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To further develop the understanding of specific pathological and histopathological phenotypes with their spatial relationships and dependencies, a more sophisticated spatial descriptive framework is required to enable integration and analysis in spatial terms.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We describe a conceptual coordinate model for the Gut Cell Atlas (small and large intestines). Here, we focus on a Gut Linear Model (1-dimensional representation based on the centreline of the gut) that represents the location semantics as typically used by clinicians and pathologists when describing location in the gut. This knowledge representation is based on a set of standardised gut anatomy ontology terms describing regions in situ, such as ileum or transverse colon, and landmarks, such as ileo-caecal valve or hepatic flexure, together with relative or absolute distance measures. We show how locations in the 1D model can be mapped to and from points and regions in both a 2D model and 3D models, such as a patient's CT scan where the gut has been segmented.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>The outputs of this work include 1D, 2D and 3D models of the human gut, delivered through publicly accessible Json and image files. We also illustrate the mappings between models using a demonstrator tool that allows the user to explore the anatomical space of the gut. All data and software is fully open-source and available online.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Small and large intestines have a natural \u201cgut coordinate\u201d system best represented as a 1D centreline through the gut tube, reflecting functional differences. Such a 1D centreline model with landmarks, visualised using viewer software allows interoperable translation to both a 2D anatomogram model and multiple 3D models of the intestines. This permits users to accurately locate samples for data comparison.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12911-023-02111-9","type":"journal-article","created":{"date-parts":[[2023,2,15]],"date-time":"2023-02-15T11:04:57Z","timestamp":1676459097000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models"],"prefix":"10.1186","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5492-8635","authenticated-orcid":false,"given":"Albert","family":"Burger","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0332-6877","authenticated-orcid":false,"given":"Richard A.","family":"Baldock","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9490-0306","authenticated-orcid":false,"given":"David J.","family":"Adams","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2855-3400","authenticated-orcid":false,"given":"Shahida","family":"Din","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7270-5470","authenticated-orcid":false,"given":"Irene","family":"Papatheodorou","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8278-5555","authenticated-orcid":false,"given":"Michael","family":"Glinka","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8988-0627","authenticated-orcid":false,"given":"Bill","family":"Hill","sequence":"additional","affiliation":[]},{"given":"Derek","family":"Houghton","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2295-9231","authenticated-orcid":false,"given":"Mehran","family":"Sharghi","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4390-4654","authenticated-orcid":false,"given":"Michael","family":"Wicks","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6826-8770","authenticated-orcid":false,"given":"Mark J.","family":"Arends","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,2,15]]},"reference":[{"key":"2111_CR1","doi-asserted-by":"publisher","first-page":"e27041","DOI":"10.7554\/eLife.27041","volume":"6","author":"A Regev","year":"2017","unstructured":"Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, et al. 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