{"id":"https://openalex.org/W4320914517","doi":"https://doi.org/10.1186/s12911-023-02111-9","title":"Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models","display_name":"Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models","publication_year":2023,"publication_date":"2023-02-15","ids":{"openalex":"https://openalex.org/W4320914517","doi":"https://doi.org/10.1186/s12911-023-02111-9","pmid":"https://pubmed.ncbi.nlm.nih.gov/36793076"},"language":"en","primary_location":{"id":"doi:10.1186/s12911-023-02111-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12911-023-02111-9","pdf_url":"https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-023-02111-9","source":{"id":"https://openalex.org/S107516304","display_name":"BMC Medical Informatics and Decision Making","issn_l":"1472-6947","issn":["1472-6947"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Medical Informatics and Decision Making","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-023-02111-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079735260","display_name":"Albert Burger","orcid":"https://orcid.org/0000-0002-5492-8635"},"institutions":[{"id":"https://openalex.org/I32062511","display_name":"Heriot-Watt University","ror":"https://ror.org/04mghma93","country_code":"GB","type":"education","lineage":["https://openalex.org/I32062511"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Albert Burger","raw_affiliation_strings":["Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK. a.g.burger@hw.ac.uk","Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK"],"raw_orcid":"https://orcid.org/0000-0002-5492-8635","affiliations":[{"raw_affiliation_string":"Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK. a.g.burger@hw.ac.uk","institution_ids":["https://openalex.org/I32062511"]},{"raw_affiliation_string":"Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK","institution_ids":["https://openalex.org/I32062511"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057893272","display_name":"Richard Baldock","orcid":"https://orcid.org/0000-0003-0332-6877"},"institutions":[{"id":"https://openalex.org/I2802581871","display_name":"Edinburgh Cancer Research","ror":"https://ror.org/05a7t9b67","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2801316944","https://openalex.org/I2802581871","https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Richard A. Baldock","raw_affiliation_strings":["Division of Pathology, Centre for Comparative Pathology, Edinburgh Cancer Research Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK"],"raw_orcid":"https://orcid.org/0000-0003-0332-6877","affiliations":[{"raw_affiliation_string":"Division of Pathology, Centre for Comparative Pathology, Edinburgh Cancer Research Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK","institution_ids":["https://openalex.org/I2802581871"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102865320","display_name":"David J. Adams","orcid":"https://orcid.org/0000-0001-9490-0306"},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"David J. Adams","raw_affiliation_strings":["Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK"],"raw_orcid":"https://orcid.org/0000-0001-9490-0306","affiliations":[{"raw_affiliation_string":"Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032672820","display_name":"Shahida Din","orcid":"https://orcid.org/0000-0003-2855-3400"},"institutions":[{"id":"https://openalex.org/I1324252669","display_name":"NHS Lothian","ror":"https://ror.org/03q82t418","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I1324252669"]},{"id":"https://openalex.org/I2800150677","display_name":"Western General Hospital","ror":"https://ror.org/009kr6r15","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I1324252669","https://openalex.org/I2800150677"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Shahida Din","raw_affiliation_strings":["Edinburgh IBD Unit Western General Hospital, NHS Lothian, Edinburgh, UK"],"raw_orcid":"https://orcid.org/0000-0003-2855-3400","affiliations":[{"raw_affiliation_string":"Edinburgh IBD Unit Western General Hospital, NHS Lothian, Edinburgh, UK","institution_ids":["https://openalex.org/I1324252669","https://openalex.org/I2800150677"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027778199","display_name":"Irene Papatheodorou","orcid":"https://orcid.org/0000-0001-7270-5470"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Irene Papatheodorou","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, Cambridge, UK"],"raw_orcid":"https://orcid.org/0000-0001-7270-5470","affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, Cambridge, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026429700","display_name":"Michael Glinka","orcid":"https://orcid.org/0000-0002-8278-5555"},"institutions":[{"id":"https://openalex.org/I2802581871","display_name":"Edinburgh Cancer Research","ror":"https://ror.org/05a7t9b67","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2801316944","https://openalex.org/I2802581871","https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Michael Glinka","raw_affiliation_strings":["Division of Pathology, Centre for Comparative