Peer-reviewedCC BYScience Advances
Standardizing Cell Ontology terms for cross-study integration in the female reproductive tract
40 affiliations
- 1Mechanobiology Institute, National University of Singapore, Singapore, Singapore.
- 2Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, USA.
- 3Department of Pediatrics, Division of Endocrinology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- 4Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- 5EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
- 6Buck Institute for Research on Aging, Novato, CA, USA.
- 7Stowers Institute for Medical Research, Kansas City, MO, USA.
- 8Chan Zuckerberg Initiative Biohub, Redwood City, CA, USA.
- 9Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
- 10Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- 11Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA.
- 12Miller School of Medicine, Medical Campus, University of Miami, Miami, FL, USA.
- 13Sylvester Comprehensive Cancer Center, Miller School of Medicine, Medical Campus, University of Miami, Miami, FL, USA.
- 14Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil.
- 15Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
- 16Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA.
- 17Aging & Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.
- 18Nutrition College, Federal University of Pelotas, Pelotas, Brazil.
- 19Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
- 20Center for Healthy Aging in Women, Buck Institute for Research on Aging, Novato, CA, USA.
- 21Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- 22Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Science, University of California, San Francisco, San Francisco, CA, USA.
- 23Bakar Aging Research Institute, University of California, San Francisco, San Francisco, CA, USA.
- 24Vitra Labs Inc., San Francisco, CA, USA.
- 25Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.
- 26Department of Medicine, Cardiovascular Research Center, Yale School of Medicine, New Haven, CT, USA.
- 27Department of Obstetrics, Gynecology and Women’s Health, School of Medicine, University of Missouri-Columbia, Columbia, MO, USA.
- 28New York Genome Center, New York, NY, USA.
- 29Cancer Biology Department, USC Keck School of Medicine, USC Norris Comprehensive Cancer Center, Los Angeles, CA, USA.
- 30Pharmacology and Pharmaceutical Sciences Department, USC Mann School of Pharmacy and Pharmacology, Los Angeles, CA, USA.
- 31USC Stem Cell Initiative, Los Angeles, CA, USA.
- 32Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
- 33Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA.
- 34Yale Center for Research on Aging, Yale School of Medicine, New Haven, CT, USA.
- 35Division of Animal Sciences, College of Agriculture, Food and Natural Resources, University of Missouri-Columbia, Columbia, MO, USA.
- 36Department of Molecular Genetics and Genome Sciences, College of Medicine, University of Oklahoma Health Campus, Oklahoma City, OK, USA.
- 37Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- 38Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- 39Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- 40Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA.
Abstract
The female reproductive tract is essential for fertility, pregnancy, and overall health, yet many of its cellular components remain poorly defined. Recent advances in single-cell and spatial transcriptomics have begun to reveal this complexity, but inconsistent naming of cell types and states has limited the ability to compare findings across studies. To address this challenge, an international group of reproductive biologists and ontology experts collaborated to harmonize annotations within Cell Ontology, focusing on the ovary, fallopian tube, and uterus. Standardized terms are proposed for major epithelial, stromal, and germ cell populations, supported by marker gene sets and anatomical linkages. This framework provides a shared reference that can be used to harmonize existing datasets and guide annotation of future studies, enabling consistent classification of oocytes, granulosa, theca, luteal, epithelial, stromal, and immune cells across tissues. By establishing a unified taxonomy, this work lays the foundation for integrating datasets, supporting cross-tissue comparisons, and advancing the understanding of reproductive biology, health, and disease.
