Index

A

add_edge() (obnb.graph.base.BaseGraph method) (obnb.graph.DirectedSparseGraph method) (obnb.graph.OntologyGraph method) (obnb.graph.SparseGraph method) add_featvec() (obnb.feature.base.BaseFeature method) add_labelset() (obnb.label.LabelsetCollection method) add_node() (obnb.graph.base.BaseGraph method) add_nodes() (obnb.graph.base.BaseGraph method) AlevinFry (class in obnb.data.experimental)

align() (obnb.feature.base.BaseFeature method) align_to_idmap() (obnb.feature.base.BaseFeature method) align_to_ids() (obnb.feature.base.BaseFeature method) AllHoldout (class in obnb.label.split) ancestors() (obnb.graph.OntologyGraph method) apply() (obnb.label.LabelsetCollection method) apply_transform() (obnb.data.annotated_ontology.base.BaseAnnotatedOntologyData method) (obnb.data.base.BaseData method) auroc() (in module obnb.metric.standard)

B

BaseAnnotatedOntologyData (class in obnb.data.annotated_ontology.base) BaseData (class in obnb.data.base) BaseFeature (class in obnb.feature.base) BaseGraph (class in obnb.graph.base)

BaseNDExData (class in obnb.data.network.base) BaseTrainer (class in obnb.model_trainer.base) BioGRID (class in obnb.data) BioPlex (class in obnb.data)

C

cache_dir (obnb.data.base.BaseData property) cache_on_static() (obnb.graph.OntologyGraph method) cast_ndarray_type() (in module obnb.metric.standard) classname (obnb.data.base.BaseData property) Compose (class in obnb.label.filters) ComPPIHumanInt (class in obnb.data)

compute_pval_mat() (obnb.label.filters.NegativeGeneratorHypergeom method) connected_components() (obnb.graph.base.BaseGraph method) (obnb.graph.DenseGraph method) (obnb.graph.DirectedSparseGraph method) (obnb.graph.SparseGraph method) ConsensusPathDB (class in obnb.data) construct_adj_vec() (obnb.graph.SparseGraph method)

D

degree() (obnb.graph.DenseGraph method) (obnb.graph.DirectedSparseGraph method) (obnb.graph.SparseGraph method) DenseGraph (class in obnb.graph) dim (obnb.feature.base.BaseFeature property) directed (obnb.graph.DirectedSparseGraph property) (obnb.graph.SparseGraph property) DirectedSparseGraph (class in obnb.graph) DISEASES (class in obnb.data) DISEASES_ExperimentsFiltered (class in obnb.data) DISEASES_ExperimentsFull (class in obnb.data) DISEASES_KnowledgeFiltered (class in obnb.data) DISEASES_KnowledgeFull (class in obnb.data) DISEASES_TextminingFiltered (class in obnb.data) DISEASES_TextminingFull (class in obnb.data)

DISEASESAnnotation (class in obnb.data) DisGeNET (class in obnb.data) DisGeNET_Animal (class in obnb.data) DisGeNET_BEFREE (class in obnb.data) DisGeNET_Curated (class in obnb.data) DisGeNET_GWAS (class in obnb.data) DisGeNETAnnotation (class in obnb.data) download() (obnb.data.annotated_ontology.base.BaseAnnotatedOntologyData method) (obnb.data.base.BaseData method) (obnb.data.experimental.AlevinFry method) (obnb.data.network.base.BaseNDExData method) download_archive() (obnb.data.base.BaseData method) download_completed() (obnb.data.annotated_ontology.base.BaseAnnotatedOntologyData method) (obnb.data.base.BaseData method) (obnb.data.experimental.AlevinFry method)

E

edge_data (obnb.graph.SparseGraph property) edge_gen() (obnb.graph.SparseGraph method) edglst_reader() (obnb.graph.SparseGraph static method) edglst_writer() (obnb.graph.SparseGraph static method) entity_ids (obnb.label.LabelsetCollection property)

