PROTEA
Cola inactiva
Los comentarios y métricas son públicos y visibles para todos los visitantes.
Cada feature del reranker tiene una única descripción canónica, compartida por la documentación, la tesis y esta página. Aquí puedes leer qué significa cada feature, quién la produce y si lleva un valor real en la exportación por defecto.
Obtenido de protea-contracts 1.7.0. 78 features en 19 familias.
distanceproducidaEmbedding distance from the query to the reference neighbour that voted this candidate term.
The PLM-embedding distance returned by the KNN retrieval step for the (query, reference) pair whose annotation contributed this candidate GO term. Smaller is a closer neighbour. Assembled onto the leaf record from the KNN runner; the metric is the one the retrieval index was built with for the active PLM.
vote_countproducidaHow many of the query's KNN neighbours annotated this candidate GO term.
Count of retrieved neighbours (within the K-neighbourhood) that carry this candidate term among their annotations. Defaults to 1 when no per-term tally is present.
k_positionproducidago_term_frequencyproducidaHow common the candidate GO term is across the reference pool.
Corpus frequency of the candidate term over the reference annotation pool, used as a base-rate prior so a ubiquitous term is not treated like a specific one. Read from the runner's precomputed term-frequency map; defaults to 0 for an unseen term.
ref_annotation_densityproducidaHow many annotations the voting reference protein carries.
Annotation count of the reference protein that supplied this candidate, a proxy for how densely studied that reference is. Read from the runner's per-reference density map; defaults to 0.
identity_nwproducidaSequence identity of the global (Needleman-Wunsch) alignment of query and reference.
Fraction of identical positions (matches / alignment length) in the parasail Needleman-Wunsch global alignment of the query and reference sequences.
Advertencia
Populated when the ``compute_alignments`` export flag is enabled; with the flag off the column is emitted null (LightGBM reads it as missing).
similarity_nwproducidaSequence similarity of the global (Needleman-Wunsch) alignment.
Fraction of similar positions (parasail comparison line characters ``|`` or ``:``) over the alignment length of the NW global alignment. Similarity counts conservative substitutions, so it is >= identity.
identity_swproducidaSequence identity of the local (Smith-Waterman) alignment of query and reference.
Fraction of identical positions (matches / alignment length) in the parasail Smith-Waterman local alignment of the query and reference sequences.
Advertencia
Populated when the ``compute_alignments`` export flag is enabled; null otherwise.
similarity_swproducidaSequence similarity of the local (Smith-Waterman) alignment.
Fraction of similar positions (comparison-line ``|`` or ``:``) over the alignment length of the SW local alignment.
length_queryproducidaAmino-acid length of the query protein.
Residue count of the query sequence, carried on the pair-feature record.
length_refproducidaAmino-acid length of the reference (neighbour) protein.
Residue count of the reference sequence, carried on the pair-feature record.
taxonomic_distanceproducidaTree distance between the query's and reference's NCBI taxa.
Distance between the query and reference organisms in the NCBI taxonomy tree, computed from their lineages (0 when identical). Null when either taxon id is missing.
Advertencia
Populated when the ``compute_taxonomy`` export flag is enabled; null otherwise.
taxonomic_common_ancestorsproducidaNumber of shared lineage nodes between the query and reference taxa.
Count of taxonomy nodes shared by the query and reference lineages (their common-ancestor path length). 1 when the taxa are the same, 0 when unrelated / unknown.
tax_voters_same_fracproducidaFraction of voting neighbours from the same organism as the query.
Over the neighbours that voted this candidate term, the fraction whose taxon equals the query's. NaN when taxonomy is disabled for the run.
tax_voters_close_fracproducidaFraction of voting neighbours taxonomically close to the query.
Over the neighbours that voted this candidate term, the fraction whose taxon is taxonomically close to the query's (near in the lineage tree). NaN when taxonomy is disabled.
anc2vec_neighbor_cosproducidaCosine of the candidate term to the neighbours' semantic centroid.
