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Datasets:
XaxiPiruli
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protea-lafa-knn-v227

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Formats:
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Size:
1M - 10M
Tags:
protein-function-prediction
gene-ontology
protein-language-model
prott5
knn
lafa
Libraries:
Datasets
Dask
Polars
License:
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go_term_id
int64
6.76M
6.8M
⌀
go_id
stringlengths
10
10
⌀
aspect
stringclasses
3 values
name
stringlengths
4
189
⌀
6,769,282
GO:0030421
P
defecation
6,786,578
GO:0070026
F
nitric oxide binding
6,790,764
GO:0097245
F
flavanol binding
6,756,631
GO:0001834
P
trophectodermal cell proliferation
6,756,632
GO:0001835
P
blastocyst hatching
6,759,363
GO:0005122
F
torso binding
6,759,845
GO:0005766
C
primary lysosome
6,759,900
GO:0005825
C
half bridge of spindle pole body
6,759,968
GO:0005907
C
obsolete HA1 clathrin adaptor
6,759,969
GO:0005908
C
obsolete HA2 clathrin adaptor
6,762,853
GO:0009492
F
obsolete 2Fe-2S electron transfer carrier
6,762,854
GO:0009493
F
obsolete adrenodoxin-type ferredoxin
6,762,855
GO:0009494
F
obsolete chloroplast-type ferredoxin
6,766,031
GO:0016802
F
trialkylsulfonium hydrolase activity
6,766,032
GO:0016803
F
ether hydrolase activity
6,769,319
GO:0030465
P
obsolete autophagic death (sensu Fungi)
6,770,295
GO:0031528
C
microvillus membrane
6,770,448
GO:0031692
F
alpha-1B adrenergic receptor binding
6,770,449
GO:0031693
F
alpha-1D adrenergic receptor binding
6,770,450
GO:0031694
F
alpha-2A adrenergic receptor binding
6,770,451
GO:0031695
F
alpha-2B adrenergic receptor binding
6,770,452
GO:0031696
F
alpha-2C adrenergic receptor binding
6,770,453
GO:0031697
F
beta-1 adrenergic receptor binding
6,770,454
GO:0031698
F
beta-2 adrenergic receptor binding
6,770,455
GO:0031699
F
beta-3 adrenergic receptor binding
6,770,456
GO:0031700
F
adrenomedullin receptor binding
6,770,457
GO:0031701
F
angiotensin receptor binding
6,770,458
GO:0031702
F
type 1 angiotensin receptor binding
6,770,459
GO:0031703
F
type 2 angiotensin receptor binding
6,770,460
GO:0031704
F
apelin receptor binding
6,770,461
GO:0031705
F
bombesin receptor binding
6,770,462
GO:0031706
F
subtype 3 bombesin receptor binding
6,770,463
GO:0031707
F
endothelin A receptor binding
6,770,464
GO:0031708
F
endothelin B receptor binding
6,770,465
GO:0031709
F
gastrin-releasing peptide receptor binding
6,770,466
GO:0031710
F
neuromedin B receptor binding
6,770,467
GO:0031711
F
bradykinin receptor binding
6,770,468
GO:0031712
F
B1 bradykinin receptor binding
6,770,469
GO:0031713
F
B2 bradykinin receptor binding
6,770,524
GO:0031771
F
type 1 orexin receptor binding
6,770,525
GO:0031772
F
type 2 orexin receptor binding
6,770,526
GO:0031773
F
kisspeptin receptor binding
6,770,527
GO:0031774
F
leukotriene receptor binding
6,770,581
GO:0031833
F
type 7 serotonin receptor binding
6,770,582
GO:0031834
F
neurokinin receptor binding
6,770,583
GO:0031835
F
substance P receptor binding
6,770,584
GO:0031836
F
neuromedin K receptor binding
6,770,585
GO:0031837
F
substance K receptor binding
6,771,126
GO:0032407
F
MutSalpha complex binding
6,771,127
GO:0032408
F
MutSbeta complex binding
6,771,888
GO:0033219
F
urea binding
6,772,832
GO:0034190
F
apolipoprotein receptor binding
6,772,833
GO:0034191
F
apolipoprotein A-I receptor binding
6,773,126
GO:0034495
C
protein storage vacuole lumen
6,778,265
GO:0045237
F
CXCR1 chemokine receptor binding
6,778,266
GO:0045238
F
CXCR2 chemokine receptor binding
6,780,878
GO:0048072
P
compound eye pigmentation
6,781,845
GO:0050204
F
oxalomalate lyase activity
6,782,122
GO:0050491
F
sulcatone reductase activity
6,782,609
GO:0051019
F
mitogen-activated protein kinase binding
6,782,610
GO:0051020
F
GTPase binding
6,782,611
GO:0051021
F
GDP-dissociation inhibitor binding
6,782,612
GO:0051022
F
Rho GDP-dissociation inhibitor binding
6,784,456
GO:0060048
P
cardiac muscle contraction
6,791,253
GO:0097753
P
membrane bending
6,791,254
GO:0097754
P
clathrin-mediated membrane bending
6,791,425
GO:0098642
C
network-forming collagen trimer
6,791,670
GO:0098896
C
postsynaptic early endosome membrane
6,791,671
GO:0098897
C
spine apparatus membrane
6,791,672
GO:0098898
C
dense core granule lumen
6,791,673
GO:0098899
C
spine apparatus lumen
6,791,755
GO:0098981
C
cholinergic synapse
6,798,213
GO:1902507
C
thiazole synthase complex
6,756,841
GO:0002052
P
positive regulation of neuroblast proliferation
6,755,670
GO:0000192
P
obsolete activation of MAPKK (pseudohyphal growth)
6,755,514
GO:0000001
P
mitochondrion inheritance
6,755,515
GO:0000002
P
obsolete mitochondrial genome maintenance
6,755,516
GO:0000003
P
obsolete reproduction
6,755,517
GO:0000005
F
obsolete ribosomal chaperone activity
6,755,518
GO:0000006
F
high-affinity zinc transmembrane transporter activity
6,755,519
GO:0000007
F
low-affinity zinc ion transmembrane transporter activity
6,755,520
GO:0000008
F
obsolete thioredoxin
6,755,521
GO:0000009
F
alpha-1,6-mannosyltransferase activity
6,755,522
GO:0000010
F
heptaprenyl diphosphate synthase activity
6,755,523
GO:0000011
P
vacuole inheritance
6,755,524
GO:0000012
P
single strand break repair
6,755,525
GO:0000014
F
single-stranded DNA endodeoxyribonuclease activity
6,755,526
GO:0000015
C
phosphopyruvate hydratase complex
6,755,527
GO:0000016
F
lactase activity
6,755,528
GO:0000017
P
alpha-glucoside transport
6,755,529
GO:0000018
P
regulation of DNA recombination
6,755,530
GO:0000019
P
regulation of mitotic recombination
6,755,531
GO:0000020
P
obsolete negative regulation of recombination within rDNA repeats
6,755,532
GO:0000022
P
mitotic spindle elongation
6,755,877
GO:0000425
P
pexophagy
6,755,533
GO:0000023
P
maltose metabolic process
6,755,534
GO:0000024
P
maltose biosynthetic process
6,755,535
GO:0000025
P
maltose catabolic process
6,755,536
GO:0000026
F
alpha-1,2-mannosyltransferase activity
6,755,537
GO:0000027
P
ribosomal large subunit assembly
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PROTEA-KNN — v227 reference bundle

