Restructure

[douweschulte]

• core (chemistry, basic types, uom, masses, peptide, modifications, protein, ontologies) [ProForma, PEFF, .dat, USI] {rustyms + mzdata}
  • proteomics ident (scores, q_values, errors) [mzTAB, mzIdentML, mzSpecLib] {rustyms}
  • annotation [mzPAF] {rustyms}
  • quant (needed?) [??]
  • spectra (feature extraction, MS1 area) {mzdata}
    • spectra files (dda + dia) [mzML, USI] {mzdata}
    • chromatograms {mzdata}
  • ontologies (needed?) [SDRF]
  • IMGT
  • mass based alignment

flowchart TD
core --> proteomics_ident
core --> annotation
core --> quant 
core --> spectra
core --> ontologies
core --> IMGT
core --> mass_alignment
annotation --> proteomics_ident
spectra --> annotation
spectra --> spectra_files
spectra --> chromatograms
spectra -- mzSpecLib --> proteomics_ident
annotation --> python
spectra --> python
core --> python
mass_alignment --> python

core -.-> ProForma
core -.-> PEFF
core -.-> .dat
core -.-> USI

annotation -.-> mzPAF

proteomics_ident -.-> mzTAB
proteomics_ident -.-> mzIdentML
proteomics_ident -.-> mzSpecLib

spectra_files -.-> USI
spectra_files -.-> mzML

ontologies -.-> SDRF

ProForma@{ shape: doc, label: "ProForma" }
PEFF@{ shape: doc, label: "PEFF+FASTA" }
.dat@{ shape: doc, label: ".dat" }
mzPAF@{ shape: doc, label: "mzPAF" }
USI@{ shape: doc, label: "USI" }
mzTAB@{ shape: doc, label: "mzTAB" }
mzIdentML@{ shape: doc, label: "mzIdentML" }
mzSpecLib@{ shape: doc, label: "mzSpecLib" }
mzML@{ shape: doc, label: "mzML" }
SDRF@{ shape: doc, label: "SDRF" }

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flowchart TD
core --> chemistry
MolecularFormula --> IsotopeDistribution
chemistry --> Molecule
chemistry--> MolecularFormula
chemistry --> Element
chemistry --> MolecularCharge
chemistry --> MassMode
MolecularFormula -.-> ChemForma
MolecularFormula -.-> UnimodFormat
MolecularFormula -.-> PSIMODFormat
MolecularFormula -.-> ResidFormat
MolecularFormula -.-> XLMODFormat
MolecularFormula -.-> pyteomicsFormat
Molecule -.-> SMILES_SMART
Element --> MonoIsotopicMass
Element --> AverageWeight
MolecularFormula --> MostAbundantIsotope

core --> sequence
sequence --> AminoAcid
sequence --> Modification
sequence --> Peptidoform
sequence --> PeptidoformIon
sequence --> CompoundPeptidoformIon
sequence --> PlacementRule
sequence --> SequencePosition
sequence --> SequenceElement
sequence --> Protease

core --> quantities
quantities --> Multi
quantities --> Tolerance

core --> glycan
glycan --> GlycanComposition
glycan --> GlycanStructure
GlycanStructure -.-> IUPAC_condensed
GlycanComposition -.-> ProformaGlycan

core --> ontology
ontology -.-> Unimod
ontology -.-> PSIMOD
ontology -.-> Resid
ontology -.-> XLMOD
ontology -.-> GNOme
ontology -.-> PSIMS

core --> fragment
fragment --> NeutralLoss
fragment --> DiagnosticIon
fragment --> Fragment
Fragment -.-> mzPAF

core --> annotation
annotation--> peakFDR
annotation --> AnnotatableSpectrum
annotation --> Statistics
annotation --> Model

core --> error
error --> CustomError
error --> Context

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thoughts:

• custom FASTA header parsing
• improve circular dependency of ontology building
• annotation+fragment could go to a separate crate