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Efforts with limited resources often encountered in academia can easily fall short of data integration best practices for processing and combining high-content imaging, proteomics, metabolomics, and other omics data. We present Phenonaut, a Python software package designed to address the data workflow needs of migration, control, integration, and auditability in the application of literature and proprietary techniques for data source and structure agnostic workflow creation.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>Source code: https:\/\/github.com\/CarragherLab\/phenonaut, Documentation: https:\/\/carragherlab.github.io\/phenonaut, PyPI package: https:\/\/pypi.org\/project\/phenonaut\/.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad143","type":"journal-article","created":{"date-parts":[[2023,3,21]],"date-time":"2023-03-21T01:45:10Z","timestamp":1679363110000},"source":"Crossref","is-referenced-by-count":7,"title":["Phenonaut: multiomics data integration for phenotypic space exploration"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6996-3663","authenticated-orcid":false,"given":"Steven","family":"Shave","sequence":"first","affiliation":[{"name":"Edinburgh Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh , Edinburgh EH4 2XR, United Kingdom"},{"name":"GlaxoSmithKline Medicines Research Centre , Stevenage SG1 2NY, United Kingdom"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5713-1026","authenticated-orcid":false,"given":"John C","family":"Dawson","sequence":"additional","affiliation":[{"name":"Edinburgh Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh , Edinburgh EH4 2XR, United Kingdom"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8326-9579","authenticated-orcid":false,"given":"Abdullah 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