{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T14:56:20Z","timestamp":1753887380210,"version":"3.41.2"},"reference-count":34,"publisher":"Walter de Gruyter GmbH","issue":"3","license":[{"start":{"date-parts":[[2024,7,12]],"date-time":"2024-07-12T00:00:00Z","timestamp":1720742400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["251654672 \u2013 TRR 161"],"award-info":[{"award-number":["251654672 \u2013 TRR 161"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>We present a method for the layout of anatomical structures and blood vessels based on information from the Foundational Model of Anatomy (FMA). Our approach integrates a novel vascular layout into the hierarchical treemap representation of anatomy as used in ApiNATOMY. Our method aims to improve the comprehension of complex anatomical and vascular data by providing readable visual representations. The effectiveness of our method is demonstrated through a prototype developed in VANTED, showing potential for application in research, education, and clinical settings.<\/jats:p>","DOI":"10.1515\/jib-2024-0023","type":"journal-article","created":{"date-parts":[[2024,7,11]],"date-time":"2024-07-11T18:44:08Z","timestamp":1720723448000},"source":"Crossref","is-referenced-by-count":2,"title":["Layout of anatomical structures and blood vessels based on the foundational model of anatomy"],"prefix":"10.1515","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-8600-6421","authenticated-orcid":false,"given":"Niklas","family":"Gr\u00f6ne","sequence":"first","affiliation":[{"name":"Department of Computer and Information Science , 570542 University of Konstanz , Konstanz , Germany"}]},{"given":"Benjamin","family":"Gr\u00fcneisen","sequence":"additional","affiliation":[{"name":"Independent Scholar , Halle (Saale) , Germany"}]},{"given":"Karsten","family":"Klein","sequence":"additional","affiliation":[{"name":"Department of Computer and Information Science , 570542 University of Konstanz , Konstanz , Germany"}]},{"given":"Bernard","family":"de Bono","sequence":"additional","affiliation":[{"name":"Whitby et\u00a0al, LLC , Indianapolis , IN , USA"},{"name":"Auckland Bioengineering Institute, University of Auckland , Auckland , New Zealand"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1788-9593","authenticated-orcid":false,"given":"Tobias","family":"Czauderna","sequence":"additional","affiliation":[{"name":"Faculty of Applied Computer Sciences & Biosciences , University of Applied Sciences Mittweida , Mittweida , Germany"}]},{"given":"Falk","family":"Schreiber","sequence":"additional","affiliation":[{"name":"Department of Computer and Information Science , 570542 University of Konstanz , Konstanz , Germany"},{"name":"Faculty of Information Technology , Monash University , Clayton , Australia"}]}],"member":"374","published-online":{"date-parts":[[2024,7,12]]},"reference":[{"key":"2024112723505291748_j_jib-2024-0023_ref_001","doi-asserted-by":"crossref","unstructured":"Rosse, C, Mejino, JL. A reference ontology for biomedical informatics: the foundational model of anatomy. J Biomed Inform 2003;36:478\u2013500. https:\/\/doi.org\/10.1016\/j.jbi.2003.11.007.","DOI":"10.1016\/j.jbi.2003.11.007"},{"key":"2024112723505291748_j_jib-2024-0023_ref_002","doi-asserted-by":"crossref","unstructured":"Rosse, C, Mejino, JL. The foundational model of anatomy ontology. London: Springer; 2008:59\u2013117 pp.","DOI":"10.1007\/978-1-84628-885-2_4"},{"key":"2024112723505291748_j_jib-2024-0023_ref_003","doi-asserted-by":"crossref","unstructured":"de