Cosine similarity between the candidate GO term's Anc2Vec embedding (GO release 2020-10-06 pretrained) and the unit centroid of the voting neighbours' embeddings. NaN when the candidate has no Anc2Vec embedding or there is no centroid.
anc2vec_neighbor_maxcosproducidaMax cosine of the candidate term to any single voting neighbour.
Maximum cosine similarity between the candidate term's Anc2Vec embedding and any individual neighbour embedding in the voting set. NaN when the candidate has no embedding or the neighbour matrix is absent.
anc2vec_query_known_cosproducidaCosine of the candidate term to the centroid of the query's known terms.
Cosine similarity between the candidate term's Anc2Vec embedding and the unit centroid of the query protein's pre-cutoff known annotations. NaN when the candidate has no embedding or the query has no known-term centroid.
anc2vec_query_known_maxcosproducidaMax cosine of the candidate term to any of the query's known terms.
Maximum cosine similarity between the candidate term's Anc2Vec embedding and any single pre-cutoff known-term embedding of the query. NaN when the candidate has no embedding or the query has no known-term matrix.
emb_pca_query_0producidaComponent 0 of the 16-dim PCA projection of the query PLM embedding.
Coordinate 0 of a 16-dimensional PCA projection of the query protein's PLM embedding. The PCA is fit over the embedding pool at export time and applied to the query vector.
Advertencia
Populated when the ``use_embedding_pca`` export flag is enabled; NaN otherwise (LightGBM reads it as missing). A training run measured this family to contribute essentially nothing; that is a property of that run, not of the feature, so no gain number is recorded here.
emb_pca_query_1producidaComponent 1 of the 16-dim PCA projection of the query PLM embedding.
Coordinate 1 of a 16-dimensional PCA projection of the query protein's PLM embedding. The PCA is fit over the embedding pool at export time and applied to the query vector.
interpro_hitproducidaWhether an InterPro signature maps the query onto this candidate GO term.
True when at least one InterPro member-database signature of the query maps onto this candidate term in the InterPro GO-prediction table. Default False for a (query, term) with no InterPro evidence.
Advertencia
The InterPro GO-prediction table is loaded by ``protea.core._interpro_features.load_interpro_go_pred``, which returns an empty table when its source env var is unset, in which case every row keeps the zero/False default and the column carries no signal. Whether the InterPro tables are populated in a given deployment is a database-state question that cannot be settled from the source tree alone, so no ``BROKEN`` status is asserted here. Note that InterPro's principal contribution to predictions enters through a separate InterPro2GO noisy-OR graft (``protea.core.operations.predict_go_terms._interpro_graft``), not through these reranker columns.
interpro_scoreproducidaStrength of the InterPro signature->GO mapping for this candidate term.
Graded InterPro2GO mapping score for the query onto this candidate term. 0.0 when there is no InterPro evidence.
classifier_scoredeclarada ausenteFull-catalogue direct classifier score for this candidate GO term.
Per-candidate score from the direct full-catalogue predictor (the first-place LAFA classifier). The producer ``protea.core.operations.predict_go_terms._classifier.apply_classifier`` (and the export post-pass ``protea.core.training_dump._classifier_postpass.apply_classifier_to_frame``) computes it, but only when the ``compute_classifier`` flag is set. It defaults to ``False`` on the export payload, so the default research-dataset export never fills this column.
Advertencia
ADR-D45: the default export emits NaN (was a well-defined 0.0 before PROTEA #710). The sealed 0.4063 champion was trained without the classifier family precisely because it was absent. The schema fingerprint pins names, not values, so a booster selecting this family still passes the schema-sha guard.
classifier_presentdeclarada ausenteWhether the direct classifier proposed this candidate GO term.
Presence flag for the direct full-catalogue classifier source. Produced by the same classifier producer, gated by ``compute_classifier`` (default False), so the default export never fills it.
self_prior_scoredeclarada ausenteScore from the query protein's own pre-cutoff non-experimental annotations.
Self-prior signal: how strongly the query protein's own pre-cutoff non-experimental annotations support this candidate term. Produced by ``protea.core.operations.predict_go_terms._post_knn_pipeline.apply_self_prior``, gated by ``compute_self_prior`` (default False), so the default research-dataset export leaves it at the NaN default.
