TogoID: an exploratory ID converter to bridge biological datasets. Ikeda, S., Ono, H., Ohta, T., Chiba, H., Naito, Y., Moriya, Y., Kawashima, S., Yamamoto, Y., Okamoto, S., Goto, S., & Katayama, T. Bioinformatics, 38(17):4194–4199, September, 2022. ![TogoID: an exploratory ID converter to bridge biological datasets [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex Abstract Motivation Understanding life cannot be accomplished without making full use of biological data, which are scattered across databases of diverse categories in life sciences. To connect such data seamlessly, identifier (ID) conversion plays a key role. However, existing ID conversion services have disadvantages, such as covering only a limited range of biological categories of databases, not keeping up with the updates of the original databases and outputs being hard to interpret in the context of biological relations, especially when converting IDs in multiple steps. Results TogoID is an ID conversion service implementing unique features with an intuitive web interface and an application programming interface (API) for programmatic access. TogoID currently supports 65 datasets covering various biological categories. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations. Availability and implementation The TogoID service is freely available on the TogoID website (https://togoid.dbcls.jp/) and the API is also provided to allow programmatic access. To encourage developers to add new dataset pairs, the system stores the configurations of pairs at the GitHub repository (https://github.com/togoid/togoid-config) and accepts the request of additional pairs. Supplementary information Supplementary data are available at Bioinformatics online.
@article{ikeda_togoid_2022,
title = {{TogoID}: an exploratory {ID} converter to bridge biological datasets},
volume = {38},
issn = {1367-4803, 1460-2059},
shorttitle = {{TogoID}},
url = {https://academic.oup.com/bioinformatics/article/38/17/4194/6633929},
doi = {10.1093/bioinformatics/btac491},
abstract = {Abstract
Motivation
Understanding life cannot be accomplished without making full use of biological data, which are scattered across databases of diverse categories in life sciences. To connect such data seamlessly, identifier (ID) conversion plays a key role. However, existing ID conversion services have disadvantages, such as covering only a limited range of biological categories of databases, not keeping up with the updates of the original databases and outputs being hard to interpret in the context of biological relations, especially when converting IDs in multiple steps.
Results
TogoID is an ID conversion service implementing unique features with an intuitive web interface and an application programming interface (API) for programmatic access. TogoID currently supports 65 datasets covering various biological categories. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations.
Availability and implementation
The TogoID service is freely available on the TogoID website (https://togoid.dbcls.jp/) and the API is also provided to allow programmatic access. To encourage developers to add new dataset pairs, the system stores the configurations of pairs at the GitHub repository (https://github.com/togoid/togoid-config) and accepts the request of additional pairs.
Supplementary information
Supplementary data are available at Bioinformatics online.},
language = {en},
number = {17},
urldate = {2022-10-12},
journal = {Bioinformatics},
author = {Ikeda, Shuya and Ono, Hiromasa and Ohta, Tazro and Chiba, Hirokazu and Naito, Yuki and Moriya, Yuki and Kawashima, Shuichi and Yamamoto, Yasunori and Okamoto, Shinobu and Goto, Susumu and Katayama, Toshiaki},
editor = {Robinson, Peter},
month = sep,
year = {2022},
pages = {4194--4199},
}
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However, existing ID conversion services have disadvantages, such as covering only a limited range of biological categories of databases, not keeping up with the updates of the original databases and outputs being hard to interpret in the context of biological relations, especially when converting IDs in multiple steps. Results TogoID is an ID conversion service implementing unique features with an intuitive web interface and an application programming interface (API) for programmatic access. TogoID currently supports 65 datasets covering various biological categories. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations. Availability and implementation The TogoID service is freely available on the TogoID website (https://togoid.dbcls.jp/) and the API is also provided to allow programmatic access. To encourage developers to add new dataset pairs, the system stores the configurations of pairs at the GitHub repository (https://github.com/togoid/togoid-config) and accepts the request of additional pairs. Supplementary information Supplementary data are available at Bioinformatics online.","language":"en","number":"17","urldate":"2022-10-12","journal":"Bioinformatics","author":[{"propositions":[],"lastnames":["Ikeda"],"firstnames":["Shuya"],"suffixes":[]},{"propositions":[],"lastnames":["Ono"],"firstnames":["Hiromasa"],"suffixes":[]},{"propositions":[],"lastnames":["Ohta"],"firstnames":["Tazro"],"suffixes":[]},{"propositions":[],"lastnames":["Chiba"],"firstnames":["Hirokazu"],"suffixes":[]},{"propositions":[],"lastnames":["Naito"],"firstnames":["Yuki"],"suffixes":[]},{"propositions":[],"lastnames":["Moriya"],"firstnames":["Yuki"],"suffixes":[]},{"propositions":[],"lastnames":["Kawashima"],"firstnames":["Shuichi"],"suffixes":[]},{"propositions":[],"lastnames":["Yamamoto"],"firstnames":["Yasunori"],"suffixes":[]},{"propositions":[],"lastnames":["Okamoto"],"firstnames":["Shinobu"],"suffixes":[]},{"propositions":[],"lastnames":["Goto"],"firstnames":["Susumu"],"suffixes":[]},{"propositions":[],"lastnames":["Katayama"],"firstnames":["Toshiaki"],"suffixes":[]}],"editor":[{"propositions":[],"lastnames":["Robinson"],"firstnames":["Peter"],"suffixes":[]}],"month":"September","year":"2022","pages":"4194–4199","bibtex":"@article{ikeda_togoid_2022,\n\ttitle = {{TogoID}: an exploratory {ID} converter to bridge biological datasets},\n\tvolume = {38},\n\tissn = {1367-4803, 1460-2059},\n\tshorttitle = {{TogoID}},\n\turl = {https://academic.oup.com/bioinformatics/article/38/17/4194/6633929},\n\tdoi = {10.1093/bioinformatics/btac491},\n\tabstract = {Abstract\n \n Motivation\n Understanding life cannot be accomplished without making full use of biological data, which are scattered across databases of diverse categories in life sciences. To connect such data seamlessly, identifier (ID) conversion plays a key role. However, existing ID conversion services have disadvantages, such as covering only a limited range of biological categories of databases, not keeping up with the updates of the original databases and outputs being hard to interpret in the context of biological relations, especially when converting IDs in multiple steps.\n \n \n Results\n TogoID is an ID conversion service implementing unique features with an intuitive web interface and an application programming interface (API) for programmatic access. TogoID currently supports 65 datasets covering various biological categories. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations.\n \n \n Availability and implementation\n The TogoID service is freely available on the TogoID website (https://togoid.dbcls.jp/) and the API is also provided to allow programmatic access. 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