This repository contains supplementary information and insights about the CFG Database. All analyses are conducted in R Programming language using multiple packages.
CFG Database, a unique and powerful tool for research and conservation of the cave fauna of Greece, was developed within the framework of the project “Conservation of the Cave Fauna of Greece” funded by MAVA foundation and WWF Greece. It was compiled after gathering, critically evaluating and integrating all taxonomic and faunistic information for species recorded in the caves of Greece. In addition, It includes all species recorded up to 2019 and currently regarded as valid. CFG Database is developed and maintained by the Hellenic Institute of Speleological Research.
Data integration is about enriching data with other types of data. This process was human curated and was supported by many computational tools. The database was checked for possible gaps in data, errors or inconsistencies in respect to the rules of zoological nomenclature, redundancy, and inconsistencies among parts. The taxonomic reference system was harmonized with the Pan-European Species directories Infrastructure (PESI, EU-nomen).
For each species, the following information is provided: scientific name and authorship; a map displaying the cave(s) location(s) recorded; higher taxonomy; distribution; distribution in caves of Greece; conservation status; protection status; links to Fauna Europaea, GBIF, IUCN red list, PESI & NCBI if available; species literature references. Species synonyms are only exceptionally provided as the user can see them at the linked databases.
Packages for the CFG Database enrichment:
- species distribution data from GBIF using the rgbif package
- species taxonomy with the taxise package
- species IUCN characterisation using the rredlist package and the red package
For each cave, the following information is provided: The Greek name of the cave in Latin characters using the Greek – ISO 843 transliteration system (see online portal ); a map displaying the location; the cave name(s) used in literature; closest settlement in the context of the 1/1/2011 administrative system established in Greece (Kallikratis reform, Greek Law 3852/2010); brief description; protection status; species list; cave literature references; species literature references.
- Greece administrative data from geodata.gov.gr
- Meteorological data of Greece using the hydroscoper package
Tidyverse is used for
For the Interactive we use the leaflet package which we incorporated in a Shiny Application.
The CFG database and the tool were designed with the KISS principle in mind while taking care to apply best coding practices.
- Programming language: PHP, Javascript
- Interface language: HTML, CSS
- Database: MySQL
- Frameworks used: CodeIgniter, Bootstrap, AngularJS
- Plug-ins & Libraries: Leaflet, Leaflet-ajax, TinyMCE
The database schema was designed so that each table holds discrete data and a separate table holds their relations . By utilizing MySQL’s “views” feature, “virtual tables” can be generated by aggregating data from the regular tables. We have carefully designed special views that contain only the necessary amount of data for most types of queries utilized in the application. For future revisions of the application, more data fields and more views could be created without breaking the existing functionality.
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Kaloust Paragamian: Gathering of literature, literature review, database design, data validation & harmonization, editing, and data uploading
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Manoussos Poulinakis: Database design and development, website development
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Savvas Paragkamian: Data cleansing and standardization, data integration, statistic analysis, spatial analysis and repository maintaining
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Ioannis Nikoloudakis: Literature review, data collection and preparation for import
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Dora Moulou: Data collection and preparation for import
All code is written in R Markdown scripts for reproducibility.