Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features
Abstract Background TogoID ( https://togoid.dbcls.jp/ ) is an identifier (ID) conversion service designed to link IDs across diverse categories of life science databases. With its ability to obtain IDs related in different semantic relationships, a user-friendly web interface, and a regular automati...
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| Format: | Article |
| Language: | English |
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BMC
2025-01-01
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| Series: | Journal of Biomedical Semantics |
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| Online Access: | https://doi.org/10.1186/s13326-024-00322-1 |
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| author | Shuya Ikeda Kiyoko F. Aoki-Kinoshita Hirokazu Chiba Susumu Goto Masae Hosoda Shuichi Kawashima Jin-Dong Kim Yuki Moriya Tazro Ohta Hiromasa Ono Terue Takatsuki Yasunori Yamamoto Toshiaki Katayama |
| author_facet | Shuya Ikeda Kiyoko F. Aoki-Kinoshita Hirokazu Chiba Susumu Goto Masae Hosoda Shuichi Kawashima Jin-Dong Kim Yuki Moriya Tazro Ohta Hiromasa Ono Terue Takatsuki Yasunori Yamamoto Toshiaki Katayama |
| author_sort | Shuya Ikeda |
| collection | DOAJ |
| description | Abstract Background TogoID ( https://togoid.dbcls.jp/ ) is an identifier (ID) conversion service designed to link IDs across diverse categories of life science databases. With its ability to obtain IDs related in different semantic relationships, a user-friendly web interface, and a regular automatic data update system, TogoID has been a valuable tool for bioinformatics. Results We have recently expanded TogoID's ability to represent semantics between datasets, enabling it to handle multiple semantic relationships within dataset pairs. This enhancement enables TogoID to distinguish relationships such as "glycans bind to proteins" or "glycans are processed by proteins" between glycans and proteins. Additional new features include the ability to display labels corresponding to database IDs, making it easier to interpret the relationships between the various IDs available in TogoID, and the ability to convert labels to IDs, extending the entry point for ID conversion. The implementation of URL parameters, which reproduces the state of TogoID's web application, allows users to share complex search results through a simple URL. Conclusions These advancements improve TogoID’s utility in bioinformatics, allowing researchers to explore complex ID relationships. By introducing the tool’s multi-semantic and label features, TogoID expands the concept of ID conversion and supports more comprehensive and efficient data integration across life science databases. |
| format | Article |
| id | doaj-art-7a46dbca70ad41cfa29b23885d50a121 |
| institution | OA Journals |
| issn | 2041-1480 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Biomedical Semantics |
| spelling | doaj-art-7a46dbca70ad41cfa29b23885d50a1212025-08-20T02:36:41ZengBMCJournal of Biomedical Semantics2041-14802025-01-0116111010.1186/s13326-024-00322-1Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label featuresShuya Ikeda0Kiyoko F. Aoki-Kinoshita1Hirokazu Chiba2Susumu Goto3Masae Hosoda4Shuichi Kawashima5Jin-Dong Kim6Yuki Moriya7Tazro Ohta8Hiromasa Ono9Terue Takatsuki10Yasunori Yamamoto11Toshiaki Katayama12Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and SystemsGraduate School of Science and Engineering, Soka UniversityDatabase Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and SystemsDatabase Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and SystemsDatabase Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and SystemsDatabase Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and SystemsDatabase Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and SystemsDatabase Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and SystemsDatabase Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and SystemsDatabase Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and SystemsDatabase Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and SystemsDatabase Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and SystemsDatabase Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and SystemsAbstract Background TogoID ( https://togoid.dbcls.jp/ ) is an identifier (ID) conversion service designed to link IDs across diverse categories of life science databases. With its ability to obtain IDs related in different semantic relationships, a user-friendly web interface, and a regular automatic data update system, TogoID has been a valuable tool for bioinformatics. Results We have recently expanded TogoID's ability to represent semantics between datasets, enabling it to handle multiple semantic relationships within dataset pairs. This enhancement enables TogoID to distinguish relationships such as "glycans bind to proteins" or "glycans are processed by proteins" between glycans and proteins. Additional new features include the ability to display labels corresponding to database IDs, making it easier to interpret the relationships between the various IDs available in TogoID, and the ability to convert labels to IDs, extending the entry point for ID conversion. The implementation of URL parameters, which reproduces the state of TogoID's web application, allows users to share complex search results through a simple URL. Conclusions These advancements improve TogoID’s utility in bioinformatics, allowing researchers to explore complex ID relationships. By introducing the tool’s multi-semantic and label features, TogoID expands the concept of ID conversion and supports more comprehensive and efficient data integration across life science databases.https://doi.org/10.1186/s13326-024-00322-1Database IntegrationWeb ApplicationOntology |
| spellingShingle | Shuya Ikeda Kiyoko F. Aoki-Kinoshita Hirokazu Chiba Susumu Goto Masae Hosoda Shuichi Kawashima Jin-Dong Kim Yuki Moriya Tazro Ohta Hiromasa Ono Terue Takatsuki Yasunori Yamamoto Toshiaki Katayama Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features Journal of Biomedical Semantics Database Integration Web Application Ontology |
| title | Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features |
| title_full | Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features |
| title_fullStr | Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features |
| title_full_unstemmed | Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features |
| title_short | Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features |
| title_sort | expanding the concept of id conversion in togoid by introducing multi semantic and label features |
| topic | Database Integration Web Application Ontology |
| url | https://doi.org/10.1186/s13326-024-00322-1 |
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