An ontology for cell types

Molecular Biology of the Cell

Alberts, B., Johnson, A., Lewis, J. H., Morgan, D. O., RAFF, M. C., Roberts, K. J., & Walter, P. (2017) · W.W. Norton eBooks · doi:10.1201/9781315735368 · Cited by 7,937

“Gray's Anatomy”

WARWICK, R., Williams, P. L., Dyson, M., & Bannister, L. (1985) · British Journal of Radiology · doi:10.1259/0007-1285-58-694-1029 · Cited by 4,532

The molecular biology of the cell

Arnstein, H. R. V. (1986) · FEBS Letters · doi:10.1016/0014-5793(86)80238-1 · Cited by 1,396

Creating the Gene Ontology Resource: Design and ImplementationPreprint

The Gene Ontology Consortium (2001) · Genome Research · doi:10.1101/gr.180801 · Cited by 957

MOLECULAR BIOLOGY OF THE CELL, 5TH EDITION

Fenderson, B. A. (2008) · Shock · doi:10.1097/01.shk.0000286288.33338.f6 · Cited by 829

Creating the gene ontology resource: design and implementation.

Blake, J. A., Corradi, J., Eppig, J. T., Hill, D. P., Richardson, J. E., & Ringwald, M. (2001) · The Mouseion at the JAXlibrary (Jackson Laboratory) · Cited by 826

Drosophila crinkled, Mutations of Which Disrupt Morphogenesis and Cause Lethality, Encodes Fly Myosin VIIA

Kiehart, D. P., Franke, J. D., Chee, M. K., Montague, R. A., Chen, T.-L., Roote, J., & Ashburner, M. (2004) · Genetics · doi:10.1534/genetics.104.026369 · Cited by 70

Phenotypic data in FlyBase

Drysdale, R. (2001) · Briefings in Bioinformatics · doi:10.1093/bib/2.1.68 · Cited by 33

Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies

Slater, L. T., Gkoutos, G. V., & Hoehndorf, R. (2020) · BMC Medical Informatics and Decision Making · doi:10.1186/s12911-020-01336-2 · Cited by 20

Systematic tissue annotations of genomics samples by modeling unstructured metadata

Hawkins, N. T., Maldaver, M., Yannakopoulos, A., Guare, L. A., & Krishnan, A. (2022) · Nature Communications · doi:10.1038/s41467-022-34435-x · Cited by 19

Ontology-Based Visualization of Hierarchical Neuroanatomical Structures

Kuß, A., Prohaska, S., Meyer, B., Rybak, J., & Hege, H. (2008) · doi:10.2312/vcbm/vcbm08/177-184 · Cited by 19

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST)

Touré, V., Vercruysse, S., Acencio, M. L., Lovering, R. C., Orchard, S. E., Bradley, G., Casals‐Casas, C., Chaouiya, C., del‐Toro, N., Flobak, Å., et al. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa622 · Cited by 19

A FAULT MODEL FOR ONTOLOGY MAPPING, ALIGNMENT, AND LINKING SYSTEMS

JOHNSON, H. L., Cohen, K. B., & Hunter, L. (2006) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789812772435_0023 · Cited by 19

Brain Data Standards - A method for building data-driven cell-type ontologies

Tan, S. Z. K., Kır, H., Aevermann, B. D., Gillespie, T., Harris, N. L., Hawrylycz, M., Jorstad, N. L., Lein, E. S., Matentzoglu, N., Miller, J. A., et al. (2023) · Scientific Data · doi:10.1038/s41597-022-01886-2 · Cited by 18

Query enhancement through the practical application of ontology: the IEDB and OBI

Vita, R., Overton, J. A., Greenbaum, J., Sette, A., & Peters, B. (2013) · Journal of Biomedical Semantics · doi:10.1186/2041-1480-4-s1-s6 · Cited by 17

An ontology for representing hematologic malignancies: the cancer cell ontology

Serra, L. M., Duncan, W. D., & Diehl, A. D. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-2722-8 · Cited by 17

