90.0,91.31,93.0,93.62,94.12,94.56,94.5,94.94,95.25,94.19,93.31,92.62,91.19,8(...TRUNCATED)
["MET","GLU","THR","LEU","GLN","MET","LYS","GLU","ALA","ALA","LEU","VAL","TYR","LEU","ASP","ARG","SE(...TRUNCATED)
[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,(...TRUNCATED)
["A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A"(...TRUNCATED)
AFDB
false
https://alphafold.ebi.ac.uk/files/AF-E9Q956-F1-model_v6.cif
"dvlvvllvllvvvcvvvvvvvvllvllqvqvvvvdqaladedegedelvvscvspvvlscccfqpvvvsqvsvlvssvvvcvvvvshvndddslrygyf(...TRUNCATED)
true
foldseek_3di_extracted
85.634043
512
512
681
true
df42818a0d49
train
afdb_structure_fot_E9Q9A9_1d058f4a4e09be98
toricblm_afdb_structure_fot
structure_function_fot_coordinate_training
E9Q9A9
OAS2_MOUSE
"2'-5'-oligoadenylate synthase 2 ((2-5')oligo(A) synthase 2) (2-5A synthase 2) (EC 2.7.7.84) (2',5'-(...TRUNCATED)
"MGNWLTGNWSSDRSSGYSSGWSPGGSSGVPSGPVHKLEKSIQANLTPNENCLKQIAVSSVPSQKLEGYIQENLKPNRESLKQIDQAVDAIWDLLRSQIP(...TRUNCATED)
"Interferon-induced, dsRNA-activated antiviral enzyme which plays a critical role in cellular innate(...TRUNCATED)
"UniProt E9Q9A9 structure-function record. Protein: 2'-5'-oligoadenylate synthase 2 ((2-5')oligo(A) (...TRUNCATED)
"{\"edges\": [{\"id\": \"protein_has_sequence\", \"source\": \"protein\", \"target\": \"sequence\", (...TRUNCATED)
"{\"edges\": [{\"source\": \"root\", \"target\": \"geometry\", \"type\": \"branch\"}, {\"source\": \(...TRUNCATED)
"{\"bcif_url\": \"\", \"cif_url\": \"https://alphafold.ebi.ac.uk/files/AF-E9Q9A9-F1-model_v6.cif\", (...TRUNCATED)
[[0.3100000023841858,55.68199920654297,-10.477999687194824],[-3.2170000076293945,54.737998962402344,(...TRUNCATED)
[[0.3100000023841858,55.68199920654297,-10.477999687194824],[-3.2170000076293945,54.737998962402344,(...TRUNCATED)
[[[1.5119999647140503,55.29899978637695,-9.706999778747559],[0.3100000023841858,55.68199920654297,-1(...TRUNCATED)
[true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true(...TRUNCATED)
[29.38,31.3,30.33,30.48,31.75,28.86,28.05,25.55,28.52,26.41,29.44,30.91,29.39,30.89,28.7,31.08,30.67(...TRUNCATED)
["MET","GLY","ASN","TRP","LEU","THR","GLY","ASN","TRP","SER","SER","ASP","ARG","SER","SER","GLY","TY(...TRUNCATED)
[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,(...TRUNCATED)
["A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A"(...TRUNCATED)
AFDB
false
https://alphafold.ebi.ac.uk/files/AF-E9Q9A9-F1-model_v6.cif
"ddddddddddddddddddddddddddpddpppdppvvqvvvvvvpppppppppddqllqaflvclvvclvvfwaadpvqlvvlvvvvvvlvvlvvvpaq(...TRUNCATED)
true
foldseek_3di_extracted
84.523887
512
512
742
true
1d058f4a4e09
train
afdb_structure_fot_E9Q9D5_a653c3323b8883f3
toricblm_afdb_structure_fot
structure_function_fot_coordinate_training
E9Q9D5
RBL2A_MOUSE
Rab-like protein 2A
"MAGDRNRHCELEQEKYDTHENVKIICLGDSAVGKSKLMERFLMDGFQPQQLSTYALTLYKHTATVDGKTILVDFWDTAGQERFQSMHASYYHKAHACIM(...TRUNCATED)
"Plays an essential role in male fertility, sperm intra-flagellar transport, and tail assembly. Bind(...TRUNCATED)
"UniProt E9Q9D5 structure-function record. Protein: Rab-like protein 2A. Function: Plays an essentia(...TRUNCATED)
"{\"edges\": [{\"id\": \"protein_has_sequence\", \"source\": \"protein\", \"target\": \"sequence\", (...TRUNCATED)
"{\"edges\": [{\"source\": \"root\", \"target\": \"geometry\", \"type\": \"branch\"}, {\"source\": \(...TRUNCATED)
"{\"bcif_url\": \"\", \"cif_url\": \"https://alphafold.ebi.ac.uk/files/AF-E9Q9D5-F1-model_v6.cif\", (...TRUNCATED)
[[-33.832000732421875,24.854000091552734,-2.8399999141693115],[-30.73699951171875,23.320999145507812(...TRUNCATED)
[[-33.832000732421875,24.854000091552734,-2.8399999141693115],[-30.73699951171875,23.320999145507812(...TRUNCATED)
[[[-33.76499938964844,26.229999542236328,-2.2929999828338623],[-33.832000732421875,24.85400009155273(...TRUNCATED)
[true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true(...TRUNCATED)
[40.78,46.34,45.12,46.28,44.25,44.28,37.22,39.91,38.03,39.59,37.66,41.44,40.19,42.72,41.94,46.38,45.(...TRUNCATED)
["MET","ALA","GLY","ASP","ARG","ASN","ARG","HIS","CYS","GLU","LEU","GLU","GLN","GLU","LYS","TYR","AS(...TRUNCATED)
[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,(...TRUNCATED)
["A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A"(...TRUNCATED)
AFDB
false
https://alphafold.ebi.ac.uk/files/AF-E9Q9D5-F1-model_v6.cif
"dpppvvvvvvvvvvvppdlqeaeeeedfdaplcqvllvcllcvvdfdwdqpppdrwiwtwdwdadpndihiytythchpvvvpvdddlvslqrhleyey(...TRUNCATED)
