diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..581e4773bb0f81b5fe154c5877d5d7420332be77 --- /dev/null +++ b/LICENSE @@ -0,0 +1,2 @@ +Human tasks: CC BY 4.0, from Figshare record 10.6084/m9.figshare.31169506 (https://creativecommons.org/licenses/by/4.0/). +Benchmark tasks metal_ion_binding, localization, ssp_q3 and ssp_q8: Apache 2.0, from huggingface.co/biomap-research. diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..f3e59837b9c90972242d9d77abd2ad2bb63b4a21 --- /dev/null +++ b/README.md @@ -0,0 +1,269 @@ +--- +license: other +license_name: cc-by-4.0-and-apache-2.0 +license_link: LICENSE +pretty_name: Protein concept probing +task_categories: +- text-classification +- token-classification +tags: +- biology +- protein +- probing +- interpretability +configs: +- config_name: functional_sites + data_files: + - split: train + path: functional_sites/train.parquet + - split: validation + path: functional_sites/validation.parquet + - split: test + path: functional_sites/test.parquet +- config_name: go_bp + data_files: + - split: train + path: go_bp/train.parquet + - split: validation + path: go_bp/validation.parquet + - split: test + path: go_bp/test.parquet +- config_name: go_cc + data_files: + - split: train + path: go_cc/train.parquet + - split: validation + path: go_cc/validation.parquet + - split: test + path: go_cc/test.parquet +- config_name: go_mf + data_files: + - split: train + path: go_mf/train.parquet + - split: validation + path: go_mf/validation.parquet + - split: test + path: go_mf/test.parquet +- config_name: interpro_active_site + data_files: + - split: train + path: interpro_active_site/train.parquet + - split: validation + path: interpro_active_site/validation.parquet + - split: test + path: interpro_active_site/test.parquet +- config_name: interpro_binding_site + data_files: + - split: train + path: interpro_binding_site/train.parquet + - split: validation + path: interpro_binding_site/validation.parquet + - split: test + path: interpro_binding_site/test.parquet +- config_name: interpro_conserved_site + data_files: + - split: train + path: interpro_conserved_site/train.parquet + - split: validation + path: interpro_conserved_site/validation.parquet + - split: test + path: interpro_conserved_site/test.parquet +- config_name: interpro_domain + data_files: + - split: train + path: interpro_domain/train.parquet + - split: validation + path: interpro_domain/validation.parquet + - split: test + path: interpro_domain/test.parquet +- config_name: interpro_family + data_files: + - split: train + path: interpro_family/train.parquet + - split: validation + path: interpro_family/validation.parquet + - split: test + path: interpro_family/test.parquet +- config_name: interpro_homologous_superfamily + data_files: + - split: train + path: interpro_homologous_superfamily/train.parquet + - split: validation + path: interpro_homologous_superfamily/validation.parquet + - split: test + path: interpro_homologous_superfamily/test.parquet +- config_name: interpro_repeat + data_files: + - split: train + path: interpro_repeat/train.parquet + - split: validation + path: interpro_repeat/validation.parquet + - split: test + path: interpro_repeat/test.parquet +- config_name: lipidation + data_files: + - split: train + path: lipidation/train.parquet + - split: validation + path: lipidation/validation.parquet + - split: test + path: lipidation/test.parquet +- config_name: localization + data_files: + - split: train + path: localization/train.parquet + - split: validation + path: localization/validation.parquet + - split: test + path: localization/test.parquet +- config_name: metal_ion_binding + data_files: + - split: train + path: metal_ion_binding/train.parquet + - split: validation + path: metal_ion_binding/validation.parquet + - split: test + path: metal_ion_binding/test.parquet +- config_name: peptide + data_files: + - split: train + path: peptide/train.parquet + - split: validation + path: peptide/validation.parquet + - split: test + path: peptide/test.parquet +- config_name: phosphorylation + data_files: + - split: train + path: phosphorylation/train.parquet + - split: validation + path: phosphorylation/validation.parquet + - split: test + path: phosphorylation/test.parquet +- config_name: post_translational_modification + data_files: + - split: train + path: post_translational_modification/train.parquet + - split: validation + path: post_translational_modification/validation.parquet + - split: test + path: post_translational_modification/test.parquet +- config_name: prot_param + data_files: + - split: train + path: prot_param/train.parquet + - split: validation + path: prot_param/validation.parquet + - split: test + path: prot_param/test.parquet +- config_name: secondary_structure + data_files: + - split: train + path: secondary_structure/train.parquet + - split: validation + path: secondary_structure/validation.parquet + - split: test + path: secondary_structure/test.parquet +- config_name: ssp_q3 + data_files: + - split: train + path: ssp_q3/train.parquet + - split: validation + path: ssp_q3/validation.parquet + - split: test + path: ssp_q3/test.parquet +- config_name: ssp_q8 + data_files: + - split: train + path: ssp_q8/train.parquet + - split: validation + path: ssp_q8/validation.parquet + - split: test + path: ssp_q8/test.parquet +- config_name: topology + data_files: + - split: train + path: topology/train.parquet + - split: validation + path: topology/validation.parquet + - split: test + path: topology/test.parquet +--- + +# Protein concept probing + +Twenty-two protein annotation tasks for probing what a protein language model's internal states encode, from +amino-acid composition to Gene Ontology terms. Thirteen tasks label a whole protein and nine label each residue. The +human tasks are reviewed *Homo sapiens* UniProtKB entries shorter than 1,024 residues; four further tasks are +xTrimoPGLM benchmark tables. + +| Config | Level | Task | Proteins | Labels | Train / validation / test | +|---|---|---|---|---|---| +| `functional_sites` | residue | multiclass | 6,893 | 6 | 4,778 / 1,106 / 1,009 | +| `go_bp` | protein | multilabel | 12,255 | 304 | 8,591 / 1,888 / 1,776 | +| `go_cc` | protein | multilabel | 16,443 | 164 | 11,409 / 2,457 / 2,577 | +| `go_mf` | protein | multilabel | 11,504 | 123 | 8,010 / 1,786 / 1,708 | +| `interpro_active_site` | protein | multilabel | 718 | 58 | 482 / 116 / 120 | +| `interpro_binding_site` | protein | multilabel | 640 | 39 | 446 / 87 / 107 | +| `interpro_conserved_site` | protein | multilabel | 2,948 | 334 | 2,062 / 450 / 436 | +| `interpro_domain` | protein | multilabel | 8,003 | 364 | 5,307 / 1,371 / 1,325 | +| `interpro_family` | protein | multilabel | 3,601 | 239 | 2,097 / 678 / 826 | +| `interpro_homologous_superfamily` | protein | multilabel | 8,198 | 100 | 5,499 / 1,368 / 1,331 | +| `interpro_repeat` | protein | multilabel | 1,189 | 65 | 819 / 189 / 181 | +| `lipidation` | residue | multiclass | 978 | 25 | 654 / 129 / 195 | +| `localization` | protein | multiclass | 7,530 | 10 | 5,321 / 590 / 1,619 | +| `metal_ion_binding` | protein | binary | 7,242 | 1 | 5,346 / 599 / 1,297 | +| `peptide` | residue | multiclass | 4,977 | 4 | 3,485 / 700 / 792 | +| `phosphorylation` | residue | multiclass | 8,648 | 6 | 6,057 / 1,304 / 1,287 | +| `post_translational_modification` | residue | multiclass | 15,349 | 12 | 10,722 / 2,400 / 2,227 | +| `prot_param` | protein | regression | 18,126 | 31 | 12,747 / 2,777 / 2,602 | +| `secondary_structure` | residue | multiclass | 8,986 | 4 | 6,310 / 1,351 / 1,325 | +| `ssp_q3` | residue | multiclass | 11,479 | 3 | 9,731 / 1,083 / 665 | +| `ssp_q8` | residue | multiclass | 11,479 | 8 | 9,731 / 1,083 / 665 | +| `topology` | residue | multiclass | 4,777 | 17 | 3,378 / 754 / 645 | + +## Homology leakage + +The human tasks keep their published cluster splits: MMseqs2 clusters at 20% identity (30% for InterPro active +site, binding site, conserved site and repeat) are assigned whole to train plus validation or to test, and +validation clusters are drawn at 50% identity from the rest, with 80% coverage of the target sequence. The four +benchmark tasks keep their published test split, and validation is a random 10% of their train split, so they hold +no homology guarantee between train and validation. + +## How it was built + +1. Read each curated human table and its recorded train, validation and test assignment. +2. Turn its targets into one `label` column: a multi-hot vector over the InterPro entries or Gene Ontology terms, + 31 ProtParam values, or one class index per residue in the contiguous order of the classes the table holds. +3. For Gene Ontology, keep the terms with more than six positive proteins in both validation and test. +4. For the four benchmark tables, split 10% of train off as validation with seed 184502, then drop sequences of + 1,024 residues or more. + +## Columns + +| Column | Meaning | +|---|---| +| `id` | UniProt accession for the human tasks; a stable sequence-derived id for the benchmark tasks | +| `sequence` | amino-acid sequence | +| `label` | multi-hot list (multilabel), list of 31 floats (regression), integer (binary or multiclass), or one integer per residue (residue tasks) | + +Each config folder also holds `metadata.json` with the task level, task type and label names. The benchmark tables +publish their classes but not the order of their integers, so their label names are `class_`. + +## What a model trained on it may say + +These are probing benchmarks. InterPro entries and many UniProt features are curated with computational evidence, +so a probe here measures agreement with the annotations, not experimentally measured function. Residue tasks count +unannotated residues as their own class (`-`), which dominates most of them. + +## Sources and licence + +The human tasks are the curated tables of Figshare record 10.6084/m9.figshare.31169506, released under CC BY 4.0, +built from UniProtKB (accessed 2025-09-09) and the InterPro entry list (accessed 2025-09-16). The