Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W A absorption (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) accession (protea.infrastructure.orm.models.protein.protein.Protein attribute) (protea.infrastructure.orm.models.query.query_set.QuerySetEntry attribute) accessions (protea.core.operations.compute_embeddings.ComputeEmbeddingsPayload attribute) active_site (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) activity_regulation (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) alignment_length_nw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) alignment_length_sw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) alignment_score_nw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) alignment_score_sw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) amqp_url (protea.infrastructure.settings.Settings attribute) annotation_date (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) annotation_set (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) annotation_set_id (protea.core.operations.predict_go_terms.PredictGOTermsBatchPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsPayload attribute) (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) annotation_sets (protea.infrastructure.orm.models.annotation.ontology_snapshot.OntologySnapshot attribute) annotations (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) (protea.infrastructure.orm.models.annotation.go_term.GOTerm attribute) AnnotationSet (class in protea.infrastructure.orm.models.annotation.annotation_set) artifacts_dir (protea.core.operations.run_cafa_evaluation.RunCafaEvaluationPayload attribute) (protea.infrastructure.settings.Settings attribute) aspect (protea.infrastructure.orm.models.annotation.go_term.GOTerm attribute) assigned_by (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) B backoff_base_seconds (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) backoff_max_seconds (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) BaseWorker (class in protea.workers.base_worker) batch_size (protea.core.operations.compute_embeddings.ComputeEmbeddingsBatchPayload attribute) (protea.core.operations.compute_embeddings.ComputeEmbeddingsPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsPayload attribute) binding_site (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) build_session_factory() (in module protea.infrastructure.session) C cancel_job() (in module protea.api.routers.jobs) CANCELLED (protea.infrastructure.orm.models.job.JobStatus attribute) canonical_accession (protea.infrastructure.orm.models.protein.protein.Protein attribute) (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) catalytic_activity (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) child (protea.infrastructure.orm.models.annotation.go_term_relationship.GOTermRelationship attribute) child_go_term_id (protea.infrastructure.orm.models.annotation.go_term_relationship.GOTermRelationship attribute) chunk_index_e (protea.core.operations.compute_embeddings.ChunkEmbedding attribute) (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) chunk_index_s (protea.core.operations.compute_embeddings.ChunkEmbedding attribute) (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) chunk_overlap (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) chunk_size (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) ChunkEmbedding (class in protea.core.operations.compute_embeddings) chunks() (in module protea.core.utils) cofactor (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) commit_every_page (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsPayload attribute) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) compressed (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) compute_alignment() (in module protea.core.feature_engineering) compute_alignments (protea.core.operations.predict_go_terms.PredictGOTermsBatchPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsPayload attribute) compute_evaluation_data() (in module protea.core.evaluation) compute_hash() (protea.infrastructure.orm.models.sequence.sequence.Sequence static method) compute_nw() (in module protea.core.feature_engineering) compute_sw() (in module protea.core.feature_engineering) compute_taxonomy (protea.core.operations.predict_go_terms.PredictGOTermsBatchPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsPayload attribute) compute_taxonomy() (in module protea.core.feature_engineering) ComputeEmbeddingsBatchOperation (class in protea.core.operations.compute_embeddings) ComputeEmbeddingsBatchPayload (class in protea.core.operations.compute_embeddings) ComputeEmbeddingsOperation (class in protea.core.operations.compute_embeddings) ComputeEmbeddingsPayload (class in protea.core.operations.compute_embeddings) create_app() (in module protea.api.app) create_embedding_config() (in module