true
foldseek_3di_extracted
80.743767
223
223
223
false
a653c3323b88
train
afdb_structure_fot_E9Q9F6_a3ee650e11e650fd
toricblm_afdb_structure_fot
structure_function_fot_coordinate_training
E9Q9F6
CTSRD_MOUSE
"Cation channel sperm-associated auxiliary subunit delta (CatSper-delta) (CatSperdelta) (Transmembra(...TRUNCATED)
"MLVLMLAAAVATMVRAHTLCRVHTVRTGKVFKSNIQLQGDPLFYAFPNTFVLKNVCKADISVYLGQKVFLTIDNFESSLLPLTVPKSLAVGVPSITSAH(...TRUNCATED)
"Auxiliary component of the CatSper complex, a complex involved in sperm cell hyperactivation. Sperm(...TRUNCATED)
"UniProt E9Q9F6 structure-function record. Protein: Cation channel sperm-associated auxiliary subuni(...TRUNCATED)
"{\"edges\": [{\"id\": \"protein_has_sequence\", \"source\": \"protein\", \"target\": \"sequence\", (...TRUNCATED)
"{\"edges\": [{\"source\": \"root\", \"target\": \"geometry\", \"type\": \"branch\"}, {\"source\": \(...TRUNCATED)
"{\"bcif_url\": \"\", \"cif_url\": \"https://alphafold.ebi.ac.uk/files/AF-E9Q9F6-F1-model_v6.cif\", (...TRUNCATED)
[[-39.63800048828125,-47.63399887084961,49.56700134277344],[-40.816001892089844,-46.784000396728516,(...TRUNCATED)
[[-39.63800048828125,-47.63399887084961,49.56700134277344],[-40.816001892089844,-46.784000396728516,(...TRUNCATED)
[[[-40.93299865722656,-47.375999450683594,50.23699951171875],[-39.63800048828125,-47.63399887084961,(...TRUNCATED)
[true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true(...TRUNCATED)
[44.41,47.06,49.91,50.38,49.44,49.44,48.84,47.75,45.84,42.94,40.81,38.47,39.62,39.81,40.38,51.69,61.(...TRUNCATED)
["MET","LEU","VAL","LEU","MET","LEU","ALA","ALA","ALA","VAL","ALA","THR","MET","VAL","ARG","ALA","HI(...TRUNCATED)
[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,(...TRUNCATED)
["A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A"(...TRUNCATED)
AFDB
false
https://alphafold.ebi.ac.uk/files/AF-E9Q9F6-F1-model_v6.cif
"dvpvvvvvvvvppvpppflwdkdwaedpppddlppdpaaafaaepdlfwewaadqqqlqwiwiharfiftgngvqnywtftdhdhcvvvlpanywlewd(...TRUNCATED)
true
foldseek_3di_extracted
88.828984
512
512
805
true
a3ee650e11e6
train
afdb_structure_fot_E9Q9U0_c032fb9c64000961
toricblm_afdb_structure_fot
structure_function_fot_coordinate_training
E9Q9U0
U17PB_MOUSE
"Ubiquitin carboxyl-terminal hydrolase 17-like protein B (USP17-B) (EC 3.4.19.12) (Deubiquitinating (...TRUNCATED)
"MVVALSFPEADPAMSPPSAPELHQDEAQVVEELAANGKHSLSWESPQGPGCGLQNTGNSCYLNAALQCLTHTPPLADYMLSQEHSQTCCSPEGCKMCAM(...TRUNCATED)
"Deubiquitinating enzyme that removes conjugated ubiquitin from specific proteins to regulate differ(...TRUNCATED)
"UniProt E9Q9U0 structure-function record. Protein: Ubiquitin carboxyl-terminal hydrolase 17-like pr(...TRUNCATED)
"{\"edges\": [{\"id\": \"protein_has_sequence\", \"source\": \"protein\", \"target\": \"sequence\", (...TRUNCATED)
"{\"edges\": [{\"source\": \"root\", \"target\": \"geometry\", \"type\": \"branch\"}, {\"source\": \(...TRUNCATED)
"{\"bcif_url\": \"\", \"cif_url\": \"https://alphafold.ebi.ac.uk/files/AF-E9Q9U0-F1-model_v6.cif\", (...TRUNCATED)
[[31.900999069213867,-30.711000442504883,8.838000297546387],[31.2189998626709,-28.468000411987305,5.(...TRUNCATED)
[[31.900999069213867,-30.711000442504883,8.838000297546387],[31.2189998626709,-28.468000411987305,5.(...TRUNCATED)
[[[32.53499984741211,-29.898000717163086,9.895999908447266],[31.900999069213867,-30.711000442504883,(...TRUNCATED)
[true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true,true(...TRUNCATED)
[33.81,28.41,29.58,29.22,31.84,33.56,34.09,35.16,32.69,39.75,34.38,36.19,36.19,32.59,35.19,36.97,37.(...TRUNCATED)
["MET","VAL","VAL","ALA","LEU","SER","PHE","PRO","GLU","ALA","ASP","PRO","ALA","MET","SER","PRO","PR(...TRUNCATED)
[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,(...TRUNCATED)
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c032fb9c6400
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toricblm_afdb_structure_fot
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S27A6_MOUSE
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[[[-51.95800018310547,-26.275999069213867,-20.391000747680664],[-50.62799835205078,-26.9120006561279(...TRUNCATED)
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AFDB
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toricblm_afdb_structure_fot
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E9Q9W7
PDZD7_MOUSE
PDZ domain-containing protein 7
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End of preview.