An Ontology for African Traditional Medicine

Atemezing, G. A., & Pavón, J. (2008) · Advances in soft computing · doi:10.1007/978-3-540-85863-8_39 · Cited by 17

DAFi: A directed recursive data filtering and clustering approach for improving and interpreting data clustering identification of cell populations from polychromatic flow cytometry data

Lee, A. J., Chang, I., Burel, J. G., Arlehamn, C. S. L., Mandava, A., Weiskopf, D., Peters, B., Sette, A., Scheuermann, R. H., & Yu, Q. (2018) · Cytometry Part A · doi:10.1002/cyto.a.23371 · Cited by 17

Identification of disease treatment mechanisms through the multiscale interactomePreprint

Ruiz, C., Žitnik, M., & Leskovec, J. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.30.069690 · Cited by 17

The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology

THACKER, R. W., Díaz, M. C., Kerner, A., Vignes‐Lebbe, R., Segerdell, E., Haendel, M. A., & Mungall, C. (2014) · Journal of Biomedical Semantics · doi:10.1186/2041-1480-5-39 · Cited by 16

CellMeSH: probabilistic cell-type identification using indexed literature

Mao, S., Zhang, Y., Seelig, G., & Kannan, S. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab834 · Cited by 18

MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation

Hermida, L. C., Schaad, O., Demougin, P., Descombes, P., & Primig, M. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-190 · Cited by 16

Proteomic resources: Integrating biomedical information in humans

Suresh, S., Mohan, S. S., Mishra, G., Hanumanthu, G., Suresh, M., Reddy, R., & Pandey, A. (2005) · Gene · doi:10.1016/j.gene.2005.07.021 · Cited by 16

Controlled vocabularies for microbial virulence factors

Korves, T. M., & Colosimo, M. (2009) · Trends in Microbiology · doi:10.1016/j.tim.2009.04.002 · Cited by 16

CELDA - an ontology for the comprehensive representation of cells in complex systems

Seltmann, S., Stachelscheid, H., Damaschun, A., Jansen, L., Lekschas, F., Fontaine, J., Nguyen-Dobinsky, T. N., Leser, U., & Kurtz, A. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-228 · Cited by 16

Exact score distribution computation for ontological similarity searches

Schulz, M. H., Köhler, S., Bauer, S., & Robinson, P. N. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-441 · Cited by 16

Systems developmental biology: the use of ontologies in annotating models and in identifying gene function within and across species

Bard, J. (2007) · Mammalian Genome · doi:10.1007/s00335-007-9027-3 · Cited by 15

Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database

Ikeda, S., Zou, Z., Bono, H. U., Moriya, Y., Kawashima, S., Katayama, T., Oki, S., & Ohta, T. (2025) · GigaScience · doi:10.1093/gigascience/giaf070 · Cited by 15

The Blood Ontology: An ontology in the domain of hematology

Almeida, M. B., Carneiro, P. A. B. D. F., Ai, J., & Smith, B. (2011) · PhilPapers (PhilPapers Foundation) · Cited by 15

Evaluation of single-cell RNAseq labelling algorithms using cancer datasets

Christensen, E., Luo, P., Turinsky, A. L., Husić, M., Mahalanabis, A., Naidas, A., Díaz-Mejía, J. J., Brudno, M., Pugh, T. J., Ramani, A. K., et al. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac561 · Cited by 15

Ontology based molecular signatures for immune cell types via gene expression analysis

Meehan, T. F., Vasilevsky, N., Mungall, C., Dougall, D. S., Haendel, M. A., Blake, J. A., & Diehl, A. D. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-263 · Cited by 15

CHARTS: a web application for characterizing and comparing tumor subpopulations in publicly available single-cell RNA-seq data sets

Bernstein, M. N., Ni, Z., Collins, M., Burkard, M. E., Kendziorski, C. M., & Stewart, R. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04021-x · Cited by 15

Structure, function, and behaviour of computational models in systems biology

Knüpfer, C. R. N., Beckstein, C., Dittrich, P., & Novère, N. G. L. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-43 · Cited by 15