Bono, B, Grenon, P, Sammut, SJ. ApiNATOMY: a novel toolkit for visualizing multiscale anatomy schematics with phenotype-related information. Hum Mutat 2012;33:837\u201348. https:\/\/doi.org\/10.1002\/humu.22065.","DOI":"10.1002\/humu.22065"},{"key":"2024112723505291748_j_jib-2024-0023_ref_004","doi-asserted-by":"crossref","unstructured":"de Bono, B, Grenon, P, Helvensteijn, M, Kok, JN, Kokash, N. ApiNATOMY: towards multiscale views of human anatomy. In: Blockeel, H, van Leeuwen, M, Vinciotti, V, editors. Advances in intelligent data analysis XIII, volume 8819 of LNCS. Springer; 2014:72\u201383 pp.","DOI":"10.1007\/978-3-319-12571-8_7"},{"key":"2024112723505291748_j_jib-2024-0023_ref_005","doi-asserted-by":"crossref","unstructured":"Scheibel, W, Limberger, D, D\u00f6llner, J. Survey of treemap layout algorithms. In: Proc. 13th international symposium on visual information communication and interaction (VINCI). ACM; 2020:1\u20139 pp.","DOI":"10.1145\/3430036.3430041"},{"key":"2024112723505291748_j_jib-2024-0023_ref_006","doi-asserted-by":"crossref","unstructured":"Kokash, N, de Bono, B, Kok, J. Template-based treemaps to preserve spatial constraints. In: Laramee, RS, Kerren, A, Braz, J, editors. 2014 international conference on information visualization theory and applications (IVAPP). IEEE; 2014:39\u201349 pp.","DOI":"10.5220\/0004684900390049"},{"key":"2024112723505291748_j_jib-2024-0023_ref_007","doi-asserted-by":"crossref","unstructured":"Zhao, H, Lu, L. Variational circular treemaps for interactive visualization of hierarchical data. In: Liu, S, Scheuermann, G, Takahashi, S, editors. IEEE pacific visualization symposium, Pacificvis 2015. IEEE; 2015:81\u20135 pp.","DOI":"10.1109\/PACIFICVIS.2015.7156360"},{"key":"2024112723505291748_j_jib-2024-0023_ref_008","doi-asserted-by":"crossref","unstructured":"Johnson, B, Shneiderman, B. Tree-maps: a space-filling approach to the visualization of hierarchical information structures. In: Proc. visualization \u201991; 1991, vol 91:284\u201391 pp.","DOI":"10.1109\/VISUAL.1991.175815"},{"key":"2024112723505291748_j_jib-2024-0023_ref_009","doi-asserted-by":"crossref","unstructured":"Bruls, M, Huizing, K, van Wijk, JJ. Squarified treemaps. In: de Leeuw, WC, van Liere, R, editors. Data visualization 2000. Springer; 2000:33\u201342 pp.","DOI":"10.1007\/978-3-7091-6783-0_4"},{"key":"2024112723505291748_j_jib-2024-0023_ref_010","doi-asserted-by":"crossref","unstructured":"Zizi, M, Beaudouin-Lafon, M. Accessing hyperdocuments through interactive dynamic maps. In: Proc. 1994 ACM european conference on hypermedia technology, ECHT \u201994. ACM; 1994:126\u201335 pp.","DOI":"10.1145\/192757.192786"},{"key":"2024112723505291748_j_jib-2024-0023_ref_011","doi-asserted-by":"crossref","unstructured":"Lu, L, Fan, S, Huang, M, Huang, W, Yang, R. Golden rectangle treemap. J Phys: Conf Ser 2017;787:012007. https:\/\/doi.org\/10.1088\/1742-6596\/787\/1\/012007.","DOI":"10.1088\/1742-6596\/787\/1\/012007"},{"key":"2024112723505291748_j_jib-2024-0023_ref_012","doi-asserted-by":"crossref","unstructured":"Tamassia, R, editor. Handbook on graph drawing and visualization. Chapman and Hall\/CRC; 2013.","DOI":"10.1201\/b15385"},{"key":"2024112723505291748_j_jib-2024-0023_ref_013","doi-asserted-by":"crossref","unstructured":"Eades, P, Klein, K. Graph visualization. Cham: Springer International Publishing; 2018:33\u201370 pp.","DOI":"10.1007\/978-3-319-96193-4_2"},{"key":"2024112723505291748_j_jib-2024-0023_ref_014","unstructured":"Bachmaier, C, Brandes, U, Schreiber, F. Biological networks. In: Tamassia, R, editor. Handbook of graph drawing and visualization. Chapman and Hall\/CRC; 2013:621\u201351 pp."