# Manual failure-mode classification of every ARBA (GO_REF:0000117) annotation # that a gene review marked REMOVE. Each entry was assigned by reading the # review's reason (see gene_side_rows.tsv). Keys are "/|". # gene_side_failures.py uses these in place of its keyword heuristic for # REMOVE rows, and reports any REMOVE row missing from this file. modes: WRONG_ACTIVITY: The protein does not have this activity (wrong reaction, wrong substrate, or wrong enzyme class). NONCATALYTIC_HOMOLOG: The family has the activity but this member has lost it. ROLE_CONFUSION: >- The protein binds, makes, regulates or is acted on by the molecule or activity, and is annotated as performing the step itself. WRONG_PROCESS: The protein's real activity is used in a different process. WRONG_DIRECTION: The regulation sign is opposite to the evidence. WRONG_PARALOG: The function belongs to a paralog or a different subfamily. WRONG_TAXON: The process does not exist in the organism's lineage. WRONG_LOCATION: The location is contradicted by the protein's topology or experiments. TERM_MISREAD: The term's definition does not mean what the rule assumed (e.g. visual perception for an eye-development factor). SPURIOUS_SIGNATURE: The annotation comes from a false domain prediction or a rule artefact. INDIRECT: The protein affects the process only indirectly. UNSUPPORTED: No evidence for the organism, or experiments argue against it. TOO_GENERAL: Removed as uninformative rather than wrong. TOO_SPECIFIC: Claims more than computational inference can support. OBSOLETE_OR_PSEUDOGENE: The term is obsolete or the gene is a pseudogene. rows: "9CAUD/g022|GO:0006259": TOO_GENERAL "9CAUD/g022|GO:0140640": TOO_GENERAL "ARATH/CYCD6-1|GO:0010440": WRONG_PARALOG "CANAL/BCY1|GO:0009267": UNSUPPORTED "CANAL/BCY1|GO:0016020": WRONG_LOCATION "DANRE/cryabb|GO:0005886": WRONG_LOCATION "DANRE/dla|GO:0005737": WRONG_LOCATION "DANRE/dla|GO:0060485": UNSUPPORTED "DANRE/fgf8b|GO:0042664": WRONG_PARALOG "DESVH/Q72F05|GO:0030001": TERM_MISREAD "DICDI/phg2|GO:0009653": UNSUPPORTED "DORPE/AP180|GO:0040011": WRONG_PROCESS "DORPE/P21613|GO:0120544": WRONG_ACTIVITY "DROME/AMPKalpha|GO:0043050": WRONG_TAXON "DROME/CG6051|GO:0004438": ROLE_CONFUSION "DROME/CG6051|GO:0004721": ROLE_CONFUSION "DROME/CG6051|GO:0046474": WRONG_PROCESS "DROME/CG6051|GO:0046856": ROLE_CONFUSION "DROME/CG6051|GO:0052629": ROLE_CONFUSION "DROME/CG6051|GO:0061952": UNSUPPORTED "DROME/N|GO:0019899": TOO_GENERAL "DROME/N|GO:0019904": TOO_GENERAL "DROME/ci|GO:0140297": WRONG_ACTIVITY "DROME/rdgBbeta|GO:0005634": WRONG_LOCATION "DROME/sws|GO:0016020": TOO_GENERAL "DROME/tin|GO:0007399": WRONG_PARALOG "EMENI/flbD|GO:0050891": WRONG_TAXON "EMENI/flbD|GO:1901002": WRONG_TAXON "EMENI/flbD|GO:1902584": WRONG_TAXON "EMENI/flbD|GO:2000037": WRONG_TAXON "EMENI/nudA|GO:0048731": WRONG_TAXON "HORSE/HSPD1|GO:0005832": WRONG_PARALOG "NEMVE/G9JWI5|GO:0003008": UNSUPPORTED "NEMVE/G9JWI5|GO:0019904": TOO_GENERAL "NEMVE/G9JWI5|GO:0030097": WRONG_TAXON "NEMVE/G9JWI5|GO:0035282": WRONG_TAXON "NICAT/NaBGL1_candidate_BGLU42|GO:0009821": WRONG_PARALOG "PSEAI/merA|GO:0006979": WRONG_PROCESS "PSEPK/PP_2320|GO:0004180": WRONG_ACTIVITY "PSEPK/catB|GO:0006518": WRONG_PROCESS "PSEPK/hisI|GO:0004636": WRONG_ACTIVITY "PSEPK/kdpD|GO:0005737": WRONG_LOCATION "PSEPK/pcaF|GO:0006629": WRONG_PROCESS "PSEPK/pedH|GO:0020037": WRONG_ACTIVITY "PSEPK/pedE|GO:0020037": WRONG_ACTIVITY "PSEPK/pgsA|GO:0005737": WRONG_LOCATION "PSEPK/pgsA|GO:0050793": WRONG_PROCESS "PSEPK/prpE|GO:0070013": WRONG_TAXON "PSEPK/pvdD|GO:0072330": TERM_MISREAD "PSEPK/pyrC'|GO:0016812": NONCATALYTIC_HOMOLOG "PSEPK/recC|GO:0140097": NONCATALYTIC_HOMOLOG "PSEPK/serA|GO:0047545": WRONG_ACTIVITY "RAMVA/RvY_01767|GO:0098803": WRONG_LOCATION "SALRS/PTSG_11235|GO:0016327": WRONG_TAXON "SCHPO/SPAC8E11.10|GO:0050085": WRONG_ACTIVITY "SCHPO/cps1|GO:0043604": UNSUPPORTED "SCHPO/cps1|GO:1990845": WRONG_TAXON "SCHPO/vas2|GO:0010496": TERM_MISREAD "SOLLC/PG2|GO:0009901": WRONG_PARALOG "SOLLC/PG2|GO:0010047": WRONG_PARALOG "SOLTU/CCOAOMT|GO:0007623": UNSUPPORTED "STRCO/actI-ORF1|GO:0030497": WRONG_PROCESS "STRPU/Delta|GO:0000902": TOO_GENERAL "STRPU/Delta|GO:0042063": UNSUPPORTED "human/ABCB7|GO:0015232": WRONG_ACTIVITY "human/ALDOB|GO:0070061": WRONG_ACTIVITY "human/AP3D1|GO:0010496": TERM_MISREAD "human/ASAH2B|GO:0046512": NONCATALYTIC_HOMOLOG "human/ASAH2B|GO:0046513": NONCATALYTIC_HOMOLOG "human/AZIN2|GO:0016831": NONCATALYTIC_HOMOLOG "human/BAK1|GO:0051049": INDIRECT "human/BAK1|GO:0051246": INDIRECT "human/BAK1|GO:1902531": INDIRECT "human/BAX|GO:0033554": INDIRECT "human/BAX|GO:1902531": INDIRECT "human/CASK|GO:0004385": NONCATALYTIC_HOMOLOG "human/CASP6|GO:0072734": UNSUPPORTED "human/CHPT1|GO:0005737": WRONG_LOCATION "human/CRY1|GO:0019902": WRONG_PARALOG "human/EIF2B4|GO:0048513": INDIRECT "human/GBA|GO:0030163": WRONG_PROCESS "human/GBA|GO:0042391": INDIRECT "human/GCK|GO:0046496": WRONG_PROCESS "human/GFPT1|GO:0006112": WRONG_PROCESS "human/GFPT2|GO:0006112": WRONG_PROCESS "human/HEXA|GO:0008375": WRONG_ACTIVITY "human/HSPA5|GO:0019899": ROLE_CONFUSION "human/KCTD18|GO:0042802": TOO_GENERAL "human/LPCAT4|GO:0042171": WRONG_ACTIVITY "human/MAP2K1|GO:0032872": WRONG_PARALOG "human/MCL1|GO:1902531": INDIRECT "human/MTRR|GO:0170033": OBSOLETE_OR_PSEUDOGENE "human/PAX6|GO:0050877": TERM_MISREAD "human/PTEN|GO:0010604": WRONG_DIRECTION "human/RASA3|GO:0006950": UNSUPPORTED "human/RDH8|GO:0006694": WRONG_PROCESS "human/RGS20|GO:0003924": ROLE_CONFUSION "human/RNF185|GO:1904380": ROLE_CONFUSION "human/RNF5|GO:1904380": ROLE_CONFUSION "human/SIX3|GO:0007601": TERM_MISREAD "human/SIX6|GO:0007601": TERM_MISREAD "human/SLC25A19|GO:0015932": WRONG_ACTIVITY "human/SNRPGP15|GO:0030532": OBSOLETE_OR_PSEUDOGENE "human/SPHK1|GO:0038036": ROLE_CONFUSION "human/SPHK2|GO:0038036": ROLE_CONFUSION "human/TRAF3|GO:0016020": WRONG_LOCATION "human/TUSC3|GO:0015095": WRONG_ACTIVITY "human/UGGT1|GO:1904380": ROLE_CONFUSION "human/XIAP|GO:0019899": TOO_GENERAL "human/XIAP|GO:0032991": TOO_GENERAL "mouse/Dll3|GO:0050768": WRONG_DIRECTION "mouse/Pax6|GO:0050877": TERM_MISREAD "mouse/Pcbd1|GO:0004505": ROLE_CONFUSION "mouse/Pcbd2|GO:0004505": ROLE_CONFUSION "worm/F44E5.4|GO:0005788": WRONG_PARALOG "worm/hip-1|GO:0005634": WRONG_LOCATION "worm/hip-1|GO:0070013": WRONG_LOCATION "worm/hsp-70|GO:0005788": WRONG_PARALOG "worm/kap-1|GO:0005634": WRONG_LOCATION "worm/lis-1|GO:0007154": WRONG_PROCESS "worm/lis-1|GO:0023052": WRONG_PROCESS "worm/lrx-1|GO:0016192": SPURIOUS_SIGNATURE "worm/mek-2|GO:0006950": TOO_GENERAL "worm/prg-1|GO:0007279": WRONG_TAXON "worm/znfx-1|GO:0005694": WRONG_LOCATION "yeast/AAD3|GO:0047681": NONCATALYTIC_HOMOLOG "yeast/DNM1|GO:0030001": SPURIOUS_SIGNATURE "yeast/EPS1|GO:0005737": WRONG_LOCATION "yeast/HDA1|GO:0010557": WRONG_DIRECTION "yeast/HSP60|GO:0005737": WRONG_LOCATION "yeast/NIT1|GO:0016836": WRONG_ACTIVITY "yeast/RAS2|GO:0097271": TOO_SPECIFIC "yeast/SPA2|GO:0051286": WRONG_TAXON