GPDE: A biological proteomic database for biomarker discovery and evaluation

Griss, J., Haudek‐Prinz, V. J., & Gerner, C. (2011) · PROTEOMICS · doi:10.1002/pmic.201000507 · Cited by 14

Flow: Statistics, visualization and informatics for flow cytometry

Frelinger, J., Kepler, T. B., & Chan, C. C. W. (2008) · Source Code for Biology and Medicine · doi:10.1186/1751-0473-3-10 · Cited by 14

An ontology of fungal subcellular traits

Kumar, T. K. A., Crow, J., Wennblom, T. J., Abril, M., Letcher, P. M., Blackwell, M., Roberson, R. W., & McLaughlin, D. J. (2011) · American Journal of Botany · doi:10.3732/ajb.1100047 · Cited by 14

The Renal Gene Ontology Annotation Initiative

Alam-Faruque, Y., Dimmer, E. C., Huntley, R. P., O’Donovan, C., Scambler, P. J., & Apweiler, R. (2010) · Organogenesis · doi:10.4161/org.6.2.11294 · Cited by 14

Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas

Herr, B. W., Hardi, J., Quardokus, E. M., Bueckle, A., Chen, L., Wang, F., Caron, A. R., Osumi-Sutherland, D., Musen, M. A., & Börner, K. (2023) · Scientific Data · doi:10.1038/s41597-023-01993-8 · Cited by 16

Composite annotations: Requirements for mapping multiscale data and models to biomedical ontologies

Cook, D. L., Mejino, J. L. V., Neal, M. L., & Gennari, J. H. (2009) · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) · doi:10.1109/iembs.2009.5333830 · Cited by 13

Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies

Alghamdi, S. M., Sundberg, B. A., Sundberg, J. P., Schofield, P. N., & Hoehndorf, R. (2019) · Scientific Reports · doi:10.1038/s41598-019-40368-1 · Cited by 13

Ontology-driven integrative analysis of omics data through Onassis

Galeota, E., Kishore, K., & Pelizzola, M. (2020) · Scientific Reports · doi:10.1038/s41598-020-57716-1 · Cited by 14

Anatomical structures, cell types, and biomarkers of the healthy human blood vasculature

Boppana, A., Lee, S., Malhotra, R. K., Halushka, M. K., Gustilo, K. S., Quardokus, E. M., Herr, B. W., Börner, K., & Weber, G. M. (2023) · Scientific Data · doi:10.1038/s41597-023-02018-0 · Cited by 14

Accessing Expert‐Curated Pharmacological Data in the IUPHAR/BPS Guide to PHARMACOLOGY

Sharman, J. L., Harding, S. D., Southan, C., Faccenda, E., Pawson, A. J., Davies, J. A., & NC‐IUPHAR (2018) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.46 · Cited by 12

Approaching the axiomatic enrichment of the Gene Ontology from a lexical perspective

Quesada-Martínez, M., Mikroyannidi, E., Fernández‐Breis, J. T., & Stevens, R. (2014) · Artificial Intelligence in Medicine · doi:10.1016/j.artmed.2014.09.003 · Cited by 12

CRAFT Shared Tasks 2019 Overview –- Integrated Structure, Semantics, and Coreference

Baumgartner, W. A., Bada, M. A., Pyysalo, S., Ciosici, M. R., Hailu, N., Pielke-Lombardo, H., Regan, M., & Hunter, L. (2019) · Workshop on BioNLP Open Shared Tasks (BioNLP-OST) · doi:10.18653/v1/d19-5725 · Cited by 12

A Cell-Cycle Knowledge Integration Framework

Antezana, E., Tsiporkova, E., Mironov, V., & Kuiper, M. T. R. (2006) · Lecture notes in computer science · doi:10.1007/11799511_4 · Cited by 12

Where to search top-K biomedical ontologies?