},{"key":"2024112723505291748_j_jib-2024-0023_ref_015","doi-asserted-by":"crossref","unstructured":"Fruchterman, T, Reingold, E. Graph drawing by force-directed placement. Softw \u2013 Pract Exp 1991;21:1129\u201364. https:\/\/doi.org\/10.1002\/spe.4380211102.","DOI":"10.1002\/spe.4380211102"},{"key":"2024112723505291748_j_jib-2024-0023_ref_016","unstructured":"Eades, P. A heuristic for graph drawing. Congr Numer 1984;42:149\u201360."},{"key":"2024112723505291748_j_jib-2024-0023_ref_017","doi-asserted-by":"crossref","unstructured":"Sugiyama, K, Tagawa, S, Toda, M. Methods for visual understanding of hierarchical system structures. IEEE Trans Syst Man Cybern 1981;SMC-11:109\u201325. https:\/\/doi.org\/10.1109\/TSMC.1981.4308636.","DOI":"10.1109\/TSMC.1981.4308636"},{"key":"2024112723505291748_j_jib-2024-0023_ref_018","doi-asserted-by":"crossref","unstructured":"Six, JM, Tollis, IG. A framework for circular drawings of networks. In: Kratochvil, J, editor. Proc. international symposium on graph drawing (GD\u201999), volume 1731 of LNCS. Springer; 1999:107\u201316 pp.","DOI":"10.1007\/3-540-46648-7_11"},{"key":"2024112723505291748_j_jib-2024-0023_ref_019","doi-asserted-by":"crossref","unstructured":"Batini, C, Nardelli, E, Tamassia, R. A layout algorithm for data flow diagrams. IEEE Trans Softw Eng 1986;SE-12:538\u201346. https:\/\/doi.org\/10.1109\/TSE.1986.6312901.","DOI":"10.1109\/TSE.1986.6312901"},{"key":"2024112723505291748_j_jib-2024-0023_ref_020","unstructured":"Schreiber, F. High quality visualization of biochemical pathways in BioPath. Silico Biol 2002;2:59\u201373."},{"key":"2024112723505291748_j_jib-2024-0023_ref_021","doi-asserted-by":"crossref","unstructured":"Genc, B, Dogrus\u00f6z, U. A constrained, force-directed layout algorithm for biological pathways. In: Liotta, G, editor. Proc. international symposium on graph drawing (GD\u201903), volume 2912 of LNCS; 2003:314\u20139 pp.","DOI":"10.1007\/978-3-540-24595-7_29"},{"key":"2024112723505291748_j_jib-2024-0023_ref_022","doi-asserted-by":"crossref","unstructured":"Dwyer, T, Marriott, K, Schreiber, F, Stuckey, PJ, Woodward, M, Wybrow, M. Exploration of networks using overview+detail with constraint-based cooperative layout. IEEE Trans Vis Comput Graph 2008;14:1293\u2013300. https:\/\/doi.org\/10.1109\/TVCG.2008.130.","DOI":"10.1109\/TVCG.2008.130"},{"key":"2024112723505291748_j_jib-2024-0023_ref_023","doi-asserted-by":"crossref","unstructured":"Schreiber, F, Dwyer, T, Marriott, K, Wybrow, M. A generic algorithm for layout of biological networks. BMC Bioinf 2009;10:375.1\u201312. https:\/\/doi.org\/10.1186\/1471-2105-10-375.","DOI":"10.1186\/1471-2105-10-375"},{"key":"2024112723505291748_j_jib-2024-0023_ref_024","doi-asserted-by":"crossref","unstructured":"Misue, K, Eades, P, Lai, W, Sugiyama, K. Layout adjustment and the mental map. J Vis Lang Comput 1995;6:183\u2013210. https:\/\/doi.org\/10.1006\/jvlc.1995.1010.","DOI":"10.1006\/jvlc.1995.1010"},{"key":"2024112723505291748_j_jib-2024-0023_ref_025","doi-asserted-by":"crossref","unstructured":"Kotlarek, J, Kwon, O-H, Ma, K, Eades, P, Kerren, A, Klein, K, et al.. A study of mental maps in immersive network visualization. In: Proc. IEEE Pacific visualization \u2013 IEEE PacificVis; 2020:1\u201310 pp.","DOI":"10.1109\/PacificVis48177.2020.4722"},{"key":"2024112723505291748_j_jib-2024-0023_ref_026","doi-asserted-by":"crossref","unstructured":"Dobkin, DP, Gansner, ER, Koutsofios, E, North, SC. Implementing