four benchmark +tasks (`metal_ion_binding`, `localization`, `ssp_q3`, `ssp_q8`) are from `biomap-research` on Hugging Face under +Apache 2.0. + +## Files + +`/train.parquet`, `/validation.parquet`, `/test.parquet` and `/metadata.json` for each +of the 22 configs. diff --git a/functional_sites/metadata.json b/functional_sites/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..8817db5bc5f297df0c31a0534461253f1b309362 --- /dev/null +++ b/functional_sites/metadata.json @@ -0,0 +1,21 @@ +{ + "config": "functional_sites", + "task_level": "residue", + "task_type": "multiclass", + "num_labels": 6, + "label_names": [ + "-", + "ACT_SITE", + "ACT_SITE,BINDING", + "BINDING", + "BINDING,DNA_BIND", + "DNA_BIND" + ], + "rows": { + "train": 4778, + "validation": 1106, + "test": 1009 + }, + "source": "Figshare record 31169506, file h_sapiens_proteome_uniprot_functional_sites_clustersplit_20_50.parquet.gz", + "licence": "CC BY 4.0" +} \ No newline at end of file diff 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b/functional_sites/validation.parquet @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8a07f8b19bd394b2f74a1149c24290a839712d7048f9dac39e4c009596b75d04 +size 532496 diff --git a/go_bp/metadata.json b/go_bp/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..283b34390fcd4d5c604e57bf91cfba1e67523756 --- /dev/null +++ b/go_bp/metadata.json @@ -0,0 +1,319 @@ +{ + "config": "go_bp", + "task_level": "protein", + "task_type": "multilabel", + "num_labels": 304, + "label_names": [ + "B cell differentiation [GO:0030183]", + "B cell proliferation [GO:0042100]", + "BMP signaling pathway [GO:0030509]", + "DNA damage response [GO:0006974]", + "DNA recombination [GO:0006310]", + "DNA repair [GO:0006281]", + "DNA replication [GO:0006260]", + "DNA-templated transcription [GO:0006351]", + "ERAD pathway [GO:0036503]", + "G protein-coupled receptor signaling pathway [GO:0007186]", + "G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger [GO:0007187]", + "Golgi organization [GO:0007030]", + "MAPK cascade [GO:0000165]", + "Notch signaling pathway [GO:0007219]", + "RNA processing [GO:0006396]", + "RNA splicing [GO:0008380]", + "Ras protein signal transduction [GO:0007265]", + "T cell activation [GO:0042110]", + "T cell differentiation in thymus [GO:0033077]", + "T cell receptor signaling pathway [GO:0050852]", + "Wnt signaling pathway [GO:0016055]", + "actin cytoskeleton organization [GO:0030036]", + "actin filament organization [GO:0007015]", + "adaptive immune response [GO:0002250]", + "adenylate cyclase-activating G protein-coupled receptor signaling pathway [GO:0007189]", + "aerobic respiration [GO:0009060]", + "anatomical structure morphogenesis [GO:0009653]", + "angiogenesis [GO:0001525]", + "animal organ morphogenesis [GO:0009887]", + "anterior/posterior pattern specification [GO:0009952]", + "antibacterial humoral response [GO:0019731]", + "antimicrobial humoral immune response mediated by antimicrobial peptide [GO:0061844]", + "antiviral innate immune response [GO:0140374]", + "apoptotic process [GO:0006915]", + "apoptotic signaling pathway [GO:0097190]", + "autophagosome assembly [GO:0000045]", + "autophagy [GO:0006914]", + "axon guidance [GO:0007411]", + "axonogenesis [GO:0007409]", + "behavioral fear response [GO:0001662]", + "blood coagulation [GO:0007596]", + "bone development [GO:0060348]", + "brain development [GO:0007420]", + "calcium ion transport [GO:0006816]", + "camera-type eye development [GO:0043010]", + "canonical Wnt signaling pathway [GO:0060070]", + "carbohydrate metabolic process [GO:0005975]", + "cell adhesion [GO:0007155]", + "cell chemotaxis [GO:0060326]", + "cell differentiation [GO:0030154]", + "cell division [GO:0051301]", + "cell migration [GO:0016477]", + "cell morphogenesis [GO:0000902]", + "cell population proliferation [GO:0008283]", + "cell surface receptor protein tyrosine kinase signaling pathway [GO:0007169]", + "cell surface receptor signaling pathway [GO:0007166]", + "cell-cell adhesion [GO:0098609]", + "cell-cell signaling [GO:0007267]", + "cellular response to cAMP [GO:0071320]", + "cellular response to calcium ion [GO:0071277]", + "cellular response to glucose stimulus [GO:0071333]", + "cellular response to hypoxia [GO:0071456]", + "cellular response to insulin stimulus [GO:0032869]", + "cellular response to leukemia inhibitory factor [GO:1990830]", + "cellular response to lipopolysaccharide [GO:0071222]", + "cellular response to mechanical stimulus [GO:0071260]", + "cellular response to oxidative stress [GO:0034599]", + "cellular response to retinoic acid [GO:0071300]", + "cellular response to tumor necrosis factor [GO:0071356]", + "cellular response to type II interferon [GO:0071346]", + "cellular response to virus [GO:0098586]", + "central nervous system development [GO:0007417]", + "cerebral cortex development [GO:0021987]", + "chemical synaptic transmission [GO:0007268]", + "chemotaxis [GO:0006935]", + "chloride transmembrane transport [GO:1902476]", + "cholesterol homeostasis [GO:0042632]", + "cholesterol metabolic process [GO:0008203]", + "chromatin organization [GO:0006325]", + "chromatin remodeling [GO:0006338]", + "chromosome segregation [GO:0007059]", + "cilium assembly [GO:0060271]", + "cytokine-mediated signaling pathway [GO:0019221]", + "cytoplasmic translation [GO:0002181]", + "cytoskeleton organization [GO:0007010]", + "defense response to Gram-negative bacterium [GO:0050829]", + "defense response to Gram-positive bacterium [GO:0050830]", + "defense response to bacterium [GO:0042742]", + "defense response to virus [GO:0051607]", + "determination of left/right symmetry [GO:0007368]", + "double-strand break repair [GO:0006302]", + "double-strand break repair via homologous recombination [GO:0000724]", + "endocytic recycling [GO:0032456]", + "endocytosis [GO:0006897]", + "endoplasmic reticulum to Golgi vesicle-mediated transport [GO:0006888]", + "endoplasmic reticulum unfolded protein response [GO:0030968]", + "energy homeostasis [GO:0097009]", + "epithelial cell proliferation [GO:0050673]", + "establishment of localization in cell [GO:0051649]", + "exocytosis [GO:0006887]", + "extracellular matrix organization [GO:0030198]", + "fat cell differentiation [GO:0045444]", + "fatty acid biosynthetic process [GO:0006633]", + "fatty acid metabolic process [GO:0006631]", + "female pregnancy [GO:0007565]", + "flagellated sperm motility [GO:0030317]", + "gene expression [GO:0010467]", + "glucose homeostasis [GO:0042593]", + "glucose metabolic process [GO:0006006]", + "glutathione metabolic process [GO:0006749]", + "heart development [GO:0007507]", + "hemopoiesis [GO:0030097]", + "heterochromatin formation [GO:0031507]", + "hippocampus development [GO:0021766]", + "immune response [GO:0006955]", + "immunoglobulin mediated immune response [GO:0016064]", + "in utero embryonic development [GO:0001701]", + "inflammatory response [GO:0006954]", + "innate immune response [GO:0045087]", + "insulin secretion [GO:0030073]", + "integrin-mediated signaling pathway [GO:0007229]", + "intracellular calcium ion homeostasis [GO:0006874]", + "intracellular protein transport [GO:0006886]", + "intracellular signal transduction [GO:0035556]", + "keratinocyte differentiation [GO:0030216]", + "killing of cells of another organism [GO:0031640]", + "lipid metabolic process [GO:0006629]", + "locomotory behavior [GO:0007626]", + "long-term synaptic potentiation [GO:0060291]", + "mRNA processing [GO:0006397]", + "mRNA splicing, via spliceosome [GO:0000398]", + "macroautophagy [GO:0016236]", + "male gonad development [GO:0008584]", + "methylation [GO:0032259]", + "microtubule cytoskeleton organization [GO:0000226]", + "mitochondrial translation [GO:0032543]", + "mitochondrion organization [GO:0007005]", + "mitotic cell cycle [GO:0000278]", + "modulation of chemical synaptic transmission [GO:0050804]", + "monoatomic ion transport [GO:0006811]", + "multicellular organism growth [GO:0035264]", + "muscle contraction [GO:0006936]", + "muscle organ development [GO:0007517]", + "negative regulation of BMP signaling pathway [GO:0030514]", + "negative regulation of DNA-templated transcription [GO:0045892]", + "negative regulation of G1/S transition of mitotic cell cycle [GO:2000134]", + "negative regulation of angiogenesis [GO:0016525]", + "negative regulation of apoptotic process [GO:0043066]", + "negative regulation of canonical NF-kappaB signal transduction [GO:0043124]", + "negative regulation of canonical Wnt signaling pathway [GO:0090090]", + "negative regulation of cell growth [GO:0030308]", + "negative regulation of cell migration [GO:0030336]", + "negative regulation of cell population proliferation [GO:0008285]", + "negative regulation of fat cell differentiation [GO:0045599]", + "negative regulation of gene expression [GO:0010629]", + "negative regulation of inflammatory response [GO:0050728]", + "negative regulation of neuron apoptotic process [GO:0043524]", + "negative regulation of neuron differentiation [GO:0045665]", + "negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction [GO:0051898]", + "negative regulation of transcription by RNA polymerase II [GO:0000122]", + "negative regulation of transforming growth factor beta receptor signaling pathway [GO:0030512]", + "negative regulation of translation [GO:0017148]", + "negative regulation of tumor necrosis factor production [GO:0032720]", + "nervous system development [GO:0007399]", + "neural tube closure [GO:0001843]", + "neurogenesis [GO:0022008]", + "neuron apoptotic process [GO:0051402]", + "neuron differentiation [GO:0030182]", + "neuron migration [GO:0001764]", + "neuron projection development [GO:0031175]", + "neuropeptide signaling pathway [GO:0007218]", + "ossification [GO:0001503]", + "osteoblast differentiation [GO:0001649]", + "osteoclast differentiation [GO:0030316]", + "phospholipase C-activating G protein-coupled receptor signaling pathway [GO:0007200]", + "phospholipid metabolic process [GO:0006644]", + "platelet activation [GO:0030168]", + "positive regulation of DNA repair [GO:0045739]", + "positive regulation of DNA-templated transcription [GO:0045893]", + "positive regulation of ERK1 and ERK2 cascade [GO:0070374]", + "positive regulation of JNK cascade [GO:0046330]", + "positive regulation of MAPK cascade [GO:0043410]", + "positive regulation of NF-kappaB transcription factor activity [GO:0051092]", + "positive regulation of T cell proliferation [GO:0042102]", + "positive regulation of angiogenesis [GO:0045766]", + "positive regulation of apoptotic process [GO:0043065]", + "positive regulation of canonical NF-kappaB signal transduction [GO:0043123]", + "positive regulation of canonical Wnt signaling pathway [GO:0090263]", + "positive regulation of cell adhesion [GO:0045785]", + "positive regulation of cell growth [GO:0030307]", + "positive regulation of cell migration [GO:0030335]", + "positive regulation of cell population proliferation [GO:0008284]", + "positive regulation of cold-induced thermogenesis [GO:0120162]", + "positive regulation of cytokine production [GO:0001819]", + "positive regulation of cytosolic calcium ion concentration [GO:0007204]", + "positive regulation of endothelial cell proliferation [GO:0001938]", + "positive regulation of gene expression [GO:0010628]", + "positive regulation of inflammatory response [GO:0050729]", + "positive regulation of insulin secretion [GO:0032024]", + "positive regulation of interleukin-6 production [GO:0032755]", + "positive regulation of interleukin-8 production [GO:0032757]", + "positive regulation of neuron differentiation [GO:0045666]", + "positive regulation of neuron projection development [GO:0010976]", + "positive regulation of osteoblast differentiation [GO:0045669]", + "positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction [GO:0051897]", + "positive regulation of proteasomal ubiquitin-dependent protein catabolic process [GO:0032436]", + "positive regulation of protein localization to plasma membrane [GO:1903078]", + "positive regulation of protein phosphorylation [GO:0001934]", + "positive regulation of protein ubiquitination [GO:0031398]", + "positive regulation of protein-containing complex assembly [GO:0031334]", + "positive regulation of transcription by RNA polymerase II [GO:0045944]", + "positive regulation of transcription elongation by RNA polymerase II [GO:0032968]", + "positive regulation of translation [GO:0045727]", + "positive regulation of tumor necrosis factor production [GO:0032760]", + "potassium ion transmembrane transport [GO:0071805]", + "potassium ion transport [GO:0006813]", + "proteasome-mediated ubiquitin-dependent protein catabolic process [GO:0043161]", + "protein K48-linked ubiquitination [GO:0070936]", + "protein O-linked glycosylation [GO:0006493]", + "protein autophosphorylation [GO:0046777]", + "protein autoubiquitination [GO:0051865]", + "protein catabolic process [GO:0030163]", + "protein destabilization [GO:0031648]", + "protein folding [GO:0006457]", + "protein glycosylation [GO:0006486]", + "protein homotetramerization [GO:0051289]", + "protein import into nucleus [GO:0006606]", + "protein localization [GO:0008104]", + "protein localization to plasma membrane [GO:0072659]", + "protein maturation [GO:0051604]", + "protein modification process [GO:0036211]", + "protein phosphorylation [GO:0006468]", + "protein polyubiquitination [GO:0000209]", + "protein processing [GO:0016485]", + "protein stabilization [GO:0050821]", + "protein transport [GO:0015031]", + "protein ubiquitination [GO:0016567]", + "protein-containing complex assembly [GO:0065003]", + "proteolysis [GO:0006508]", + "proton motive force-driven mitochondrial ATP synthesis [GO:0042776]", + "proton transmembrane transport [GO:1902600]", + "rRNA processing [GO:0006364]", + "receptor internalization [GO:0031623]", + "receptor-mediated endocytosis [GO:0006898]", + "regulation of DNA repair [GO:0006282]", + "regulation of DNA replication [GO:0006275]", + "regulation of DNA-templated transcription [GO:0006355]", + "regulation of apoptotic process [GO:0042981]", + "regulation of blood pressure [GO:0008217]", + "regulation of cell cycle [GO:0051726]", + "regulation of cell growth [GO:0001558]", + "regulation of cell migration [GO:0030334]", + "regulation of cell population proliferation [GO:0042127]", + "regulation of cell shape [GO:0008360]", + "regulation of circadian rhythm [GO:0042752]", + "regulation of cytokine production [GO:0001817]", + "regulation of embryonic development [GO:0045995]", + "regulation of gene expression [GO:0010468]", + "regulation of inflammatory response [GO:0050727]", + "regulation of insulin secretion [GO:0050796]", + "regulation of mitotic cell cycle [GO:0007346]", + "regulation of protein stability [GO:0031647]", + "regulation of transcription by RNA polymerase II [GO:0006357]", + "regulation of translation [GO:0006417]", + "response to bacterium [GO:0009617]", + "response to endoplasmic reticulum stress [GO:0034976]", + "response to estradiol [GO:0032355]", + "response to estrogen [GO:0043627]", + "response to ethanol [GO:0045471]", + "response to hydrogen peroxide [GO:0042542]", + "response to hypoxia [GO:0001666]", + "response to insulin [GO:0032868]", + "response to ischemia [GO:0002931]", + "response to lipopolysaccharide [GO:0032496]", + "response to oxidative stress [GO:0006979]", + "response to retinoic acid [GO:0032526]", + "response to toxic substance [GO:0009636]", + "response to virus [GO:0009615]", + "response to xenobiotic stimulus [GO:0009410]", + "retina development in camera-type eye [GO:0060041]", + "retrograde transport, endosome to Golgi [GO:0042147]", + "retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum [GO:0006890]", + "ribosomal small subunit biogenesis [GO:0042274]", + "roof of mouth development [GO:0060021]", + "sensory perception of sound [GO:0007605]", + "signal transduction [GO:0007165]", + "skeletal system development [GO:0001501]", + "smoothened signaling pathway [GO:0007224]", + "social behavior [GO:0035176]", + "sodium ion transmembrane transport [GO:0035725]", + "sodium ion transport [GO:0006814]", + "somatic stem cell population maintenance [GO:0035019]", + "spermatid development [GO:0007286]", + "spermatogenesis [GO:0007283]", + "synapse assembly [GO:0007416]", + "telomere maintenance [GO:0000723]", + "transcription by RNA polymerase II [GO:0006366]", + "transforming growth factor beta receptor signaling pathway [GO:0007179]", + "translation [GO:0006412]", + "ubiquitin-dependent protein catabolic process [GO:0006511]", + "vasodilation [GO:0042311]", + "vesicle-mediated transport [GO:0016192]", + "visual perception [GO:0007601]", + "xenobiotic metabolic process [GO:0006805]" + ], + "rows": { + "train": 8591, + "validation": 1888, + "test": 1776 + }, + "source": 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[GO:0005635]", + "nuclear matrix [GO:0016363]", + "nuclear membrane [GO:0031965]", + "nuclear speck [GO:0016607]", + "nucleolus [GO:0005730]", + "nucleoplasm [GO:0005654]", + "nucleosome [GO:0000786]", + "nucleus [GO:0005634]", + "perikaryon [GO:0043204]", + "perinuclear region of cytoplasm [GO:0048471]", + "peroxisomal membrane [GO:0005778]", + "peroxisome [GO:0005777]", + "photoreceptor outer segment [GO:0001750]", + "plasma membrane [GO:0005886]", + "postsynapse [GO:0098794]", + "postsynaptic density [GO:0014069]", + "postsynaptic density membrane [GO:0098839]", + "postsynaptic membrane [GO:0045211]", + "presynapse [GO:0098793]", + "proteasome complex [GO:0000502]", + "protein-containing complex [GO:0032991]", + "receptor complex [GO:0043235]", + "recycling endosome [GO:0055037]", + "recycling endosome membrane [GO:0055038]", + "ribonucleoprotein complex [GO:1990904]", + "ribosome [GO:0005840]", + "ruffle [GO:0001726]", + "ruffle membrane [GO:0032587]", + "sarcolemma [GO:0042383]", 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"IPR003016__2-oxo_acid_dehydrogenase,_lipoyl-binding_site", + "IPR004163__coenzyme_a_transferase_binding_site", + "IPR004838__aminotransferases,_class-i,_pyridoxal-phosphate-binding_site", + "IPR013838__beta_tubulin,_autoregulation_binding_site", + "IPR016192__apobec/cmp_deaminase,_zinc-binding", + "IPR017441__protein_kinase,_atp_binding_site", + "IPR018064__metallothionein,_vertebrate,_metal_binding_site", + "IPR018136__aconitase_family,_4fe-4s_cluster_binding_site", + "IPR018152__superoxide_dismutase,_copper/zinc,_binding_site", + "IPR018195__transferrin_family,_iron_binding_site", + "IPR018220__adenylosuccinate_synthase,_gtp-binding_site", + "IPR018247__ef-hand_1,_calcium-binding_site", + "IPR018298__adrenodoxin,_iron-sulphur_binding_site", + "IPR018301__aromatic_amino_acid_hydroxylase,_iron/copper_binding_site", + "IPR018349__peptidase_m24a,_methionine_aminopeptidase,_subfamily_2,_binding_site", + "IPR018506__cytochrome_b5,_heme-binding_site", + "IPR019798__serine_hydroxymethyltransferase,_pyridoxal_phosphate_binding_site", + "IPR019807__hexokinase,_binding_site", + "IPR019843__dna_polymerase_family_x,_binding_site", + "IPR020537__atp_synthase,_f0_complex,_subunit_c,_dccd-binding_site", + "IPR020578__aminotransferase_class-v,_pyridoxal-phosphate_binding_site", + "IPR020583__inositol_monophosphatase,_metal-binding_site", + "IPR020826__transketolase_binding_site", + "IPR020833__lipoxygenase,_iron_binding_site", + "IPR020847__ap_endonuclease_1,_binding_site", + "IPR020855__ureohydrolase,_manganese-binding_site", + "IPR020969__ankyrin-g_binding_site", + "IPR021115__pyridoxal-phosphate_binding_site", + "IPR021158__peptidase_m10a,_cysteine_switch,_zinc_binding_site", + "IPR022653__orn/dap/arg_decarboxylase_2,_pyridoxal-phosphate_binding_site", + "IPR025662__sigma-54_interaction_domain,_atp-binding_site_1", + "IPR025735__rip_homotypic_interaction_motif", + "IPR027430__visual_pigments_(opsins)_retinal_binding_site" + ], + "rows": { + "train": 446, + "validation": 87, + "test": 107 + }, + "source": "Figshare record 31169506, file h_sapiens_proteome_interpro_InterPro_binding_site_clustersplit_30_50.parquet.gz", + "licence": "CC BY 4.0" +} \ No newline at end of file diff --git a/interpro_binding_site/test.parquet b/interpro_binding_site/test.parquet new file mode 100644 index 0000000000000000000000000000000000000000..f18da84bde3401375db347d865455f64a52d2db2 --- /dev/null +++ b/interpro_binding_site/test.parquet @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8dffbcd3ffa09ac26d9e4f1d52a9912e8c4fced1b97dc68df0df6454040c7297 +size 55787 diff --git a/interpro_binding_site/train.parquet b/interpro_binding_site/train.parquet new file mode 100644 index 0000000000000000000000000000000000000000..e466811c5fe030e5c580ca72f586898138ec9ae2 --- /dev/null +++ b/interpro_binding_site/train.parquet @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e891a477d5e67016488f8971e98cd70c84f79d10eefc9e40f02dd696fd14d82f +size 234373 diff --git a/interpro_binding_site/validation.parquet b/interpro_binding_site/validation.parquet new file mode 100644 index 0000000000000000000000000000000000000000..e7b70f1f41f8661094f8878908a6517ab8c2a6f6 --- /dev/null +++ b/interpro_binding_site/validation.parquet @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1a43da648ee8cf2a43546a90c5c78b67dc126a5eae3ecca788a60dda78061738 +size 50456 diff --git a/interpro_conserved_site/metadata.json b/interpro_conserved_site/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..1bc76bac0b0562a06fc54d3687a3ff7d8e2b705f --- /dev/null +++ b/interpro_conserved_site/metadata.json @@ -0,0 +1,349 @@ +{ + "config": "interpro_conserved_site", + "task_level": "protein", + "task_type": "multilabel", + "num_labels": 334, + "label_names": [ + "IPR000047__helix-turn-helix_motif", + "IPR000111__glycoside_hydrolase_family_27/36,_conserved_site", + "IPR000203__gps_motif", + "IPR000445__helix-hairpin-helix_motif", + "IPR000629__atp-dependent_rna_helicase_dead-box,_conserved_site", + "IPR000633__vinculin,_conserved_site", + "IPR000637__hmg-i/hmg-y,_dna-binding,_conserved_site", + "IPR000804__clathrin_adaptor_complex,_small_chain", + "IPR000808__iron-sulfur_cluster_carrier_protein-like,_conserved_site", + "IPR000827__cc_chemokine,_conserved_site", + "IPR000842__phosphoribosyl_pyrophosphate_synthetase,_conserved_site", + "IPR000952__ab_hydrolase_4,_conserved_site", + "IPR001006__procollagen-lysine_5-dioxygenase,_conserved_site", + "IPR001131__peptidase_m24b,_x-pro_dipeptidase/aminopeptidase_p,_conserved_site", + "IPR001261__arge/dape/acy1/cpg2/yscs,_conserved_site", + "IPR001307__thiosulphate_sulfurtransferase,_conserved_site", + "IPR001326__translation_elongation_factor_ef1b,_beta/delta_chains,_conserved_site", + "IPR001331__guanine-nucleotide_dissociation_stimulator,_cdc24,_conserved_site", + "IPR001363__proteinase_inhibitor_i25c,_fetuin,_conserved_site", + "IPR001412__aminoacyl-trna_synthetase,_class_i,_conserved_site", + "IPR001426__tyrosine-protein_kinase,_receptor_class_v,_conserved_site", + "IPR001514__dna-directed_rna_polymerase,_30-40kda_subunit,_conserved_site", + "IPR001522__fatty_acid_desaturase_type_1,_conserved_site", + "IPR001562__zinc_finger,_btk_motif", + "IPR001589__actinin-type_actin-binding_domain,_conserved_site", + "IPR001751__s100/calcium_binding_protein_7/8-like,_conserved_site", + "IPR001824__tyrosine-protein_kinase,_receptor_class_iii,_conserved_site", + "IPR001827__homeobox_protein,_antennapedia_type,_conserved_site", + "IPR001858__phosphatidylethanolamine-binding,_conserved_site", + "IPR001999__osteonectin-like,_conserved_site", + "IPR002011__tyrosine-protein_kinase,_receptor_class_ii,_conserved_site", + "IPR002012__gonadotropin-releasing_hormone", + "IPR002052__dna_methylase,_n-6_adenine-specific,_conserved_site", + "IPR002173__carbohydrate/purine_kinase,_pfkb,_conserved_site", + "IPR002194__chaperonin_tcp-1,_conserved_site", + "IPR002328__alcohol_dehydrogenase,_zinc-type,_conserved_site", + "IPR002364__quinone_oxidoreductase/zeta-crystallin,_conserved_site", + "IPR002464__dna/rna_helicase,_atp-dependent,_deah-box_type,_conserved_site", + "IPR003006__immunoglobulin/major_histocompatibility_complex,_conserved_site", + "IPR003109__goloco_motif", + "IPR003527__mitogen-activated_protein_(map)_kinase,_conserved_site", + "IPR003528__long_hematopoietin_receptor,_single_chain,_conserved_site", + "IPR003529__long_hematopoietin_receptor,_gp130_family_2,_conserved_site", + "IPR003530__long_hematopoietin_receptor,_soluble_alpha_chain,_conserved_site", + "IPR003531__short_hematopoietin_receptor,_family_1,_conserved_site", + "IPR003532__short_hematopoietin_receptor,_family_2,_conserved_site", + "IPR003651__endonuclease_iii-like,_iron-sulphur_cluster_loop_motif", + "IPR003903__ubiquitin_interacting_motif", + "IPR003960__atpase,_aaa-type,_conserved_site", + "IPR004001__actin,_conserved_site", + "IPR004036__endonuclease_iii-like,_conserved_site-2", + "IPR004037__large_ribosomal_subunit_protein_el8-like,_conserved_site", + "IPR005108__help_motif", + "IPR005825__large_ribosomal_subunit_protein_ul24,_conserved_site", + "IPR005829__sugar_transporter,_conserved_site", + "IPR006012__syntaxin/epimorphin,_conserved_site", + "IPR006074__gtp1/obg,_conserved_site", + "IPR006089__acyl-coa_dehydrogenase,_conserved_site", + "IPR006117__2-5-oligoadenylate_synthetase,_c-terminal_conserved_site", + "IPR006180__3-hydroxyacyl-coa_dehydrogenase,_conserved_site", + "IPR006181__d-amino_acid_oxidase,_conserved_site", + "IPR006203__ghmp_kinase,_atp-binding,_conserved_site", + "IPR006224__pseudouridine_synthase,_rlua-like,_conserved_site", + "IPR006594__lis1_homology_motif", + "IPR007577__glycosyltransferase,_dxd_sugar-binding_motif", + "IPR007858__dpy-30_motif", + "IPR008193__dna-directed_rna_polymerase_rpb11,_13-16kda_subunit,_conserved_site", + "IPR008918__helix-hairpin-helix_motif,_class_2", + "IPR009818__pam2_motif", + "IPR013032__egf-like,_conserved_site", + "IPR013055__tachykinin/neurokinin-like,_conserved_site", + "IPR013152__gastrin/cholecystokinin,_conserved_site", + "IPR013992__adenylate_cyclase-associated_cap,_n-terminal", + "IPR014034__ferritin,_conserved_site", + "IPR014762__dna_mismatch_repair,_conserved_site", + "IPR014783__copper_type_ii,_ascorbate-dependent_monooxygenase,_histidine-cluster-2_conserved_site", + "IPR015875__imp_dehydrogenase_/_gmp_reductase,_conserved_site", + "IPR015884__malic_enzyme,_conserved_site", + "IPR015911__phosphoglycerate_kinase,_conserved_site", + "IPR015912__phosphofructokinase,_conserved_site", + "IPR016050__proteasome_beta-type_subunit,_conserved_site", + "IPR016059__dna_ligase,_atp-dependent,_conserved_site", + "IPR016066__alpha-d-phosphohexomutase,_conserved_site", + "IPR016157__cullin,_conserved_site", + "IPR016160__aldehyde_dehydrogenase,_cysteine_active_site", + "IPR017864__arrestin,_conserved_site", + "IPR017865__f-actin_capping_protein,_alpha_subunit,_conserved_site", + "IPR017866__succinyl-coa_synthetase,_beta_subunit,_conserved_site", + "IPR017870__fes_cluster_insertion,_c-terminal,_conserved_site", + "IPR017871__abc_transporter-like,_conserved_site", + "IPR017891__insulin-like_growth_factor_binding_protein,_n-terminal,_cys-rich_conserved_site", + "IPR017900__4fe-4s_ferredoxin,_iron-sulphur_binding,_conserved_site", + "IPR017907__zinc_finger,_ring-type,_conserved_site", + "IPR017937__thioredoxin,_conserved_site", + "IPR017948__transforming_growth_factor_beta,_conserved_site", + "IPR017954__lipid-binding_serum_glycoprotein,_conserved_site", + "IPR017956__at_hook,_dna-binding_motif", + "IPR017957__p-type_trefoil,_conserved_site", + "IPR017967__hmg_box_a_dna-binding_domain,_conserved_site", + "IPR017968__acylphosphatase,_conserved_site", + "IPR017970__homeobox,_conserved_site", + "IPR017972__cytochrome_p450,_conserved_site", + "IPR017974__claudin,_conserved_site", + "IPR017975__tubulin,_conserved_site", + "IPR017977__zona_pellucida_domain,_conserved_site", + "IPR017979__gpcr,_family_3,_conserved_site", + "IPR017983__gpcr,_family_2,_secretin-like,_conserved_site", + "IPR017990__connexin,_conserved_site", + "IPR018000__neurotransmitter-gated_ion-channel,_conserved_site", + "IPR018016__nucleoside_phosphorylase,_conserved_site", + "IPR018038__large_ribosomal_subunit_protein_ul30,_conserved_site", + "IPR018039__intermediate_filament_protein,_conserved_site", + "IPR018045__sulphate_anion_transporter,_conserved_site", + "IPR018048__cxc_chemokine,_conserved_site", + "IPR018049__interleukin-7/interleukin-9,_conserved_site", + "IPR018054__chromogranin,_conserved_site", + "IPR018056__kringle,_conserved_site", + "IPR018066__tubby,_c-terminal,_conserved_site", + "IPR018067__protein_phosphatase_2a_regulatory_subunit_pr55,_conserved_site", + "IPR018073__proteinase_inhibitor_i25,_cystatin,_conserved_site", + "IPR018080__band_7/stomatin-like,_conserved_site", + "IPR018083__sterol_reductase,_conserved_site", + "IPR018091__phosphoenolpyruvate_carboxykinase,_gtp-utilising,_conserved_site", + "IPR018096__interleukin-4/interleukin-13,_conserved_site", + "IPR018097__egf-like_calcium-binding,_conserved_site", + "IPR018099__purine_phosphorylase,_family_2,_conserved_site", + "IPR018102__small_ribosomal_subunit_protein_us11,_conserved_site", + "IPR018103__translationally_controlled_tumour_protein,_conserved_site", + "IPR018104__translation_initiation_factor_1a_(eif-1a),_conserved_site", + "IPR018106__cap,_conserved_site,_n-terminal", + "IPR018107__sodium:dicarboxylate_symporter,_conserved_site", + "IPR018116__somatotropin_hormone,_conserved_site", + "IPR018122__fork_head_domain_conserved_site1", + "IPR018124__calreticulin/calnexin,_conserved_site", + "IPR018130__small_ribosomal_subunit_protein_us2,_conserved_site", + "IPR018134__lysosome-associated_membrane_glycoprotein,_conserved_site", + "IPR018161__wnt_protein,_conserved_site", + "IPR018170__aldo/keto_reductase,_conserved_site", + "IPR018181__heat_shock_protein_70,_conserved_site", + "IPR018186__transcription_factor,_t-box,_conserved_site", + "IPR018192__small_ribosomal_subunit_protein_us5,_n-terminal,_conserved_site", + "IPR018199__small_ribosomal_subunit_protein_es4,_n-terminal,_conserved_site", + "IPR018200__ubiquitin_specific_protease,_conserved_site", + "IPR018207__haem_oxygenase_conserved_site", + "IPR018212__sodium/solute_symporter,_conserved_site", + "IPR018228__deoxyribonuclease,_tatd-related,_conserved_site", + "IPR018233__calsequestrin,_conserved_site", + "IPR018237__myelin_proteolipid_protein_plp,_conserved_site", + "IPR018240__clathrin_adaptor,_mu_subunit,_conserved_site", + "IPR018244__allergen_v5/tpx-1-related,_conserved_site", + "IPR018245__gonadotropin,_beta_subunit,_conserved_site", + "IPR018252__annexin_repeat,_conserved_site", + "IPR018253__dnaj_domain,_conserved_site", + "IPR018255__large_ribosomal_subunit_protein_ul16,_conserved_site,_eukaryotes/archaea", + "IPR018295__flap/gst2/ltc4s,_conserved_site", + "IPR018297__adenylyl_cyclase_class-4/guanylyl_cyclase,_conserved_site", + "IPR018300__aminotransferase,_class_iv,_conserved_site", + "IPR018314__rsmb/nol1/nop2-like,_conserved_site", + "IPR018321__glucosamine-6-phosphate_isomerase,_conserved_site", + "IPR018338__carbonic_anhydrase,_alpha-class,_conserved_site", + "IPR018350__transcription_factor_coe,_conserved_site", + "IPR018357__hexapeptide_transferase,_conserved_site", + "IPR018358__disintegrin,_conserved_site", + "IPR018359__bromodomain,_conserved_site", + "IPR018360__calcitonin,_conserved_site", + "IPR018361__caveolin,_conserved_site", + "IPR018363__cd59_antigen,_conserved_site", + "IPR018376__enoyl-coa_hydratase/isomerase,_conserved_site", + "IPR018378__c-type_lectin,_conserved_site", + "IPR018446__corticotropin-releasing_factor_conserved_site", + "IPR018456__ptr2_family_proton/oligopeptide_symporter,_conserved_site", + "IPR018483__carbohydrate_kinase,_fggy,_conserved_site", + "IPR018486__hemopexin,_conserved_site", + "IPR018488__cyclic_nucleotide-binding,_conserved_site", + "IPR018494__oxysterol-binding_protein,_conserved_site", + "IPR018498__peripherin/rom-1,_conserved_site", + "IPR018503__tetraspanin,_conserved_site", + "IPR018507__cytochrome_c_oxidase,_subunit_via,_conserved_site", + "IPR018517__trna-dihydrouridine_synthase,_conserved_site", + "IPR018525__mini-chromosome_maintenance,_conserved_site", + "IPR018526__glycoside_hydrolase,_family_29,_conserved_site", + "IPR018935__rio_kinase,_conserved_site", + "IPR018936__phosphatidylinositol_3-/4-kinase,_conserved_site", + "IPR018938__glycophorin,_conserved_site", + "IPR019041__ssxrd_motif", + "IPR019735__synapsin,_conserved_site", + "IPR019737__homeobox_engrailed-type,_conserved_site", + "IPR019739__ctf_transcription_factor/nuclear_factor_1,_conserved_site", + "IPR019741__galactokinase,_conserved_site", + "IPR019744__amyloidogenic_glycoprotein,_copper-binding_domain_conserved_site", + "IPR019745__amyloidogenic_glycoprotein,_intracellular_domain,_conserved_site", + "IPR019747__ferm_conserved_site", + "IPR019758__peptidase_s26a,_signal_peptidase_i,_conserved_site", + "IPR019761__dna-directed_rna_polymerase_m,_15kda_subunit,_conserved_site", + "IPR019762__dynamin,_gtpase_region,_conserved_site", + "IPR019763__dynein_light_chain,_type_1/2,_conserved_site", + "IPR019764__endothelin-like_toxin,_conserved_site", + "IPR019765__ephrin,_conserved_site", + "IPR019767__erythropoietin/thrombopoeitin,_conserved_site", + "IPR019770__eukaryotic_translation_initiation_factor_4e_(eif-4e),_conserved_site", + "IPR019775__wd40_repeat,_conserved_site", + "IPR019786__zinc_finger,_phd-type,_conserved_site", + "IPR019801__glycoside_hydrolase,_family_35,_conserved_site", + "IPR019803__glypican,_conserved_site", + "IPR019804__ras_guanine-nucleotide_exchange_factor,_conserved_site", + "IPR019805__heat_shock_protein_hsp90,_conserved_site", + "IPR019808__histidine_triad,_conserved_site", + "IPR019817__interferon_regulatory_factor,_conserved_site", + "IPR019818__isocitrate/isopropylmalate_dehydrogenase,_conserved_site", + "IPR019819__carboxylesterase_type_b,_conserved_site", + "IPR019821__kinesin_motor_domain,_conserved_site", + "IPR019827__leukemia_inhibitory_factor_/oncostatin,_conserved_site", + "IPR019828__lysyl_oxidase,_conserved_site", + "IPR019829__macrophage_migration_inhibitory_factor,_conserved_site", + "IPR019844__cold-shock_domain,_conserved_site", + "IPR019846__nerve_growth_factor_conserved_site", + "IPR019926__large_ribosomal_subunit_protein_ul3,_conserved_site", + "IPR019954__ubiquitin_conserved_site", + "IPR019974__xpg_conserved_site", + "IPR020082__s-adenosyl-l-homocysteine_hydrolase,_conserved_site", + "IPR020083__large_ribosomal_subunit_protein_el39,_conserved_site", + "IPR020084__nudix_hydrolase,_conserved_site", + "IPR020092__pleiotrophin/midkine_heparin-binding_growth_factor,_conserved_site", + "IPR020392__pancreatic_hormone-like,_conserved_site", + "IPR020423__interleukin-10,_conserved_site", + "IPR020550__inositol_monophosphatase,_conserved_site", + "IPR020556__amidase,_conserved_site", + "IPR020557__fumarate_lyase,_conserved_site", + "IPR020574__small_ribosomal_subunit_protein_us9,_conserved_site", + "IPR020590__guanylate_kinase,_conserved_site", + "IPR020596__ribosomal_rna_adenine_methylase_transferase,_conserved_site", + "IPR020611__copper_type_ii,_ascorbate-dependent_monooxygenase,_histidine-cluster-1_conserved_site", + "IPR020612__methylthiotransferase,_conserved_site", + "IPR020613__thiolase,_conserved_site", + "IPR020628__formate-tetrahydrofolate_ligase,_fthfs,_conserved_site", + "IPR020717__apoptosis_regulator,_bcl-2,_bh1_motif,_conserved_site", + "IPR020719__rna_3'-terminal_phosphate_cyclase-like,_conserved_site", + "IPR020726__apoptosis_regulator,_bcl-2,_bh2_motif,_conserved_site", + "IPR020728__apoptosis_regulator,_bcl-2,_bh3_motif,_conserved_site", + "IPR020731__apoptosis_regulator,_bcl-2,_bh4_motif,_conserved_site", + "IPR020809__enolase,_conserved_site", + "IPR020813__fibrillarin,_conserved_site", + "IPR020834__lipoxygenase,_conserved_site", + "IPR020837__fibrinogen,_conserved_site", + "IPR020845__amp-binding,_conserved_site", + "IPR020857__serum_albumin,_conserved_site", + "IPR020863__membrane_attack_complex_component/perforin_domain,_conserved_site", + "IPR020867__tetrahydrofolate_dehydrogenase/cyclohydrolase,_conserved_site", + "IPR020877__interleukin-1_conserved_site", + "IPR020892__cyclophilin-type_peptidyl-prolyl_cis-trans_isomerase,_conserved_site", + "IPR020894__cadherin_conserved_site", + "IPR020901__proteinase_inhibitor_i2,_kunitz,_conserved_site", + "IPR020902__actin/actin-like_conserved_site", + "IPR020903__epithelial_sodium_channel,_conserved_site", + "IPR020904__short-chain_dehydrogenase/reductase,_conserved_site", + "IPR021184__tumour_necrosis_factor,_conserved_site", + "IPR021939__kank_n-terminal_motif", + "IPR022272__lipocalin_family_conserved_site", + "IPR022353__insulin,_conserved_site", + "IPR022357__major_intrinsic_protein,_conserved_site", + "IPR022408__acyl-coa-binding_protein,_acbp,_conserved_site", + "IPR022423__neurohypophysial_hormone,_conserved_site", + "IPR022631__s-adenosylmethionine_synthetase,_conserved_site", + "IPR022657__orn/dap/arg_decarboxylase_2,_conserved_site", + "IPR022678__glycylpeptide_n-tetradecanoyltransferase,_conserved_site", + "IPR022966__ribonuclease_ii/r,_conserved_site", + "IPR023152__ras_gtpase-activating_protein,_conserved_site", + "IPR023174__3'5'-cyclic_nucleotide_phosphodiesterase,_conserved_site", + "IPR023409__14-3-3_protein,_conserved_site", + "IPR023415__low-density_lipoprotein_(ldl)_receptor_class_a,_conserved_site", + "IPR023442__large_ribosomal_subunit_protein_el24,_conserved_site", + "IPR023563__large_ribosomal_subunit_protein_ul13,_conserved_site", + "IPR023576__ubie/coq5_methyltransferase,_conserved_site", + "IPR023581__platelet-derived_growth_factor,_conserved_site", + "IPR023779__chromo_domain,_conserved_site", + "IPR023795__serpin,_conserved_site", + "IPR024607__sulfatase,_conserved_site", + "IPR025820__methyltransferase_nnmt/pnmt/temt,_conserved_site", + "IPR027310__profilin_conserved_site", + "IPR028322__proline-rich_nuclear_receptor_coactivator-like,_proline_rich_region", + "IPR028417__cap,_conserved_site,_c-terminal", + "IPR029162__trp-interacting_helix,_inaf_motif", + "IPR029510__aldehyde_dehydrogenase,_glutamic_acid_active_site", + "IPR029752__d-isomer_specific_2-hydroxyacid_dehydrogenase,_nad-binding_domain_conserved_site_1", + "IPR029753__d-isomer_specific_2-hydroxyacid_dehydrogenase,_nad-binding_domain_conserved_site", + "IPR029760__glutathione_peroxidase_conserved_site", + "IPR029768__fructose-bisphosphate_aldolase_class-i_active_site", + "IPR030373__polyamine_biosynthesis_domain,_conserved_site", + "IPR030456__fork_head_domain_conserved_site_2", + "IPR030457__elo_family,_conserved_site", + "IPR030459__glycosyl_hydrolases_family_31,_conserved_site", + "IPR030470__ubia_prenyltransferase_conserved_site", + "IPR030473__interleukin-6/gcsf/mgf,_conserved_site", + "IPR030476__pentaxin,_conserved_site", + "IPR030479__syndecan,_conserved_site", + "IPR030480__natriuretic_peptide,_conserved_site", + "IPR030490__tissue_inhibitor_of_metalloproteinase,_conserved_site", + "IPR030491__tata-box_binding_protein,_conserved_site", + "IPR030492__rel_homology_domain,_conserved_site", + "IPR030514__stathmin,_conserved_site", + "IPR030659__secy_conserved_site", + "IPR031157__tr-type_g_domain,_conserved_site", + "IPR031305__casein_alpha/beta,_conserved_site", + "IPR031312__sodium/sulphate_symporter,_conserved_site", + "IPR032458__histone_h2a_conserved_site", + "IPR033125__deoxyribonuclease_i,_conservied_site", + "IPR033132__glycosyl_hydrolases_family_1,_n-terminal_conserved_site", + "IPR033466__cornichon,_conserved_site", + "IPR033690__adenylate_kinase,_conserved_site", + "IPR033749__polyprenyl_synthetase,_conserved_site", + "IPR033773__cbx_family_c-terminal_motif", + "IPR033774__yaf2/rybp_c-terminal_binding_motif", + "IPR035090__phosphorylase_pyridoxal-phosphate_attachment_site", + "IPR035595__udp-glycosyltransferase_family,_conserved_site", + "IPR043518__2-5-oligoadenylate_synthetase,_n-terminal_conserved_site", + "IPR043937__golgin_subfamily_a_,_c-terminal_binding_motif", + "IPR045668__fhf_complex_subunit_hook-interacting_protein,_kelaa_motif", + "IPR046790__kbtb,_w-type_lir_motif", + "IPR046793__cysteine_protease_atg4,_f-type_lir_motif", + "IPR047297__ion-transport_regulator,_fxyd_motif", + "IPR047862__tsc22/bun,_conserved_site", + "IPR047864__ribosomal_protein_es26,_conserved_site", + "IPR048254__cdp-alcohol_phosphatidyltransferase,_conserved_site", + "IPR048258__cyclins,_cyclin-box", + "IPR048559__disabled_homolog_1/2,_sulfatide-binding_motif", + "IPR049704__aminotransferases_class-iii_pyridoxal-phosphate_attachment_site", + "IPR049947__copper_amine_oxidase,_copper-binding_site", + "IPR049948__copper_amine_oxidase,_tpq-binding_site", + "IPR053790__pyrroline-5-carboxylate_reductase-like_conserved_site", + "IPR053792__atp_p2x_receptor,_conserved_site", + "IPR053819__tead_interacting_region_3,_omega_loop", + "IPR055262__gamma-glutamyltranspeptidase,_conserved_site", + "IPR055333__histone_h2b,_conserved_site", + "IPR057254__ubiquitin_carboxyl-terminal_hydrolase_family_1,_cysteine_active-site" + ], + "rows": { + "train": 