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This poses challenges in building unified hierarchical cell-type structures and hinders integration of large-scale datasets. To address this, several computational methods have been developed to harmonize cell type annotations across datasets and build data-driven hierarchies of cell types.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we benchmarked three state-of-the-art methods: scHPL, treeArches, and CellHint. We evaluated these methods across five simulated scenarios and five real-world scenarios across cell types and organs. To assess harmonization results, we designed three metrics, Annotation Harmonization F1-score (AH-F1), Tree Edit Distance Similarity and Parent\u2013Children Branches Similarity, comparing the constructed cell-type hierarchies and the knowledge-based ones. Based on the benchmarking results, we found that methods performed well in simulated scenarios but still have room for improvement in complex real-world data. Thus, we developed OTHarmonizer, a tool based on partial optimal transport (OT) for cell-type harmonization and hierarchy construction. OTHarmonizer excels in accurately capturing equivalent and hierarchical relationships between cell types, offering a more effective approach for the cell-type hierarchy construction across datasets.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The simulated and real-world datasets in the benchmark are available on https:\/\/figshare.com\/articles\/dataset\/OTHarmonizer\/28243205. The source codes for the benchmark and OTHarmonizer are available online on GitHub at\u00a0https:\/\/github.com\/Duck-Boss\/OTHarmonizer.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag506","type":"journal-article","created":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T11:46:57Z","timestamp":1783424817000},"source":"Crossref","is-referenced-by-count":0,"title":["Cross-dataset annotation harmonization for cell-type hierarchy construction"],"prefix":"10.1093","volume":"42","author":[{"given":"Tianhong","family":"Zhou","sequence":"first","affiliation":[{"name":"MOE Key Laboratory of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University , Beijing 100084,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2946-5122","authenticated-orcid":false,"given":"Yixin","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Biomedical 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