{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T21:22:09Z","timestamp":1775596929307,"version":"3.50.1"},"reference-count":41,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2022,3,22]],"date-time":"2022-03-22T00:00:00Z","timestamp":1647907200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2022,3,22]],"date-time":"2022-03-22T00:00:00Z","timestamp":1647907200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["P41 HD064556"],"award-info":[{"award-number":["P41 HD064556"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["P41 HD064556"],"award-info":[{"award-number":["P41 HD064556"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["P41 HD064556"],"award-info":[{"award-number":["P41 HD064556"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["P41 HD064556"],"award-info":[{"award-number":["P41 HD064556"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["P41 HD064556"],"award-info":[{"award-number":["P41 HD064556"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["P41 HD064556"],"award-info":[{"award-number":["P41 HD064556"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["P41 HD064556"],"award-info":[{"award-number":["P41 HD064556"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["P41 HD064556"],"award-info":[{"award-number":["P41 HD064556"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["P41 HD064556"],"award-info":[{"award-number":["P41 HD064556"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["P41 HD064556"],"award-info":[{"award-number":["P41 HD064556"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["P41 HD064556"],"award-info":[{"award-number":["P41 HD064556"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["P41 HD064556"],"award-info":[{"award-number":["P41 HD064556"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["P41 HD064556"],"award-info":[{"award-number":["P41 HD064556"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["P41 HD064556"],"award-info":[{"award-number":["P41 HD064556"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["P41 HD064556"],"award-info":[{"award-number":["P41 HD064556"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["P41 HD064556"],"award-info":[{"award-number":["P41 HD064556"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["P41 HD064556"],"award-info":[{"award-number":["P41 HD064556"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009633","name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","doi-asserted-by":"publisher","award":["P41 HD064556"],"award-info":[{"award-number":["P41 HD064556"]}],"id":[{"id":"10.13039\/100009633","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["1RM1HG010860-01"],"award-info":[{"award-number":["1RM1HG010860-01"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["1RM1HG010860-01"],"award-info":[{"award-number":["1RM1HG010860-01"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2022,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Ontologies of precisely defined, controlled vocabularies are essential to curate the results of biological experiments such that the data are machine searchable, can be computationally analyzed, and are interoperable across the biomedical research continuum. There is also an increasing need for methods to interrelate phenotypic data easily and accurately from experiments in animal models with human development and disease.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Here we present the\n                      <jats:italic>Xenopus<\/jats:italic>\n                      phenotype ontology (XPO) to annotate phenotypic data from experiments in\n                      <jats:italic>Xenopus<\/jats:italic>\n                      , one of the major vertebrate model organisms used to study gene function in development and disease. The XPO implements design patterns from the Unified Phenotype Ontology (uPheno), and the principles outlined by the Open Biological and Biomedical Ontologies (OBO Foundry) to maximize interoperability with other species and facilitate ongoing ontology management. Constructed in Web Ontology Language (OWL) the XPO combines the existing uPheno library of ontology design patterns with additional terms from the\n                      <jats:italic>Xenopus<\/jats:italic>\n                      Anatomy Ontology (XAO), the Phenotype and Trait Ontology (PATO) and the Gene Ontology (GO). The integration of these different ontologies into the XPO enables rich phenotypic curation, whilst the uPheno bridging axioms allows phenotypic data from\n                      <jats:italic>Xenopus<\/jats:italic>\n                      experiments to be related to phenotype data from other model organisms and human disease. Moreover, the simple post-composed uPheno design patterns facilitate ongoing XPO development as the generation of new terms and classes of terms can be substantially automated.