Advertencia
ADR-D45: DECLARED_ABSENT in the default export. See classifier_score.
association_totaldeclarada ausenteConditional probability of the candidate term given the query's known terms.
Total cross-aspect association: the conditional probability of the candidate term given the query protein's pre-cutoff known terms, over all branches. Produced by ``protea.core.operations.predict_go_terms._post_knn_pipeline.apply_association``, gated by ``compute_association`` (default False), so the default export leaves it at the NaN default.
Advertencia
ADR-D45: DECLARED_ABSENT in the default export. See classifier_score.
association_crossdeclarada ausenteCross-branch-only conditional probability of the candidate given known terms.
Cross-branch component of the association signal: the conditional probability of the candidate term given the query's known terms, restricted to terms in a different GO aspect. Same producer and gating as ``association_total``.
protst_text_scoredeclarada ausenteProtST text-to-GO transfer score for this candidate GO term.
Normalised cosine-weighted vote for the candidate term from the query protein's ProtST kNN neighbourhood. The producer takes the query's ProtST protein embedding, retrieves its top-30 cosine-nearest reference proteins (both banks L2-normalised), casts a vote per reference GO term weighted by the neighbour cosine, and normalises by the per-query maximum vote. Reference GO terms are restricted to the pre-cutoff annotation set (leakage-free). Produced by ``protea.core.operations.predict_go_terms._protst_text.apply_protst_text``, gated by ``compute_protst`` (default False), so the default research-dataset export leaves it at the NaN default.
Advertencia
ADR-D45: DECLARED_ABSENT in the default export. The ProtST reference bank is a separate EmbeddingConfig; whether it is populated in a given deployment is a database-state question, so no BROKEN status is asserted here. See classifier_score.
protst_vote_fractiondeclarada ausenteFraction of the query's ProtST neighbours that carry this candidate term.
qualifierproducidaGO annotation qualifier carried by the reference annotation.
The GO qualifier string of the reference annotation that supplied this candidate term (for example ``enables``, ``NOT``), empty when absent. Categorical: encoded to a stable integer code by the lab.
Advertencia
Categorical feature.
evidence_codeproducidaGO evidence code of the reference annotation.
The GO evidence code of the reference annotation that supplied this candidate term (for example ``EXP``, ``IEA``), empty when absent. Categorical: encoded to a stable integer code by the lab.
plm_idinyectada en el poolWhich protein language model produced the embeddings used for KNN retrieval.
Categorical code identifying the PLM whose embeddings retrieved the candidate. The PROTEA dump does not write this column; the lab's pooled multi-manifest loader injects it as a per-source constant at stage time so the universal multi-PLM booster sees which PLM a row came from.
Advertencia
Categorical feature. See PROTEA FEATURE_LEAKAGE_AUDIT.md for the GO/NO-GO ruling on this column.
k_contextinyectada en el poolKNN neighbourhood size (K) used to retrieve this candidate.
The K-neighbourhood size for the manifest source that produced this row. The PROTEA dump does not write this column; the lab's pooled loader injects it as a per-source constant at stage time so a booster trained over several K settings can condition on K.
lineage_is_ancestor_of_knownproducidaWhether the candidate GO term is an ancestor of at least one term the protein is already known to have.
1.0 when the candidate appears in the is_a / part_of ancestor closure of any pre-cutoff known term of the query protein, else 0.0. A candidate identical to a known term does not count as its own ancestor: the self-overlap is subtracted before the test. A protein with no known terms scores 0.0, a true absence rather than a missing measurement, so this feature is identically zero across the no-knowledge evaluation cell.
Advertencia
Opt-in through the compute_lineage_features payload flag. In the sealed v227 to v230 champion it is the second most important feature of the previously-known cell by LightGBM gain, and the third overall, while contributing exactly zero in the no-knowledge cell, where by construction there is nothing to be an ancestor of.
lineage_is_descendant_of_knownproducidaWhether the candidate GO term is a descendant of at least one term the protein is already known to have.
