PT - JOURNAL ARTICLE AU - Safiye Celik AU - Jan-Christian Hütter AU - Sandra Melo Carlos AU - Nathan H Lazar AU - Rahul Mohan AU - Conor Tillinghast AU - Tommaso Biancalani AU - Marta Fay AU - Berton A Earnshaw AU - Imran S Haque TI - Biological Cartography: Building and Benchmarking Representations of Life AID - 10.1101/2022.12.09.519400 DP - 2022 Jan 01 TA - bioRxiv PG - 2022.12.09.519400 4099 - http://biorxiv.org/content/early/2022/12/12/2022.12.09.519400.short 4100 - http://biorxiv.org/content/early/2022/12/12/2022.12.09.519400.full AB - The continued scaling of genetic perturbation technologies combined with high-dimensional assays (microscopy and RNA-sequencing) has enabled genome-scale reverse-genetics experiments that go beyond single-endpoint measurements of growth or lethality. Datasets emerging from these experiments can be combined to construct “maps of biology”, in which perturbation readouts are placed in unified, relatable embedding spaces to capture known biological relationships and discover new ones. Construction of maps involves many technical choices in both experimental and computational protocols, motivating the design of benchmark procedures by which to evaluate map quality in a systematic, unbiased manner.In this work, we propose a framework for the steps involved in map building and demonstrate key classes of benchmarks to assess the quality of a map. We describe univariate benchmarks assessing perturbation quality and multivariate benchmarks assessing recovery of known biological relationships from large-scale public data sources. We demonstrate the application and interpretation of these benchmarks through example maps of scRNA-seq and phenomic imaging data.Competing Interest StatementThe authors have declared no competing interest.