Frozen, inference-only reference data for the protea-knn-v1 LAFA submission. Lets anyone reproduce PROTEA's simple KNN baseline without any PROTEA infrastructure (no database, no queues): mount this bundle into the container and run.

  • Embedding model: Rostlab/prot_t5_xl_half_uniref50-enc (mean pooled, 1024-dim) — the same model as LAFA's own ProtT5 baseline. The difference is the data: PROTEA's reference protein set.
  • Cutoff: GOA release v227 (Sep 2025) — annotations as of t0 only, no post-cutoff leakage. Fair under LAFA/CAFA rules (each method brings its own pre-t0 data).
  • Method: per-aspect cosine K-nearest-neighbour transfer of GO annotations, score = max(0, 1 - cosine_distance). No learned reranker, no v6 features.

Contents

File What
reference_embeddings.parquet (accession, ProtT5 embedding) for the reference set
reference_annotations.parquet (accession, GO term) labels at v227
go_term_metadata.parquet GO id / aspect / name / information-accretion weight
pca_state.npz query-PCA mean+components (optional, unused by knn-v1)
anc2vec.npz Anc2Vec GO embeddings (optional, unused by knn-v1)
manifest.json provenance: embedding config, annotation set, cutoff

Usage 

docker run --rm \
  -v /path/to/this/bundle:/bundle:ro \
  -v $HOME/.cache/huggingface:/hf-cache \
  -v $PWD/queries.fasta:/input/queries.fasta:ro \
  -v $PWD/out:/output \
  ghcr.io/frapercan/protea/knn-v1:latest

Writes /output/predictions.tsv (query_accession <TAB> GO_id <TAB> score).

Container source + method card: PROTEA (apps/lafa_knn_v1). Submission to LAFA and correspondence owned by the author (Francisco Miguel Pérez Canales).
Downloads last month
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Number of rows:
6,498,821
Total file size:
1.08 GB