Database: The Journal of Biological Databases and Curation最新文献

{"title":"Localizatome: a database for stress-dependent subcellular localization changes in proteins.","authors":"Takahide Matsushima, Yuki Naito, Tomoki Chiba, Ryota Kurimoto, Keiko Itano, Koji Ochiai, Koichi Takahashi, Naoki Goshima, Hiroshi Asahara","doi":"10.1093/database/baaf028","DOIUrl":"10.1093/database/baaf028","url":null,"abstract":"<p><p>Understanding protein subcellular localization and its dynamic changes is crucial for elucidating cellular function and disease mechanisms, particularly under stress conditions, where protein localization changes can modulate cellular responses. Currently available databases provide insights into protein localization under steady-state conditions; however, stress-related dynamic localization changes remain poorly understood. Here, we present the Localizatome, a comprehensive database that captures stress-induced protein localization dynamics in living cells. Using an original high-throughput microscopy system and machine learning algorithms, we analysed the localization patterns of 10 287 fluorescent protein-fused human proteins in HeLa cells before and after exposure to oxidative stress. Our analysis revealed that 1910 proteins exhibited oxidative stress-dependent localization changes, particularly forming distinct foci. Among them, there were stress granule assembly factors and autophagy-related proteins, as well as components of various signalling pathways. Subsequent characterization identified some specific amino acid motifs and intrinsically disordered regions associated with stress-induced protein redistribution. The Localizatome provides open access to these data through a web-based interface, supporting a wide range of studies on cellular stress response and disease mechanisms. Database URL https://localizatome.embrys.jp/.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12010962/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143984325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Localizatome: a database for stress-dependent subcellular localization changes in proteins.","authors":"Takahide Matsushima, Yuki Naito, Tomoki Chiba, Ryota Kurimoto, Keiko Itano, Koji Ochiai, Koichi Takahashi, Naoki Goshima, Hiroshi Asahara","doi":"10.1093/database/baaf028","DOIUrl":"https://doi.org/10.1093/database/baaf028","url":null,"abstract":"<p><p>Understanding protein subcellular localization and its dynamic changes is crucial for elucidating cellular function and disease mechanisms, particularly under stress conditions, where protein localization changes can modulate cellular responses. Currently available databases provide insights into protein localization under steady-state conditions; however, stress-related dynamic localization changes remain poorly understood. Here, we present the Localizatome, a comprehensive database that captures stress-induced protein localization dynamics in living cells. Using an original high-throughput microscopy system and machine learning algorithms, we analysed the localization patterns of 10 287 fluorescent protein-fused human proteins in HeLa cells before and after exposure to oxidative stress. Our analysis revealed that 1910 proteins exhibited oxidative stress-dependent localization changes, particularly forming distinct foci. Among them, there were stress granule assembly factors and autophagy-related proteins, as well as components of various signalling pathways. Subsequent characterization identified some specific amino acid motifs and intrinsically disordered regions associated with stress-induced protein redistribution. The Localizatome provides open access to these data through a web-based interface, supporting a wide range of studies on cellular stress response and disease mechanisms. Database URL https://localizatome.embrys.jp/.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AFED, a comprehensive resource for Aspergillus flavus gene expression profiling.","authors":"Brian M Mack, Matthew D Lebar","doi":"10.1093/database/baaf033","DOIUrl":"https://doi.org/10.1093/database/baaf033","url":null,"abstract":"<p><p>The Aspergillus flavus expression database (AFED) is a comprehensive resource dedicated to exploring gene expression in A. flavus, a significant fungal pathogen that threatens food security by contaminating crops with aflatoxin. Given the complex regulation of aflatoxin biosynthesis and the lack of centralized expression data resources for this important pathogen, a database integrating diverse experimental conditions is essential for understanding its biology and developing control strategies. Public RNA sequencing data were used to quantify gene expression abundance for 604 A. flavus samples from 52 experiments. Using abundance data, we created an AFED accessible through a web-based interface that allows for the expression profiles of genes to be conveniently examined across different growth conditions and life cycle stages. Expression profiles can be visualized through either an interactive bar plot for single gene queries or a heatmap for multiple gene queries. A gene co-expression network based on samples containing at least 10 million mapped reads is also available, which allows users to identify genes that are co-expressed with an individual gene or set of genes and displays the functional enrichment among the co-expressed genes. Database URL: https://a-flavus-expression-db-jyqnpeuvta-uc.a.run.app.