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      The XPO serves as an example of current best practices to help overcome many of the inherent challenges in harmonizing phenotype data between different species. The XPO currently consists of approximately 22,000 terms and is being used to curate phenotypes by Xenbase, the\n                      <jats:italic>Xenopus<\/jats:italic>\n                      Model Organism Knowledgebase, forming a standardized corpus of genotype\u2013phenotype data that can be directly related to other uPheno compliant resources.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-022-04636-8","type":"journal-article","created":{"date-parts":[[2022,3,22]],"date-time":"2022-03-22T02:02:51Z","timestamp":1647914571000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development"],"prefix":"10.1186","volume":"23","author":[{"given":"Malcolm E.","family":"Fisher","sequence":"first","affiliation":[]},{"given":"Erik","family":"Segerdell","sequence":"additional","affiliation":[]},{"given":"Nicolas","family":"Matentzoglu","sequence":"additional","affiliation":[]},{"given":"Mardi J.","family":"Nenni","sequence":"additional","affiliation":[]},{"given":"Joshua D.","family":"Fortriede","sequence":"additional","affiliation":[]},{"given":"Stanley","family":"Chu","sequence":"additional","affiliation":[]},{"given":"Troy J.","family":"Pells","sequence":"additional","affiliation":[]},{"given":"David","family":"Osumi-Sutherland","sequence":"additional","affiliation":[]},{"given":"Praneet","family":"Chaturvedi","sequence":"additional","affiliation":[]},{"given":"Christina","family":"James-Zorn","sequence":"additional","affiliation":[]},{"given":"Nivitha","family":"Sundararaj","sequence":"additional","affiliation":[]},{"given":"Vaneet S.","family":"Lotay","sequence":"additional","affiliation":[]},{"given":"Virgilio","family":"Ponferrada","sequence":"additional","affiliation":[]},{"given":"Dong Zhuo","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Eugene","family":"Kim","sequence":"additional","affiliation":[]},{"given":"Sergei","family":"Agalakov","sequence":"additional","affiliation":[]},{"given":"Bradley I.","family":"Arshinoff","sequence":"additional","affiliation":[]},{"given":"Kamran","family":"Karimi","sequence":"additional","affiliation":[]},{"given":"Peter D.","family":"Vize","sequence":"additional","affiliation":[]},{"given":"Aaron M.","family":"Zorn","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2022,3,22]]},"reference":[{"issue":"11","key":"4636_CR1","doi-asserted-by":"publisher","first-page":"e1000247","DOI":"10.1371\/journal.pbio.1000247","volume":"7","author":"NL Washington","year":"2009","unstructured":"Washington NL, Haendel MA, Mungall CJ, Ashburner M, Westerfield M, Lewis SE. Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol. 2009;7(11):e1000247.","journal-title":"PLoS Biol"},{"issue":"11","key":"4636_CR2","doi-asserted-by":"publisher","first-page":"1251","DOI":"10.1038\/nbt1346","volume":"25","author":"B Smith","year":"2007","unstructured":"Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, et al. The OBO foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007;25(11):1251\u20135.","journal-title":"Nat Biotechnol"},{"key":"4636_CR3","unstructured":"The Gene Ontology. http:\/\/purl.obolibrary.org\/obo\/go.obo. Accessed 26 Aug 2021."},{"key":"4636_CR4","unstructured":"PATO\u2014The Phenotype And Trait Ontology. http:\/\/purl.obolibrary.org\/obo\/pato.obo. Accessed 26 Aug 2021."},{"key":"4636_CR5","unstructured":"The Relations Ontology. http:\/\/purl.obolibrary.org\/obo\/ro.obo. Accessed 26 Aug 2021."},{"key":"4636_CR6","unstructured":"The Human Phenotype Ontology. http:\/\/purl.obolibrary.org\/obo\/hp.owl. Accessed 26 Aug 2021."},{"issue":"6","key":"4636_CR7","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1111\/j.1399-0004.2010.01436.x","volume":"77","author":"PN Robinson","year":"2010","unstructured":"Robinson PN, Mundlos S. The human phenotype ontology. Clin Genet. 