a general-purpose edge router. In: DiBattista, G, editor. Graph drawing (GD 1997). Berlin, Heidelberg: Springer; 1997:262\u201371 pp.","DOI":"10.1007\/3-540-63938-1_68"},{"key":"2024112723505291748_j_jib-2024-0023_ref_027","doi-asserted-by":"crossref","unstructured":"Wybrow, M, Marriott, K, Stuckey, PJ. Orthogonal connector routing. In: Eppstein, D, Gansner, ER, editors. Graph drawing (GD 2009). Berlin, Heidelberg: Springer; 2010:219\u201331 pp.","DOI":"10.1007\/978-3-642-11805-0_22"},{"key":"2024112723505291748_j_jib-2024-0023_ref_028","doi-asserted-by":"crossref","unstructured":"Freivalds, K. Curved edge routing. In: Freivalds, R, editor. Fundamentals of computation theory (FCT 2001). Berlin, Heidelberg: Springer; 2001:126\u201337 pp.","DOI":"10.1007\/3-540-44669-9_14"},{"key":"2024112723505291748_j_jib-2024-0023_ref_029","doi-asserted-by":"crossref","unstructured":"Wybrow, M, Marriott, K, Stuckey, PJ. Incremental connector routing. In: Healy, P, Nikolov, NS, editors. Graph drawing (GD 2005). Berlin, Heidelberg: Springer; 2006:446\u201357 pp.","DOI":"10.1007\/11618058_40"},{"key":"2024112723505291748_j_jib-2024-0023_ref_030","doi-asserted-by":"crossref","unstructured":"Holten, D, Van Wijk, JJ. Force-directed edge bundling for graph visualization. Comput Graph Forum 2009;28:983\u201390. https:\/\/doi.org\/10.1111\/j.1467-8659.2009.01450.x.","DOI":"10.1111\/j.1467-8659.2009.01450.x"},{"key":"2024112723505291748_j_jib-2024-0023_ref_031","doi-asserted-by":"crossref","unstructured":"Gansner, ER, Hu, Y, North, S, Scheidegger, C. Multilevel agglomerative edge bundling for visualizing large graphs. In: IEEE Pacific visualization symposium (PacificVis); 2011:187\u201394 pp.","DOI":"10.1109\/PACIFICVIS.2011.5742389"},{"key":"2024112723505291748_j_jib-2024-0023_ref_032","doi-asserted-by":"crossref","unstructured":"Guven, G, Hilty, M, Ince, C. Microcirculation: physiology, pathophysiology, and clinical application. Blood Purif 2020;49:143\u201350. https:\/\/doi.org\/10.1159\/000503775.","DOI":"10.1159\/000503775"},{"key":"2024112723505291748_j_jib-2024-0023_ref_033","doi-asserted-by":"crossref","unstructured":"Junker, BH, Klukas, C, Schreiber, F. VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinf 2006;7:109.1\u201313. https:\/\/doi.org\/10.1186\/1471-2105-7-109.","DOI":"10.1186\/1471-2105-7-109"},{"key":"2024112723505291748_j_jib-2024-0023_ref_034","doi-asserted-by":"crossref","unstructured":"Rohn, H, Junker, A, Hartmann, A, Grafahrend-Belau, E, Treutler, H, Klapperst\u00fcck, M, et al.. VANTED v2: a framework for systems biology applications. BMC Syst Biol 2012;6:139.1\u201313. https:\/\/doi.org\/10.1186\/1752-0509-6-139.","DOI":"10.1186\/1752-0509-6-139"}],"container-title":["Journal of Integrative Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2024-0023\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2024-0023\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,27]],"date-time":"2024-11-27T23:52:09Z","timestamp":1732751529000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/jib-2024-0023\/html"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,7,12]]},"references-count":34,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2024,7,15]]},"published-print":{"date-parts":[[2024,11,27]]}},"alternative-id":["10.1515\/jib-2024-0023"],"URL":"https:\/\/doi.org\/10.1515\/jib-2024-0023","relation":{},"ISSN":["1613-4516"],"issn-type":[{"type":"electronic","value":"1613-4516"}],"subject":[],"published":{"date-parts":[[2024,7,12]]},"article-number":"20240023"}}