Related
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BibTeX
@article{ong2026standardizing,
title = {{Standardizing Cell Ontology terms for cross-study integration in the female reproductive tract}},
author = {Huan Ting Ong and Diane C. Saunders and Caroline Eastwood and Aleix Puig-Barbe and Alison Kochersberger and Anna Galligos and Bailey Marshall and Benjamin K. Johnson and Caroline E. Kratka and Chen Jin and Daniela Betancur and Gabriela Rapozo Guimarães and Jordan H. Machlin and Jose V. V. Isola and Katelyn M. Adam and Osmaray Morales-Casanova and Svetlana Djirackor and Taylor Schissel and Valentina Lorenzi and Xifan Wang and Xingyu Shen and Bikem Soygur and Brian Aevermann and Eliza A. Gaylord and Mariko H. Foecke and Norbert K. Tavares and Ryan M. Samuel and Sophia Szady and Srinivasan Mahalingam and Subhasri Biswas and Will Liao and Bérénice A. Benayoun and Hattie Chung and Wipawee Winuthayanon and Jun Z. Li and Matteo A. Molè and Michael Angelo and Patricia Jeudin and Ronny Drapkin and Ariella Shikanov and Diana J. Laird and Francesca Duncan and Hui Shen and Jennifer L. Garrison and Mariana Boroni and Michael B. Stout and Roser Vento-Tormo and Sophia H. L. George and Yousin Suh and Jennifer L. Young and Monica M. Laronda},
journal = {Science Advances},
year = {2026},
month = oct,
doi = {10.1126/sciadv.aef2358},
url = {https://www.science.org/doi/10.1126/sciadv.aef2358},
note = {CC BY},
}
RIS
TY - JOUR
TI - Standardizing Cell Ontology terms for cross-study integration in the female reproductive tract
AU - Huan Ting Ong
AU - Diane C. Saunders
AU - Caroline Eastwood
AU - Aleix Puig-Barbe
AU - Alison Kochersberger
AU - Anna Galligos
AU - Bailey Marshall
AU - Benjamin K. Johnson
AU - Caroline E. Kratka
AU - Chen Jin
AU - Daniela Betancur
AU - Gabriela Rapozo Guimarães
AU - Jordan H. Machlin
AU - Jose V. V. Isola
AU - Katelyn M. Adam
AU - Osmaray Morales-Casanova
AU - Svetlana Djirackor
AU - Taylor Schissel
AU - Valentina Lorenzi
AU - Xifan Wang
AU - Xingyu Shen
AU - Bikem Soygur
AU - Brian Aevermann
AU - Eliza A. Gaylord
AU - Mariko H. Foecke
AU - Norbert K. Tavares
AU - Ryan M. Samuel
AU - Sophia Szady
AU - Srinivasan Mahalingam
AU - Subhasri Biswas
AU - Will Liao
AU - Bérénice A. Benayoun
AU - Hattie Chung
AU - Wipawee Winuthayanon
AU - Jun Z. Li
AU - Matteo A. Molè
AU - Michael Angelo
AU - Patricia Jeudin
AU - Ronny Drapkin
AU - Ariella Shikanov
AU - Diana J. Laird
AU - Francesca Duncan
AU - Hui Shen
AU - Jennifer L. Garrison
AU - Mariana Boroni
AU - Michael B. Stout
AU - Roser Vento-Tormo
AU - Sophia H. L. George
AU - Yousin Suh
AU - Jennifer L. Young
AU - Monica M. Laronda
PY - 2026
DA - 2026/10/09
JO - Science Advances
DO - 10.1126/sciadv.aef2358
UR - https://www.science.org/doi/10.1126/sciadv.aef2358
AB - The female reproductive tract is essential for fertility, pregnancy, and overall health, yet many of its cellular components remain poorly defined. Recent advances in single-cell and spatial transcriptomics have begun to reveal this complexity, but inconsistent naming of cell types and states has limited the ability to compare findings across studies. To address this challenge, an international group of reproductive biologists and ontology experts collaborated to harmonize annotations within Cell Ontology, focusing on the ovary, fallopian tube, and uterus. Standardized terms are proposed for major epithelial, stromal, and germ cell populations, supported by marker gene sets and anatomical linkages. This framework provides a shared reference that can be used to harmonize existing datasets and guide annotation of future studies, enabling consistent classification of oocytes, granulosa, theca, luteal, epithelial, stromal, and immune cells across tissues. By establishing a unified taxonomy, this work lays the foundation for integrating datasets, supporting cross-tissue comparisons, and advancing the understanding of reproductive biology, health, and disease.
SN - 2375-2548
ER -