ToricBLM Bio Forest-of-Thought Graphification for ToricGT

This repository stores Parquet-first biological graph/FoT curation artifacts for ToricGT/ToricBLM. The upload contains deterministic graph/FoT rows plus any locally curated real-coordinate structure shards selected by the publish command.

Raw upstream Parquet data is not uploaded in this initial push. Local raw sources remain organized by symlink under the ToricGT data tree and require separate license review before redistribution.

Files

  • derived/*.parquet graphified source-data slices
  • splits/*/*.parquet leakage-aware or ProTrek-aware graph/FoT splits when present
  • structures/*/{train,validation,test}/*.parquet real coordinate-bearing AFDB/PDB/PubChem3D shards when present
  • authored/accepted/accepted_records.parquet when authored records are present
  • authored/accepted/validation_report.json
  • authored/records/*.json inspectable handwritten source records
  • authored/source_anchors/*.parquet source-row anchors for future handwritten batches
  • manifests/uniprot_fot_build_manifest.json
  • schema/uniprot_fot_record.schema.json
  • LOCAL_README.md
  • authored/README.md
  • authored/progress_log.md
  • GOAL.md

Current Local Build

  • Repository: AmelieSchreiber/toricblm_fot
  • Derived sample records: 3072
  • Raw datasets scanned: 6
  • Raw Parquet files scanned: 168
  • Readable raw Parquet files: 167
  • Raw rows indexed in manifest: 99138803

Format

Each row contains flat loader columns plus graph_json, forest_json, thought_forest_json, convextok_dag_json, training_views_json, enrichment_status_json, metadata_json, hashes, split cluster metadata, and quality flags.

thought_forest_json materializes source-grounded Forest-of-Thought trees with expansion, self-correction, and consensus edges. convextok_dag_json stores a compact ConvexTok byte-boundary DAG with free byte fallback edges, matched priced-token edges, and a min-plus shortest path. Graph JSON records include directed nodes/edges, GFlowNet reward metadata, continuous embedding proxies, TokenGT/TropicalGT/ToricGT fields, active support nodes, and leakage-resistant split metadata.

Safety And License Notes

Biomedical content is for model-training curation and mechanism-focused annotation reasoning, not patient-specific medical advice. Coordinate-native structure shards are generated only from real AFDB/PDB/PubChem3D records; raw upstream caches such as mmCIF/SDF downloads are not uploaded by this script.
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Total file size:
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