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# Mutants
#########

- name: mutant_sub1
  label: SubstitutionMutant
  priority: 1
  type: token
  action: unpackRelations
  example: "K182L"
  keep: false
  pattern: |
    [lemma=/^(mutant|mutation)/]? (?[word=/(?i)^[ACDEFGHIKLMNPQRSTVWY]\d+[ACDEFGHIKLMNPQRSTVWY](\/[ACDEFGHIKLMNPQRSTVWY]\d+[ACDEFGHIKLMNPQRSTVWY])*$/]) [lemma=/^(mutant|mutation)/]?

#- name: mutant_sub2
#  label: SubstitutionMutant
#  priority: 1
#  type: token
#  action: unpackRelations
#  example: "P88i" # TODO: Is this a legal mutation name?
#  keep: false
#  pattern: |
#    [lemma=/^(mutant|mutation)/]? (?[word=/^P\d+[ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy]$/]) [lemma=/^(mutant|mutation)/]?

- name: mutant_sub3long
  label: SubstitutionMutant
  priority: 1
  type: token
  action: unpackRelations
  example: "Ser43Val"
  keep: false
  pattern: |
    [lemma=/^(mutant|mutation)/]? (?[word=/(?i)^(Ala|Arg|Asn|Asp|Cys|Gln|Glu|Gly|His|Ile|Leu|Lys|Met|Phe|Pro|Ser|Thr|Trp|Tyr|Val)\d+(Ala|Arg|Asn|Asp|Cys|Gln|Glu|Gly|His|Ile|Leu|Lys|Met|Phe|Pro|Ser|Thr|Trp|Tyr|Val)(\/(Ala|Arg|Asn|Asp|Cys|Gln|Glu|Gly|His|Ile|Leu|Lys|Met|Phe|Pro|Ser|Thr|Trp|Tyr|Val)\d+(Ala|Arg|Asn|Asp|Cys|Gln|Glu|Gly|His|Ile|Leu|Lys|Met|Phe|Pro|Ser|Thr|Trp|Tyr|Val))*$/]) [lemma=/^(mutant|mutation)/]?

- name: mutant_sub4rangle
  label: SubstitutionMutant
  priority: 1
  type: token
  action: unpackRelations
  example: "91T>Y"
  keep: false
  pattern: |
    [lemma=/^(mutant|mutation)/]? (?[word=/^\d+[ACDEFGHIKLMNPQRSTVWY]$/] ">" [word=/^[ACDEFGHIKLMNPQRSTVWY]$/]) [lemma=/^(mutant|mutation)/]?

- name: mutant_del1range
  label: DeletionMutant
  priority: 1
  type: token
  action: unpackRelations
  example: "W34_A36del"
  keep: false
  pattern: |
    [lemma=/^(mutant|mutation)/]? (?[word=/^([ACDEFGHIKLMNPQRSTVWY]?\d+_)?[ACDEFGHIKLMNPQRSTVWY]?\d+del[ACDEFGHIKLMNPQRSTVWY]?(\/([ACDEFGHIKLMNPQRSTVWY]?\d+_)?[ACDEFGHIKLMNPQRSTVWY]?\d+del[ACDEFGHIKLMNPQRSTVWY]?)*$/]) [lemma=/^(mutant|mutation)/]?

- name: mutant_del2rangelong
  label: DeletionMutant
  priority: 1
  type: token
  action: unpackRelations
  example: "414delCys"
  keep: false
  pattern: |
    [lemma=/^(mutant|mutation)/]? (?[word=/^((Ala|Arg|Asn|Asp|Cys|Gln|Glu|Gly|His|Ile|Leu|Lys|Met|Phe|Pro|Ser|Thr|Trp|Tyr|Val)?\d+_)?(Ala|Arg|Asn|Asp|Cys|Gln|Glu|Gly|His|Ile|Leu|Lys|Met|Phe|Pro|Ser|Thr|Trp|Tyr|Val)?\d+del(Ala|Arg|Asn|Asp|Cys|Gln|Glu|Gly|His|Ile|Leu|Lys|Met|Phe|Pro|Ser|Thr|Trp|Tyr|Val)?(\/((Ala|Arg|Asn|Asp|Cys|Gln|Glu|Gly|His|Ile|Leu|Lys|Met|Phe|Pro|Ser|Thr|Trp|Tyr|Val)?\d+_)?(Ala|Arg|Asn|Asp|Cys|Gln|Glu|Gly|His|Ile|Leu|Lys|Met|Phe|Pro|Ser|Thr|Trp|Tyr|Val)?\d+del(Ala|Arg|Asn|Asp|Cys|Gln|Glu|Gly|His|Ile|Leu|Lys|Met|Phe|Pro|Ser|Thr|Trp|Tyr|Val)?)*$/]) [lemma=/^(mutant|mutation)/]?

