Flora Samples Import and Taxonomy Update to Database

This workflow aims to efficiently integrate floral sample data from Excel files into a MongoDB database for botanical projects. It involves verifying and updating taxonomic information, importing georeferenced floral samples, converting data to JSON format, and uploading it to the database. This process ensures accurate taxonomy and enriches the database with comprehensive sample information, supporting robust data analysis and enhancing the project's overall dataset.<div><br></div><div>Background</div><div>Efficient management of flora sample data is essential in botanical projects, especially when integrating diverse information into a MongoDB database. This workflow addresses the challenge of incorporating floral samples, collected at various sampling points, into the MongoDB database. The database is divided into two segments: one storing taxonomic information and common characteristics of taxa, and the other containing georeferenced floral samples with relevant information. The workflow ensures that, upon importing new samples, taxonomic information is verified and updated, if necessary, before storing the sample data.</div><div><br></div><div>Introduction</div><div>In botanical projects, effective data handling is pivotal, particularly when incorporating diverse flora samples into a MongoDB database. This workflow focuses on importing floral samples from an Excel file into MongoDB, ensuring data integrity and taxonomic accuracy. The database is structured into taxonomic information and a collection of georeferenced floral samples, each with essential details about the collection location and the species' nativity. The workflow dynamically updates taxonomic records and stores new samples in the appropriate database sections, enriching the overall floral sample collection.</div><div><br></div><div>Aims</div><div>The primary aim of this workflow is to streamline the integration of floral sample data into the MongoDB database, maintaining taxonomic accuracy and enhancing the overall collection. The workflow includes the following key components:

- Taxonomy Verification and Update: Checks and updates taxonomic information in the MongoDB database, ensuring accuracy before importing new floral samples.

- Georeferenced Sample Import: Imports floral samples from the Excel file, containing georeferenced information and additional sample details.

- JSON Transformation and Database Upload: Transforms the floral sample information from the Excel file into JSON format and uploads it to the appropriate sections of the MongoDB database.</div><div><br></div><div>Scientific Questions</div><div>- Taxonomy Verification Process: How effectively does the workflow verify and update taxonomic information before importing new floral samples?</div><div>- Georeferenced Sample Storage: How does the workflow handle the storage of georeferenced floral samples, considering collection location and species nativity?

- JSON Transformation Accuracy: How successful is the transformation of floral sample information from the Excel file into JSON format for MongoDB integration?

- Database Enrichment: How does the workflow contribute to enriching the taxonomic and sample collections in the MongoDB database, and how is this reflected in the overall project dataset?</div>

Date ( Publication): 2023-12-31T00:00:00

Status: On going / operational

Principal investigator

University of Malaga - Ismael Navas Delgado

Publisher

LifeWatch ERIC ICT Core - Francisco Manuel SÁNCHEZ-CANO

Custodian

LifeWatch ERIC ICT Core - Antonio José SÁENZ-ALBANÉS

Principal investigator

LifeWatch ERIC ICT Core - ICT Core Group

Keywords: Flora samples

Keywords: Taxonomy update

Keywords: Data integration

Keywords: MongoDB database

Keywords: Excel file

Keywords: JSON conversion

Keywords: Georeferenced samples

Keywords: Data integrity

Keywords: Botanical projects

Keywords: Taxonomic information

Access constraints: Copyright

Other constraints: Copyright 2023 Khaos Research Group

Protocol: DOI

Service Name: Import excel file

Service Description: Import a xlsx file from an online source given its URL. Extract floral sample data from Excel files.

Service Reference (id): https://gitlab.lifewatch.dev/lfw002-khaos/wrapper-library/-/tree/develop/core/ImportFile/0.0.5

Service Name: Excel to Sample and Taxon JSONs

Service Description: Convert the excel file to JSON files with sample and taxons. Extract floral sample data from Excel files. Verify and update taxonomic information in the MongoDB database to ensure accuracy before importing new samples. Convert the extracted floral sample data from Excel format to JSON format for compatibility with MongoDB. Import floral samples containing georeferenced information and additional sample details into the MongoDB database.