1.0 when any pre-cutoff known term of the query protein appears in the candidate's own ancestor closure, else 0.0. Self-overlap is subtracted, so a candidate equal to a known term scores 0.0. A protein with no known terms scores 0.0.
Rank of the closest neighbour that voted this candidate term.
The 1-based position, in the distance-sorted neighbour list, of the nearest neighbour that annotated this candidate term. Lower means the term was proposed by a closer neighbour. Defaults to 1.
neighbor_distance_stdproducidaSpread of the query's neighbour distances.
Standard deviation of the distances of the query's retrieved neighbours. A per-query quantity (same for every candidate of that query) describing how tight or diffuse the neighbourhood is. Defaults to 0.0.
neighbor_vote_fractionproducidaFraction of the K-neighbourhood that voted this candidate term.
``vote_count`` divided by the retrieval neighbourhood size ``runner.k_limit``. A normalised consensus strength: 1.0 means every neighbour in the K-neighbourhood annotated this term.
neighbor_min_distanceproducidaDistance of the closest neighbour that voted this candidate term.
Minimum over the voting neighbours of their query distance, for this candidate term. Falls back to the row's own ``distance`` when no per-term minimum is recorded.
neighbor_mean_distanceproducidaMean distance of the neighbours that voted this candidate term.
Sum of the voting neighbours' distances divided by ``vote_count`` (clamped to at least 1) for this candidate term. Falls back to the row's own ``distance`` when no per-term sum is recorded.
Advertencia
Populated when the ``compute_alignments`` export flag is enabled; null otherwise.
alignment_score_nwproducidaRaw score of the global (Needleman-Wunsch) alignment.
The parasail substitution-matrix score of the NW global alignment of query and reference. An unnormalised score that grows with alignment length and similarity.
Advertencia
Populated when the ``compute_alignments`` export flag is enabled; null otherwise.
gaps_pct_nwproducidaGap percentage of the global (Needleman-Wunsch) alignment.
Fraction of the NW alignment columns that are gaps in either sequence.
Advertencia
Populated when the ``compute_alignments`` export flag is enabled; null otherwise.
alignment_length_nwproducidaLength of the global (Needleman-Wunsch) alignment.
Number of columns in the NW global alignment (matched positions plus gaps).
Advertencia
Populated when the ``compute_alignments`` export flag is enabled; null otherwise.
Advertencia
Populated when the ``compute_alignments`` export flag is enabled; null otherwise.
alignment_score_swproducidaRaw score of the local (Smith-Waterman) alignment.
The parasail substitution-matrix score of the SW local alignment of query and reference. Unnormalised.
Advertencia
Populated when the ``compute_alignments`` export flag is enabled; null otherwise.
gaps_pct_swproducidaGap percentage of the local (Smith-Waterman) alignment.
Fraction of the SW alignment columns that are gaps in either sequence.
Advertencia
Populated when the ``compute_alignments`` export flag is enabled; null otherwise.
alignment_length_swproducidaLength of the local (Smith-Waterman) alignment.
Number of columns in the SW local alignment (matched positions plus gaps).
Advertencia
Populated when the ``compute_alignments`` export flag is enabled; null otherwise.
Advertencia
Populated when the ``compute_taxonomy`` export flag is enabled.
taxonomic_relationproducidaCategorical relationship of the query and reference taxa.
One of ``same``, ``ancestor``, ``descendant``, ``child``, ``parent``, ``root-only`` or ``unrelated``, derived from the two lineages. Categorical: the lab encodes it to a stable integer code for LightGBM.
Advertencia
Categorical feature. Populated when the ``compute_taxonomy`` export flag is enabled.
tax_voters_mean_common_ancestorsproducidaMean shared-lineage depth between the query and its voting neighbours.
Average, over the neighbours that voted this candidate term, of the count of taxonomy nodes shared with the query. NaN when taxonomy is disabled.
anc2vec_has_embproducidaWhether the candidate GO term has an Anc2Vec embedding.
1.0 when the candidate term is present in the Anc2Vec index (so the cosine features are meaningful), 0.0 otherwise. Lets the booster tell a real 0 cosine from an absent embedding.
anc2vec_query_known_countproducidaHow many pre-cutoff known terms the query protein has.
