Dataset Information

Medna-metadata: an open-source data management system for tracking environmental DNA samples and metadata.

ABSTRACT:

Motivation

Environmental DNA (eDNA), as a rapidly expanding research field, stands to benefit from shared resources including sampling protocols, study designs, discovered sequences, and taxonomic assignments to sequences. High-quality community shareable eDNA resources rely heavily on comprehensive metadata documentation that captures the complex workflows covering field sampling, molecular biology lab work, and bioinformatic analyses. There are limited sources that provide documentation of database development on comprehensive metadata for eDNA and these workflows and no open-source software.

Results

We present medna-metadata, an open-source, modular system that aligns with Findable, Accessible, Interoperable, and Reusable guiding principles that support scholarly data reuse and the database and application development of a standardized metadata collection structure that encapsulates critical aspects of field data collection, wet lab processing, and bioinformatic analysis. Medna-metadata is showcased with metabarcoding data from the Gulf of Maine (Polinski et al., 2019).

Availability and implementation

The source code of the medna-metadata web application is hosted on GitHub (https://github.com/Maine-eDNA/medna-metadata). Medna-metadata is a docker-compose installable package. Documentation can be found at https://medna-metadata.readthedocs.io/en/latest/?badge=latest. The application is implemented in Python, PostgreSQL and PostGIS, RabbitMQ, and NGINX, with all major browsers supported. A demo can be found at https://demo.metadata.maine-edna.org/.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Kimble M

PROVIDER: S-EPMC9524998 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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Publications

medna-metadata: an open-source data management system for tracking environmental DNA samples and metadata.

Kimble M M Allers S S Campbell K K Chen C C Jackson L M LM King B L BL Silverbrand S S York G G Beard K K

Bioinformatics (Oxford, England) 20220901 19

<h4>Motivation</h4>Environmental DNA (eDNA), as a rapidly expanding research field, stands to benefit from shared resources including sampling protocols, study designs, discovered sequences, and taxonomic assignments to sequences. High-quality community shareable eDNA resources rely heavily on comprehensive metadata documentation that captures the complex workflows covering field sampling, molecular biology lab work, and bioinformatic analyses. There are limited sources that provide documentatio ...[more]

PMID: 35960154

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