Oliveira, D., Butt, A. S., Armin Haller, A., Rebholz‐Schuhmann, D., & Sahay, R. (2018) · Briefings in Bioinformatics · doi:10.1093/bib/bby015 · Cited by 11

An infrastructure for ontology-based information systems in biomedicine: RICORDO case study

Wimalaratne, S., Grenon, P., Hoehndorf, R., Gkoutos, G. V., & de Bono, B. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr662 · Cited by 11

Plant-Pathogen Interactions Ontology (PPIO)

Iglesias, A. R., Aranguren, M. E., Rodríguez‐González, A., & Wilkinson, M. D. (2013) · IWBBIO · Cited by 11

Better living through ontologies at the Immune Epitope Database

Vita, R., Overton, J. A., Sette, A., & Peters, B. (2017) · Database · doi:10.1093/database/bax014 · Cited by 11

Developing an Ontology

Harris, M. A. (2008) · Methods in molecular biology · doi:10.1007/978-1-60327-159-2_5 · Cited by 11

Bioinformatics

(2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6622-6 · Cited by 11

A Proposal for a Gene Functions Wiki

Hoehndorf, R., Prüfer, K., Backhaus, M., Heinrich Herre, B., Kelso, J. F., Frank Loebe, A., & Visagie, J. (2006) · Lecture notes in computer science · doi:10.1007/11915034_91 · Cited by 11

Thematic series on biomedical ontologies in JBMS: challenges and new directions

Hoehndorf, R., Haendel, M. A., Stevens, R., & Rebholz‐Schuhmann, D. (2014) · Journal of Biomedical Semantics · doi:10.1186/2041-1480-5-15 · Cited by 10

Knowledge sharing and collaboration in translational research, and the DC-THERA Directory

Splendiani, A., Gündel, M., Austyn, J. M., Cavalieri, D., Scognamiglio, C., & Brandizi, M. (2011) · Briefings in Bioinformatics · doi:10.1093/bib/bbr051 · Cited by 10

Building reference alignments for compound matching of multiple ontologies using OBO cross-products

Pesquita, C., Cheatham, M., Faria, D., Barros, J., dos Santos, E. M., & Couto, F. M. (2014) · International Conference on Ontology Matching · Cited by 10

Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes

Gkoutos, G. V., & Hoehndorf, R. (2012) · Journal of Biomedical Semantics · doi:10.1186/2041-1480-3-s2-s6 · Cited by 10

A Literature-Derived Knowledge Graph Augments the Interpretation of Single Cell RNA-seq Datasets

Doddahonnaiah, D., Lenehan, P. J., Hughes, T. K., Zemmour, D., Garcia-Rivera, E., Venkatakrishnan, A., Chilaka, R., Khare, A., Kasaraneni, A., Garg, A., et al. (2021) · Genes · doi:10.3390/genes12060898 · Cited by 11

Development of an Ontology for Periodontitis

Suzuki, A., Takai‐Igarashi, T., Nakaya, J., & Tanaka, H. (2015) · Journal of Biomedical Semantics · doi:10.1186/s13326-015-0028-y · Cited by 10

PIDO: the primary immunodeficiency disease ontology

Adams, N., Hoehndorf, R., Gkoutos, G. V., Hansen, G., & Hennig, C. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr531 · Cited by 10

OBO to UML: Support for the development of conceptual models in the biomedical domain

Waldemarin, R. C., & de Farias, C. R. G. (2018) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2018.02.015 · Cited by 10

A survey on automatically constructed universal knowledge bases

Hossain, B. A., Salam, A., & Schwitter, R. (2020) · Journal of Information Science · doi:10.1177/0165551520921342 · Cited by 10

Knowledge‐Based Bioinformatics

Neumann, E. (2010) · Wiley eBooks · doi:10.1002/9780470669716.ch1 · Cited by 10

Digital evolution: Novo Nordisk’s shift to ontology-based data management

Tan, S. Z. K., Baksi, S., Bjerregaard, T. G., Elangovan, P., Gopalakrishnan, T., Hric, D., Joumaa, J., Li, B., Rabbani, K., Venkatesan, S. K., et al. (2025) · Journal of Biomedical Semantics · doi:10.1186/s13326-025-00327-4 · Cited by 9

