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Research Reproducibility Issues

Follows the list of information that is retrieved from online sources, therefore, they may cause issues regarding research reproducibility.

  • compounds with HMDB IDs HMDB29244, HMDB29245, and HMDB29246 are excluded from pathway evaluation (annotation of unannotated features which are part of some pathway that is present in the analyzed sample).
    • possible explanation: these compounds are very similar and they probably cause errors since they are non-specifically related to various pathways (very late stage biosynthesis)
    • primary affected functions: multilevelannotationstep3
    • transitively affected functions: multilevelannotation
  • attributes BRITE, PATHWAYS, and DBLINKS are retrieved from online KEGG database
    • conditionally (defaults to not to) the HMDB ID and LipidMaps ID are extracted from DBLINKS if present
    • implications: since these are not important attributes and are added to the result just for convenience, the annotation algorithm is unaffected
    • primary affected functions: Annotationbychemical_IDschild, Annotationbychemical_IDschildsimple, Annotationbychemical_IDschild_multilevel
    • transitively affected functions: simpleAnnotation, multilevelannotation, Annotationbychemical_IDs
  • attributes FORMULA, NAME, and EXACT_MASS are retrieved from online KEGG database
    • primary affected functions: get_mz_by_KEGGcompoundIDs, get_mz_by_KEGGdrugIDs
  • attributes COMPOUND, MODULE are retrieved from online KEGG database
    • primary affected function: get_mz_by_KEGGpathwayIDs
    • transitively affected functions: get_mz_by_KEGGspecies
  • based on the KEGG's species code a list of pathways is retrieved from online KEGG database
    • primary affected function: get_mz_by_KEGGspecies
  • legacy KEGG annotation (needs verification in case of interest)
    • all data is retrieved from various online sources: Adduct, Query.m/z, Search mass tolerance range (+/-), Metlin, Compound.Name, Chemical.Formula, Exact Mass, CASID, KEGG.Compound.ID, KEGG.Pathway.ID, KEGG.Pathway.Name, HMDB.ID, PubChem.Substance.ID, ChEBI.ID, LIPID.MAPS.ID, KEGG.Brite.Category, KEGG.Disease.ID, KEGG.Drug.ID, KEGG.Environ.ID
    • primary affected function: feat.batch.annotation.child
    • transitively affected functions: KEGG.annotationvold
  • ChemSpider annotation (needs verification in case of interest)
    • all data is retrieved from various online sources: Adduct, Query.m/z, Search mass tolerance range (+/-), ChemspiderID, CommonName, Molecular.Formula, SMILES, InChI, InChIKey, AverageMass, MolecularWeight, MonoisotopicMass, NominalMass, ALogP, XLogP, Structure, KEGG.Compound.ID, HMDB, LipidMAPS, PubChem, MassBank, BioCyc, SMPDB, EPA.DSSTox, EPA.Toxcast, Pesticide.Common.Names, ChEMBL, ChEBI, NIST.Chem.WebBook, WikiPathways, DrugBank, Comparative Toxicogenomics Database, ACToR: Aggregated Computational Toxicology Resource
    • primary affected functions:chspider.batch.annotation.child
    • transitively affected functions: ChemSpider.annotation