{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T12:58:38Z","timestamp":1780577918039,"version":"3.54.1"},"reference-count":29,"publisher":"Springer Science and Business Media LLC","issue":"S17","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12859-017-1980-6","type":"journal-article","created":{"date-parts":[[2017,12,21]],"date-time":"2017-12-21T08:48:51Z","timestamp":1513846131000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Cell ontology in an age of data-driven cell classification"],"prefix":"10.1186","volume":"18","author":[{"given":"David","family":"Osumi-Sutherland","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,12,21]]},"reference":[{"key":"1980_CR1","doi-asserted-by":"crossref","first-page":"1308","DOI":"10.1016\/j.cell.2016.07.054","volume":"166","author":"K Shekhar","year":"2016","unstructured":"Shekhar K, Lapan SW, Whitney IE, Tran NM, Macosko EZ, Kowalczyk M, et al. Comprehensive classification of retinal bipolar neurons by single-cell Transcriptomics. Cell. 2016;166:1308\u201323. e30","journal-title":"Cell"},{"key":"1980_CR2","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1016\/j.neuron.2016.10.001","volume":"92","author":"S Shah","year":"2016","unstructured":"Shah S, Lubeck E, Zhou W, Cai L. In situ transcription profiling of single cells reveals spatial Organization of Cells in the mouse hippocampus. Neuron. 2016;92:342\u201357.","journal-title":"Neuron."},{"key":"1980_CR3","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1016\/j.neuron.2016.06.012","volume":"91","author":"M Costa","year":"2016","unstructured":"Costa M, Manton JD, Ostrovsky AD, Prohaska S, Jefferis GSXE. NBLAST: rapid, sensitive comparison of neuronal structure and construction of neuron family databases. Neuron. 2016;91:293\u2013311.","journal-title":"Neuron."},{"key":"1980_CR4","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1038\/nature16468","volume":"529","author":"T Baden","year":"2016","unstructured":"Baden T, Berens P, Franke K, Rom\u00e1n Ros\u00f3n M, Bethge M, Euler T. The functional diversity of retinal ganglion cells in the mouse. Nature. 2016;529:345\u201350.","journal-title":"Nature"},{"key":"1980_CR5","doi-asserted-by":"crossref","first-page":"1243259","DOI":"10.1126\/science.1243259","volume":"342","author":"R Zenobi","year":"2013","unstructured":"Zenobi R. Single-cell metabolomics: analytical and biological perspectives. Science. 2013;342:1243259.","journal-title":"Science"},{"key":"1980_CR6","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1038\/nature14297","volume":"520","author":"T Ohyama","year":"2015","unstructured":"Ohyama T, Schneider-Mizell CM, Fetter RD, Aleman JV, Franconville R, Rivera-Alba M, et al. A multilevel multimodal circuit enhances action selection in drosophila. Nature. 2015;520:633\u20139.","journal-title":"Nature"},{"key":"1980_CR7","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1038\/nature12346","volume":"500","author":"M Helmstaedter","year":"2013","unstructured":"Helmstaedter M, Briggman KL, Turaga SC, Jain V, Seung HS, Denk W. Connectomic reconstruction of the inner plexiform layer in the mouse retina. Nature. 2013;500:168\u201374.","journal-title":"Nature"},{"key":"1980_CR8","unstructured":"Human Cell Atlas [Internet]. [cited 28 Jun 2017]. Available: https:\/\/www.humancellatlas.org\/"},{"key":"1980_CR9","unstructured":"Fly Cell Atlas. In: FLY CELL ATLAS [Internet]. [cited 28 Jun 2017]. Available: http:\/\/flycellatlas.org"},{"key":"1980_CR10","doi-asserted-by":"publisher","unstructured":"Kiselev VY, Hemberg M. Scmap - a tool for unsupervised projection of single cell RNA-seq data. bioRxiv. 2017:150292. https:\/\/doi.org\/10.1101\/150292 .","DOI":"10.1101\/150292"},{"key":"1980_CR11","doi-asserted-by":"crossref","first-page":"1867","DOI":"10.1016\/j.cell.2016.11.048","volume":"167","author":"B Adamson","year":"2016","unstructured":"Adamson B, Norman TM, Jost M, Cho MY, Nu\u00f1ez JK, Chen Y, et al. A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response. Cell. 2016;167:1867\u201382. e21","journal-title":"Cell"},{"key":"1980_CR12","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/s13326-016-0088-7","volume":"7","author":"AD Diehl","year":"2016","unstructured":"Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, et al. The cell ontology 2016: enhanced content, modularization, and ontology interoperability. J Biomed Semantics. 2016;7:44.","journal-title":"J Biomed Semantics."},{"key":"1980_CR13","doi-asserted-by":"crossref","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 Semantics. 2014;5:12.","journal-title":"J Biomed Semantics."},{"key":"1980_CR14","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1186\/2041-1480-4-32","volume":"4","author":"M Costa","year":"2013","unstructured":"Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. The drosophila anatomy ontology. J Biomed Semantics. 2013;4:32.","journal-title":"J Biomed Semantics"},{"key":"1980_CR15","doi-asserted-by":"publisher","unstructured":"Rosse C, Mejino JLV. The Foundational Model of Anatomy Ontology. In: Burger A, Davidson D, Baldock R. (eds) Anatomy Ontologies for Bioinformatics. Computational Biology. London: Springer. 