protea.api.routers.embeddings) create_job() (in module protea.api.routers.jobs) create_query_set() (in module protea.api.routers.query_sets) created_at (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) (protea.infrastructure.orm.models.job.Job attribute) (protea.infrastructure.orm.models.protein.protein.Protein attribute) (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) (protea.infrastructure.orm.models.query.query_set.QuerySet attribute) (protea.infrastructure.orm.models.query.query_set.QuerySetEntry attribute) (protea.infrastructure.orm.models.sequence.sequence.Sequence attribute) CreateJobRequest (class in protea.api.routers.jobs) D db_reference (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) db_url (protea.infrastructure.settings.Settings attribute) deferred (protea.core.contracts.operation.OperationResult attribute) definition (protea.infrastructure.orm.models.annotation.go_term.GOTerm attribute) delete_annotation_set() (in module protea.api.routers.annotations) delete_embedding_config() (in module protea.api.routers.embeddings) delete_job() (in module protea.api.routers.jobs) delete_prediction_set() (in module protea.api.routers.embeddings) delete_query_set() (in module protea.api.routers.query_sets) delta_proteins (protea.core.evaluation.EvaluationData property) description (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) (protea.infrastructure.orm.models.query.query_set.QuerySet attribute) device (protea.core.operations.compute_embeddings.ComputeEmbeddingsBatchPayload attribute) (protea.core.operations.compute_embeddings.ComputeEmbeddingsPayload attribute) distance (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) distance_threshold (protea.core.operations.predict_go_terms.PredictGOTermsBatchPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsPayload attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) dna_binding (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) download_delta_fasta() (in module protea.api.routers.annotations) download_evaluation_artifacts() (in module protea.api.routers.annotations) download_evaluation_metrics() (in module protea.api.routers.annotations) download_gt_lk() (in module protea.api.routers.annotations) download_gt_nk() (in module protea.api.routers.annotations) download_gt_pk() (in module protea.api.routers.annotations) download_known_terms() (in module protea.api.routers.annotations) download_predictions_cafa() (in module protea.api.routers.embeddings) download_predictions_tsv() (in module protea.api.routers.embeddings) E ec_number (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) eco_mapping_url (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) embedding (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) embedding_config (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) embedding_config_id (protea.core.operations.compute_embeddings.ComputeEmbeddingsBatchPayload attribute) (protea.core.operations.compute_embeddings.ComputeEmbeddingsPayload attribute) (protea.core.operations.compute_embeddings.StoreEmbeddingsPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsBatchPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsPayload attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) embedding_dim (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) EmbeddingConfig (class in protea.infrastructure.orm.models.embedding.embedding_config) entries (protea.infrastructure.orm.models.query.query_set.QuerySet attribute) entry_name (protea.infrastructure.orm.models.protein.protein.Protein attribute) error_code (protea.infrastructure.orm.models.job.Job attribute) error_message (protea.infrastructure.orm.models.job.Job attribute) evaluation_set_id (protea.core.operations.run_cafa_evaluation.RunCafaEvaluationPayload attribute) EvaluationData (class in protea.core.evaluation) event (protea.infrastructure.orm.models.job.JobEvent attribute) events (protea.infrastructure.orm.models.job.Job attribute) evidence_code (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) execute() (protea.core.contracts.operation.Operation method) (protea.core.operations.compute_embeddings.ComputeEmbeddingsBatchOperation method) (protea.core.operations.compute_embeddings.ComputeEmbeddingsOperation method) (protea.core.operations.compute_embeddings.StoreEmbeddingsOperation method) (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataOperation method) (protea.core.operations.generate_evaluation_set.GenerateEvaluationSetOperation method) (protea.core.operations.insert_proteins.InsertProteinsOperation method) (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsOperation method) (protea.core.operations.load_ontology_snapshot.LoadOntologySnapshotOperation method) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsOperation method) (protea.core.operations.ping.PingOperation method) (protea.core.operations.predict_go_terms.PredictGOTermsBatchOperation