2010;77(6):525\u201334.","journal-title":"Clin Genet"},{"key":"4636_CR8","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1186\/s13326-015-0009-1","volume":"6","author":"CL Smith","year":"2015","unstructured":"Smith CL, Eppig JT. Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens. J Biomed Semant. 2015;6:11.","journal-title":"J Biomed Semant"},{"issue":"1","key":"4636_CR9","doi-asserted-by":"publisher","first-page":"R7","DOI":"10.1186\/gb-2004-6-1-r7","volume":"6","author":"CL Smith","year":"2005","unstructured":"Smith CL, Goldsmith CA, Eppig JT. The Mammalian phenotype ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol. 2005;6(1):R7.","journal-title":"Genome Biol"},{"issue":"D1","key":"4636_CR10","doi-asserted-by":"publisher","first-page":"D867","DOI":"10.1093\/nar\/gky1090","volume":"47","author":"L Ruzicka","year":"2019","unstructured":"Ruzicka L, Howe DG, Ramachandran S, Toro S, Van Slyke CE, Bradford YM, Eagle A, Fashena D, Frazer K, Kalita P, et al. The Zebrafish information network: new support for non-coding genes, richer gene ontology annotations and the alliance of genome resources. Nucl Acids Res. 2019;47(D1):D867\u201373.","journal-title":"Nucl Acids Res"},{"issue":"1","key":"4636_CR11","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/2041-1480-5-12","volume":"5","author":"CE Van Slyke","year":"2014","unstructured":"Van Slyke CE, Bradford YM, Westerfield M, Haendel MA. The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. J Biomed Semant. 2014;5(1):12.","journal-title":"J Biomed Semant"},{"issue":"4","key":"4636_CR12","doi-asserted-by":"publisher","first-page":"1491","DOI":"10.1534\/genetics.116.188870","volume":"203","author":"JA McMurry","year":"2016","unstructured":"McMurry JA, Kohler S, Washington NL, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, et al. Navigating the phenotype frontier: the monarch initiative. Genetics. 2016;203(4):1491\u20135.","journal-title":"Genetics"},{"issue":"D1","key":"4636_CR13","doi-asserted-by":"publisher","first-page":"D704","DOI":"10.1093\/nar\/gkz997","volume":"48","author":"KA Shefchek","year":"2020","unstructured":"Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, et al. The monarch initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucl Acids Res. 2020;48(D1):D704\u201315.","journal-title":"Nucl Acids Res"},{"key":"4636_CR14","unstructured":"Matentzoglu NB, James P, Bello SM, Boerkoel CF, Bradford YM, Carmody LC, Cooper LD, Grove CA, Harris NL, K\u00f6hler S, Laporte M-A, Laulederkind SLF, Lee R, Mazandu GK, McMurry JA, Mungall C, Osumi-Sutherland D, Pilgrim C, Rageth K, Robb SMC, Robinson PN, Segerdell E, Thessen A, Vasilevsky N, Zhang XA, Haendel MA. Phenotype ontologies traversing all the organisms (POTATO) workshop aims to reconcile logical definitions across species. 2018."},{"issue":"D1","key":"4636_CR15","first-page":"D776","volume":"48","author":"JD Fortriede","year":"2020","unstructured":"Fortriede JD, Pells TJ, Chu S, Chaturvedi P, Wang D, Fisher ME, James-Zorn C, Wang Y, Nenni MJ, Burns KA, et al. Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database. Nucl Acids Res. 2020;48(D1):D776\u201382.","journal-title":"Nucl Acids Res"},{"key":"4636_CR16","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1007\/978-1-4939-7737-6_10","volume":"1757","author":"C James-Zorn","year":"2018","unstructured":"James-Zorn C, Ponferrada V, Fisher ME, Burns K, Fortriede J, Segerdell E, Karimi K, Lotay V, Wang DZ, Chu S, et al. Navigating Xenbase: an integrated Xenopus genomics and gene expression database. Methods Mol Biol. 2018;1757:251\u2013305.","journal-title":"Methods Mol Biol"},{"key":"4636_CR17","doi-asserted-by":"publisher","first-page":"154","DOI":"10.3389\/fphys.2019.00154","volume":"10","author":"MJ Nenni","year":"2019","unstructured":"Nenni MJ, Fisher ME, James-Zorn C, Pells TJ, Ponferrada V, Chu S, Fortriede JD, Burns KA, Wang Y, Lotay VS, et al. Xenbase: facilitating the use of Xenopus to model human disease. Front Physiol. 2019;10:154.","journal-title":"Front Physiol"},{"key":"4636_CR18","unstructured":"Web Ontology Language (OWL). https:\/\/www.w3.org\/OWL\/. Accessed 29 Oct 2021."