tima_parameters.yaml

annotations:
  candidates:
    final: 500
  ms1only: no
  ms2approx: no
  thresholds:
    consistency: 0
    ms1:
      biological: 0
      chemical: 0
      condition: OR
    ms2:
      similarity:
        annotation: 0
        edges: 0.7
files:
  pattern: mia
  annotations:
    raw:
      spectral:
        gnps: data/interim/annotations/mia_gnps.tsv
        spectral: data/interim/annotations/mia_spectralMatches.tsv.gz
    filtered: data/interim/annotations/mia_annotationsFiltered.tsv.gz
    prepared:
      canopus: data/interim/annotations/mia_canopusPrepared.tsv.gz
      formula: data/interim/annotations/mia_formulaPrepared.tsv.gz
      structural:
        gnps: data/interim/annotations/mia_gnpsPrepared.tsv.gz
        ms1: data/interim/annotations/mia_ms1Prepared.tsv.gz
        sirius: data/interim/annotations/mia_siriusPrepared.tsv.gz
        spectral: data/interim/annotations/mia_spectralMatchesPrepared.tsv.gz
    processed: example_results.tsv
  features:
    raw: data/source/3f8c133554914f429401ea999086cc75.csv
    prepared: data/interim/features/mia_features.tsv.gz
  libraries:
    sop:
      raw:
        closed: ../lotus-processor/data/processed/230106_closed_metadata.csv.gz
        ecmdb: data/source/libraries/sop/ecmdb.json.zip
        hmdb: data/source/libraries/sop/hmdb/structures.zip
        lotus: data/source/libraries/sop/lotus.csv.gz
      prepared:
        closed: data/interim/libraries/sop/closed_prepared.tsv.gz
        ecmdb: data/interim/libraries/sop/ecmdb_prepared.tsv.gz
        hmdb: data/interim/libraries/sop/hmdb_prepared.tsv.gz
        lotus: data/interim/libraries/sop/lotus_prepared.tsv.gz
        rt: data/interim/libraries/sop/rt_prepared.tsv.gz
        spectral: data/interim/libraries/sop/spectral_prepared.tsv.gz
      merged:
        keys: data/interim/libraries/sop/merged/keys.tsv.gz
        organisms:
          names: data/interim/libraries/sop/merged/organisms/names.tsv.gz
          taxonomies:
            ott: data/interim/libraries/sop/merged/organisms/taxonomies/ott.tsv.gz
        structures:
          stereo: data/interim/libraries/sop/merged/structures/stereo.tsv.gz
          metadata: data/interim/libraries/sop/merged/structures/metadata.tsv.gz
          names: data/interim/libraries/sop/merged/structures/names.tsv.gz
          taxonomies:
            cla: data/interim/libraries/sop/merged/structures/taxonomies/classyfire.tsv.gz
            npc: data/interim/libraries/sop/merged/structures/taxonomies/npc.tsv.gz
    spectral:
      neg: data/interim/libraries/spectra/exp/internal_neg.rds
      pos: data/interim/libraries/spectra/exp/internal_pos.rds
    temporal:
      exp:
        mgf:
          neg: []
          pos: []
      is:
        mgf:
          neg: []
          pos: []
      prepared: data/interim/libraries/rt/prepared.tsv.gz
  networks:
    spectral:
      edges:
        raw:
          ms1: data/interim/features/mia_edgesMasses.tsv
          spectral: data/interim/features/mia_edgesSpectra.tsv
        prepared: data/interim/features/mia_edges.tsv