method) (protea.core.operations.predict_go_terms.PredictGOTermsOperation method) (protea.core.operations.predict_go_terms.StorePredictionsOperation method) (protea.core.operations.run_cafa_evaluation.RunCafaEvaluationOperation method) F FAILED (protea.infrastructure.orm.models.job.JobStatus attribute) faiss_hnsw_ef_search (protea.core.operations.predict_go_terms.PredictGOTermsBatchPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsPayload attribute) faiss_hnsw_m (protea.core.operations.predict_go_terms.PredictGOTermsBatchPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsPayload attribute) faiss_index_type (protea.core.operations.predict_go_terms.PredictGOTermsBatchPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsPayload attribute) faiss_nlist (protea.core.operations.predict_go_terms.PredictGOTermsBatchPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsPayload attribute) faiss_nprobe (protea.core.operations.predict_go_terms.PredictGOTermsBatchPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsPayload attribute) features (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) FetchUniProtMetadataOperation (class in protea.core.operations.fetch_uniprot_metadata) FetchUniProtMetadataPayload (class in protea.core.operations.fetch_uniprot_metadata) FIELD_MAP (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataOperation attribute) field_validator() (protea.core.operations.load_ontology_snapshot.LoadOntologySnapshotPayload method) fields (protea.infrastructure.orm.models.job.JobEvent attribute) finished_at (protea.infrastructure.orm.models.job.Job attribute) force_relationships (protea.core.operations.load_ontology_snapshot.LoadOntologySnapshotPayload attribute) function_cc (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) G gaf_url (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsPayload attribute) gaps_pct_nw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) gaps_pct_sw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) gene_name (protea.infrastructure.orm.models.protein.protein.Protein attribute) gene_product_batch_size (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) gene_product_ids (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) generate_evaluation_set() (in module protea.api.routers.annotations) GenerateEvaluationSetOperation (class in protea.core.operations.generate_evaluation_set) GenerateEvaluationSetPayload (class in protea.core.operations.generate_evaluation_set) get() (protea.core.contracts.registry.OperationRegistry method) get_amqp_url() (in module protea.api.routers.annotations) (in module protea.api.routers.embeddings) (in module protea.api.routers.jobs) get_annotation_set() (in module protea.api.routers.annotations) get_artifacts_dir() (in module protea.api.routers.annotations) get_embedding_config() (in module protea.api.routers.embeddings) get_evaluation_set() (in module protea.api.routers.annotations) get_go_subgraph() (in module protea.api.routers.annotations) get_go_term_distribution() (in module protea.api.routers.embeddings) get_job() (in module protea.api.routers.jobs) get_job_events() (in module protea.api.routers.jobs) get_prediction_set() (in module protea.api.routers.embeddings) get_protein() (in module protea.api.routers.proteins) get_protein_annotations() (in module protea.api.routers.proteins) get_protein_predictions() (in module protea.api.routers.embeddings) get_protein_stats() (in module protea.api.routers.proteins) get_query_set() (in module protea.api.routers.query_sets) get_session_factory() (in module protea.api.routers.annotations) (in module protea.api.routers.embeddings) (in module protea.api.routers.jobs) (in module protea.api.routers.proteins) (in module protea.api.routers.query_sets) get_snapshot() (in module protea.api.routers.annotations) go_id (protea.infrastructure.orm.models.annotation.go_term.GOTerm attribute) go_term (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) go_term_id (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) go_terms (protea.infrastructure.orm.models.annotation.ontology_snapshot.OntologySnapshot attribute) GOPrediction (class in protea.infrastructure.orm.models.embedding.go_prediction) GOTerm (class in protea.infrastructure.orm.models.annotation.go_term) GOTermRelationship (class in protea.infrastructure.orm.models.annotation.go_term_relationship) H handle_job() (protea.workers.base_worker.BaseWorker method) I id (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) (protea.infrastructure.orm.models.annotation.go_term.GOTerm attribute) (protea.infrastructure.orm.models.annotation.go_term_relationship.GOTermRelationship attribute) (protea.infrastructure.orm.models.annotation.ontology_snapshot.OntologySnapshot attribute) (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) (protea.infrastructure.orm.models.job.Job