EntityExistenceFilter (class in obnb.label.filters) EntityRangeFilterNoccur (class in obnb.label.filters) evaluate() (obnb.model_trainer.gnn.SimpleGNNTrainer method) export() (obnb.label.LabelsetCollection method) export_gmt() (obnb.label.LabelsetCollection method)

F

feature_ids (obnb.feature.MultiFeatureVec property) FeatureVec (class in obnb.feature) from_anndata() (obnb.feature.base.BaseFeature class method) from_cx_stream_file() (obnb.graph.DenseGraph class method) (obnb.graph.SparseGraph class method) from_dict() (obnb.label.LabelsetCollection class method) from_edglst() (obnb.graph.DenseGraph class method) from_gmt() (obnb.label.LabelsetCollection class method) from_mat() (obnb.feature.base.BaseFeature class method) (obnb.feature.MultiFeatureVec class method) (obnb.graph.DenseGraph class method) (obnb.graph.SparseGraph class method)

from_mats() (obnb.feature.MultiFeatureVec class method) from_npy() (obnb.graph.DenseGraph class method) from_npz() (obnb.graph.SparseGraph class method) from_obo() (obnb.graph.OntologyGraph class method) from_ontology_graph() (obnb.label.LabelsetCollection class method) FunCoup (class in obnb.data)

G

GeneOntology (class in obnb.data) GeneOntologyAnnotation (class in obnb.data) get_column_names() (obnb.data.DISEASESAnnotation method) get_edge() (obnb.graph.DenseGraph method) get_features() (obnb.feature.MultiFeatureVec method) get_features_from_idx() (obnb.feature.MultiFeatureVec method) get_featvec() (obnb.feature.base.BaseFeature method) (obnb.feature.FeatureVec method) get_featvec_from_idx() (obnb.feature.base.BaseFeature method) get_info() (obnb.label.LabelsetCollection method) get_labelset() (obnb.label.LabelsetCollection method) get_negative() (obnb.label.LabelsetCollection method) get_neighbors() (obnb.graph.base.BaseGraph method) get_noccur() (obnb.label.LabelsetCollection method) get_node_attr() (obnb.graph.OntologyGraph method)

get_node_id() (obnb.graph.base.BaseGraph method) get_node_idx() (obnb.graph.base.BaseGraph method) get_node_name() (obnb.graph.OntologyGraph method) get_nonred_label_ids() (obnb.label.filters.LabelsetNonRedFilter method) get_split_idx() (obnb.label.split.RatioHoldout method) (obnb.label.split.RatioPartition method) (obnb.label.split.ThresholdHoldout method) (obnb.label.split.ThresholdPartition method) get_val_getter() (obnb.label.filters.LabelsetRangeFilterSplit method) get_y() (obnb.label.LabelsetCollection method) GOBP (class in obnb.data) GOCC (class in obnb.data) GOMF (class in obnb.data) graphgym_auroc() (in module obnb.metric.graphgym_metric) graphgym_log2_auprc_prior() (in module obnb.metric.graphgym_metric) graphgym_precision_at_topk() (in module obnb.metric.graphgym_metric)

H

HIPPIE (class in obnb.data) HPO (class in obnb.data) HumanBaseTopGlobal (class in obnb.data) HumanNet (class in obnb.data)

HumanNet_CC (class in obnb.data) HumanNet_FN (class in obnb.data) HumanPhenotypeOntologyAnnotation (class in obnb.data) HuMAP (class in obnb.data) HuRI (class in obnb.data)

I

iapply() (obnb.label.LabelsetCollection method) idmap (obnb.feature.base.BaseFeature property) (obnb.graph.base.BaseGraph property) ids (obnb.feature.base.BaseFeature property) induced_subgraph() (obnb.graph.base.BaseGraph method) (obnb.graph.DenseGraph method) (obnb.graph.SparseGraph method)

info_dir (obnb.data.base.BaseData property) info_log_path (obnb.data.base.BaseData property) is_connected() (obnb.graph.base.BaseGraph method) isempty() (obnb.feature.base.BaseFeature method) (obnb.graph.base.BaseGraph method) items() (obnb.label.LabelsetCollection method) iter_terms() (obnb.graph.OntologyGraph static method)