Count of the query protein's own pre-cutoff (non-experimental-leakage-free) known annotations, cast to float. Zero for a protein with no prior annotations.
Advertencia
Populated when the ``use_embedding_pca`` export flag is enabled; NaN otherwise (LightGBM reads it as missing). A training run measured this family to contribute essentially nothing; that is a property of that run, not of the feature, so no gain number is recorded here.
emb_pca_query_2producidaComponent 2 of the 16-dim PCA projection of the query PLM embedding.
Coordinate 2 of a 16-dimensional PCA projection of the query protein's PLM embedding. The PCA is fit over the embedding pool at export time and applied to the query vector.
Advertencia
Populated when the ``use_embedding_pca`` export flag is enabled; NaN otherwise (LightGBM reads it as missing). A training run measured this family to contribute essentially nothing; that is a property of that run, not of the feature, so no gain number is recorded here.
emb_pca_query_3producidaComponent 3 of the 16-dim PCA projection of the query PLM embedding.
Coordinate 3 of a 16-dimensional PCA projection of the query protein's PLM embedding. The PCA is fit over the embedding pool at export time and applied to the query vector.
Advertencia
Populated when the ``use_embedding_pca`` export flag is enabled; NaN otherwise (LightGBM reads it as missing). A training run measured this family to contribute essentially nothing; that is a property of that run, not of the feature, so no gain number is recorded here.
emb_pca_query_4producidaComponent 4 of the 16-dim PCA projection of the query PLM embedding.
Coordinate 4 of a 16-dimensional PCA projection of the query protein's PLM embedding. The PCA is fit over the embedding pool at export time and applied to the query vector.
Advertencia
Populated when the ``use_embedding_pca`` export flag is enabled; NaN otherwise (LightGBM reads it as missing). A training run measured this family to contribute essentially nothing; that is a property of that run, not of the feature, so no gain number is recorded here.
emb_pca_query_5producidaComponent 5 of the 16-dim PCA projection of the query PLM embedding.
Coordinate 5 of a 16-dimensional PCA projection of the query protein's PLM embedding. The PCA is fit over the embedding pool at export time and applied to the query vector.
Advertencia
Populated when the ``use_embedding_pca`` export flag is enabled; NaN otherwise (LightGBM reads it as missing). A training run measured this family to contribute essentially nothing; that is a property of that run, not of the feature, so no gain number is recorded here.
emb_pca_query_6producidaComponent 6 of the 16-dim PCA projection of the query PLM embedding.
Coordinate 6 of a 16-dimensional PCA projection of the query protein's PLM embedding. The PCA is fit over the embedding pool at export time and applied to the query vector.
Advertencia
Populated when the ``use_embedding_pca`` export flag is enabled; NaN otherwise (LightGBM reads it as missing). A training run measured this family to contribute essentially nothing; that is a property of that run, not of the feature, so no gain number is recorded here.
emb_pca_query_7producidaComponent 7 of the 16-dim PCA projection of the query PLM embedding.
Coordinate 7 of a 16-dimensional PCA projection of the query protein's PLM embedding. The PCA is fit over the embedding pool at export time and applied to the query vector.
Advertencia
Populated when the ``use_embedding_pca`` export flag is enabled; NaN otherwise (LightGBM reads it as missing). A training run measured this family to contribute essentially nothing; that is a property of that run, not of the feature, so no gain number is recorded here.
emb_pca_query_8producidaComponent 8 of the 16-dim PCA projection of the query PLM embedding.
Coordinate 8 of a 16-dimensional PCA projection of the query protein's PLM embedding. The PCA is fit over the embedding pool at export time and applied to the query vector.
Advertencia
Populated when the ``use_embedding_pca`` export flag is enabled; NaN otherwise (LightGBM reads it as missing). A training run measured this family to contribute essentially nothing; that is a property of that run, not of the feature, so no gain number is recorded here.
emb_pca_query_9producidaComponent 9 of the 16-dim PCA projection of the query PLM embedding.