attribute) (protea.infrastructure.orm.models.job.JobEvent attribute) (protea.infrastructure.orm.models.query.query_set.QuerySet attribute) (protea.infrastructure.orm.models.query.query_set.QuerySetEntry attribute) (protea.infrastructure.orm.models.sequence.sequence.Sequence attribute) identity_nw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) identity_sw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) include_isoforms (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) InsertProteinsOperation (class in protea.core.operations.insert_proteins) InsertProteinsPayload (class in protea.core.operations.insert_proteins) is_canonical (protea.infrastructure.orm.models.protein.protein.Protein attribute) is_obsolete (protea.infrastructure.orm.models.annotation.go_term.GOTerm attribute) isoform_index (protea.infrastructure.orm.models.protein.protein.Protein attribute) J jitter_seconds (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) Job (class in protea.infrastructure.orm.models.job) job (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) (protea.infrastructure.orm.models.job.JobEvent attribute) job_id (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) (protea.infrastructure.orm.models.job.JobEvent attribute) JobEvent (class in protea.infrastructure.orm.models.job) JobStatus (class in protea.infrastructure.orm.models.job) K keywords (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) kinetics (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) known (protea.core.evaluation.EvaluationData attribute) known_terms_count (protea.core.evaluation.EvaluationData property) L layer_agg (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) layer_indices (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) length (protea.infrastructure.orm.models.protein.protein.Protein attribute) length_query (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) length_ref (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) level (protea.infrastructure.orm.models.job.JobEvent attribute) limit_per_entry (protea.core.operations.predict_go_terms.PredictGOTermsBatchPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsPayload attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) list_annotation_sets() (in module protea.api.routers.annotations) list_embedding_configs() (in module protea.api.routers.embeddings) list_evaluation_results() (in module protea.api.routers.annotations) list_evaluation_sets() (in module protea.api.routers.annotations) list_jobs() (in module protea.api.routers.jobs) list_prediction_set_proteins() (in module protea.api.routers.embeddings) list_prediction_sets() (in module protea.api.routers.embeddings) list_proteins() (in module protea.api.routers.proteins) list_query_sets() (in module protea.api.routers.query_sets) list_snapshots() (in module protea.api.routers.annotations) lk (protea.core.evaluation.EvaluationData attribute) lk_annotations (protea.core.evaluation.EvaluationData property) lk_proteins (protea.core.evaluation.EvaluationData property) load_goa_annotations() (in module protea.api.routers.annotations) load_ontology_snapshot() (in module protea.api.routers.annotations) load_quickgo_annotations() (in module protea.api.routers.annotations) load_settings() (in module protea.infrastructure.settings) loaded_at (protea.infrastructure.orm.models.annotation.ontology_snapshot.OntologySnapshot attribute) LoadGOAAnnotationsOperation (class in protea.core.operations.load_goa_annotations) LoadGOAAnnotationsPayload (class in protea.core.operations.load_goa_annotations) LoadOntologySnapshotOperation (class in protea.core.operations.load_ontology_snapshot) LoadOntologySnapshotPayload (class in protea.core.operations.load_ontology_snapshot) LoadQuickGOAnnotationsOperation (class in protea.core.operations.load_quickgo_annotations) LoadQuickGOAnnotationsPayload (class in protea.core.operations.load_quickgo_annotations) M max_distance (protea.core.operations.run_cafa_evaluation.RunCafaEvaluationPayload attribute) max_length (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) max_retries (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) message (protea.infrastructure.orm.models.job.JobEvent attribute) meta (protea.api.routers.jobs.CreateJobRequest attribute) (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) (protea.infrastructure.orm.models.job.Job attribute) metric (protea.core.operations.predict_go_terms.PredictGOTermsBatchPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsPayload attribute) model_backend (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) model_config (protea.api.routers.jobs.CreateJobRequest attribute) (protea.core.contracts.operation.ProteaPayload attribute) (protea.core.operations.compute_embeddings.ComputeEmbeddingsBatchPayload attribute) (protea.core.operations.compute_embeddings.ComputeEmbeddingsPayload