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AFED, a comprehensive resource for Aspergillus flavus gene expression profiling.","authors":"Brian M Mack, Matthew D Lebar","doi":"10.1093/database/baaf033","DOIUrl":"10.1093/database/baaf033","url":null,"abstract":"<p><p>The Aspergillus flavus expression database (AFED) is a comprehensive resource dedicated to exploring gene expression in A. flavus, a significant fungal pathogen that threatens food security by contaminating crops with aflatoxin. Given the complex regulation of aflatoxin biosynthesis and the lack of centralized expression data resources for this important pathogen, a database integrating diverse experimental conditions is essential for understanding its biology and developing control strategies. Public RNA sequencing data were used to quantify gene expression abundance for 604 A. flavus samples from 52 experiments. Using abundance data, we created an AFED accessible through a web-based interface that allows for the expression profiles of genes to be conveniently examined across different growth conditions and life cycle stages. Expression profiles can be visualized through either an interactive bar plot for single gene queries or a heatmap for multiple gene queries. A gene co-expression network based on samples containing at least 10 million mapped reads is also available, which allows users to identify genes that are co-expressed with an individual gene or set of genes and displays the functional enrichment among the co-expressed genes. Database URL: https://a-flavus-expression-db-jyqnpeuvta-uc.a.run.app.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12007493/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143984209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data.","authors":"Sharon Wei, Kapeel Chougule, Andrew Olson, Zhenyuan Lu, Marcela K Tello-Ruiz, Vivek Kumar, Sunita Kumari, Lifang Zhang, Audra Olson, Catherine Kim, Nick Gladman, Doreen Ware","doi":"10.1093/database/baaf021","DOIUrl":"https://doi.org/10.1093/database/baaf021","url":null,"abstract":"<p><p>Rice is a vital staple crop, sustaining over half of the global population, and is a key model for genetic research. To support the growing need for comprehensive and accessible rice genomic data, GrameneOryza (https://oryza.gramene.org) was developed as an online resource adhering to FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data management. It distinguishes itself through its comprehensive multispecies focus, encompassing a wide variety of Oryza genomes and related species, and its integration with FAIR principles to ensure data accessibility and usability. It offers a community curated selection of high-quality Oryza genomes, genetic variation, gene function, and trait data. The latest release, version 8, includes 28 Oryza genomes, covering wild rice and domesticated cultivars. These genomes, along with Leersia perrieri and seven additional outgroup species, form the basis for 38 K protein-coding gene family trees, essential for identifying orthologs, paralogs, and developing pan-gene sets. GrameneOryza's genetic variation data features 66 million single-nucleotide variants (SNVs) anchored to the Os-Nipponbare-Reference-IRGSP-1.0 genome, derived from various studies, including the Rice Genome 3 K (RG3K) project. The RG3K sequence reads were also mapped to seven additional platinum-quality Asian rice genomes, resulting in 19 million SNVs for each genome, significantly expanding the coverage of genetic variation beyond the Nipponbare reference. Of the 66 million SNVs on IRGSP-1.0, 27 million acquired standardized reference SNP cluster identifiers (rsIDs) from the European Variation Archive release v5. Additionally, 1200 distinct phenotypes provide a comprehensive overview of quantitative trait loci (QTL) features. The newly introduced Oryza CLIMtools portal offers insights into environmental impacts on genome adaptation. The platform's integrated search interface, along with a BLAST server and curation tools, facilitates user access to genomic, phylogenetic, gene function, and QTL data, supporting broad research applications. Database URL: https://oryza.gramene.org.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126836","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data.","authors":"Sharon Wei, Kapeel Chougule, Andrew Olson, Zhenyuan Lu, Marcela K Tello-Ruiz, Vivek Kumar, Sunita Kumari, Lifang Zhang, Audra Olson, Catherine Kim, Nick Gladman, Doreen Ware","doi":"10.1093/database/baaf021","DOIUrl":"10.1093/database/baaf021","url":null,"abstract":"<p><p>Rice is a vital staple crop, sustaining over half of the global population, and is a key model for genetic research. To support the growing need for comprehensive and accessible rice genomic data, GrameneOryza (https://oryza.gramene.org) was developed as an online resource adhering to FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data management. It distinguishes itself through its comprehensive multispecies focus, encompassing a wide variety of Oryza genomes and related species, and its integration with FAIR principles to ensure data accessibility and usability. It offers a community curated selection of high-quality Oryza genomes, genetic variation, gene function, and trait data. The