TogoID: an exploratory ID converter to bridge biological datasets.
TogoID: an exploratory ID converter to bridge biological datasets.
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DOI：
10.1093/bioinformatics/btac491
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发表时间：
2022-09-02
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影响因子：
--
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如果不充分利用生物数据，就无法理解生命，这些数据分散在生命科学的各种数据库中。为了无缝连接这些数据，标识符（ID）转换起着关键作用。但是，现有的ID转换服务存在缺点，例如仅覆盖有限范围的数据库的生物类别，不能跟上原始数据库的更新，并且在生物关系的上下文中难以解释输出，特别是在多步骤转换ID时。TogoID是一种ID转换服务，通过直观的web界面和用于编程访问的应用程序编程接口（API）实现了独特的功能。TogoID目前支持65个涵盖各种生物类别的数据集。TogoID用户可以执行探索性多步骤转换，以在id之间找到路径。为了指导转换中生物学意义的解释，我们制作了一个本体来定义数据集关系的语义。TogoID服务在TogoID网站（https://togoid.dbcls.jp/）上免费提供，并且还提供API以允许编程访问。为了鼓励开发人员添加新的数据集对，系统将数据对的配置存储在GitHub存储库（https://github.com/togoid/togoid-config）中，并接受其他数据对的请求。补充数据可在生物信息学网站获得。
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. 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. 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 data are available at Bioinformatics online.
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影响因子：
14.9
作者：
Smedley D;Haider S;Durinck S;Pandini L;Provero P;Allen J;Arnaiz O;Awedh MH;Baldock R;Barbiera G;Bardou P;Beck T;Blake A;Bonierbale M;Brookes AJ;Bucci G;Buetti I;Burge S;Cabau C;Carlson JW;Chelala C;Chrysostomou C;Cittaro D;Collin O;Cordova R;Cutts RJ;Dassi E;Di Genova A;Djari A;Esposito A;Estrella H;Eyras E;Fernandez-Banet J;Forbes S;Free RC;Fujisawa T;Gadaleta E;Garcia-Manteiga JM;Goodstein D;Gray K;Guerra-Assunção JA;Haggarty B;Han DJ;Han BW;Harris T;Harshbarger J;Hastings RK;Hayes RD;Hoede C;Hu S;Hu ZL;Hutchins L;Kan Z;Kawaji H;Keliet A;Kerhornou A;Kim S;Kinsella R;Klopp C;Kong L;Lawson D;Lazarevic D;Lee JH;Letellier T;Li CY;Lio P;Liu CJ;Luo J;Maass A;Mariette J;Maurel T;Merella S;Mohamed AM;Moreews F;Nabihoudine I;Ndegwa N;Noirot C;Perez-Llamas C;Primig M;Quattrone A;Quesneville H;Rambaldi D;Reecy J;Riba M;Rosanoff S;Saddiq AA;Salas E;Sallou O;Shepherd R;Simon R;Sperling L;Spooner W;Staines DM;Steinbach D;Stone K;Stupka E;Teague JW;Dayem Ullah AZ;Wang J;Ware D;Wong-Erasmus M;Youens-Clark K;Zadissa A;Zhang SJ;Kasprzyk A
通讯作者：
Kasprzyk A
影响因子：
14.9
作者：
Howe KL;Achuthan P;Allen J;Allen J;Alvarez-Jarreta J;Amode MR;Armean IM;Azov AG;Bennett R;Bhai J;Billis K;Boddu S;Charkhchi M;Cummins C;Da Rin Fioretto L;Davidson C;Dodiya K;El Houdaigui B;Fatima R;Gall A;Garcia Giron C;Grego T;Guijarro-Clarke C;Haggerty L;Hemrom A;Hourlier T;Izuogu OG;Juettemann T;Kaikala V;Kay M;Lavidas I;Le T;Lemos D;Gonzalez Martinez J;Marugán JC;Maurel T;McMahon AC;Mohanan S;Moore B;Muffato M;Oheh DN;Paraschas D;Parker A;Parton A;Prosovetskaia I;Sakthivel MP;Salam AIA;Schmitt BM;Schuilenburg H;Sheppard D;Steed E;Szpak M;Szuba M;Taylor K;Thormann A;Threadgold G;Walts B;Winterbottom A;Chakiachvili M;Chaubal A;De Silva N;Flint B;Frankish A;Hunt SE;IIsley GR;Langridge N;Loveland JE;Martin FJ;Mudge JM;Morales J;Perry E;Ruffier M;Tate J;Thybert D;Trevanion SJ;Cunningham F;Yates AD;Zerbino DR;Flicek P
通讯作者：
Flicek P
影响因子：
14.9
作者：
Gene Ontology Consortium
通讯作者：
Gene Ontology Consortium
影响因子：
14.9
作者：
Mistry J;Chuguransky S;Williams L;Qureshi M;Salazar GA;Sonnhammer ELL;Tosatto SCE;Paladin L;Raj S;Richardson LJ;Finn RD;Bateman A
通讯作者：
Bateman A
影响因子：
8.6
作者：
Heller SR;McNaught A;Pletnev I;Stein S;Tchekhovskoi D
通讯作者：
Tchekhovskoi D