attribute) (protea.core.operations.compute_embeddings.StoreEmbeddingsPayload attribute) (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.generate_evaluation_set.GenerateEvaluationSetPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsPayload attribute) (protea.core.operations.load_ontology_snapshot.LoadOntologySnapshotPayload attribute) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsBatchPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsPayload attribute) (protea.core.operations.predict_go_terms.StorePredictionsPayload attribute) (protea.core.operations.run_cafa_evaluation.RunCafaEvaluationPayload attribute) model_name (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) module protea.api.app protea.api.routers.annotations protea.api.routers.embeddings protea.api.routers.jobs protea.api.routers.proteins protea.api.routers.query_sets protea.core.contracts.operation protea.core.contracts.registry protea.core.evaluation protea.core.feature_engineering protea.core.knn_search protea.core.operations.compute_embeddings protea.core.operations.fetch_uniprot_metadata protea.core.operations.generate_evaluation_set protea.core.operations.insert_proteins protea.core.operations.load_goa_annotations protea.core.operations.load_ontology_snapshot protea.core.operations.load_quickgo_annotations protea.core.operations.ping protea.core.operations.predict_go_terms protea.core.operations.run_cafa_evaluation protea.core.utils protea.infrastructure.orm.models.annotation.annotation_set protea.infrastructure.orm.models.annotation.go_term protea.infrastructure.orm.models.annotation.go_term_relationship protea.infrastructure.orm.models.annotation.ontology_snapshot protea.infrastructure.orm.models.annotation.protein_go_annotation protea.infrastructure.orm.models.embedding.embedding_config protea.infrastructure.orm.models.embedding.go_prediction protea.infrastructure.orm.models.embedding.prediction_set protea.infrastructure.orm.models.embedding.sequence_embedding protea.infrastructure.orm.models.job protea.infrastructure.orm.models.protein.protein protea.infrastructure.orm.models.protein.protein_metadata protea.infrastructure.orm.models.query.query_set protea.infrastructure.orm.models.sequence.sequence protea.infrastructure.queue.consumer protea.infrastructure.queue.publisher protea.infrastructure.session protea.infrastructure.settings protea.workers.base_worker must_be_non_empty() (protea.core.operations.compute_embeddings.ComputeEmbeddingsPayload class method) (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload class method) (protea.core.operations.generate_evaluation_set.GenerateEvaluationSetPayload class method) (protea.core.operations.insert_proteins.InsertProteinsPayload class method) (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsPayload class method) (protea.core.operations.load_ontology_snapshot.LoadOntologySnapshotPayload class method) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload class method) (protea.core.operations.predict_go_terms.PredictGOTermsPayload class method) (protea.core.operations.run_cafa_evaluation.RunCafaEvaluationPayload class method) N name (protea.core.contracts.operation.Operation attribute) (protea.core.operations.compute_embeddings.ComputeEmbeddingsBatchOperation attribute) (protea.core.operations.compute_embeddings.ComputeEmbeddingsOperation attribute) (protea.core.operations.compute_embeddings.StoreEmbeddingsOperation attribute) (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataOperation attribute) (protea.core.operations.generate_evaluation_set.GenerateEvaluationSetOperation attribute) (protea.core.operations.insert_proteins.InsertProteinsOperation attribute) (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsOperation attribute) (protea.core.operations.load_ontology_snapshot.LoadOntologySnapshotOperation attribute) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsOperation attribute) (protea.core.operations.ping.PingOperation attribute) (protea.core.operations.predict_go_terms.PredictGOTermsBatchOperation attribute) (protea.core.operations.predict_go_terms.PredictGOTermsOperation attribute) (protea.core.operations.predict_go_terms.StorePredictionsOperation attribute) (protea.core.operations.run_cafa_evaluation.RunCafaEvaluationOperation attribute) (protea.infrastructure.orm.models.annotation.go_term.GOTerm attribute) (protea.infrastructure.orm.models.query.query_set.QuerySet attribute) new_annotation_set_id (protea.core.operations.generate_evaluation_set.GenerateEvaluationSetPayload attribute) nk (protea.core.evaluation.EvaluationData attribute) nk_annotations (protea.core.evaluation.EvaluationData property) nk_proteins (protea.core.evaluation.EvaluationData property) normalize (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) normalize_residues (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) O obo_url (protea.core.operations.load_ontology_snapshot.LoadOntologySnapshotPayload attribute) (protea.infrastructure.orm.models.annotation.ontology_snapshot.OntologySnapshot attribute) obo_version (protea.infrastructure.orm.models.annotation.ontology_snapshot.OntologySnapshot attribute) old_annotation_set_id (protea.core.operations.generate_evaluation_set.GenerateEvaluationSetPayload attribute) ontology_snapshot (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) (protea.infrastructure.orm.models.annotation.go_term.GOTerm attribute) (protea.infrastructure.orm.models.annotation.go_term_relationship.GOTermRelationship attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) ontology_snapshot_id (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsPayload attribute) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsPayload attribute) (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) (protea.infrastructure.orm.models.annotation.go_term.GOTerm attribute) (protea.infrastructure.orm.models.annotation.go_term_relationship.GOTermRelationship attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) OntologySnapshot (class in protea.infrastructure.orm.models.annotation.ontology_snapshot) Operation (class in protea.core.contracts.operation) operation (protea.api.routers.jobs.CreateJobRequest attribute) (protea.infrastructure.orm.models.job.Job attribute) OperationConsumer (class in protea.infrastructure.queue.consumer) OperationRegistry (class in protea.core.contracts.registry) OperationResult (class in protea.core.contracts.operation) organism (protea.infrastructure.orm.models.protein.protein.Protein attribute) P page_size (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsPayload attribute) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) parent (protea.infrastructure.orm.models.annotation.go_term_relationship.GOTermRelationship attribute) parent_go_term_id (protea.infrastructure.orm.models.annotation.go_term_relationship.GOTermRelationship attribute) parent_job_id (protea.core.operations.compute_embeddings.ComputeEmbeddingsBatchPayload attribute) (protea.core.operations.compute_embeddings.StoreEmbeddingsPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsBatchPayload attribute) (protea.core.operations.predict_go_terms.StorePredictionsPayload attribute) (protea.infrastructure.orm.models.job.Job attribute) parse_isoform() (protea.infrastructure.orm.models.protein.protein.Protein static method) pathway (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) payload (protea.api.routers.jobs.CreateJobRequest attribute) (protea.infrastructure.orm.models.job.Job attribute) ph_dependence (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) PingOperation (class in protea.core.operations.ping) pk (protea.core.evaluation.EvaluationData attribute) pk_annotations (protea.core.evaluation.EvaluationData property) pk_known (protea.core.evaluation.EvaluationData attribute) pk_proteins (protea.core.evaluation.EvaluationData property) pooling (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) predict_go_terms() (in module protea.api.routers.embeddings) PredictGOTermsBatchOperation (class in protea.core.operations.predict_go_terms) PredictGOTermsBatchPayload (class in protea.core.operations.predict_go_terms) PredictGOTermsOperation (class in protea.core.operations.predict_go_terms) PredictGOTermsPayload (class in protea.core.operations.predict_go_terms) prediction_set (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) prediction_set_id (protea.core.operations.predict_go_terms.PredictGOTermsBatchPayload attribute) (protea.core.operations.predict_go_terms.StorePredictionsPayload attribute) (protea.core.operations.run_cafa_evaluation.RunCafaEvaluationPayload attribute) (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) predictions (protea.core.operations.predict_go_terms.StorePredictionsPayload attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) PredictionSet (class in protea.infrastructure.orm.models.embedding.prediction_set) progress_current (protea.core.contracts.operation.OperationResult attribute) (protea.infrastructure.orm.models.job.Job attribute) progress_total (protea.core.contracts.operation.OperationResult attribute) (protea.infrastructure.orm.models.job.Job attribute) protea.api.app module protea.api.routers.annotations module protea.api.routers.embeddings module protea.api.routers.jobs module protea.api.routers.proteins module protea.api.routers.query_sets module protea.core.contracts.operation module protea.core.contracts.registry module protea.core.evaluation module protea.core.feature_engineering module protea.core.knn_search module protea.core.operations.compute_embeddings module protea.core.operations.fetch_uniprot_metadata module protea.core.operations.generate_evaluation_set module protea.core.operations.insert_proteins module protea.core.operations.load_goa_annotations module