High-precision cell-type mapping and annotation of single-cell spatial transcriptomics with STAMapper

Shen, Q., Dong, K., Zhang, S., & Zhang, S. (2025) · Genome biology · doi:10.1186/s13059-025-03773-6 · Cited by 9

Using ontologies for life science text-based resource organization

Panzarella, G., Veltri, P., & Alcaro, S. (2023) · Artificial Intelligence in the Life Sciences · doi:10.1016/j.ailsci.2023.100059 · Cited by 9

The Open Physiology workflow: modeling processes over physiology circuitboards of interoperable tissue units

de Bono, B., Safaei, S., Grenon, P., Nickerson, D. P., Alexander, S., Helvensteijn, M., Kok, J. N., Kokash, N., Wu, A., Yu, T., et al. (2015) · Frontiers in Physiology · doi:10.3389/fphys.2015.00024 · Cited by 9

The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms

Parikh, P., Zheng, J., Logan-Klumpler, F., Stoeckert, C. J., Louis, C., Topalis, P., Protasio, A. V., Sheth, A., Carrington, M., Berriman, M., et al. (2012) · Journal of Biomedical Semantics · doi:10.1186/2041-1480-3-5 · Cited by 9

An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets

Schmidt, F., List, M., Cukuroglu, E., Köhler, S., Göke, J., & Schulz, M. H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty553 · Cited by 9

scDOT: enhancing single-cell RNA-Seq data annotation and uncovering novel cell types through multi-reference integration

Xiong, Y.-X., & Zhang, X.-F. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae072 · Cited by 10

Statistical Tests for Associations between Two Directed Acyclic Graphs

Hoehndorf, R., Ngomo, A.-C. N., Dannemann, M., & Kelso, J. F. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010996 · Cited by 9

Guidelines for managing data and processes in bone and cartilage tissue engineering

Viti, F., Scaglione, S., Orro, A., & Milanesi, L. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-s1-s14 · Cited by 9

Evolutionary Cell Biology of Proteins from Protists to Humans and Plants

Plattner, H. (2017) · Journal of Eukaryotic Microbiology · doi:10.1111/jeu.12449 · Cited by 9

Parallel sequence tagging for concept recognition

Furrer, L., Cornelius, J., & Rinaldi, F. (2022) · BMC Bioinformatics · doi:10.1186/s12859-021-04511-y · Cited by 9

Developmental Anatomy Ontology of Zebrafish: an Integrative semantic framework

Belmamoune, M., & Verbeek, F. J. (2007) · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics · doi:10.1515/jib-2007-65 · Cited by 9

GoPubMed: Ontology-based literature search for the life sciences

Doms, A. (2008) · Qucosa (Saxon State and University Library Dresden) · Cited by 9

The Physiome Project, open EHR Archetypes, and the Digital Patient

Nickerson, D. P., Atalağ, K., de Bono, B., & Hunter, P. J. (2016) · Wiley eBooks · doi:10.1002/9781118952788.ch9 · Cited by 9

NS-Forest: A machine learning method for the objective identification of minimum marker gene combinations for cell type determination from single cell RNA sequencingPreprint

Aevermann, B. D., Zhang, Y., Novotny, M. A., Bakken, T. E., Miller, J. A., Hodge, R. D., Lelieveldt, B. P. F., Lein, E. S., & Scheuermann, R. H. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.23.308932 · Cited by 9

A curated collection of human vaccination response signatures

Smith, K. C., Chawla, D. G., Dhillon, B. K., Ji, Z., Vita, R., van der Leest, E. C., Weng, J. Y., Tang, E., Abid, A., Peters, B., et al. (2022) · Scientific Data · doi:10.1038/s41597-022-01558-1 · Cited by 9

On the use of QDE-SVM for gene feature selection and cell type classification from scRNA-seq data

Ng, G. Y. L., Tan, S. C., & Ong, C. S. (2023) · PLoS ONE · doi:10.1371/journal.pone.0292961 · Cited by 8

uHAF: a unified hierarchical annotation framework for cell type standardization and harmonization

