Sodb facilitates comprehensive exploration of spatial omics data

ABSTRACT Spatial omics technologies generate wealthy but highly complex datasets. Here we present Spatial Omics DataBase (SODB), a web-based platform providing both rich data resources and a

suite of interactive data analytical modules. SODB currently maintains >2,400 experiments from >25 spatial omics technologies, which are freely accessible as a unified data format

compatible with various computational packages. SODB also provides multiple interactive data analytical modules, especially a unique module, Spatial Omics View (SOView). We conduct

comprehensive statistical analyses and illustrate the utility of both basic and advanced analytical modules using multiple spatial omics datasets. We demonstrate SOView utility with brain

spatial transcriptomics data and recover known anatomical structures. We further delineate functional tissue domains with associated marker genes that were obscured when analyzed using

previous methods. We finally show how SODB may efficiently facilitate computational method development. The SODB website is https://gene.ai.tencent.com/SpatialOmics/. The command-line

package is available at https://pysodb.readthedocs.io/en/latest/. Access through your institution Buy or subscribe This is a preview of subscription content, access via your institution

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FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS NEUROMAPS: STRUCTURAL AND FUNCTIONAL INTERPRETATION OF BRAIN MAPS Article Open access 06 October 2022 DECIPHERING

SPATIAL DOMAINS FROM SPATIAL MULTI-OMICS WITH SPATIALGLUE Article Open access 21 June 2024 INTRACELLULAR SPATIAL TRANSCRIPTOMIC ANALYSIS TOOLKIT (INSTANT) Article Open access 06 September

2024 DATA AVAILABILITY All the primary links of raw data are provided on the web page of datasets. All processed data can be downloaded via the SODB website

(https://gene.ai.tencent.com/SpatialOmics/) or pysodb package (https://pysodb.readthedocs.io/en/latest/). CODE AVAILABILITY The SODB website is available at

https://gene.ai.tencent.com/SpatialOmics/. Code for the SODB project is available at https://github.com/yuanzhiyuan/SODB_analysis/. Code for pysodb is available at

https://github.com/TencentAILabHealthcare/pysodb. Please refer to Supplementary Table 9 for detailed information on code and resources. CHANGE HISTORY * _ 17 MARCH 2023 A Correction to this

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Article  CAS  PubMed  PubMed Central  Google Scholar  Download references ACKNOWLEDGEMENTS Z.Y. acknowledges the support from the Shanghai Municipal Science and Technology Major Project (no.

2018SHZDZX01), ZJ Laboratory, Shanghai Center for Brain Science and Brain-Inspired Technology and 111 Project (no. B18015). M.Q.Z. acknowledges support by the Cecil H. and Ida Green

Distinguished Chair. We thank L. Wang of Tencent for technical support. AUTHOR INFORMATION Author notes * These authors contributed equally: Zhiyuan Yuan, Wentao Pan. AUTHORS AND

AFFILIATIONS * Institute of Science and Technology for Brain-Inspired Intelligence; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence; MOE Frontiers Center for

Brain Science, Fudan University, Shanghai, China Zhiyuan Yuan * Tencent AI Lab, Shenzhen, China Zhiyuan Yuan, Wentao Pan, Xuan Zhao, Zhimeng Xu & Jianhua Yao * Shenzhen International

Graduate School, Tsinghua University, Shenzen, China Wentao Pan & Xiu Li * Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China Fangyuan Zhao & Yi Zhao *

University of Chinese Academy of Sciences, Beijing, China Fangyuan Zhao & Yi Zhao * Department of Biological Sciences, Center for Systems Biology, The University of Texas, Richardson,

TX, USA Michael Q. Zhang Authors * Zhiyuan Yuan View author publications You can also search for this author inPubMed Google Scholar * Wentao Pan View author publications You can also search

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publications You can also search for this author inPubMed Google Scholar * Jianhua Yao View author publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS

J.Y., Z.Y. and M.Q.Z. designed the project. Z.Y. performed data collection. Website design was by Z.Y. and X.Z. J.Y., X.L. and Y.Z. provided technical support. Biological interpretation was

by M.Q.Z. and Y.Z. Data statistics were performed by Z.Y. Website implementation was by X.Z. and W.P. Figure generation was by Z.Y. and F.Z. Z.Y. and W.P. wrote the manuscript. Z.X.

maintains the website. J.Y. and M.Q.Z. reviewed the manuscript. All authors approved the final manuscript. CORRESPONDING AUTHORS Correspondence to Zhiyuan Yuan, Michael Q. Zhang or Jianhua

Yao. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing interests. PEER REVIEW PEER REVIEW INFORMATION _Nature Methods_ thanks the anonymous reviewers for their

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remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION Supplementary Figs. 1–42, Notes 1

and 2 and Tables 7–10. REPORTING SUMMARY SUPPLEMENTARY TABLE 1 Experiment information of SODB. SUPPLEMENTARY TABLE 2 Dataset information of SODB. SUPPLEMENTARY TABLE 3 Biotechnology

information of SODB. SUPPLEMENTARY TABLE 4 Review article containing computational methods. SUPPLEMENTARY TABLE 5 Computational methods and their categories. SUPPLEMENTARY TABLE 6 Datasets

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and applicable law. Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Yuan, Z., Pan, W., Zhao, X. _et al._ SODB facilitates comprehensive exploration of spatial omics data. _Nat

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