protea.core.operations.load_ontology_snapshot module protea.core.operations.load_quickgo_annotations module protea.core.operations.ping module protea.core.operations.predict_go_terms module protea.core.operations.run_cafa_evaluation module protea.core.utils module protea.infrastructure.orm.models.annotation.annotation_set module protea.infrastructure.orm.models.annotation.go_term module protea.infrastructure.orm.models.annotation.go_term_relationship module protea.infrastructure.orm.models.annotation.ontology_snapshot module protea.infrastructure.orm.models.annotation.protein_go_annotation module protea.infrastructure.orm.models.embedding.embedding_config module protea.infrastructure.orm.models.embedding.go_prediction module protea.infrastructure.orm.models.embedding.prediction_set module protea.infrastructure.orm.models.embedding.sequence_embedding module protea.infrastructure.orm.models.job module protea.infrastructure.orm.models.protein.protein module protea.infrastructure.orm.models.protein.protein_metadata module protea.infrastructure.orm.models.query.query_set module protea.infrastructure.orm.models.sequence.sequence module protea.infrastructure.queue.consumer module protea.infrastructure.queue.publisher module protea.infrastructure.session module protea.infrastructure.settings module protea.workers.base_worker module ProteaPayload (class in protea.core.contracts.operation) Protein (class in protea.infrastructure.orm.models.protein.protein) protein (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) protein_accession (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) ProteinGOAnnotation (class in protea.infrastructure.orm.models.annotation.protein_go_annotation) proteins (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) (protea.infrastructure.orm.models.sequence.sequence.Sequence attribute) ProteinUniProtMetadata (class in protea.infrastructure.orm.models.protein.protein_metadata) publish_after_commit (protea.core.contracts.operation.OperationResult attribute) publish_job() (in module protea.infrastructure.queue.publisher) publish_operation() (in module protea.infrastructure.queue.publisher) publish_operations (protea.core.contracts.operation.OperationResult attribute) Q qualifier (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) query_accessions (protea.core.operations.predict_go_terms.PredictGOTermsBatchPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsPayload attribute) query_set (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) (protea.infrastructure.orm.models.query.query_set.QuerySetEntry attribute) query_set_id (protea.core.operations.compute_embeddings.ComputeEmbeddingsPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsBatchPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsPayload attribute) (protea.infrastructure.orm.models.embedding.prediction_set.PredictionSet attribute) (protea.infrastructure.orm.models.query.query_set.QuerySetEntry attribute) query_taxonomy_id (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) QuerySet (class in protea.infrastructure.orm.models.query.query_set) QuerySetEntry (class in protea.infrastructure.orm.models.query.query_set) queue_name (protea.api.routers.jobs.CreateJobRequest attribute) (protea.infrastructure.orm.models.job.Job attribute) QueueConsumer (class in protea.infrastructure.queue.consumer) QUEUED (protea.infrastructure.orm.models.job.JobStatus attribute) quickgo_base_url (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) R redox_potential (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) ref_protein_accession (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) ref_taxonomy_id (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) register() (protea.core.contracts.registry.OperationRegistry method) relation_type (protea.infrastructure.orm.models.annotation.go_term_relationship.GOTermRelationship attribute) result (protea.core.contracts.operation.OperationResult attribute) RetryLaterError reviewed (protea.infrastructure.orm.models.protein.protein.Protein attribute) rhea_id (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) run() (protea.infrastructure.queue.consumer.OperationConsumer method) (protea.infrastructure.queue.consumer.QueueConsumer method) run_cafa_evaluation() (in module protea.api.routers.annotations) RunCafaEvaluationOperation (class in protea.core.operations.run_cafa_evaluation) RunCafaEvaluationPayload (class in protea.core.operations.run_cafa_evaluation) RUNNING (protea.infrastructure.orm.models.job.JobStatus attribute) S search_backend (protea.core.operations.predict_go_terms.PredictGOTermsBatchPayload attribute) (protea.core.operations.predict_go_terms.PredictGOTermsPayload attribute) search_criteria (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) search_knn() (in module protea.core.knn_search) Sequence (class in