      components:
        raw: data/interim/features/mia_components.tsv
        prepared: data/interim/features/mia_componentsPrepared.tsv
  metadata:
    raw: data/source/fichier_metadata.tsv
    prepared: data/interim/taxa/mia_taxed.tsv.gz
  spectral:
    raw: data/source/specs_ms.mgf
gnps:
  id: ec37fe7e20764d38924c881ab9dd006e
  workflow: fbmn
ms:
  adducts:
    neg:
    - '[M-H2]2-'
    - '[M-H]-'
    - '[2M-H]-'
    pos:
    - '[M+H2]2+'
    - '[M+H]+'
    - '[M+H4N]+'
    - '[M+Na]+'
    - '[2M+H]+'
  clusters:
    neg:
    - H2O
    - CH2O2
    - H2PO4
    pos:
    - H2O
    - C2H3N
  neutral_losses:
  - O
  - H3N (ammonia)
  - H2O (water)
  - CO
  - C2H5 (CH2-CH3)
  - H4O2 (2xH2O)
  - CO2
  - CHO2
  - H6O3 (3xH2O)
  - C2O2 (2xCO)
  - CH6O3 (combination)
  - H8O4 (4xH2O)
  - C3H6O3 (sugar)
  - H2O4S (sulfuric)
  - H3O4P (phosphoric)
  - C4H8O4 (sugar)
  - C6H6O3 (HRF)
  - C5H8O4 (pentose-H2O)
  - C8H8O2 (RDA-1)
  - C6H8O4 (HRF)
  - C6H10O4 (methylpentose/desoxyhexose-H2O)
  - C8H8O3 (RDA-2)
  - C6H10O5 (hexose-H2O)
  - C8H8O4 (RDA-3)
  - C8H10O4 (RDA-2-H2O)
  - C6H12O6 (hexose)
  - C11H10O4 (sinapoyl)
  - C16H30O (pamitoyl)
  - C12H20O8 (2xmethylpentose/desoxyhexose-H2O)
  - C12H20O10 (2xhexose-H2O)
  polarity: pos
  thresholds:
    ms2:
      intensity: 5
  tolerances:
    mass:
      ppm:
        ms1: 10
        ms2: 10
      dalton:
        ms1: 0.01
        ms2: 0.01
    rt:
      adducts: 0.02
      library: 0.1
names:
  adduct: best ion
  extension: yes
  features: row ID
  filename: sample_filename_pos
  libraries: internal
  inchikey: inchikey
  mgf:
    adduct: ''
    collision_energy: ''
    compound_id: SPECTRUMID
    exact_mass: EXACTMASS
    inchi: INCHI
    inchi_no_stereo: ''
    inchikey: ''
    inchikey_no_stereo: ''
    molecular_formula: ''
    name: ''
    polarity: IONMODE
    retention_time: RTINSECONDS
    smiles: SMILES
    smiles_no_stereo: ''
    spectrum_id: ''
    splash: ''
    synonyms: ''
    xlogp: ''
  precursor: row m/z
  rt:
    features: row retention time
    library: rt
  smiles: smiles
  source: CLUSTERID1
  target: CLUSTERID2
  taxon: source_taxon
organisms:
  candidates: 1
  filter:
    mode: no
    level: phylum
    value: Streptophyta
tools:
  metadata: gnps
  networks:
    spectral:
      components: gnps
      edges: gnps
  sirius:
    version: '6'
  taxonomies:
    biological: otl
    chemical: npc
units:
  rt: seconds
weights:
  global:
    biological: 0.5
    chemical: 0.166
    spectral: 0.333
  biological:
    domain: 0.1
    kingdom: 0.2
    phylum: 0.3
    class: 0.4
    order: 0.5
    infraorder: 0.55
    family: 0.6
    subfamily: 0.65
    tribe: 0.7
    subtribe: 0.75
    genus: 0.8
    subgenus: 0.85
    species: 0.9
    subspecies: 0.95
    variety: 1
  chemical:
    cla:
      kingdom: 0.25
      superclass: 0.5
      class: 0.75
      parent: 1
    npc:
      pathway: 0.333
      superclass: 0.666
      class: 1
options:
  compounds_names: yes
  force: no
  high_confidence: no
  remove_ties: no
  summarise: yes