Pathology, Edinburgh Cancer Research Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK"],"raw_orcid":"https://orcid.org/0000-0002-8278-5555","affiliations":[{"raw_affiliation_string":"Division of Pathology, Centre for Comparative Pathology, Edinburgh Cancer Research Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK","institution_ids":["https://openalex.org/I2802581871"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074966091","display_name":"Bill Hill","orcid":"https://orcid.org/0000-0002-8988-0627"},"institutions":[{"id":"https://openalex.org/I32062511","display_name":"Heriot-Watt University","ror":"https://ror.org/04mghma93","country_code":"GB","type":"education","lineage":["https://openalex.org/I32062511"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Bill Hill","raw_affiliation_strings":["Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK"],"raw_orcid":"https://orcid.org/0000-0002-8988-0627","affiliations":[{"raw_affiliation_string":"Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK","institution_ids":["https://openalex.org/I32062511"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021849832","display_name":"Derek Houghton","orcid":null},"institutions":[{"id":"https://openalex.org/I32062511","display_name":"Heriot-Watt University","ror":"https://ror.org/04mghma93","country_code":"GB","type":"education","lineage":["https://openalex.org/I32062511"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Derek Houghton","raw_affiliation_strings":["Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK","institution_ids":["https://openalex.org/I32062511"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062718449","display_name":"Mehran Sharghi","orcid":"https://orcid.org/0000-0003-2295-9231"},"institutions":[{"id":"https://openalex.org/I32062511","display_name":"Heriot-Watt University","ror":"https://ror.org/04mghma93","country_code":"GB","type":"education","lineage":["https://openalex.org/I32062511"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mehran Sharghi","raw_affiliation_strings":["Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK"],"raw_orcid":"https://orcid.org/0000-0003-2295-9231","affiliations":[{"raw_affiliation_string":"Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK","institution_ids":["https://openalex.org/I32062511"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089518375","display_name":"Michael N Wicks","orcid":"https://orcid.org/0000-0002-4390-4654"},"institutions":[{"id":"https://openalex.org/I2802581871","display_name":"Edinburgh Cancer Research","ror":"https://ror.org/05a7t9b67","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2801316944","https://openalex.org/I2802581871","https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Michael Wicks","raw_affiliation_strings":["Division of Pathology, Centre for Comparative Pathology, Edinburgh Cancer Research Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK"],"raw_orcid":"https://orcid.org/0000-0002-4390-4654","affiliations":[{"raw_affiliation_string":"Division of Pathology, Centre for Comparative Pathology, Edinburgh Cancer Research Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK","institution_ids":["https://openalex.org/I2802581871"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019378167","display_name":"Mark J. Arends","orcid":"https://orcid.org/0000-0002-6826-8770"},"institutions":[{"id":"https://openalex.org/I2802581871","display_name":"Edinburgh Cancer Research","ror":"https://ror.org/05a7t9b67","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2801316944","https://openalex.org/I2802581871","https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mark J. Arends","raw_affiliation_strings":["Division of Pathology, Centre for Comparative Pathology, Edinburgh Cancer Research Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK. m.arends@ed.ac.uk","Division of Pathology, Centre for Comparative Pathology, Edinburgh Cancer Research Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK"],"raw_orcid":"https://orcid.org/0000-0002-6826-8770","affiliations":[{"raw_affiliation_string":"Division of Pathology, Centre for Comparative Pathology, Edinburgh Cancer Research Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK. m.arends@ed.ac.uk","institution_ids":["https://openalex.org/I2802581871"]},{"raw_affiliation_string":"Division of Pathology, Centre for Comparative Pathology, Edinburgh Cancer Research Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK","institution_ids":["https://openalex.org/I2802581871"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5079735260"],"corresponding_institution_ids":["https://openalex.org/I32062511"],"apc_list":{"value":1570,"currency":"GBP","value_usd":1925},"apc_paid":{"value":1570,"currency":"GBP","value_usd":1925},"fwci":0.9513,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.74627925,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"23","issue":"1","first_page":"36","last_page":"36"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9602000117301941,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9602000117301941,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10336","display_name":"Cancer