protea.infrastructure.orm.models.sequence.sequence) sequence (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) (protea.infrastructure.orm.models.protein.protein.Protein attribute) (protea.infrastructure.orm.models.query.query_set.QuerySetEntry attribute) (protea.infrastructure.orm.models.sequence.sequence.Sequence attribute) sequence_hash (protea.infrastructure.orm.models.sequence.sequence.Sequence attribute) sequence_id (protea.infrastructure.orm.models.embedding.sequence_embedding.SequenceEmbedding attribute) (protea.infrastructure.orm.models.protein.protein.Protein attribute) (protea.infrastructure.orm.models.query.query_set.QuerySetEntry attribute) sequence_ids (protea.core.operations.compute_embeddings.ComputeEmbeddingsBatchPayload attribute) SequenceEmbedding (class in protea.infrastructure.orm.models.embedding.sequence_embedding) sequences (protea.core.operations.compute_embeddings.StoreEmbeddingsPayload attribute) sequences_per_job (protea.core.operations.compute_embeddings.ComputeEmbeddingsPayload attribute) session_scope() (in module protea.infrastructure.session) Settings (class in protea.infrastructure.settings) similarity_nw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) similarity_sw (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) site (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) skip_existing (protea.core.operations.compute_embeddings.ComputeEmbeddingsBatchPayload attribute) (protea.core.operations.compute_embeddings.ComputeEmbeddingsPayload attribute) (protea.core.operations.compute_embeddings.StoreEmbeddingsPayload attribute) source (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) source_version (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsPayload attribute) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) (protea.infrastructure.orm.models.annotation.annotation_set.AnnotationSet attribute) started_at (protea.infrastructure.orm.models.job.Job attribute) stats() (protea.core.evaluation.EvaluationData method) status (protea.infrastructure.orm.models.job.Job attribute) StoreEmbeddingsOperation (class in protea.core.operations.compute_embeddings) StoreEmbeddingsPayload (class in protea.core.operations.compute_embeddings) StorePredictionsOperation (class in protea.core.operations.predict_go_terms) StorePredictionsPayload (class in protea.core.operations.predict_go_terms) strip_and_require() (protea.api.routers.jobs.CreateJobRequest class method) SUCCEEDED (protea.infrastructure.orm.models.job.JobStatus attribute) T taxonomic_common_ancestors (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) taxonomic_distance (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) taxonomic_lca (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) taxonomic_relation (protea.infrastructure.orm.models.embedding.go_prediction.GOPrediction attribute) taxonomy_id (protea.infrastructure.orm.models.protein.protein.Protein attribute) temperature_dependence (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) timeout_seconds (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsPayload attribute) (protea.core.operations.load_ontology_snapshot.LoadOntologySnapshotPayload attribute) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) total_limit (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) (protea.core.operations.load_goa_annotations.LoadGOAAnnotationsPayload attribute) (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) ts (protea.infrastructure.orm.models.job.JobEvent attribute) U uniprot_metadata (protea.infrastructure.orm.models.protein.protein.Protein attribute) UNIPROT_SEARCH_URL (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataOperation attribute) (protea.core.operations.insert_proteins.InsertProteinsOperation attribute) UniProtHttpMixin (class in protea.core.utils) update_protein_core (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) updated_at (protea.infrastructure.orm.models.protein.protein.Protein attribute) (protea.infrastructure.orm.models.protein.protein_metadata.ProteinUniProtMetadata attribute) (protea.infrastructure.orm.models.sequence.sequence.Sequence attribute) use_chunking (protea.infrastructure.orm.models.embedding.embedding_config.EmbeddingConfig attribute) use_db_accessions (protea.core.operations.load_quickgo_annotations.LoadQuickGOAnnotationsPayload attribute) user_agent (protea.core.operations.fetch_uniprot_metadata.FetchUniProtMetadataPayload attribute) (protea.core.operations.insert_proteins.InsertProteinsPayload attribute) utcnow() (in module protea.core.utils) (in module protea.infrastructure.orm.models.job) V vector (protea.core.operations.compute_embeddings.ChunkEmbedding attribute) W with_from (protea.infrastructure.orm.models.annotation.protein_go_annotation.ProteinGOAnnotation attribute) worker_name (protea.workers.base_worker.WorkerConfig attribute) WorkerConfig (class in protea.workers.base_worker)