Coordinate 9 of a 16-dimensional PCA projection of the query protein's PLM embedding. The PCA is fit over the embedding pool at export time and applied to the query vector.
Advertencia
Populated when the ``use_embedding_pca`` export flag is enabled; NaN otherwise (LightGBM reads it as missing). A training run measured this family to contribute essentially nothing; that is a property of that run, not of the feature, so no gain number is recorded here.
emb_pca_query_10producidaComponent 10 of the 16-dim PCA projection of the query PLM embedding.
Coordinate 10 of a 16-dimensional PCA projection of the query protein's PLM embedding. The PCA is fit over the embedding pool at export time and applied to the query vector.
Advertencia
Populated when the ``use_embedding_pca`` export flag is enabled; NaN otherwise (LightGBM reads it as missing). A training run measured this family to contribute essentially nothing; that is a property of that run, not of the feature, so no gain number is recorded here.
emb_pca_query_11producidaComponent 11 of the 16-dim PCA projection of the query PLM embedding.
Coordinate 11 of a 16-dimensional PCA projection of the query protein's PLM embedding. The PCA is fit over the embedding pool at export time and applied to the query vector.
Advertencia
Populated when the ``use_embedding_pca`` export flag is enabled; NaN otherwise (LightGBM reads it as missing). A training run measured this family to contribute essentially nothing; that is a property of that run, not of the feature, so no gain number is recorded here.
emb_pca_query_12producidaComponent 12 of the 16-dim PCA projection of the query PLM embedding.
Coordinate 12 of a 16-dimensional PCA projection of the query protein's PLM embedding. The PCA is fit over the embedding pool at export time and applied to the query vector.
Advertencia
Populated when the ``use_embedding_pca`` export flag is enabled; NaN otherwise (LightGBM reads it as missing). A training run measured this family to contribute essentially nothing; that is a property of that run, not of the feature, so no gain number is recorded here.
emb_pca_query_13producidaComponent 13 of the 16-dim PCA projection of the query PLM embedding.
Coordinate 13 of a 16-dimensional PCA projection of the query protein's PLM embedding. The PCA is fit over the embedding pool at export time and applied to the query vector.
Advertencia
Populated when the ``use_embedding_pca`` export flag is enabled; NaN otherwise (LightGBM reads it as missing). A training run measured this family to contribute essentially nothing; that is a property of that run, not of the feature, so no gain number is recorded here.
emb_pca_query_14producidaComponent 14 of the 16-dim PCA projection of the query PLM embedding.
Coordinate 14 of a 16-dimensional PCA projection of the query protein's PLM embedding. The PCA is fit over the embedding pool at export time and applied to the query vector.
Advertencia
Populated when the ``use_embedding_pca`` export flag is enabled; NaN otherwise (LightGBM reads it as missing). A training run measured this family to contribute essentially nothing; that is a property of that run, not of the feature, so no gain number is recorded here.
emb_pca_query_15producidaComponent 15 of the 16-dim PCA projection of the query PLM embedding.
Coordinate 15 of a 16-dimensional PCA projection of the query protein's PLM embedding. The PCA is fit over the embedding pool at export time and applied to the query vector.
Advertencia
Populated when the ``use_embedding_pca`` export flag is enabled; NaN otherwise (LightGBM reads it as missing). A training run measured this family to contribute essentially nothing; that is a property of that run, not of the feature, so no gain number is recorded here.
Advertencia
Env-gated table; carries no signal when the InterPro GO-prediction table is unpopulated (see interpro_hit).
interpro_n_signaturesproducidaNumber of InterPro signatures supporting this candidate term.
Count of distinct InterPro member-database signatures of the query that map onto this candidate term. 0 when there is no InterPro evidence.
Advertencia
Env-gated table; 0 for every row when the InterPro table is unpopulated (see interpro_hit).
interpro_db_pfamproducidaWhether a Pfam signature supplied the InterPro mapping.
One-hot: True when a Pfam member-database signature contributed the mapping for this candidate term.
Advertencia
Env-gated table (see interpro_hit).
interpro_db_pantherproducidaWhether a PANTHER signature supplied the InterPro mapping.