2062, + "validation": 450, + "test": 436 + }, + "source": "Figshare record 31169506, file h_sapiens_proteome_interpro_InterPro_conserved_site_clustersplit_30_50.parquet.gz", + "licence": "CC BY 4.0" +} \ No newline at end of file diff --git a/interpro_conserved_site/test.parquet b/interpro_conserved_site/test.parquet new file mode 100644 index 0000000000000000000000000000000000000000..4aec95e6e1f869c922e5974baed50322c34d7672 --- /dev/null +++ b/interpro_conserved_site/test.parquet @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:43daba6fe51732a2418d30afa14d78221b5f89af2334403eff8149b15a185dae +size 193252 diff --git a/interpro_conserved_site/train.parquet b/interpro_conserved_site/train.parquet new file mode 100644 index 0000000000000000000000000000000000000000..24ee62aea1b7d461e04077cda7b1a809c036c434 --- /dev/null +++ b/interpro_conserved_site/train.parquet @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:98c75e40bb3bd586b3090e6efd7202367c838d4ce7057d74259b6532ec6593ed +size 987116 diff --git a/interpro_conserved_site/validation.parquet b/interpro_conserved_site/validation.parquet new file mode 100644 index 0000000000000000000000000000000000000000..47107cb96e3750fa78db1b616117a966c833dd42 --- /dev/null +++ b/interpro_conserved_site/validation.parquet @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:55d060f67beb0c2192d220e60ef75e518c08a5ac2360bceb6f903ed484668bcd +size 216484 diff --git a/interpro_domain/metadata.json b/interpro_domain/metadata.json new file mode 100644 index 0000000000000000000000000000000000000000..2ab504ad05d6dc16775334ec79c093a38695d688 --- /dev/null +++ b/interpro_domain/metadata.json @@ -0,0 +1,379 @@ +{ + "config": "interpro_domain", + "task_level": "protein", + "task_type": "multilabel", + "num_labels": 364, + "label_names": [ + "IPR000008__c2_domain", + "IPR000014__pas_domain", + "IPR000072__pdgf/vegf_domain", + "IPR000073__alpha/beta_hydrolase_fold-1", + "IPR000086__nudix_hydrolase_domain", + "IPR000095__crib_domain", + "IPR000157__toll/interleukin-1_receptor_homology_(tir)_domain", + "IPR000159__ras-associating_domain", + "IPR000182__gnat_domain", + "IPR000195__rab-gap-tbc_domain", + "IPR000210__btb/poz_domain", + "IPR000219__dbl_homology_domain", + "IPR000232__heat_shock_factor_(hsf)-type,_dna-binding", + "IPR000242__tyrosine-specific_protein_phosphatase,_ptpase_domain", + "IPR000253__forkhead-associated_(fha)_domain", + "IPR000294__gamma-carboxyglutamic_acid-rich_(gla)_domain", + "IPR000299__ferm_domain", + "IPR000306__fyve_zinc_finger", + "IPR000315__b-box-type_zinc_finger", + "IPR000326__phosphatidic_acid_phosphatase_type_2/haloperoxidase", + "IPR000330__snf2,_n-terminal", + "IPR000340__dual_specificity_phosphatase,_catalytic_domain", + "IPR000372__leucine-rich_repeat_n-terminal_domain", + "IPR000387__tyrosine-specific_protein_phosphatases_domain", + "IPR000418__ets_domain", + "IPR000433__zinc_finger,_zz-type", + "IPR000436__sushi/scr/ccp_domain", + "IPR000467__g-patch_domain", + "IPR000483__cysteine-rich_flanking_region,_c-terminal", + "IPR000488__death_domain", + "IPR000504__rna_recognition_motif_domain", + "IPR000532__glucagon/gip/secretin/vip", + "IPR000535__major_sperm_protein_(msp)_domain", + "IPR000536__nuclear_hormone_receptor,_ligand-binding_domain", + "IPR000555__jab1/mpn/mov34_metalloenzyme_domain", + "IPR000566__lipocalin/cytosolic_fatty-acid_binding_domain", + "IPR000569__hect_domain", + "IPR000571__zinc_finger,_ccch-type", + "IPR000582__acyl-coa-binding_protein,_acbp", + "IPR000585__hemopexin-like_domain", + "IPR000608__ubiquitin-conjugating_(ubc),_catalytic_core_domain", + "IPR000626__ubiquitin-like_domain", + "IPR000644__cbs_domain", + "IPR000651__ras-like_guanine_nucleotide_exchange_factor,_n-terminal", + "IPR000690__matrin/u1-c,_c2h2-type_zinc_finger", + "IPR000717__proteasome_component_(pci)_domain", + "IPR000719__protein_kinase_domain", + "IPR000727__target_snare_coiled-coil_homology_domain", + "IPR000742__egf-like_domain", + "IPR000772__ricin_b,_lectin_domain", + "IPR000859__cub_domain", + "IPR000863__sulfotransferase_domain", + "IPR000873__amp-dependent_synthetase/ligase_domain", + "IPR000909__phosphatidylinositol-specific_phospholipase_c,_x_domain", + "IPR000953__chromo/chromo_shadow_domain", + "IPR000961__agc-kinase,_c-terminal", + "IPR000980__sh2_domain", + "IPR001005__sant/myb_domain", + "IPR001039__mhc_class_i_alpha_chain,_alpha1_alpha2_domains", + "IPR001064__beta/gamma_crystallin", + "IPR001107__band_7_domain", + "IPR001111__tgf-beta,_propeptide", + "IPR001124__lipid-binding_serum_glycoprotein,_c-terminal", + "IPR001148__alpha_carbonic_anhydrase_domain", + "IPR001163__sm_domain,_eukaryotic/archaea-type", + "IPR001164__arf_gtpase_activating_protein", + "IPR001173__glycosyltransferase_2-like", + "IPR001202__ww_domain", + "IPR001206__diacylglycerol_kinase,_catalytic_domain", + "IPR001212__somatomedin_b_domain", + "IPR001214__set_domain", + "IPR001245__serine-threonine/tyrosine-protein_kinase,_catalytic_domain", + "IPR001247__exoribonuclease,_phosphorolytic_domain_1", + "IPR001251__cral-trio_lipid_binding_domain", + "IPR001279__metallo-beta-lactamase", + "IPR001293__zinc_finger,_traf-type", + "IPR001296__glycosyl_transferase,_family_1", + "IPR001304__c-type_lectin-like", + "IPR001309__peptidase_c14,_p20_domain", + "IPR001315__card_domain", + "IPR001356__homeodomain", + "IPR001357__brct_domain", + "IPR001365__adenosine_deaminase_domain", + "IPR001368__tnfr/ngfr_cysteine-rich_region", + "IPR001394__peptidase_c19,_ubiquitin_carboxyl-terminal_hydrolase", + "IPR001452__sh3_domain", + "IPR001478__pdz_domain", + "IPR001494__importin-beta,_n-terminal_domain", + "IPR001507__zona_pellucida_domain", + "IPR001565__synaptotagmin", + "IPR001594__palmitoyltransferase,_dhhc_domain", + "IPR001607__zinc_finger,_ubp-type", + "IPR001623__dnaj_domain", + "IPR001628__zinc_finger,_nuclear_hormone_receptor-type", + "IPR001650__helicase,_c-terminal_domain-like", + "IPR001660__sterile_alpha_motif_domain", + "IPR001683__phox_homology", + "IPR001715__calponin_homology_domain", + "IPR001739__methyl-cpg_dna_binding", + "IPR001752__kinesin_motor_domain", + "IPR001763__rhodanese-like_domain", + "IPR001766__fork_head_domain", + "IPR001781__zinc_finger,_lim-type", + "IPR001810__f-box_domain", + "IPR001811__chemokine_interleukin-8-like_domain", + "IPR001818__peptidase_m10,_metallopeptidase", + "IPR001839__transforming_growth_factor-beta,_c-terminal", + "IPR001841__zinc_finger,_ring-type", + "IPR001849__pleckstrin_homology_domain", + "IPR001870__b30.2/spry_domain", + "IPR001878__zinc_finger,_cchc-type", + "IPR001881__egf-like_calcium-binding_domain", + "IPR001895__ras_guanine-nucleotide_exchange_factors_catalytic_domain", + "IPR001909__krueppel-associated_box", + "IPR001932__ppm-type_phosphatase-like_domain", + "IPR001965__zinc_finger,_phd-type", + "IPR002014__vhs_domain", + "IPR002018__carboxylesterase,_type_b", + "IPR002035__von_willebrand_factor,_type_a", + "IPR002048__ef-hand_domain", + "IPR002058__pap/25a-associated", + "IPR002068__alpha_crystallin/hsp20_domain", + "IPR002073__3'5'-cyclic_nucleotide_phosphodiesterase,_catalytic_domain", + "IPR002123__phospholipid/glycerol_acyltransferase", + "IPR002125__cytidine_and_deoxycytidylate_deaminase_domain", + "IPR002126__cadherin-like", + "IPR002138__peptidase_c14,_caspase_non-catalytic_subunit_p10", + "IPR002219__protein_kinase_c-like,_phorbol_ester/diacylglycerol-binding_domain", + "IPR002314__aminoacyl-trna_synthetase,_class_ii_(g/_p/_s/t)", + "IPR002350__kazal_domain", + "IPR002498__phosphatidylinositol-4-phosphate_4/5-kinase,_core", + "IPR002562__3'-5'_exonuclease_domain", + "IPR002589__macro_domain", + "IPR002645__stas_domain", + "IPR002867__ibr_domain", + "IPR002893__zinc_finger,_mynd-type", + "IPR002913__start_domain", + "IPR002931__transglutaminase-like", + "IPR003029__s1_domain", + "IPR003103__bag_domain", + "IPR003112__olfactomedin-like_domain", + "IPR003124__wh2_domain", + "IPR003137__pa_domain", + "IPR003172__md-2-related_lipid-recognition_domain", + "IPR003309__scan_domain", + "IPR003316__e2f/dp_family,_winged-helix_dna-binding_domain", + "IPR003323__otu_domain", + "IPR003347__jmjc_domain", + "IPR003439__abc_transporter-like,_atp-binding_domain", + "IPR003533__doublecortin_domain", + "IPR003593__aaa+_atpase_domain", + "IPR003595__protein-tyrosine_phosphatase,_catalytic", + "IPR003597__immunoglobulin_c1-set", + "IPR003598__immunoglobulin_subtype_2", + "IPR003599__immunoglobulin_domain_subtype", + "IPR003604__matrin/u1-c-like,_c2h2-type_zinc_finger", + "IPR003607__hd/pdease_domain", + "IPR003617__transcription_elongation_factor,_tfiis/crsp70,_n-terminal,_sub-type", + "IPR003618__transcription_elongation_factor_s-ii,_central_domain", + "IPR003645__follistatin-like,_n-terminal", + "IPR003649__b-box,_c-terminal", + "IPR003650__orange_domain", + "IPR003654__oar_domain", + "IPR003877__spry_domain", + "IPR003879__butyrophylin-like,_spry_domain", + "IPR003887__lem_domain", + "IPR003890__mif4g-like,_type_3", + "IPR003891__initiation_factor_eif-4_gamma,_ma3", + "IPR003892__ubiquitin_system_component_cue", + "IPR003954__rna_recognition_motif_domain,_eukaryotic-type", + "IPR003958__transcription_factor_cbf/nf-y/archaeal_histone_domain", + "IPR003959__atpase,_aaa-type,_core", + "IPR003961__fibronectin_type_iii", + "IPR004012__run_domain", + "IPR004043__lccl_domain", + "IPR004045__glutathione_s-transferase,_n-terminal", + "IPR004046__glutathione_s-transferase,_c-terminal", + "IPR004087__k_homology_domain", + "IPR004088__k_homology_domain,_type_1", + "IPR004113__fad-binding_oxidoreductase/transferase,_type_4,_c-terminal", + "IPR004182__gram_domain", + "IPR004217__tim10-like", + "IPR004364__aminoacyl-trna_synthetase,_class_ii_(d/k/n)", + "IPR004365__ob-fold_nucleic_acid_binding_domain,_aa-trna_synthetase-type", + "IPR004367__cyclin,_c-terminal_domain", + "IPR004826__basic_leucine_zipper_domain,_maf-type", + "IPR004827__basic-leucine_zipper_domain", + "IPR004853__sugar_phosphate_transporter_domain", + "IPR005036__cbm21_(carbohydrate_binding_type-21)_domain", + "IPR005123__oxoglutarate/iron-dependent_dioxygenase_domain", + "IPR005135__endonuclease/exonuclease/phosphatase", + "IPR005225__small_gtp-binding_domain", + "IPR005576__rna_polymerase_rpb7-like_,_n-terminal", + "IPR005821__ion_transport_domain", + "IPR006011__syntaxin,_n-terminal_domain", + "IPR006020__ptb/pi_domain", + "IPR006026__peptidase,_metallopeptidase", + "IPR006052__tumour_necrosis_factor_domain", + "IPR006073__gtp_binding_domain", + "IPR006094__fad_linked_oxidase,_n-terminal", + "IPR006195__aminoacyl-trna_synthetase,_class_ii", + "IPR006208__glycoprotein_hormone_subunit_beta", + "IPR006574__spry-associated", + "IPR006575__rwd_domain", + "IPR006620__prolyl_4-hydroxylase,_alpha_subunit", + "IPR006634__tram/lag1/cln8_homology_domain", + "IPR006640__sprt-like", + "IPR006642__rad18,_zinc_finger_ubz4-type", + "IPR006671__cyclin,_n-terminal", + "IPR006680__amidohydrolase-related", + "IPR006694__fatty_acid_hydroxylase", + "IPR006861__hyaluronan/mrna-binding_protein", + "IPR006909__rad21/rec8-like_protein,_c-terminal,_eukaryotic", + "IPR006910__rad21/rec8-like_protein,_n-terminal", + "IPR007052__cs_domain", + "IPR007110__immunoglobulin-like_domain", + "IPR007330__mit_domain", + "IPR007527__zinc_finger,_swim-type", + "IPR007529__zinc_finger,_hit-type", + "IPR008174__galanin", + "IPR008197__wap-type_'four-disulfide_core'_domain", + "IPR008422__kn_homeodomain", + "IPR010513__ken_domain", + "IPR010569__myotubularin-like,_phosphatase_domain", + "IPR010909__plac", + "IPR010987__glutathione_s-transferase,_c-terminal-like", + "IPR011016__zinc_finger,_ring-ch-type", + "IPR011072__hr1_rho-binding_domain", + "IPR011124__zinc_finger,_cw-type", + "IPR011161__mhc_class_i-like_antigen_recognition-like", + "IPR011545__dead/deah-box_helicase_domain", + "IPR011547__slc26a/sulp_transporter_domain", + "IPR011598__myc-type,_basic_helix-loop-helix_(bhlh)_domain", + "IPR011600__peptidase_c14,_caspase_domain", + "IPR011611__carbohydrate_kinase_pfkb", + "IPR011650__peptidase_m20,_dimerisation_domain", + "IPR012319__formamidopyrimidine-dna_glycosylase,_catalytic_domain", + "IPR013087__zinc_finger_c2h2-type", + "IPR013098__immunoglobulin_i-set", + "IPR013099__potassium_channel_domain", + "IPR013106__immunoglobulin_v-set_domain", + "IPR013137__zinc_finger,_tfiib-type", + "IPR013151__immunoglobulin-like_beta-sandwich_domain", + "IPR013162__cd80-like,_immunoglobulin_c2-set", + "IPR013164__cadherin,_n-terminal", + "IPR013216__methyltransferase_type_11", + "IPR013520__ribonuclease_h-like_domain", + "IPR013568__sefir_domain", + "IPR013655__pas_fold-3", + "IPR013763__cyclin-like_domain", + "IPR013766__thioredoxin_domain", + "IPR013767__pas_fold", + "IPR014001__helicase_superfamily_1/2,_atp-binding_domain", + "IPR014014__rna_helicase,_dead-box_type,_q_motif", + "IPR014020__tensin_phosphatase,_c2_domain", + "IPR014044__cap_domain", + "IPR014720__double-stranded_rna-binding_domain", + "IPR015338__glycosyl_transferase_64_domain", + "IPR015369__follistatin/osteonectin_egf_domain", + "IPR015590__aldehyde_dehydrogenase_domain", + "IPR015847__exoribonuclease,_phosphorolytic_domain_2", + "IPR015886__formamidopyrimidine-dna_glycosylase,_h2th_dna-binding", + "IPR015898__g-protein,_gamma_subunit-like_domain", + "IPR015917__peptidase_c14a,_caspase_catalytic_domain", + "IPR015940__ubiquitin-associated_domain", + "IPR016040__nad(p)-binding_domain", + "IPR016054__ly-6_antigen/upa_receptor-like", + "IPR016137__rgs_domain", + "IPR016166__fad-binding_domain,_pcmh-type", + "IPR016179__insulin-like", + "IPR016201__psi_domain", + "IPR017452__gpcr,_rhodopsin-like,_7tm", + "IPR017455__zinc_finger,_fyve-related", + "IPR017884__sant_domain", + "IPR017892__protein_kinase,_c-terminal", + "IPR017896__4fe-4s_ferredoxin-type,_iron-sulphur_binding_domain", + "IPR017920__comm_domain", + "IPR017923__transcription_factor_iis,_n-terminal", + "IPR017942__lipid-binding_serum_glycoprotein,_n-terminal", + "IPR017981__gpcr,_family_2-like,_7tm", + "IPR018484__carbohydrate_kinase_fggy,_n-terminal", + "IPR018957__zinc_finger,_c3hc4_ring-type", + "IPR018979__ferm,_n-terminal", + "IPR018980__ferm,_c-terminal_ph-like_domain", + "IPR019339__cbf1-interacting_co-repressor_cir,_n-terminal_domain", + "IPR019383__golgin_subfamily_a_member_7/erf4", + "IPR019748__ferm_central_domain", + "IPR019749__band_4.1_domain", + "IPR019787__zinc_finger,_phd-finger", + "IPR020067__frizzled_domain", + "IPR020422__dual_specificity_protein_phosphatase_domain", + "IPR020479__homeodomain,_metazoa", + "IPR020635__tyrosine-protein_kinase,_catalytic_domain", + "IPR020846__major_facilitator_superfamily_domain", + "IPR022049__fam69,_protein-kinase_domain", + "IPR022666__large_ribosomal_subunit_protein_ul2,_rna-binding_domain", + "IPR022669__large_ribosomal_subunit_protein_ul2,_c-terminal", + "IPR022764__peptidase_s54,_rhomboid_domain", + "IPR022775__ap_complex,_mu/sigma_subunit", + "IPR023340__uma_domain", + "IPR023412__ribonuclease_a-domain", + "IPR023780__chromo_domain", + "IPR023796__serpin_domain", + "IPR023801__histone_deacetylase_domain", + "IPR024771__suz_domain", + "IPR025110__amp-binding_enzyme,_c-terminal_domain", + "IPR025256__tm7s3/tm198-like_domain", + "IPR025933__beta-defensin_domain", + "IPR027370__zinc_finger,_ring-type,_eukaryotic", + "IPR027450__alpha-ketoglutarate-dependent_dioxygenase_alkb-like", + "IPR027791__galactosyltransferase,_c-terminal", + "IPR027995__galactosyltransferase,_n-terminal", + "IPR028002__myb/sant-like_dna-binding_domain_5", + "IPR028021__katanin_p80_subunit,_c-terminal", + "IPR028565__mu_homology_domain", + "IPR028889__ubiquitin_specific_protease_ups,_catalytic_domain", + "IPR028933__lebercilin_domain", + "IPR029244__fam69,_n-terminal", + "IPR029281__fam194,_c-terminal", + "IPR030379__septin-type_guanine_nucleotide-binding_(g)_domain", + "IPR031315__lns2/pitp", + "IPR031320__gage", + "IPR032098__acyltransferase,_c-terminal_domain", + "IPR032198__e2f_transcription_factor,_cc-mb_domain", + "IPR033729__serine-trna_ligase_catalytic_core_domain", + "IPR033739__peptidase_m10a,_catalytic_domain", + "IPR033899__cxc_chemokine_domain", + "IPR033989__cd209-like,_c-type_lectin-like_domain", + "IPR033992__natural_killer_cell_receptor-like,_c-type_lectin-like_domain", + "IPR034085__tog_domain", + "IPR034133__chemokine_cc,_dccl_motif-cointaining_domain", + "IPR034732__extended_phd_(ephd)_domain", + "IPR035076__snake_toxin/toxin-like", + "IPR035587__dus-like,_fmn-binding_domain", + "IPR037516__tripartite_denn_domain", + "IPR037518__mpn_domain", + "IPR041418__sam_domain", + "IPR041569__aaa_atpase,_aaa+_lid_domain", + "IPR041698__methyltransferase_domain_25", + "IPR044744__znrf4_/rnf13/rnf167,_pa_domain", + "IPR044822__myb/sant-like_dna-binding_domain_4", + "IPR044865__mrh_domain", + "IPR045135__26s_proteasome_regulatory_subunit_rpn7,_n-terminal", + "IPR045885__n-acetylgalactosaminyltransferase", + "IPR046371__bcl-2,_bcl-2_homology_region_1-3", + "IPR047575__sm_domain", + "IPR048271__paraneoplastic_antigen_ma-like,_n-terminal_domain", + "IPR048287__thrombospondin-like,_n-terminal_domain", + "IPR048290__zona_pellucida_domain,_chordate-type", + "IPR049730__snf2/rad5-like,_c-terminal_helicase_domain", + "IPR049883__notch1_egf-like_calcium-binding_domain", + "IPR049899__zinc_finger,_c2hc/c3h-type", + "IPR053891__shisa,_n-terminal_domain", + "IPR053896__butyrophilin_subfamily_3_member_a2-like,_ig-c_domain", + "IPR054076__zuotin-like,_zuotin_homology_domain", + "IPR054708__poly(a)_rna_polymerase,_mitochondrial-like,_central_palm_domain", + "IPR055256__khdc4/bbp-like,_kh-domain_type_i", + "IPR055355__zp-c_domain", + "IPR055356__zp-n_domain", + "IPR055414__disease_resistance_r13l4/shoc-2-like,_lrr_domain", + "IPR055439__eml-like,_first_beta-propeller_domain", + "IPR055442__eml-like,_second_beta-propeller_domain", + "IPR056436__zic1-5/gli1-3like,_c2h2_zinc_finger", + "IPR057244__gain,_subdomain_b" + ], + "rows": { + "train": 5307, + "validation": 1371, + "test": 1325 + }, + "source": "Figshare record 31169506, file h_sapiens_proteome_interpro_InterPro_domain_clustersplit_20_50.parquet.gz", + "licence": "CC BY 4.0" +} \ No newline at end of file diff --git a/interpro_domain/test.parquet b/interpro_domain/test.parquet new file mode 100644 index 0000000000000000000000000000000000000000..aa8758b7f7b7ea4f03eedf714a49d79ae151afcb --- /dev/null +++ b/interpro_domain/test.parquet @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:dc498a05067dd8adb827486740a4a6123e7d5c2c02d8c8b7ef38e5a1bb965de7 +size 598858 diff --git a/interpro_domain/train.parquet b/interpro_domain/train.parquet new file mode 100644 index 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"task_type": "multilabel", + "num_labels": 239, + "label_names": [ + "IPR000006__metallothionein,_vertebrate", + "IPR000276__g_protein-coupled_receptor,_rhodopsin-like", + "IPR000286__histone_deacetylase_hdac", + "IPR000301__tetraspanin,_animals", + "IPR000558__histone_h2b", + "IPR000560__histidine_phosphatase_superfamily,_clade-2", + "IPR000615__bestrophin", + "IPR000725__olfactory_receptor", + "IPR000734__triacylglycerol_lipase_family", + "IPR000798__ezrin/radixin/moesin-like", + "IPR000832__gpcr,_family_2,_secretin-like", + "IPR000837__ap-1_transcription_factor", + "IPR000874__bombesin/neuromedin-b/ranatensin_peptide_family", + "IPR000911__ribosomal_protein_ul11", + "IPR000920__myelin_p0_protein-related", + "IPR000929__dopamine_receptor_family", + "IPR001067__nuclear_translocator", + "IPR001128__cytochrome_p450", + "IPR001314__peptidase_s1a,_chymotrypsin_family", + "IPR001353__proteasome,_subunit_alpha/beta", + "IPR001388__synaptobrevin-like", + "IPR001392__clathrin_adaptor,_mu_subunit", + "IPR001545__gonadotropin,_beta_subunit", + "IPR001564__nucleoside_diphosphate_kinase", + "IPR001613__flavin_amine_oxidase", + "IPR001675__glycosyl_transferase_family_29", + "IPR001753__enoyl-coa_hydratase/isomerase", + "IPR001806__small_gtpase", + "IPR001958__tetracycline_resistance_protein_teta/multidrug_resistance_protein_mdtg-like", + "IPR002051__haem_oxygenase", + "IPR002067__mitochondrial_carrier_protein", + "IPR002164__nucleosome_assembly_protein_(nap)", + "IPR002209__fibroblast_growth_factor_family", + "IPR002345__lipocalin", + "IPR002347__short-chain_dehydrogenase/reductase_sdr", + "IPR002398__peptidase_c14_family", + "IPR002401__cytochrome_p450,_e-class,_group_i", + "IPR002423__chaperonin_cpn60/groel/tcp-1_family", + "IPR002450__von_ebner's_gland_protein/_bos/can_allergen", + "IPR002494__keratin-associated_protein", + "IPR002495__glycosyl_transferase,_family_8", + "IPR002659__glycosyl_transferase,_family_31", + "IPR002777__prefoldin_beta-like", + "IPR002957__keratin,_type_i", + "IPR003092__two_pore_domain_potassium_channel,_task_family", + "IPR003177__cytochrome_c_oxidase_subunit_viia,_metazoa", + "IPR003280__two_pore_domain_potassium_channel", + "IPR003406__glycosyl_transferase,_family_14", + "IPR003578__small_gtpase_rho", + "IPR003689__zinc/iron_permease", + "IPR003968__potassium_channel,_voltage_dependent,_kv", + "IPR003971__potassium_channel,_voltage_dependent,_kv5/kv9", + "IPR004031__pmp-22/emp/mp20/claudin", + "IPR004156__organic_anion_transporter_polypeptide", + "IPR004171__camp-dependent_protein_kinase_inhibitor", + "IPR004299__membrane_bound_o-acyl_transferase,_mboat", + "IPR004301__nucleoplasmin_family", + "IPR004752__ampg-like_permease/acetyl-coenzyme_a_transporter_1", + "IPR005334__dynein_light_chain_tctex-1_like", + "IPR005828__major_facilitator,_sugar_transporter-like", + "IPR006028__gamma-aminobutyric_acid_a_receptor/glycine_receptor_alpha", + "IPR006187__claudin", + "IPR006201__neurotransmitter-gated_ion-channel", + "IPR006439__had_hydrolase,_subfamily_ia", + "IPR006838__adtrp/aig1", + "IPR006876__lmbr1-like_membrane_protein", + "IPR007237__cd20-like_family", + "IPR007305__vesicle_transport_protein,_got1/sft2-like", + "IPR007593__cd225/dispanin_family", + "IPR007659__keratin,_high-sulphur_matrix_protein", + "IPR007951__keratin-associated_protein,_pmg_type", + "IPR008428__chondroitin_n-acetylgalactosaminyltransferase", + "IPR009262__solute_carrier_family_35_member_slc35f1/f2/f6", + "IPR009637__transmembrane_protein_gpr107/gpr108-like", + "IPR010345__interleukin-17_family", + "IPR010548__bnip3", + "IPR011701__major_facilitator_superfamily", + "IPR012163__sialyltransferase", + "IPR013128__peptidase_c1a", + "IPR013273__adamts/adamts-like", + "IPR013836__cd34/podocalyxin", + "IPR014631__cellular_repressor_of_e1a-stimulated_genes_(creg)", + "IPR015496__ubiquilin", + "IPR015526__frizzled/secreted_frizzled-related_protein", + "IPR015615__transforming_growth_factor-beta-related", + "IPR015631__cd2/slam_family_receptor", + "IPR015812__integrin_beta_subunit", + "IPR016053__haem_oxygenase-like", + "IPR016272__lipase,_liph-type", + "IPR016469__carbohydrate_sulfotransferase", + "IPR016491__septin", + "IPR018154__tlv/env_coat_polyprotein", + "IPR018499__tetraspanin/peripherin", + "IPR019585__26s_proteasome_regulatory_subunit_rpn7/cop9_signalosome_complex_subunit_1", + "IPR021134__bestrophin-like", + "IPR021190__peptidase_m10a", + "IPR021743__keratin-associated_protein,_type8/19/20/21/22", + "IPR022352__insulin/igf/relaxin", + "IPR023235__fam105", + "IPR023333__proteasome_b-type_subunit", + "IPR024810__mab21l/cyclic_gmp-amp_synthase-like_receptor", + "IPR024936__cyclophilin-type_peptidyl-prolyl_cis-trans_isomerase", + "IPR026512__rgs7bp/rgs9bp_family", + "IPR026617__transmembrane_and_coiled-coil_domain-containing_protein_2/5", + "IPR027640__kinesin-like_protein", + "IPR027971__elongin_bc_and_polycomb_repressive_complex_2-associated_protein_epop-like", + "IPR028118__chibby_family", + "IPR028325__voltage-gated_potassium_channel", + "IPR028751__cation_channel_sperm-associated_auxiliary_subunit_delta/epsilon", + "IPR029684__schlafen_family", + "IPR030417__membrane-spanning_4-domains_subfamily_a", + "IPR030564__myotubularin", + "IPR031127__e3_ubiquitin_ligase_rbr_family", + "IPR031328__ephrin", + "IPR031627__pdzk1-interacting_protein_1/smim24", + "IPR032801__peroxiredoxin-like_2a/b/c", + "IPR037359__heparan_sulfate_sulfotransferase", + "IPR037796__transcription_initiation_factor_tfiid_subunit_6", + "IPR037936__netrin_receptor_unc5a-d", + "IPR039297__cytochrome_c_oxidase_subunit_vii", + "IPR039361__cyclin", + "IPR039809__chemokine_beta/gamma/delta", + "IPR040079__glutathione_transferase_family", + "IPR040167__transcription_factor_cp2-like", + "IPR040255__non-specific_endonuclease", + "IPR043183__dnaj_homolog_subfamily_b_member_2/6-like", + "IPR043198__cyclin/cyclin-like_subunit_ssn8", + "IPR043210__cd44_antigen-like", + "IPR043378__paired_mesoderm_homeobox_protein_1/2", + "IPR043563__nuclear_body_protein_sp110/sp140/sp140l-like", + "IPR044156__galectin-like", + "IPR045046__vacuolar_protein_sorting-associated_protein_9-like", + "IPR045103__e3_ubiquitin-protein_ligase_rnf5/rnf185-like", + "IPR045119__sun_domain-containing_protein_1-5", + "IPR046327__homeobox_protein_hox-a1/b1/d1", + "IPR046965__cyclin_a/b-like", + "IPR046985__inositol_5-phosphatase", + "IPR047132__olfactory_receptor_subfamily_6c-like", + "IPR048280__cytochrome_oxidase_c_subunit_vib-like", + "IPR050108__cyclin-dependent_kinase", + "IPR050111__c-type_lectin_and_snaclec_domain-containing_protein", + "IPR050113__ubiquitin-conjugating_enzyme", + "IPR050117__mitogen-activated_protein_(map)_kinase", + "IPR050122__receptor_tyrosine_kinase", + "IPR050125__g-protein_coupled_receptor_opsins", + "IPR050140__sry-related_hmg-box_transcription_factor-like", + "IPR050143__tripartite_motif-containing", + "IPR050150__immunoglobulin_variable_light_chain", + "IPR050160__major_histocompatibility_complex/immunoglobulin", + "IPR050164__ubiquitin_carboxyl-terminal_hydrolases", + "IPR050169__krueppel_c2h2-type_zinc-finger", + "IPR050185__ubiquitin_carboxyl-terminal_hydrolase", + "IPR050186__triose_phosphate/phosphate_translocator", + "IPR050199__immunoglobulin_heavy_variable", + "IPR050216__leucine-rich_repeat_domain-containing_protein", + "IPR050224__three_amino_acid_loop_extension_(tale)_homeobox", + "IPR050241__nad-capped_rna_hydrolase_nudc_subfamily", + "IPR050255__pou_domain_transcription_factor", + "IPR050281__flavin_monoamine_oxidase_and_related_enzymes", + "IPR050307__sterol_desaturase_and_related_enzymes", + "IPR050309__type-b_carboxylesterase/lipase", + "IPR050329__gli_c2h2-type_zinc-finger", + "IPR050331__zinc_finger", + "IPR050333__small_leucine-rich_proteoglycans", + "IPR050365__mitochondrial_import_inner_membrane_translocase_subunit_tim50", + "IPR050372__neurexin-related_cell_adhesion_and_synaptic_protein", + "IPR050373__fibrinogen_c-terminal_domain-containing_protein", + "IPR050380__immune_recognition_and_response_modulators", + "IPR050384__endophilin/sh3rf", + "IPR050394__homeobox_nk-like_transcription_regulators", + "IPR050402__olfactory_receptor_51/52/56-like", + "IPR050410__ccr4/nocturin_mrna_turnover_and_transcription", + "IPR050412__immunoglobulin-like_receptors_in_immune_regulation", + "IPR050427__human_olfactory_receptors", + "IPR050431__adaptor_complexes_medium_subunit", + "IPR050439__adamts_and_adamts-like", + "IPR050441__rna-binding_motif", + "IPR050457__zinc_finger_and_btb_domain-containing", + "IPR050467__leucine-rich_repeat_and_fibronectin_type-iii_domain-containing", + "IPR050502__eukaryotic_rna-binding", + "IPR050504__immunoglobulin_superfamily_btn/mog_domain-containing_protein", + "IPR050516__olfactory_g-protein_coupled_receptor", + "IPR050527__snail/krueppel_c2h2-type_zinc-finger", + "IPR050541__leucine-rich_repeat_and_transmembrane_domain-containing_protein", + "IPR050548__polycomb_group_and_chromatin_remodeling_factors", + "IPR050568__transcription/dna_replication_regulator", + "IPR050576__ciliary_and_flagellar_integrity-associated_protein", + "IPR050578__marvel_domain-containing_and_chemokine-like_factor_proteins", + "IPR050589__ikaros_c2h2-type_zinc-finger", + "IPR050617__e3_ubiquitin-protein_ligases_and_fn3/spry_domain-containing_proteins", + "IPR050636__c2h2-type_zinc_finger_domain-containing_protein", + "IPR050645__histidine_acid_phosphatase", + "IPR050649__paired_homeobox_transcription_factors", + "IPR050650__type_ii_cytokine_and_tissue_factor_receptors", + "IPR050653__protease_inhibitors_and_growth_factor_antagonists", + "IPR050663__ankyrin_repeat_and_socs_box", + "IPR050666__epithelial_splicing_regulatory", + "IPR050671__cd300_family_immune_receptors", + "IPR050685__low-density_lipoprotein_receptor", + "IPR050752__c2h2-type_zinc-finger_domain-containing_protein", + "IPR050754__peptidyl-prolyl_cis-trans_isomerase_fkbp4/5/8-like", + "IPR050755__trafac_ylqf/yawg_gtpases,_ribosome_maturation", + "IPR050758__zinc_finger_protein,_c2h2-type", + "IPR050774__kcmf1_and_dystrophin", + "IPR050776__ankyrin_repeat_and_cyclin-dependent_kinase_inhibitor", + "IPR050826__krueppel_c2h2-type_zinc_finger", + "IPR050840__adaptor_complexes_large_subunit", + "IPR050870__fast_kinase_domain-containing", + "IPR050888__zinc_finger_c2h2-type_transcription_regulators", + "IPR050918__cnf-like_phospholipase_a2_inhibitor", + "IPR050930__major_facilitator_superfamily_vesicular_transporter", + "IPR050933__circadian_clock_transcription_factors", + "IPR050944__family_with_sequence_similarity_83_(fam83)", + "IPR051002__ubiquitin-binding_and_autophagy-associated_domain-containing_protein", + 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