Cells and Metastasis","score":0.004900000058114529,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.00419999985024333,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/atlas","display_name":"Atlas (anatomy)","score":0.7354192137718201},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6285120248794556},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.43829280138015747},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3321380019187927},{"id":"https://openalex.org/keywords/anatomy","display_name":"Anatomy","score":0.2984444499015808},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2520340085029602}],"concepts":[{"id":"https://openalex.org/C2776673561","wikidata":"https://www.wikidata.org/wiki/Q655357","display_name":"Atlas (anatomy)","level":2,"score":0.7354192137718201},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6285120248794556},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43829280138015747},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3321380019187927},{"id":"https://openalex.org/C105702510","wikidata":"https://www.wikidata.org/wiki/Q514","display_name":"Anatomy","level":1,"score":0.2984444499015808},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2520340085029602}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12911-023-02111-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12911-023-02111-9","pdf_url":"https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-023-02111-9","source":{"id":"https://openalex.org/S107516304","display_name":"BMC Medical Informatics and Decision Making","issn_l":"1472-6947","issn":["1472-6947"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Medical Informatics and Decision Making","raw_type":"journal-article"},{"id":"pmid:36793076","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36793076","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC medical informatics and decision making","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9933383","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9933383","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9933383/pdf/12911_2023_Article_2111.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Med Inform Decis Mak","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:5036c98cb2794b52894100234eea3c03","is_oa":true,"landing_page_url":"https://doaj.org/article/5036c98cb2794b52894100234eea3c03","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Medical Informatics and Decision Making, Vol 23, Iss 1, Pp 1-17 (2023)","raw_type":"article"},{"id":"pmh:oai:pure.ed.ac.uk:openaire/dc48607d-b098-4a0b-b53c-ef74680de4d7","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/files/328311150/Towards_a_clinically_based_common_coordinate_framework_for_the_human_gut_cell_atlas_the_gut_models.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Burger, A, Baldock, R, Adams, D J, Din, S, Papatheodorou, I, Glinka, M, Hill, B, Houghton, D, Sharghi, M, Wicks, M & Arends, M J 2023, 'Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models', Nature. https://doi.org/10.1186/s12911-023-02111-9","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pure.ed.ac.uk:publications/dc48607d-b098-4a0b-b53c-ef74680de4d7","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/dc48607d-b098-4a0b-b53c-ef74680de4d7","pdf_url":null,"source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Burger, A, Baldock, R, Adams, D J, Din, S, Papatheodorou, I, Glinka, M, Hill, B, Houghton, D, Sharghi, M, Wicks, M & Arends, M J 2023, 'Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models', Nature. https://doi.org/10.1186/s12911-023-02111-9","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.1186/s12911-023-02111-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12911-023-02111-9","pdf_url":"https://bmcmedinformdecismak.biomedcentral.com/counter/pdf/10.1186/s12911-023-02111-9","source":{"id":"https://openalex.org/S107516304","display_name":"BMC Medical Informatics and Decision Making","issn_l":"1472-6947","issn":["1472-6947"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Medical Informatics and Decision Making","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309446","display_name":"Leona M. and Harry B. Helmsley Charitable Trust","ror":"https://ror.org/011x6n313"},{"id":"https://openalex.org/F4320311518","display_name":"Heriot-Watt University","ror":"https://ror.org/04mghma93"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4320914517.pdf"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W228639233","https://openalex.org/W1524554374","https://openalex.org/W1614089981","https://openalex.org/W1835820463","https://openalex.org/W1901129140","https://openalex.org/W1903029394","https://openalex.org/W2024927934","https://openalex.org/W2055655674","https://openalex.org/W2120087768","https://openalex.org/W2137362149","https://openalex.org/W2143742443","https://openalex.org/W2163670493","https://openalex.org/W2229919701","https://openalex.org/W2395611524","https://openalex.org/W2462007197","https://openalex.org/W2612519453","https://openalex.org/W2742995736","https://openalex.org/W2749814893","https://openalex.org