},{"key":"4636_CR19","doi-asserted-by":"publisher","unstructured":"Ontology Development Kit. https:\/\/doi.org\/10.5281\/zenodo.5564481. Accessed 29 Oct 2021.","DOI":"10.5281\/zenodo.5564481"},{"issue":"1","key":"4636_CR20","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1186\/s12859-019-3002-3","volume":"20","author":"RC Jackson","year":"2019","unstructured":"Jackson RC, Balhoff JP, Douglass E, Harris NL, Mungall CJ, Overton JA. ROBOT: a tool for automating ontology workflows. BMC Bioinform. 2019;20(1):407.","journal-title":"BMC Bioinform"},{"key":"4636_CR21","unstructured":"YAML\u2122 Specification Index. https:\/\/yaml.org\/spec\/. Accessed 25 Oct 2021."},{"key":"4636_CR22","unstructured":"The Xenopus Anatomy Ontology http:\/\/purl.obolibrary.org\/obo\/xao.obo. Accessed 26 Aug 2021."},{"key":"4636_CR23","unstructured":"The Basic Formal Ontology. http:\/\/purl.obolibrary.org\/obo\/bfo.obo. Accessed 26 Aug 2021."},{"issue":"6","key":"4636_CR24","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1242\/dmm.024661","volume":"9","author":"N Gouignard","year":"2016","unstructured":"Gouignard N, Maccarana M, Strate I, von Stedingk K, Malmstrom A, Pera EM. Musculocontractural Ehlers\u2013Danlos syndrome and neurocristopathies: dermatan sulfate is required for Xenopus neural crest cells to migrate and adhere to fibronectin. Dis Models Mech. 2016;9(6):607\u201320.","journal-title":"Dis Models Mech"},{"key":"4636_CR25","unstructured":"Phenotype Ontologies Reconciliation Effort. https:\/\/github.com\/obophenotype\/upheno\/wiki\/Phenotype-Ontologies-Reconciliation-Effort. Accessed 26 Aug 2021."},{"key":"4636_CR26","unstructured":"The Neuro Behavior Ontology. http:\/\/purl.obolibrary.org\/obo\/nbo.owl. Accessed 26 Aug 2021."},{"issue":"1","key":"4636_CR27","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/s13326-017-0172-7","volume":"9","author":"N Matentzoglu","year":"2018","unstructured":"Matentzoglu N, Malone J, Mungall C, Stevens R. MIRO: guidelines for minimum information for the reporting of an ontology. J Biomed Semant. 2018;9(1):6.","journal-title":"J Biomed Semant"},{"key":"4636_CR28","doi-asserted-by":"publisher","first-page":"35264","DOI":"10.1038\/srep35264","volume":"6","author":"T Naert","year":"2016","unstructured":"Naert T, Colpaert R, Van Nieuwenhuysen T, Dimitrakopoulou D, Leoen J, Haustraete J, Boel A, Steyaert W, Lepez T, Deforce D, et al. CRISPR\/Cas9 mediated knockout of rb1 and rbl1 leads to rapid and penetrant retinoblastoma development in Xenopus tropicalis. Sci Rep. 2016;6:35264.","journal-title":"Sci Rep"},{"issue":"3","key":"4636_CR29","first-page":"1","volume":"11","author":"SM Bello","year":"2018","unstructured":"Bello SM, Shimoyama M, Mitraka E, Laulederkind SJF, Smith CL, Eppig JT, Schriml LM. Disease ontology: improving and unifying disease annotations across species. Dis Models Mech. 2018;11(3):1\u20139.","journal-title":"Dis Models Mech"},{"issue":"Suppl 2","key":"4636_CR30","doi-asserted-by":"publisher","first-page":"S1","DOI":"10.1186\/2041-1480-3-S2-S1","volume":"3","author":"A Oellrich","year":"2012","unstructured":"Oellrich A, Gkoutos GV, Hoehndorf R, Rebholz-Schuhmann D. Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology. J Biomed Semant. 2012;3(Suppl 2):S1.","journal-title":"J Biomed Semant"},{"issue":"1","key":"4636_CR31","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1016\/0012-1606(80)90082-2","volume":"79","author":"SR Scharf","year":"1980","unstructured":"Scharf SR, Gerhart JC. Determination of the dorsal-ventral axis in eggs of Xenopus laevis: complete rescue of uv-impaired eggs by oblique orientation before first cleavage. Dev Biol. 1980;79(1):181\u201398.","journal-title":"Dev Biol"},{"issue":"1","key":"4636_CR32","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1016\/0012-1606(83)90255-5","volume":"99","author":"SR Scharf","year":"1983","unstructured":"Scharf SR, Gerhart JC. Axis determination in eggs of Xenopus laevis: a critical period before first cleavage, identified by the common effects of cold, pressure and ultraviolet irradiation. Dev Biol. 1983;99(1):75\u201387.","journal-title":"Dev Biol"},{"key":"4636_CR33","volume-title":"Symposium on the application of short-term bioassays in the analysis of complex environmental mixtures: III","author":"JN Dumont","year":"1983","unstructured":"Dumont JN, Schultz TW, Buchanan MV, Kao GL. Frog embryo teratogenesis assay Xenopus: FETAX\u2014a short-term assay applicable to complex environmental mixtures. In: Sandhu SS, Lewtas J, Claxton L, Chernoff N, Nesnow S, editors. Symposium on the application of short-term bioassays in the analysis of complex environmental mixtures: III. New York: Springer; 1983."