ReDU: a framework to find and reanalyze public mass spectrometry data.
Alan K JarmuschMingxun WangChristine M AcevesRohit S AdvaniShaden AguirreAlexander A AksenovGajender AletiAllegra T AronAnelize BauermeisterSanjana BolledduAmina BouslimaniAndres Mauricio Caraballo RodriguezRama ChaarRoxana CorasEmmanuel O ElijahMadeleine ErnstJulia M GauglitzEmily C GentryMakhai HusbandScott A JarmuschKenneth L JonesZdeněk KameníkAudrey Le GouëllecAileen LuLaura-Isobel McCallKerry L McPhailMichael J MeehanAlexey V MelnikRiya C MenezesYessica Alejandra Montoya GiraldoNgoc Hung NguyenLouis-Felix NothiasMélissa Nothias-EspositoMorgan PanitchpakdiDaniel PetrasRobert A QuinnNicole SikoraJustin Johan Jozias van der HooftFernando VargasAlison VrbanacKelly C WeldonRob KnightNuno BandeiraPieter C DorresteinPublished in: Nature methods (2020)
We present ReDU ( https://redu.ucsd.edu/ ), a system for metadata capture of public mass spectrometry-based metabolomics data, with validated controlled vocabularies. Systematic capture of knowledge enables the reanalysis of public data and/or co-analysis of one's own data. ReDU enables multiple types of analyses, including finding chemicals and associated metadata, comparing the shared and different chemicals between groups of samples, and metadata-filtered, repository-scale molecular networking.