latest release, version 8, includes 28 Oryza genomes, covering wild rice and domesticated cultivars. These genomes, along with Leersia perrieri and seven additional outgroup species, form the basis for 38 K protein-coding gene family trees, essential for identifying orthologs, paralogs, and developing pan-gene sets. GrameneOryza's genetic variation data features 66 million single-nucleotide variants (SNVs) anchored to the Os-Nipponbare-Reference-IRGSP-1.0 genome, derived from various studies, including the Rice Genome 3 K (RG3K) project. The RG3K sequence reads were also mapped to seven additional platinum-quality Asian rice genomes, resulting in 19 million SNVs for each genome, significantly expanding the coverage of genetic variation beyond the Nipponbare reference. Of the 66 million SNVs on IRGSP-1.0, 27 million acquired standardized reference SNP cluster identifiers (rsIDs) from the European Variation Archive release v5. Additionally, 1200 distinct phenotypes provide a comprehensive overview of quantitative trait loci (QTL) features. The newly introduced Oryza CLIMtools portal offers insights into environmental impacts on genome adaptation. The platform's integrated search interface, along with a BLAST server and curation tools, facilitates user access to genomic, phylogenetic, gene function, and QTL data, supporting broad research applications. Database URL: https://oryza.gramene.org.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11986821/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143968793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"mirTarCLASH: a comprehensive miRNA target database based on chimeric read-based experiments.","authors":"Tzu-Hsien Yang, Xiang-Wei Li, Yuan-Han Lee, Shang-Yi Lu, Wei-Sheng Wu, Heng-Chi Lee","doi":"10.1093/database/baaf023","DOIUrl":"10.1093/database/baaf023","url":null,"abstract":"<p><p>MicroRNAs (miRNAs) can target messenger RNAs to control their degradation or translation repression effects. Therefore, identifying the target and binding sites of different miRNAs is essential for understanding miRNA functions. To investigate these interactions, researchers have employed the cross-linking, ligation, and sequencing of hybrids (CLASH-seq) and similar CLASH-like approaches to generate chimeric reads formed by miRNAs and their targeting segments. These chimeric reads allow for the direct extraction of both the miRNA-target gene pairs and their corresponding binding sites. Nevertheless, these studies lack user-friendly platforms for researchers to investigate these interactions efficiently, thus hindering scientists' ability to explore miRNA functions. To address this gap, we developed mirTarCLASH, a comprehensive database that deposits 502 061/322 707/224 452 unique hybrid reads from human/mouse/worm miRNA chimeric read-based experiments. In mirTarCLASH, the chimera analysis algorithm ChiRA and two distinct binding site inference tools, RNAup and miRanda, were adopted to facilitate the exploration of miRNA-target pairs derived from CLASH-like experiments. Compared with existing similar repositories, mirTarCLASH further enables several confidence evaluation filters with visualization functions for the extracted results. The results can be further refined based on the key properties of the miRNA targeting sites, including read depths, numbers of supporting algorithms, and cross-linking-induced mutations, to enhance confidence levels. In addition, these miRNA-binding sites are visually represented through an integrated transcript atlas. Finally, we demonstrated the biological applicability of mirTarCLASH via the well-characterized example interaction between cel-let-7-5p and lin-41 in Caenorhabditis elegans, showcasing the potential of mirTarCLASH to provide novel insights for subsequent experimental research designs. The constructed mirTarCLASH database is freely available at https://cosbi.ee.ncku.edu.tw/MirTarClash. Database URL: https://cosbi.ee.ncku.edu.tw/MirTarClash.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11971479/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143787788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"mirTarCLASH: a comprehensive miRNA target database based on chimeric read-based experiments.","authors":"Tzu-Hsien Yang, Xiang-Wei Li, Yuan-Han Lee, Shang-Yi Lu, Wei-Sheng Wu, Heng-Chi Lee","doi":"10.1093/database/baaf023","DOIUrl":"https://doi.org/10.1093/database/baaf023","url":null,"abstract":"<p><p>MicroRNAs (miRNAs) can target messenger RNAs to control their degradation or translation repression effects. Therefore, identifying the target and binding sites of different miRNAs is essential for understanding miRNA functions. To investigate these interactions, researchers have employed the cross-linking, ligation, and sequencing of hybrids (CLASH-seq) and similar CLASH-like approaches to generate chimeric reads formed by miRNAs and their targeting segments. These chimeric reads allow for the direct extraction of both the miRNA-target gene pairs and their corresponding binding sites. Nevertheless, these studies lack user-friendly platforms for researchers to investigate these interactions efficiently, thus hindering scientists' ability to explore miRNA functions. To address this gap, we developed mirTarCLASH, a comprehensive database that deposits 502 061/322 707/224 452 unique hybrid reads