},{"key":"4636_CR34","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1007\/978-1-4939-7172-5_17","volume":"1641","author":"I Mouche","year":"2017","unstructured":"Mouche I, Malesic L, Gillardeaux O. FETAX assay for evaluation of developmental toxicity. Methods Mol Biol. 2017;1641:311\u201324.","journal-title":"Methods Mol Biol"},{"issue":"11","key":"4636_CR35","doi-asserted-by":"publisher","first-page":"e193","DOI":"10.1371\/journal.pgen.0020193","volume":"2","author":"AA Rana","year":"2006","unstructured":"Rana AA, Collart C, Gilchrist MJ, Smith JC. Defining synphenotype groups in Xenopus tropicalis by use of antisense morpholino oligonucleotides. PLoS Genet. 2006;2(11):e193.","journal-title":"PLoS Genet"},{"key":"4636_CR36","doi-asserted-by":"publisher","first-page":"30","DOI":"10.12688\/f1000research.2-30.v1","volume":"2","author":"S Kohler","year":"2013","unstructured":"Kohler S, Doelken SC, Ruef BJ, Bauer S, Washington N, Westerfield M, Gkoutos G, Schofield P, Smedley D, Lewis SE, et al. Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000Res. 2013;2:30.","journal-title":"F1000Res"},{"key":"4636_CR37","doi-asserted-by":"publisher","first-page":"D1207","DOI":"10.1093\/nar\/gkaa1043","volume":"49","author":"S Kohler","year":"2020","unstructured":"Kohler S, Gargano M, Matentzoglu N, Carmody LC, Lewis-Smith D, Vasilevsky NA, Danis D, Balagura G, Baynam G, Brower AM, et al. The Human Phenotype Ontology in 2021. Nucleic Acids Res. 2020;49:D1207\u201317.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"4636_CR38","first-page":"1","volume":"13","author":"AM Shah","year":"2020","unstructured":"Shah AM, Krohn P, Baxi AB, Tavares ALP, Sullivan CH, Chillakuru YR, Majumdar HD, Neilson KM, Moody SA. Six1 proteins with human branchio-oto-renal mutations differentially affect cranial gene expression and otic development. Dis Models Mech. 2020;13(3):1\u201314.","journal-title":"Dis Models Mech"},{"issue":"12","key":"4636_CR39","doi-asserted-by":"publisher","first-page":"2393","DOI":"10.1002\/humu.23895","volume":"40","author":"J Li","year":"2019","unstructured":"Li J, Zhang J, Tang W, Mizu RK, Kusumoto H, XiangWei W, Xu Y, Chen W, Amin JB, Hu C, et al. De novo GRIN variants in NMDA receptor M2 channel pore-forming loop are associated with neurological diseases. Hum Mutat. 2019;40(12):2393\u2013413.","journal-title":"Hum Mutat"},{"key":"4636_CR40","doi-asserted-by":"publisher","first-page":"134","DOI":"10.3389\/fphys.2019.00134","volume":"10","author":"T Ott","year":"2019","unstructured":"Ott T, Kaufmann L, Granzow M, Hinderhofer K, Bartram CR, Theiss S, Seitz A, Paramasivam N, Schulz A, Moog U, et al. The frog Xenopus as a model to study joubert syndrome: the case of a human patient with compound heterozygous variants in PIBF1. Front Physiol. 2019;10:134.","journal-title":"Front Physiol"},{"key":"4636_CR41","doi-asserted-by":"publisher","first-page":"1094","DOI":"10.1016\/j.cels.2021.07.009","volume":"12","author":"SB Rosenthal","year":"2021","unstructured":"Rosenthal SB, Willsey HR, Xu Y, Mei Y, Dea J, Wang S, Curtis C, Sempou E, Khokha MK, Chi NC, et al. A convergent molecular network underlying autism and congenital heart disease. Cell Syst. 2021;12:1094\u2013107.","journal-title":"Cell Syst"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-022-04636-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-022-04636-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-022-04636-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,20]],"date-time":"2024-09-20T15:52:39Z","timestamp":1726847559000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-022-04636-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,3,22]]},"references-count":41,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2022,12]]}},"alternative-id":["4636"],"URL":"https:\/\/doi.org\/10.1186\/s12859-022-04636-8","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.11.12.467727","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,3,22]]},"assertion":[{"value":"12 November 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 March 2022","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 March 2022","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing Interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"99"}}