Bian, H., Chen, Y., Wei, L., & Zhang, X. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf149 · Cited by 9

Semantic integration of information about orthologs and diseases: The OGO system

Miñarro-Giménez, J. A., Aranguren, M. E., Martínez‐Béjar, R., Fernández‐Breis, J. T., & Madrid, M. (2011) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2011.08.002 · Cited by 8

The IUPHAR Guide to Immunopharmacology: connecting immunology and pharmacology

Harding, S. D., Faccenda, E., Southan, C., Pawson, A. J., Maffia, P., Alexander, S. P. H., Davenport, A. P., Fabbro, D., Levi‐Schaffer, F., Spedding, M., et al. (2020) · Immunology · doi:10.1111/imm.13175 · Cited by 8

Populous: A tool for populating ontology templates

Jupp, S., Matthew Horridge, A., Iannone, L., Klein, J., Owen, S., Schanstra, J. P., Stevens, R., & Wolstencroft, K. (2010) · Research Explorer (The University of Manchester) · doi:10.48550/arxiv.1012.1745 · Cited by 8

The bio-zen plus ontology

Matthias Samwald, A., & Adlassnig, K.-P. (2008) · Applied Ontology · doi:10.3233/ao-2008-0053 · Cited by 8

Ontological realism and classification: Structures and concepts in the G ene O ntology

Mayor, C., & Robinson, L. (2014) · Journal of the Association for Information Science and Technology · doi:10.1002/asi.23057 · Cited by 8

A scale-out RDF molecule store for improved co-identification, querying and inferencing

Newman, A. F., Li, Y.-F., & Hunter, J. (2008) · Cited by 8

Advancement in Sustainable Agriculture: Computational and Bioinformatics Tools

Parray, J. A., Mir, M. Y., & Shameem, N. (2019) · Springer eBooks · doi:10.1007/978-981-13-8840-8_10 · Cited by 8

Jupyter notebook-based tools for building structured datasets from the Sequence Read Archive

Bernstein, M. N., Gladstein, A. L., Latt, K. Z., Clough, E., Busby, B., & Dillman, A. (2020) · F1000Research · doi:10.12688/f1000research.23180.1 · Cited by 8

Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge From Anatomy Ontologies

Porto, D. S., Dahdul, W., Lapp, H., Balhoff, J. P., Vision, T., Mabee, P., & Uyeda, J. C. (2022) · Systematic Biology · doi:10.1093/sysbio/syac022 · Cited by 8

Linking Scattered Stem Cell-Based Data to Advance Therapeutic Development

Kurtz, A., Elsallab, M., Sanzenbacher, R., & Abou‐El‐Enein, M. (2018) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2018.10.008 · Cited by 8

Biomedical Ontologies: Coverage, Access and Use

Ferreira, J. D., Teixeira, D. C., & Pesquita, C. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-801238-3.11664-2 · Cited by 7

ApiNATOMY: Towards Multiscale Views of Human Anatomy

de Bono, B., Grenon, P., Helvensteijn, M., Kok, J. N., & Kokash, N. (2014) · Lecture notes in computer science · doi:10.1007/978-3-319-12571-8_7 · Cited by 7

A semantic model of events for integrating photovoltaic monitoring data

Dagnely, P., Tsiporkova, E., Tourwé, T., Ruette, T., Brabandere, K. D., & Assiandi, F. (2015) · IEEE International Conference on Industrial Informatics (INDIN) · doi:10.1109/indin.2015.7281705 · Cited by 7

New concepts for building vocabulary for cell image ontologies

Plant, A. L., Elliott, J. T., & Bhat, T. N. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-487 · Cited by 7

Representing Normal and Abnormal Physiology as Routes of Flow in ApiNATOMY

de Bono, B., Gillespie, T., Surles-Zeigler, M. C., Kokash, N., Grethe, J. S., & Martone, M. E. (2022) · Frontiers in Physiology · doi:10.3389/fphys.2022.795303 · Cited by 7

Ontologies for data and knowledge sharing in biology: plant ROS signaling as a case study