L

label_ids (obnb.label.LabelsetCollection property) LabelPropagationTrainer (class in obnb.model_trainer.label_propagation) LabelsetCollection (class in obnb.label) LabelsetExistenceFilter (class in obnb.label.filters) LabelsetNonRedFilter (class in obnb.label.filters) LabelsetPairwiseFilterJaccard (class in obnb.label.filters) LabelsetPairwiseFilterOverlap (class in obnb.label.filters) LabelsetRangeFilterSize (class in obnb.label.filters) LabelsetRangeFilterSplit (class in obnb.label.filters) largest_connected_subgraph() (obnb.graph.base.BaseGraph method)

load_entity_properties() (obnb.label.LabelsetCollection method) load_processed_data() (obnb.data.annotated_ontology.base.BaseAnnotatedOntologyData method) (obnb.data.base.BaseData method) (obnb.data.DISEASESAnnotation method) (obnb.data.DisGeNETAnnotation method) (obnb.data.experimental.AlevinFry method) (obnb.data.GeneOntologyAnnotation method) (obnb.data.HumanPhenotypeOntologyAnnotation method) (obnb.data.network.base.BaseNDExData method) log2_auprc_prior() (in module obnb.metric.standard)

M

mat (obnb.graph.DenseGraph property) mod_name (obnb.label.filters.EntityExistenceFilter property) (obnb.label.filters.EntityRangeFilterNoccur property) (obnb.label.filters.LabelsetExistenceFilter property) (obnb.label.filters.LabelsetNonRedFilter property) (obnb.label.filters.LabelsetRangeFilterSize property) (obnb.label.filters.LabelsetRangeFilterSplit property) module obnb.data obnb.data.experimental obnb.feature obnb.graph obnb.graph.base obnb.label.filters obnb.label.split obnb.metric.graphgym_metric obnb.metric.standard obnb.model_trainer.label_propagation obnb.model_trainer.supervised_learning

MondoDiseaseOntology (class in obnb.data) MultiFeatureVec (class in obnb.feature) MultiSupervisedLearningTrainer (class in obnb.model_trainer.supervised_learning)

N

NegativeGeneratorHypergeom (class in obnb.label.filters) new_labelset() (obnb.label.LabelsetCollection method) node_ids (obnb.graph.base.BaseGraph property) nonzeros (obnb.graph.DenseGraph property) norm_mat (obnb.graph.DenseGraph property)

npy_reader() (obnb.graph.SparseGraph static method) num_edges (obnb.graph.base.BaseGraph property) (obnb.graph.DenseGraph property) (obnb.graph.SparseGraph property) num_nodes (obnb.graph.base.BaseGraph property)

O

obnb.data module obnb.data.experimental module obnb.feature module obnb.graph module obnb.graph.base module obnb.label.filters module

obnb.label.split module obnb.metric.graphgym_metric module obnb.metric.standard module obnb.model_trainer.label_propagation module obnb.model_trainer.supervised_learning module OmniPath (class in obnb.data) OntologyGraph (class in obnb.graph)

P

params (obnb.label.filters.LabelsetNonRedFilter property) (obnb.label.filters.LabelsetRangeFilterSplit property) (obnb.label.filters.NegativeGeneratorHypergeom property) parse_stanza_simplified() (obnb.graph.OntologyGraph static method) PCNet (class in obnb.data) pop_entity() (obnb.label.LabelsetCollection method) pop_labelset() (obnb.label.LabelsetCollection method) precision_at_topk() (in module obnb.metric.standard) prior() (in module obnb.metric.standard) process() (obnb.data.annotated_ontology.base.BaseAnnotatedOntologyData method) (obnb.data.base.BaseData method) (obnb.data.network.base.BaseNDExData method)

process_completed() (obnb.data.base.BaseData method) (obnb.data.experimental.AlevinFry method) processed_dir (obnb.data.base.BaseData property) processed_file_path() (obnb.data.base.BaseData method) processed_files (obnb.data.annotated_ontology.base.BaseAnnotatedOntologyData property) (obnb.data.base.BaseData property) (obnb.data.HumanNet property) (obnb.data.network.base.BaseNDExData property) propagate() (obnb.graph.DenseGraph method) propagate_node_attrs() (obnb.graph.OntologyGraph method) ProteomeHD (class in obnb.data)

