{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/demeter-efficient-simultaneous-curation-of","title":"DEMETER: Efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations","arxiv_id":"2106.06638","date":"2021-06-11","proceeding":null,"authors":["Almut Heinken","Stefanía Magnúsdóttir","Ronan M. T. Fleming","Ines Thiele"],"abstract":"Motivation: Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools typically do not take species-specific experimental data and manually refined genome annotations into account. Results: We developed DEMETER, a COBRA Toolbox extension that enables the efficient simultaneous refinement of thousands of draft genome-scale reconstructions while ensuring adherence to the quality standards in the field, agreement with available experimental data, and refinement of pathways based on manually refined genome annotations. Availability: DEMETER and tutorials are available at https://github.com/opencobra/cobratoolbox.","url_abs":"https://arxiv.org/abs/2106.06638v1","url_pdf":"https://arxiv.org/pdf/2106.06638v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"demeter-efficient-simultaneous-curation-of","repo_url":"https://github.com/opencobra/cobratoolbox","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}