Стриж, И. Г. (2006) · BioEssays · doi:10.1002/bies.20368 · Cited by 7

Gold-standard ontology-based anatomical annotation in the CRAFT Corpus

Bada, M. A., Vasilevsky, N., Baumgartner, W. A., Haendel, M. A., & Hunter, L. (2017) · Database · doi:10.1093/database/bax087 · Cited by 6

Exploring Zebrafish Genomic, Functional and Phenotypic Data Using ZFIN

Ramachandran, S., Ruef, B. J., Pich, C., & Sprague, J. (2010) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0118s31 · Cited by 6

Data Extraction, Transformation, and Dissemination through ZFIN

Howe, D. G., Frazer, K., Fashena, D. S., Ruzicka, L., Bradford, Y. M., Ramachandran, S., Ruef, B. J., Slyke, C. E. V., Singer, A., & Westerfield, M. (2011) · Methods in cell biology · doi:10.1016/b978-0-12-374814-0.00017-3 · Cited by 6

Cytoview: Development of a cell modelling framework

Khodade, P., Malhotra, S., Kumar, N., Iyengar, M. S., Balakrishnan, N., & Chandra, N. R. (2007) · Journal of Biosciences · doi:10.1007/s12038-007-0096-y · Cited by 6

Integration of Biological Data with Semantic Networks

Hsing, M., & Cherkasov, A. R. (2006) · Current Bioinformatics · doi:10.2174/157489306777827946 · Cited by 6

Compound matching of biomedical ontologies.

Oliveira, D., & Pesquita, C. (2015) · Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) · Cited by 6

Role and application of Ontology Design Patterns in bio-ontologies

Aranguren, M. E. (2010) · OpenGrey (Institut de l'Information Scientifique et Technique) · Cited by 6

Populous: A Tool for Populating Templates for OWL Ontologies.

Jupp, S., Matthew Horridge, A., Iannone, L., Klein, J., Owen, S., Schanstra, J. P., Stevens, R., & Wolstencroft, K. (2010) · SWAT4LS · Cited by 5

The Immunopeptidomics Ontology (ImPO)

Faria, D., Eugénio, P., Silva, M. C., Balbi, L., Bedran, G., Kallor, A. A., Nunes, S., Pałkowski, A., Waleron, M. M., Alfaro, J. A., et al. (2024) · Database · doi:10.1093/database/baae014 · Cited by 5

Bluima: a UIMA-based NLP Toolkit for Neuroscience.

Richardet, R., Chappelier, J.-C., & Telefont, M. (2013) · Cited by 5

Leveraging Ontologies for Knowledge Graph Schemas

Oliveira, D., Sahay, R., & d’Aquin, M. (2019) · Cited by 5

Evaluation of the Cell Ontology (CL)Preprint

Cowell, L. G. (2009) · Nature Precedings · doi:10.1038/npre.2009.3971.1

CELDA - an ontology for the comprehensive representation of cells in complex systems

Seltmann, S., Stachelscheid, H., Damaschun, A., Jansen, L., Lekschas, F., Fontaine, J., Nguyen-Dobinsky, T. N., Leser, U., & Kurtz, A. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-228 · Cited by 16

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability

Diehl, A. D., Meehan, T. F., Bradford, Y. M., Brush, M., Dahdul, W., Dougall, D. S., He, Y. O., Osumi-Sutherland, D., Ruttenberg, A., Sarntivijai, S., et al. (2016) · Journal of Biomedical Semantics · doi:10.1186/s13326-016-0088-7 · Cited by 332

Development of an ontology for the comprehensive representation of cells in complex systems

Seltmann, S. (2015) · Universitätsbibliothek der FU Berlin Hochschulschriftenstelle u. Dokumentenserver · doi:10.17169/refubium-9844

CellFinder: a cell data repository

Stachelscheid, H., Seltmann, S., Lekschas, F., Fontaine, J., Mah, N., Neves, M., Andrade-Navarro, M. A., Leser, U., & Kurtz, A. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1264 · Cited by 31