One-hot: True when a PANTHER member-database signature contributed the mapping for this candidate term.
Advertencia
Env-gated table (see interpro_hit).
interpro_db_superfamilyproducidaWhether a SUPERFAMILY signature supplied the InterPro mapping.
One-hot: True when a SUPERFAMILY member-database signature contributed the mapping for this candidate term.
Advertencia
Env-gated table (see interpro_hit).
interpro_db_smartproducidaWhether a SMART signature supplied the InterPro mapping.
One-hot: True when a SMART member-database signature contributed the mapping for this candidate term.
Advertencia
Env-gated table (see interpro_hit).
interpro_db_cddproducidaWhether a CDD signature supplied the InterPro mapping.
One-hot: True when a CDD member-database signature contributed the mapping for this candidate term.
Advertencia
Env-gated table (see interpro_hit).
interpro_db_prositeproducidaWhether a PROSITE signature supplied the InterPro mapping.
One-hot: True when a PROSITE member-database signature contributed the mapping for this candidate term.
Advertencia
Env-gated table (see interpro_hit).
knn_presentproducidaWhether the KNN source proposed this candidate for the (protein, term).
Presence flag: True when the KNN retrieval source contributed this candidate. Used when pooling KNN and InterPro candidates so a true zero is distinguishable from an absent source. True on every KNN leaf record.
interpro_presentproducidaWhether the InterPro source proposed this candidate for the (protein, term).
Presence flag: True when the InterPro source contributed this candidate. Default False on a KNN leaf record with no InterPro evidence; set True by the InterPro post-pass / union path.
Advertencia
Env-gated table (see interpro_hit).
Advertencia
ADR-D45: DECLARED_ABSENT in the default export. See classifier_score.
Advertencia
ADR-D45: DECLARED_ABSENT in the default export. See classifier_score.
association_presentdeclarada ausenteWhether the association source proposed this candidate GO term.
Presence flag for the cross-aspect association source. Same producer and gating as ``association_total`` (``compute_association``, default False), so the default export leaves it at the NaN default.
Advertencia
ADR-D45: DECLARED_ABSENT in the default export. See classifier_score.
Coverage feature for the ProtST transfer: the fraction of the query's 30 ProtST cosine-nearest neighbours whose pre-cutoff annotations include the candidate term. Decouples a single very close neighbour from a broad consensus, mirroring ``neighbor_vote_fraction``. Same producer and gating as ``protst_text_score`` (``compute_protst``, default False), so the default export leaves it at the NaN default.
Advertencia
ADR-D45: DECLARED_ABSENT in the default export. See protst_text_score.
protst_presentdeclarada ausenteWhether the ProtST source contributed to this candidate at all.
Presence flag for the ProtST transfer source: 1.0 when at least one ProtST neighbour voted the candidate term (so the score is a measured value), 0.0 when ProtST had coverage but no support. Distinguishes a measured zero from an absent source, letting the booster gate on ProtST coverage, mirroring ``interpro_present`` / ``knn_present``. Same producer and gating as ``protst_text_score`` (``compute_protst``, default False).
Advertencia
ADR-D45: DECLARED_ABSENT in the default export. See protst_text_score.
Advertencia
Categorical feature.
aspectproducidaGO aspect (BP / MF / CC) of the candidate term.
The GO aspect of the candidate term, read from the runner's aspect map (biological process, molecular function or cellular component). Categorical: encoded to a stable integer code by the lab. Also a reserved column.
Advertencia
Categorical feature; also present in RESERVED_COLUMNS.
lineage_ancestor_of_countproducidaHow many of the protein's known terms have this candidate among their ancestors.
Number of pre-cutoff known terms whose ancestor closure contains the candidate, minus one when the candidate is itself a known term. The graded counterpart of lineage_is_ancestor_of_known.
lineage_descendant_of_countproducidaHow many of the protein's known terms are ancestors of this candidate.
Number of pre-cutoff known terms present in the candidate's ancestor closure, minus one when the candidate is itself a known term. The graded counterpart of lineage_is_descendant_of_known.