Pladias platform: Technical description of the database structure

Novotný, P.; Bruna, J; Chytrý, Milan; Kalčík, Vojtěch; Kaplan, Zdeněk; Kebert, Tomáš; Rohn, Martin; Řezníčková, Marcela; Štech, Milan; Wild, Jan

doi:10.3897/bdj.10.e80167

Cited by 4 publications

(3 citation statements)

References 11 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The basis of the infrastructure is a relational database (= RDBMS; Relational Database Management System) PostgreSQL with PostGIS extension allowing us to process spatial data. A description of the database information model is provided by Novotný et al (2022) . Professional botanists use a web application* 12 written in Java, the public having read-only access to the data provided by a web portal* 13 written in PHP.…”

Section: Project Descriptionmentioning

confidence: 99%

“…It does not use persistent identifiers other than the pure database level IDs, i.e. the model situation of just correcting a typo in a scientific name does not lead to a new ID ( Novotný et al 2022 ).…”

Section: Project Descriptionmentioning

confidence: 99%

“…The occurrences are limited strictly to the Czech Republic area, allowing only a technical buffer (50 m) across the country border. The platform had been developed with this limitation to store only those data which can be validated and curated by local experts ( Novotný et al 2022 ).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Software infrastructure and data pipelines established for technical interoperability within a cross-border cooperation for the flora of the Bohemian Forest

Novotný¹,

Seifert²,

Rohn³

et al. 2022

BDJ

Self Cite

View full text Add to dashboard Cite

The timely and geographical resolutions, as well as the quantity and taxon concepts of records on the occurrence of plants near national borders is often ambiguous. This is due to the regional focus and different approaches of the contributing national and regional databases and networks of the neighbouring countries. Careful data transformation between national data providers is essential for understanding distribution patterns and its dynamics for organisms in areas along the national borders. Sharing occurrence data through the international data aggregator Global Biodiversity Information Facility (GBIF) is also complicated and has to consider that the underlying taxonomic concept and geographic information system of each single GBIF dataset might be different. In addition, some regional data providers have a restrictive (non-cc) licensing policy which does not allow data publication via the GBIF network. Therefore, it is necessary to investigate new ways to make data fit for use for a better and comprehensive understanding of the Flora of the Bohemian Forest. In this paper, we present a bilateral technical interoperability solution for vascular plant occurrence data for the area between the Czech Republic and Bavaria. We describe the initial state of data providers in both countries and the factual and technical challenges in finding a sustainable concept to establish mutual data sharing. The resulting solution for a functional infrastructure and an agreed data pipeline is described in a step-by-step approach. The new distributed infrastructure allows botanists and other stakeholders from both countries to work within the cross-border context of historical and current plants' distribution.

show abstract

Section: Project Descriptionmentioning

confidence: 99%

Section: Project Descriptionmentioning

confidence: 99%

See 1 more Smart Citation

Software infrastructure and data pipelines established for technical interoperability within a cross-border cooperation for the flora of the Bohemian Forest

Novotný¹,

Seifert²,

Rohn³

et al. 2022

BDJ

Self Cite

View full text Add to dashboard Cite

show abstract

The relational modeling of hierarchical data in biodiversity databases

Novotný,

Wild

2024

Database

View full text Add to dashboard Cite

The unifying element of all biodiversity data is the issue of taxon hierarchy modeling. We compared 25 existing databases in terms of handling taxa hierarchy and presentation of this data. We used documentation or demo installations of databases as a source of information and next in line was the analysis of structures using R packages provided by inspected platforms. If neither of these was available, we used the public interface of individual databases. For almost half (12) of the databases analyzed, we did not find any formalized taxa hierarchy data structure, providing only biological information about taxon membership in higher ranks, which is not fully formalizable and thus not generally usable. The least effective Adjacency List model (storing parentId of a taxon) dominates among the remaining providers. This study demonstrates the lack of attention paid by current biodiversity databases to modeling taxon hierarchy, particularly to making it available to researchers in the form of a hierarchical data structure within the data provided. For biodiversity relational databases, the Closure Table type is the most suitable of the known data models, which also corresponds to the ontology concept. However, its use is rather sporadic within the biodiversity databases ecosystem.

show abstract

FloraVeg.EU — An online database of European vegetation, habitats and flora

Chytrý,

Řezníčková,

Novotný

et al. 2024

Applied Vegetation Science

View full text Add to dashboard Cite

This article describes FloraVeg.EU, a new online database with open‐access information on European vegetation units (phytosociological syntaxa), vegetated habitats, and plant taxa. It consists of three modules. (1) The Vegetation module includes 149 phytosociological classes, 378 orders and 1305 alliances of an updated version of the EuroVegChecklist modified based on the decisions of the European Vegetation Classification Committee. Vegetation units dominated by vascular plants are characterized by country‐based distribution maps and data on the dominant life forms, phenology, soil properties, relationships to vegetation regions, elevational vegetation belts and azonal habitats, successional status, and degree of naturalness. A list of diagnostic taxa is also provided for each class. (2) The Habitats module includes vascular‐plant‐dominated terrestrial, freshwater, and marine habitat types from the first to the third or fourth highest hierarchical levels of the EUNIS classification. Of these, 249 vegetated habitats are characterized by a brief description, a point‐based distribution map, diagnostic, constant, and dominant taxa, and a list of the corresponding alliances. (3) The Species module provides information on 37 characteristics of European vascular plant species and some infrageneric or infraspecific taxa, including functional traits (habitus and growth type, leaf, flower, fruit and seed traits, and trophic mode), taxon origin (native vs alien), and ecological information (environmental relationships, Ellenberg‐type indicator values, disturbance indicator values, and relationships to vegetation units and habitat types). Values for at least three variables are available for 36,404 species. Individual taxa, vegetation units, and habitats in these three modules are illustrated by more than 34,000 photographs. The Download section of FloraVeg.EU provides open‐access data sets in a spreadsheet format that can be used for analyses. FloraVeg.EU is a new resource with easily accessible data that can be used for research in vegetation science, ecology, and biogeography, as well as for education and conservation applications.

show abstract

Pladias platform: Technical description of the database structure

Cited by 4 publications

References 11 publications

Software infrastructure and data pipelines established for technical interoperability within a cross-border cooperation for the flora of the Bohemian Forest

Software infrastructure and data pipelines established for technical interoperability within a cross-border cooperation for the flora of the Bohemian Forest

The relational modeling of hierarchical data in biodiversity databases

FloraVeg.EU — An online database of European vegetation, habitats and flora

Contact Info

Product

Resources

About