- name: mutant_del3Delta
  label: DeletionMutant
  priority: 1
  type: token
  action: unpackRelations
  example: "DeltaN663"
  keep: false
  pattern: |
    [lemma=/^(mutant|mutation)/]? (?[word=/^Delta[ACDEFGHIKLMNPQRSTVWY]\d+(\/(Delta)?[ACDEFGHIKLMNPQRSTVWY]\d+)*$/]) [lemma=/^(mutant|mutation)/]?

- name: mutant_dup1
  label: DuplicationMutant
  priority: 1
  type: token
  action: unpackRelations
  example: "Q18_H33dup"
  keep: false
  pattern: |
    [lemma=/^(mutant|mutation)/]? (?[word=/^([ACDEFGHIKLMNPQRSTVWY]?\d+_)?[ACDEFGHIKLMNPQRSTVWY]?\d+dup$/]) [lemma=/^(mutant|mutation)/]?

- name: mutant_dup2long
  label: DuplicationMutant
  priority: 1
  type: token
  action: unpackRelations
  example: "Gly101dup"
  keep: false
  pattern: |
    [lemma=/^(mutant|mutation)/]? (?[word=/^((Ala|Arg|Asn|Asp|Cys|Gln|Glu|Gly|His|Ile|Leu|Lys|Met|Phe|Pro|Ser|Thr|Trp|Tyr|Val)?\d+_)?(Ala|Arg|Asn|Asp|Cys|Gln|Glu|Gly|His|Ile|Leu|Lys|Met|Phe|Pro|Ser|Thr|Trp|Tyr|Val)?\d+dup?$/]) [lemma=/^(mutant|mutation)/]?

- name: mutant_ins1
  label: InsertionMutant
  priority: 1
  type: token
  action: unpackRelations
  example: "K66_A67insEMYQ"
  keep: false
  pattern: |
    [lemma=/^(mutant|mutation)/]? (?[word=/^[ACDEFGHIKLMNPQRSTVWY]?\d+_[ACDEFGHIKLMNPQRSTVWY]?\d+ins[ACDEFGHIKLMNPQRSTVWY]+$/]) [lemma=/^(mutant|mutation)/]?

- name: mutant_ins2long
  label: InsertionMutant
  priority: 1
  type: token
  action: unpackRelations
  example: "Glu66_Tyr67insHis"
  keep: false
  pattern: |
    [lemma=/^(mutant|mutation)/]? (?[word=/^(Ala|Arg|Asn|Asp|Cys|Gln|Glu|Gly|His|Ile|Leu|Lys|Met|Phe|Pro|Ser|Thr|Trp|Tyr|Val)?\d+_(Ala|Arg|Asn|Asp|Cys|Gln|Glu|Gly|His|Ile|Leu|Lys|Met|Phe|Pro|Ser|Thr|Trp|Tyr|Val)?\d+ins(Ala|Arg|Asn|Asp|Cys|Gln|Glu|Gly|His|Ile|Leu|Lys|Met|Phe|Pro|Ser|Thr|Trp|Tyr|Val)+$/]) [lemma=/^(mutant|mutation)/]?

- name: mutant_fs1
  label: FrameshiftMutant
  priority: 1
  type: token
  action: unpackRelations
  example: "S228fs"
  keep: false
  pattern: |
    [lemma=/^(mutant|mutation)/]? (?[word=/^[ACDEFGHIKLMNPQRSTVWY]\d+fs$/]) [lemma=/^(mutant|mutation)/]?

- name: mutant_fs2long
  label: FrameshiftMutant
  priority: 1
  type: token
  action: unpackRelations
  example: "Leu81fs"
  keep: false
  pattern: |
    [lemma=/^(mutant|mutation)/]? (?[word=/^(Ala|Arg|Asn|Asp|Cys|Gln|Glu|Gly|His|Ile|Leu|Lys|Met|Phe|Pro|Ser|Thr|Trp|Tyr|Val)\d+fs$/]) [lemma=/^(mutant|mutation)/]?

#NOTE: mutantlate_.+ should happen AFTER mutant_.+, because they are generic
- name: mutantlate_1
  label: GenericMutant
  priority: 2
  action: mkBioMention
  type: token
  keep: false
  pattern: |
    (?<= [mention=/^Family|MacroMolecule$/]) [lemma=/^(mutant|mutation)/ & !mention=Mutant] (?! of [mention=/^Family|MacroMolecule$/]) (?! ("("? [mention=Mutant] ")"?))

- name: mutantlate_2
  label: GenericMutant
  priority: 2
  action: mkBioMention
  type: token
  keep: false
  pattern: |
    (?