Ježek Petr, Teeters Jeffery L, Sommer Friedrich T
Faculty of Applied Sciences, New Technologies for the Information Society, University of West Bohemia, Plzeň, Czechia.
Redwood Center for Theoretical Neuroscience & Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States.
Front Neuroinform. 2020 Sep 11;14:27. doi: 10.3389/fninf.2020.00027. eCollection 2020.
The Neurodata Without Borders (abbreviation NWB) format is a current technology for storing neurophysiology data along with the associated metadata. Data stored in the format is organized into separate HDF5 files, each file usually storing the data associated with a single recording session. While the NWB format provides a structured method for storing data, so far there have not been tools which enable searching a collection of NWB files in order to find data of interest for a particular purpose. We describe here three tools to enable searching NWB files. The tools have different features making each of them most useful for a particular task. The first tool, called the NWB Query Engine, is written in Java. It allows searching the complete content of NWB files. It was designed for the first version of NWB (NWB 1) and supports most (but not all) features of the most recent version (NWB 2). For some searches, it is the fastest tool. The second tool, called "search_nwb" is written in Python and also allow searching the complete contents of NWB files. It works with both NWB 1 and NWB 2, as does the third tool. The third tool, called "nwbindexer" enables searching a collection of NWB files using a two-step process. In the first step, a utility is run which creates an SQLite database containing the metadata in a collection of NWB files. This database is then searched in the second step, using another utility. Once the index is built, this two-step processes allows faster searches than are done by the other tools, but does not enable as complete of searches. All three tools use a simple query language which was developed for this project. Software integrating the three tools into a web-interface is provided which enables searching NWB files by submitting a web form.
无国界神经数据（缩写为NWB）格式是一种用于存储神经生理学数据及相关元数据的当前技术。以这种格式存储的数据被组织成单独的HDF5文件，每个文件通常存储与单个记录会话相关的数据。虽然NWB格式提供了一种结构化的数据存储方法，但到目前为止，还没有能够搜索NWB文件集合以找到特定目的所需数据的工具。我们在此描述三种用于搜索NWB文件的工具。这些工具具有不同的特性，使得它们各自对于特定任务最为有用。第一个工具称为NWB查询引擎，用Java编写。它允许搜索NWB文件的完整内容。它是为NWB的第一个版本（NWB 1）设计的，支持最新版本（NWB 2）的大多数（但不是全部）特性。对于某些搜索，它是最快的工具。第二个工具称为“search_nwb”，用Python编写，也允许搜索NWB文件的完整内容。它与NWB 1和NWB 2都兼容，第三个工具也是如此。第三个工具称为“nwbindexer”，它通过两步过程来搜索NWB文件集合。在第一步中，运行一个实用程序，该程序创建一个包含NWB文件集合中元数据的SQLite数据库。然后在第二步中使用另一个实用程序搜索该数据库。一旦建立索引，这个两步过程比其他工具的搜索速度更快，但不能进行像其他工具那样完整的搜索。所有这三个工具都使用为该项目开发的简单查询语言。提供了将这三个工具集成到一个Web界面中的软件，通过提交Web表单即可搜索NWB文件。