/W2914189536","https://openalex.org/W2922020904","https://openalex.org/W2946804769","https://openalex.org/W2958721929","https://openalex.org/W2959566316","https://openalex.org/W2976362764","https://openalex.org/W2981768636","https://openalex.org/W2996615913","https://openalex.org/W3010741079","https://openalex.org/W3045964436","https://openalex.org/W3097200033","https://openalex.org/W3099559583","https://openalex.org/W3137406645","https://openalex.org/W3149417142","https://openalex.org/W3169239564","https://openalex.org/W3177911292","https://openalex.org/W3188531180","https://openalex.org/W3201734479","https://openalex.org/W3212552860","https://openalex.org/W3217192868","https://openalex.org/W4213108508","https://openalex.org/W4220837089","https://openalex.org/W4221113039","https://openalex.org/W4226172016","https://openalex.org/W4244131281","https://openalex.org/W4246739026","https://openalex.org/W4293498815","https://openalex.org/W4295136141","https://openalex.org/W4361205254","https://openalex.org/W6950726717"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2011187995","https://openalex.org/W2314146950","https://openalex.org/W2373521488","https://openalex.org/W4284509","https://openalex.org/W606911313","https://openalex.org/W4229506690","https://openalex.org/W4244549571","https://openalex.org/W638747717","https://openalex.org/W4243557525"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,219],"Human":[2],"Cell":[3,100],"Atlas":[4,101],"resource":[5],"will":[6,28],"deliver":[7],"single":[8],"cell":[9,44],"transcriptome":[10],"data":[11,38,266,334],"spatially":[12],"organised":[13],"in":[14,87,138,157,185,198],"terms":[15,154],"of":[16,24,32,43,62,120,149,221,230,262,323],"gross":[17],"anatomy,":[18],"tissue":[19],"location":[20,126,137],"and":[21,37,49,65,72,85,103,133,165,193,196,203,227,239,267,272,277,319],"with":[22,68,175,304],"images":[23],"cellular":[25,51],"histology.":[26],"This":[27,141,326],"enable":[29,83],"the":[30,60,98,118,121,125,139,186,213,231,245,255,259,263,293,324],"application":[31],"bioinformatics":[33],"analysis,":[34],"machine":[35],"learning":[36],"mining":[39],"revealing":[40],"an":[41],"atlas":[42],"types,":[45],"sub-types,":[46],"varying":[47],"states":[48],"ultimately":[50],"changes":[52],"related":[53],"to":[54,82,192,257,313,329],"disease":[55],"conditions.":[56],"To":[57],"further":[58],"develop":[59],"understanding":[61],"specific":[63],"pathological":[64],"histopathological":[66],"phenotypes":[67],"their":[69],"spatial":[70,77,88],"relationships":[71],"dependencies,":[73],"a":[74,93,110,147,200,208,250,281,289,300,315],"more":[75],"sophisticated":[76],"descriptive":[78],"framework":[79],"is":[80,144,269],"required":[81],"integration":[84],"analysis":[86],"terms.":[89],"METHODS:":[90],"We":[91,181,242],"describe":[92],"conceptual":[94],"coordinate":[95],"model":[96,188,202,303,318],"for":[97,333],"Gut":[99,111],"(small":[102],"large":[104,278],"intestines).":[105],"Here,":[106],"we":[107],"focus":[108],"on":[109,117,146],"Linear":[112],"Model":[113],"(1-dimensional":[114],"representation":[115,143],"based":[116,145],"centreline":[119,291,302],"gut)":[122],"that":[123,253],"represents":[124],"semantics":[127],"as":[128,160,168,207,288],"typically":[129],"used":[130],"by":[131],"clinicians":[132],"pathologists":[134],"when":[135],"describing":[136,155],"gut.":[140,264],"knowledge":[142],"set":[148],"standardised":[150],"gut":[151,214,294],"anatomy":[152],"ontology":[153],"regions":[156,197],"situ,":[158],"such":[159,167,206],"ileum":[161],"or":[162,171,177],"transverse":[163],"colon,":[164],"landmarks,":[166,305],"ileo-caecal":[169],"valve":[170],"hepatic":[172],"flexure,":[173],"together":[174],"relative":[176],"absolute":[178],"distance":[179],"measures.":[180],"show":[182],"how":[183],"locations":[184],"1D":[187,290,301],"can":[189],"be":[190],"mapped":[191],"from":[194],"points":[195],"both":[199,314],"2D":[201,226,316],"3D":[204,228,321],"models,":[205],"patient's":[209],"CT":[210],"scan":[211],"where":[212],"has":[215],"been":[216],"segmented.":[217],"RESULTS:":[218],"outputs":[220],"this":[222],"work":[223],"include":[224],"1D,":[225],"models":[229,248,322],"human":[232],"gut,":[233],"delivered":[234],"through":[235,292],"publicly":[236],"accessible":[237],"Json":[238],"image":[240],"files.":[241],"also":[243],"illustrate":[244],"mappings":[246],"between":[247],"using":[249,307],"demonstrator":[251],"tool":[252],"allows":[254,310],"user":[256],"explore":[258],"anatomical":[260],"space":[261],"All":[265],"software":[268,309],"fully":[270],"open-source":[271],"available":[273],"online.":[274],"CONCLUSIONS:":[275],"Small":[276],"intestines":[279],"have":[280],"natural":[282],"\"gut":[283],"coordinate\"":[284],"system":[285],"best":[286],"represented":[287],"tube,":[295],"reflecting":[296],"functional":[297],"differences.":[298],"Such":[299],"visualised":[306],"viewer":[308],"interoperable":[311],"translation":[312],"anatomogram":[317],"multiple":[320],"intestines.":[325],"permits":[327],"users":[328],"accurately":[330],"locate":[331],"samples":[332],"comparison.":[335]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