2008;6. doi: 10.1007\/978-1-84628-885-2_4 .","DOI":"10.1007\/978-1-84628-885-2_4"},{"key":"1980_CR16","unstructured":"Hitzler P, Kr\u00f6tzsch M, Parsia B, Patel-Schneider - W3C \u2026 PF, 2009. OWL 2 web ontology language primer. w3.org . 2009; Available: https:\/\/www.w3.org\/TR\/2009\/PR-owl2-primer-20090922\/all.pdf"},{"key":"1980_CR17","doi-asserted-by":"crossref","unstructured":"Mungall CJ, Dietze H, Osumi-Sutherland D. Use of OWL within the gene ontology. In: Maria Keet C, editor. Proceedings of OWLED 2014, vol. 2014. p. 25\u201336.","DOI":"10.1101\/010090"},{"key":"1980_CR18","doi-asserted-by":"crossref","first-page":"1262","DOI":"10.1093\/bioinformatics\/bts113","volume":"28","author":"D Osumi-Sutherland","year":"2012","unstructured":"Osumi-Sutherland D, Reeve S, Mungall CJ, Neuhaus F, Ruttenberg A, Jefferis GSXE, et al. A strategy for building neuroanatomy ontologies. Bioinformatics. 2012;28:1262\u20139.","journal-title":"Bioinformatics"},{"key":"1980_CR19","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1093\/bioinformatics\/btr677","volume":"28","author":"N Milyaev","year":"2012","unstructured":"Milyaev N, Osumi-Sutherland D, Reeve S, Burton N, Baldock RA, Armstrong JD. The virtual fly brain browser and query interface. Bioinformatics. 2012;28:411\u20135.","journal-title":"Bioinformatics"},{"key":"1980_CR20","unstructured":"Osumi-Sutherland D, Costa M, Court R, O\u2019Kane C. Virtual fly brain-using OWL to support the mapping and genetic dissection of the drosophila brain. In: C Maria Keet, editor. Proceedings of OWLED 2014. 2014. pp. 85\u201396."},{"key":"1980_CR21","unstructured":"Virtual Fly Brain. In: Virtual Fly Brain [Internet]. [cited 30 Jun 2017]. Available: http:\/\/www.virtualflybrain.org"},{"key":"1980_CR22","first-page":"121","volume-title":"Modularisation of domain Ontologies implemented in description logics and related formalisms including OWL. Proceedings of the 2Nd international conference on knowledge capture","author":"AL Rector","year":"2003","unstructured":"Rector AL. Modularisation of domain Ontologies implemented in description logics and related formalisms including OWL. Proceedings of the 2Nd international conference on knowledge capture. New York: ACM; 2003. p. 121\u20138."},{"key":"1980_CR23","doi-asserted-by":"publisher","unstructured":"Li H, Horns F, Wu B, Xie Q, Li J, Li T, et al. Classifying drosophila olfactory projection neuron subtypes by single-cell RNA sequencing. bioRxiv. 2017:145045. https:\/\/doi.org\/10.1101\/145045 .","DOI":"10.1101\/145045"},{"key":"1980_CR24","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1038\/nrn3783","volume":"15","author":"T Euler","year":"2014","unstructured":"Euler T, Haverkamp S, Schubert T, Baden T. Retinal bipolar cells: elementary building blocks of vision. Nat Rev Neurosci. 2014;15:507\u201319.","journal-title":"Nat Rev Neurosci"},{"key":"1980_CR25","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1146\/annurev-neuro-062111-150533","volume":"36","author":"RI Wilson","year":"2013","unstructured":"Wilson RI. Early olfactory processing in drosophila: mechanisms and principles. Annu Rev Neurosci. 2013;36:217\u201341.","journal-title":"Annu Rev Neurosci"},{"key":"1980_CR26","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1006\/ijhc.1995.1081","volume":"43","author":"TR Gruber","year":"1995","unstructured":"Gruber TR. Toward principles for the design of ontologies used for knowledge sharing? Int J Hum Comput Stud. 1995;43:907\u201328.","journal-title":"Int J Hum Comput Stud"},{"key":"1980_CR27","first-page":"4","volume":"1","author":"MA Musen","year":"2015","unstructured":"Musen MA. The Prot\u00c9G\u00c9 project: a look back and a look forward. AI matters. New York, NY. USA: ACM. 2015;1:4\u201312.","journal-title":"USA: ACM"},{"key":"1980_CR28","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s10817-013-9296-3","volume":"53","author":"Y Kazakov","year":"2014","unstructured":"Kazakov Y, Kr\u00f6tzsch M, Siman\u010d\u00edk F. The incredible ELK. J Automat Reason. Springer Netherlands. 2014;53:1\u201361.","journal-title":"J Automat Reason"},{"key":"1980_CR29","doi-asserted-by":"crossref","unstructured":"Chiang AS, Lin CY, Chuang CC, Chang HM, Hsieh CH, Yeh CW, Shih CT, et al. \u201cThree-Dimensional Reconstruction of Brain-Wide Wiring Networks in Drosophila at Single-Cell Resolution\u201d. Current Biology: CB 21. 2011;(1):1\u201311.","DOI":"10.1016\/j.cub.2010.11.056"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1980-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,8]],"date-time":"2019-10-08T10:54:25Z","timestamp":1570532065000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1980-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,12]]},"references-count":29,"journal-issue":{"issue":"S17","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["1980"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1980-6","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,12]]},"article-number":"558"}}