from human/mouse/worm miRNA chimeric read-based experiments. In mirTarCLASH, the chimera analysis algorithm ChiRA and two distinct binding site inference tools, RNAup and miRanda, were adopted to facilitate the exploration of miRNA-target pairs derived from CLASH-like experiments. Compared with existing similar repositories, mirTarCLASH further enables several confidence evaluation filters with visualization functions for the extracted results. The results can be further refined based on the key properties of the miRNA targeting sites, including read depths, numbers of supporting algorithms, and cross-linking-induced mutations, to enhance confidence levels. In addition, these miRNA-binding sites are visually represented through an integrated transcript atlas. Finally, we demonstrated the biological applicability of mirTarCLASH via the well-characterized example interaction between cel-let-7-5p and lin-41 in Caenorhabditis elegans, showcasing the potential of mirTarCLASH to provide novel insights for subsequent experimental research designs. The constructed mirTarCLASH database is freely available at https://cosbi.ee.ncku.edu.tw/MirTarClash. Database URL: https://cosbi.ee.ncku.edu.tw/MirTarClash.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Post-composing ontology terms for efficient phenotyping in plant breeding.","authors":"Naama Menda, Bryan J Ellerbrock, Christiano C Simoes, Srikanth Kumar Karaikal, Christine Nyaga, Mirella Flores-Gonzalez, Isaak Y Tecle, David Lyon, Afolabi Agbona, Paterne A Agre, Prasad Peteti, Violet Akech, Amos Asiimwe, Eglantine Fauvelle, Karima Meghar, Thierry Tran, Dominique Dufour, Laurel Cooper, Marie-Angélique Laporte, Elizabeth Arnaud, Lukas A Mueller","doi":"10.1093/database/baaf020","DOIUrl":"https://doi.org/10.1093/database/baaf020","url":null,"abstract":"<p><p>Ontologies are widely used in databases to standardize data, improving data quality, integration, and ease of comparison. Within ontologies tailored to diverse use cases, post-composing user-defined terms reconciles the demands for standardization on the one hand and flexibility on the other. In many instances of Breedbase, a digital ecosystem for plant breeding designed for genomic selection, the goal is to capture phenotypic data using highly curated and rigorous crop ontologies, while adapting to the specific requirements of plant breeders to record data quickly and efficiently. For example, post-composing enables users to tailor ontology terms to suit specific and granular use cases such as repeated measurements on different plant parts and special sample preparation techniques. To achieve this, we have implemented a post-composing tool based on orthogonal ontologies providing users with the ability to introduce additional levels of phenotyping granularity tailored to unique experimental designs. Post-composed terms are designed to be reused by all breeding programs within a Breedbase instance but are not exported to the crop reference ontologies. Breedbase users can post-compose terms across various categories, such as plant anatomy, treatments, temporal events, and breeding cycles, and, as a result, generate highly specific terms for more accurate phenotyping.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Post-composing ontology terms for efficient phenotyping in plant breeding.","authors":"Naama Menda, Bryan J Ellerbrock, Christiano C Simoes, Srikanth Kumar Karaikal, Christine Nyaga, Mirella Flores-Gonzalez, Isaak Y Tecle, David Lyon, Afolabi Agbona, Paterne A Agre, Prasad Peteti, Violet Akech, Amos Asiimwe, Eglantine Fauvelle, Karima Meghar, Thierry Tran, Dominique Dufour, Laurel Cooper, Marie-Angélique Laporte, Elizabeth Arnaud, Lukas A Mueller","doi":"10.1093/database/baaf020","DOIUrl":"10.1093/database/baaf020","url":null,"abstract":"<p><p>Ontologies are widely used in databases to standardize data, improving data quality, integration, and ease of comparison. Within ontologies tailored to diverse use cases, post-composing user-defined terms reconciles the demands for standardization on the one hand and flexibility on the other. In many instances of Breedbase, a digital ecosystem for plant breeding designed for genomic selection, the goal is to capture phenotypic data using highly curated and rigorous crop ontologies, while adapting to the specific requirements of plant breeders to record data quickly and efficiently. For example, post-composing enables users to tailor ontology terms to suit specific and granular use cases such as repeated measurements on different plant parts and special sample preparation techniques. To achieve this, we have implemented a post-composing tool based on orthogonal ontologies providing users with the ability to introduce additional levels of phenotyping granularity tailored to unique experimental designs. Post-composed terms are designed to be reused by all breeding programs within a Breedbase instance but are not exported to the crop reference ontologies. Breedbase users can post-compose terms across various categories, such as plant anatomy, treatments, temporal events, and breeding cycles, and, as a result, generate highly specific terms for more accurate phenotyping.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927528/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143673564","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}