NWB Query Engines: Tools to Search Data Stored in Neurodata Without Borders Format
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F49777513%3A23520%2F20%3A43959618" target="_blank" >RIV/49777513:23520/20:43959618 - isvavai.cz</a>
Result on the web
<a href="https://www.frontiersin.org/articles/10.3389/fninf.2020.00027/full" target="_blank" >https://www.frontiersin.org/articles/10.3389/fninf.2020.00027/full</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.3389/fninf.2020.00027" target="_blank" >10.3389/fninf.2020.00027</a>
Alternative languages
Result language
angličtina
Original language name
NWB Query Engines: Tools to Search Data Stored in Neurodata Without Borders Format
Original language description
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.
Czech name
—
Czech description
—
Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Result continuities
Project
<a href="/en/project/LO1506" target="_blank" >LO1506: Sustainability support of the centre NTIS - New Technologies for the Information Society</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2020
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Frontiers in Neuroinformatics
ISSN
1662-5196
e-ISSN
—
Volume of the periodical
14
Issue of the periodical within the volume
27
Country of publishing house
CH - SWITZERLAND
Number of pages
16
Pages from-to
1-16
UT code for WoS article
000576329400001
EID of the result in the Scopus database
2-s2.0-85091940691