ARBA annotations in gene reviews: failure breakdown

ARBA annotations in gene reviews: failure breakdown

Generated by gene_side_failures.py; do not edit by hand. Per-row detail is in
gene_side_rows.tsv; per-rule counts in gene_side_rules.tsv.

Outcome by how general the ARBA term is

term generality rows kept modify over-annotated remove
very general (>200 descendants) 1347 55% 15% 25% 3%
general (21-200) 1642 75% 11% 12% 2%
specific (1-20) 1984 83% 8% 4% 2%
leaf (0) 1078 86% 5% 4% 3%

What went wrong (1394 rows not kept)

kind of failure rows share
true but uninformative 867 62%
overreach 179 13%
wrong 125 9%
unclassified 118 8%
different term needed 105 8%

Annotations judged wrong (133 REMOVE rows, classified by hand)

failure mode rows meaning
WRONG_LOCATION 15 The location is contradicted by the protein's topology or experiments.
WRONG_ACTIVITY 15 The protein does not have this activity (wrong reaction, wrong substrate, or wrong enzyme class).
WRONG_PROCESS 14 The protein's real activity is used in a different process.
WRONG_TAXON 13 The process does not exist in the organism's lineage.
ROLE_CONFUSION 13 The protein binds, makes, regulates or is acted on by the molecule or activity, and is annotated as performing the step itself.
TOO_GENERAL 11 Removed as uninformative rather than wrong.
WRONG_PARALOG 11 The function belongs to a paralog or a different subfamily.
UNSUPPORTED 10 No evidence for the organism, or experiments argue against it.
TERM_MISREAD 8 The term's definition does not mean what the rule assumed (e.g. visual perception for an eye-development factor).
INDIRECT 8 The protein affects the process only indirectly.
NONCATALYTIC_HOMOLOG 7 The family has the activity but this member has lost it.
WRONG_DIRECTION 3 The regulation sign is opposite to the evidence.
OBSOLETE_OR_PSEUDOGENE 2 The term is obsolete or the gene is a pseudogene.
SPURIOUS_SIGNATURE 2 The annotation comes from a false domain prediction or a rule artefact.
TOO_SPECIFIC 1 Claims more than computational inference can support.

Failure categories, all rows not kept

REMOVE rows use the hand classification; other rows use the keyword heuristic.

category rows REMOVE over-annotated MODIFY
NEEDS_MORE_SPECIFIC (true but uninformative) 468 0 0 468
TOO_GENERAL (true but uninformative) 399 11 387 1
INDIRECT_EFFECT (overreach) 118 0 118 0
UNCLASSIFIED (unclassified) 118 0 117 1
OTHER_TERM (different term needed) 105 0 0 105
TOO_SPECIFIC (overreach) 29 1 0 28
WRONG_PARALOG (wrong) 23 11 12 0
WRONG_TAXON (wrong) 20 13 7 0
WRONG_LOCATION (wrong) 16 15 1 0
WRONG_ACTIVITY (wrong) 15 15 0 0
NO_EVIDENCE (overreach) 14 0 14 0
WRONG_PROCESS (wrong) 14 14 0 0
ROLE_CONFUSION (wrong) 13 13 0 0
UNSUPPORTED (overreach) 10 10 0 0
TERM_MISREAD (wrong) 8 8 0 0
INDIRECT (overreach) 8 8 0 0
NONCATALYTIC_HOMOLOG (wrong) 7 7 0 0
WRONG_DIRECTION (wrong) 3 3 0 0
OBSOLETE_OR_PSEUDOGENE (wrong) 2 2 0 0
SPURIOUS_SIGNATURE (wrong) 2 2 0 0
NONCATALYTIC (wrong) 1 0 1 0
SUBSTRATE_OR_CARGO (wrong) 1 0 1 0

Examples per category

NEEDS_MORE_SPECIFIC

TOO_GENERAL

INDIRECT_EFFECT

UNCLASSIFIED

OTHER_TERM

TOO_SPECIFIC

WRONG_PARALOG

WRONG_TAXON

WRONG_LOCATION

WRONG_ACTIVITY

NO_EVIDENCE

WRONG_PROCESS

ROLE_CONFUSION

UNSUPPORTED

TERM_MISREAD

INDIRECT

NONCATALYTIC_HOMOLOG

WRONG_DIRECTION

OBSOLETE_OR_PSEUDOGENE

SPURIOUS_SIGNATURE

NONCATALYTIC

SUBSTRATE_OR_CARGO

Rules with the most rows not kept

rule rows kept modify rejected
ARBA00026971 155 112 19 23
ARBA00027533 39 5 21 13
ARBA00028902 35 9 13 11
ARBA00028763 46 25 6 15
ARBA00027702 29 10 5 14
ARBA00028334 38 21 9 8
ARBA00029247 32 15 3 14
ARBA00098139 29 13 0 15
ARBA00027557 15 0 14 1
ARBA00029050 29 16 9 4
ARBA00026300 33 20 3 9
ARBA00028953 30 19 5 6
ARBA00026583 29 18 1 10
ARBA00028747 15 4 2 9
ARBA00027126 13 3 3 7
ARBA00028689 24 15 3 6
ARBA00027316 11 3 8 0
ARBA00027930 43 34 3 5
ARBA00027200 17 9 7 1
ARBA00028665 14 6 0 8
ARBA00028859 14 6 0 8
ARBA00027483 11 3 0 7
ARBA00027429 26 18 3 4
ARBA00028065 13 6 3 4
ARBA00027236 9 2 2 5