Institute of Biochemistry, Computational Systems Biochemistry Group, Universitätsmedizin Berlin (Charité), Reinickendorfer Strasse 61, D-13347 Berlin, Germany.
Bioinformatics. 2011 Oct 1;27(19):2763-4. doi: 10.1093/bioinformatics/btr456. Epub 2011 Aug 8.
Semantic annotations of the biochemical entities constituting a biological reaction network are indispensable to create biologically meaningful networks. They further heighten efficient exchange, reuse and merging of existing models which concern present-day systems biology research more often. Two types of tools for the reconstruction of biological networks currently exist: (i) several sophisticated programs support graphical network editing and visualization. (ii) Data management systems permit reconstruction and curation of huge networks in a team of scientists including data integration, annotation and cross-referencing. We seeked ways to combine the advantages of both approaches.
Metannogen, which was previously developed for network reconstruction, has been considerably improved. From now on, Metannogen provides sbml import and annotation of networks created elsewhere. This permits users of other network reconstruction platforms or modeling software to annotate their networks using Metannogen's advanced information management. We implemented word-autocompletion, multipattern highlighting, spell check, brace-expansion and publication management, and improved annotation, cross-referencing and team work requirements. Unspecific enzymes and transporters acting on a spectrum of different substrates are efficiently handled. The network can be exported in sbml format where the annotations are embedded in line with the miriam standard. For more comfort, Metannogen may be tightly coupled with the network editor such that Metannogen becomes an additional view for the focused reaction in the network editor. Finally, Metannogen provides local single user, shared password protected multiuser or public access to the annotation data.
Metannogen is available free of charge at: http://www.bioinformatics.org/strap/metannogen/ or http://3d-alignment.eu/metannogen/.
Supplementary data are available at Bioinformatics online.
构成生物反应网络的生化实体的语义注释对于创建具有生物学意义的网络是必不可少的。它们进一步提高了现有模型的有效交换、重用和合并，这些模型更多地涉及当今的系统生物学研究。目前存在两种用于重建生物网络的工具：（i）一些复杂的程序支持图形网络编辑和可视化。（ii）数据管理系统允许包括数据集成、注释和交叉引用在内的科学家团队重建和管理庞大的网络。我们寻求结合这两种方法的优势。
Metannogen 以前是为网络重建而开发的，已经得到了相当大的改进。从现在开始，Metannogen 提供了对在其他地方创建的网络的 sbml 导入和注释。这允许使用其他网络重建平台或建模软件的用户使用 Metannogen 的高级信息管理来注释他们的网络。我们实现了单词自动完成、多模式突出显示、拼写检查、括号扩展和出版物管理，并改进了注释、交叉引用和团队工作要求。能够有效地处理作用于不同底物谱的非特异性酶和转运蛋白。该网络可以以 sbml 格式导出，其中注释与 miriam 标准嵌入在同一行中。为了更舒适，Metannogen 可以与网络编辑器紧密耦合，以便 Metannogen 成为网络编辑器中聚焦反应的附加视图。最后，Metannogen 提供了本地单个用户、共享密码保护的多用户或公共访问注释数据的权限。
Metannogen 可免费在以下网址获得：http://www.bioinformatics.org/strap/metannogen/或 http://3d-alignment.eu/metannogen/。
补充数据可在 Bioinformatics 在线获得。