R

RandomRatioHoldout (class in obnb.label.split) RandomRatioPartition (class in obnb.label.split) ratio (obnb.label.split.RatioHoldout property) RatioHoldout (class in obnb.label.split) RatioPartition (class in obnb.label.split) ratios (obnb.label.split.RatioPartition property) raw_dir (obnb.data.base.BaseData property) raw_file_path() (obnb.data.base.BaseData method) raw_files (obnb.data.base.BaseData property) (obnb.data.ConsensusPathDB property) (obnb.data.HumanNet property) (obnb.data.network.base.BaseNDExData property) (obnb.data.OmniPath property) read() (obnb.graph.SparseGraph method)

read_anndata() (obnb.feature.base.BaseFeature method) read_cx_stream_file() (obnb.graph.SparseGraph method) read_gmt() (obnb.label.LabelsetCollection method) read_npz() (obnb.graph.SparseGraph method) read_obo() (obnb.graph.OntologyGraph method) read_ontology_graph() (obnb.label.LabelsetCollection method) release_cache() (obnb.graph.OntologyGraph method) remove_edge() (obnb.graph.base.BaseGraph method) (obnb.graph.DirectedSparseGraph method) (obnb.graph.SparseGraph method) reset() (obnb.label.LabelsetCollection method) reset_labelset() (obnb.label.LabelsetCollection method) restrict_to_branch() (obnb.graph.OntologyGraph method) rev_edge_data (obnb.graph.DirectedSparseGraph property)

S

save() (obnb.data.annotated_ontology.base.BaseAnnotatedOntologyData method) (obnb.data.base.BaseData method) (obnb.graph.SparseGraph method) save_npz() (obnb.graph.SparseGraph method) set_node_attr() (obnb.graph.OntologyGraph method) set_node_name() (obnb.graph.OntologyGraph method) SIGNOR (class in obnb.data) SimpleGNNTrainer (class in obnb.model_trainer.gnn)

size (obnb.feature.base.BaseFeature property) (obnb.graph.base.BaseGraph property) sizes (obnb.label.LabelsetCollection property) SparseGraph (class in obnb.graph) split() (obnb.label.LabelsetCollection method) stats() (obnb.label.LabelsetCollection method) STRING (class in obnb.data) SupervisedLearningTrainer (class in obnb.model_trainer.supervised_learning)

T

threshold (obnb.label.split.ThresholdHoldout property) ThresholdHoldout (class in obnb.label.split) ThresholdPartition (class in obnb.label.split) thresholds (obnb.label.split.ThresholdPartition property) to_adjmat() (obnb.graph.SparseGraph method) to_config() (obnb.data.base.BaseData method) (obnb.label.filters.Compose method) to_coo() (obnb.graph.DenseGraph method) (obnb.graph.SparseGraph method)

to_dense_graph() (obnb.graph.SparseGraph method) to_df() (obnb.label.LabelsetCollection method) to_feature() (obnb.graph.DenseGraph method) to_sparse_graph() (obnb.graph.DenseGraph method) to_undirected_sparse_graph() (obnb.graph.DirectedSparseGraph method) train() (obnb.model_trainer.base.BaseTrainer method) (obnb.model_trainer.gnn.SimpleGNNTrainer method) (obnb.model_trainer.supervised_learning.MultiSupervisedLearningTrainer method) train_epoch() (obnb.model_trainer.gnn.SimpleGNNTrainer method)

U

update_labelset() (obnb.label.LabelsetCollection method)

update_node_attr() (obnb.graph.OntologyGraph method)

W

weighted (obnb.graph.SparseGraph property)

wrap_metric() (in module obnb.metric.standard)