scholarly journals Mangal: An open infrastructure for ecological interactions

2019 ◽  
Vol 3 ◽  
Author(s):  
Steve Vissault ◽  
Dominique Gravel ◽  
Timothée Poisot
Keyword(s):  
Information System ◽  
Case Studies ◽  
Source Code ◽  
Data Access ◽  
Ecological Interactions ◽  
Global Biodiversity Information Facility ◽  
Scientific Publications ◽  
Standard Information ◽  
Global Biodiversity ◽  
Biodiversity Information

Interactions among species is at the heart of ecology. Despite their importance, studying ecological interactions remains difficult due to the lack of standard information and the disparity of formats in which ecological interactions are stored (Poisot et al. 2015). Historically, ecologists have used matrices to store interactions, which tend to easily decontextualize interactions from fieldwork when metadata is missing. To overcome these limitations, we designed Mangal - a global ecological interactions database - which serialize ecological interaction matrices into nodes (e.g. taxon, individuals or population) and edges. This database offers the opportunity to store information on traits, environment and homogenized taxonomy through unique taxonomic identifiers such as Encyclopedia of Life (EOL), Catalogue of Life (COL), Global Biodiversity Information Facility (GBIF) and Integrated Taxonomic Information System (ITIS). Here, we present the new release of Mangal including more than 120,000 interactions, 1,300 networks from 172 scientific publications distributed across the globe. We explore the content, illustrate case studies and present templates in order to contribute to this open infrastructure. For this purpose, we developed and maintained two packages/clients from popular scientific languages: R and Julia to facilitate data access, curation and network deposits on the database (Source code).

scholarly journals Updated checklist of the extant Chondrichthyes within the Exclusive Economic Zone of Mexico

ZooKeys ◽  
2018 ◽  
Vol 774 ◽  
pp. 17-39 ◽  
Author(s):  
Nicolás Roberto Ehemann ◽  
Lorem del Valle González-González ◽  
Jorge Guillermo Chollet-Villalpando ◽  
José De La Cruz-Agüero
Keyword(s):  
Information System ◽  
Gulf Of California ◽  
Marine Species ◽  
Exclusive Economic Zone ◽  
Global Biodiversity Information Facility ◽  
Scientific Publications ◽  
Mexican Pacific ◽  
California Academy ◽  
Economic Zone ◽  
Biodiversity Information

The checklist presented in this study includes the latest taxonomic and systematic modifications and updates (early 2018) for the Chondrichthyes that inhabit the Exclusive Economic Zone (EEZ) of Mexico. The list is based on a literature review of field-specific books, scientific publications and database information from collections and museums worldwide available online such as, the Ocean Biogeographic Information System (OBIS), Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EOL), iSpecies, FishBase and the National Biodiversity Information System (SNIB–CONABIO). Information was cross-referenced with digital taxonomic systems such as the Catalog of Fishes of the California Academy of Sciences, the World Register of Marine Species (WoRMS), and the Integrated Taxonomic Information System (ITIS). There is a total of two subclasses two divisions, 13 orders, 44 families, 84 genera, and 217 species that represent approximately 18% of all living and described species of chondrichthyans worldwide. For the Mexican Pacific and the Gulf of California, 92 species of chondrichthyans are listed compared to 94 species for the Gulf of Mexico and the Caribbean Sea. Additionally, 31 species listed occur on both coasts of Mexico. The species richness of the Mexican chondrichthyans will surely continue to increase, due to the exploration of deep-water fishing areas in the EEZ.

scholarly journals Aplicación de índices filogenéticos para la definición de prioridades de conservación en los páramos del noroeste de los Andes

2018 ◽  
Vol 66 (4) ◽  
pp. 1353
Author(s):  
Fernando Alzate ◽  
Astrid Álvarez ◽  
Daniel Rafael Miranda-Esquivel ◽  
Juan J. Morrone
Keyword(s):  
Information System ◽  
Species Richness ◽  
Conservation Priorities ◽  
Global Biodiversity Information Facility ◽  
Subsequent Loss ◽  
Global Biodiversity ◽  
The Individual ◽  
Available Information ◽  
Biodiversity Information ◽  
Data Priority

Paramos are High Andean ecosystems that harbor a diverse biota and have high endemicity, as a result of their extreme environmental conditions. We used different phylogenetic indices to define conservation priorities in the paramos of the department of Antioquia, Colombia, based on measures of their evolutionary individuality and richness complimentary. To perform the analyses, we generated a data base including 416 angiosperm taxa and 1 951 localities for a total of 12 897 distributional records compiled from surveys and reviews. Additionally, the available information in the Global Biodiversity Information Facility and the Colombian Biodiversity Information System were included. From these data, priority areas for the conservation of the paramos located in the state of Antioquia were identified, using measures of evolutionary individuality based on nodes and biotic complementarity. Taking into account only the individual phylogenetic indices, the most important paramo for conservation was Frontino-Urrao, followed by Farallones de Citará. If biotic complementarity is considered, the second most important paramo is Sonsón. Priority classifications of areas based on individuality are congruent with areas of greatest species richness. We conclude that it is necessary and urgent to preserve the paramos given their vulnerability and the subsequent loss of the ecosystem services that they provide, if they are exposed to degradation or disappearance.

scholarly journals The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 01

2020 ◽  
Vol 8 ◽  
Author(s):  
Sonia Ferreira ◽  
Rui Andrade ◽  
Ana Gonçalves ◽  
Pedro Sousa ◽  
Joana Paupério ◽  
...  
Keyword(s):  
Species Level ◽  
Distribution Data ◽  
Dna Barcodes ◽  
Online Database ◽  
Global Biodiversity Information Facility ◽  
Life Data ◽  
Tagus River ◽  
Global Biodiversity ◽  
Biodiversity Information ◽  
Dipteran Species

The InBIO Barcoding Initiative (IBI) Diptera 01 dataset contains records of 203 specimens of Diptera. All specimens have been morphologically identified to species level, and belong to 154 species in total. The species represented in this dataset correspond to about 10% of continental Portugal dipteran species diversity. All specimens were collected north of the Tagus river in Portugal. Sampling took place from 2014 to 2018, and specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources. This dataset contributes to the knowledge on the DNA barcodes and distribution of 154 species of Diptera from Portugal and is the first of the planned IBI database public releases, which will make available genetic and distribution data for a series of taxa. All specimens have their DNA barcodes made publicly available in the Barcode of Life Data System (BOLD) online database and the distribution dataset can be freely accessed through the Global Biodiversity Information Facility (GBIF).

scholarly journals Using Global Biodiversity Information Facility Occurrence Data for Automated Invasive Alien Species Risk Mapping 

2020 ◽  
Vol 4 ◽  
Author(s):  
Amy Davis ◽  
Tim Adriaens ◽  
Rozemien De Troch ◽  
Peter Desmet ◽  
Quentin Groom ◽  
...  
Keyword(s):  
Alien Species ◽  
Vascular Plants ◽  
Invasive Alien Species ◽  
Risk Assessments ◽  
Sampling Effort ◽  
Global Biodiversity Information Facility ◽  
Global Biodiversity ◽  
Risk Maps ◽  
Species Occurrences ◽  
Biodiversity Information

To support invasive alien species risk assessments, the Tracking Invasive Alien Species (TrIAS) project has developed an automated, open, workflow incorporating state-of-the-art species distribution modelling practices to create risk maps using the open source language R. It is based on Global Biodiversity Information Facility (GBIF) data and openly published environmental data layers characterizing climate and land cover. Our workflow requires only a species name and generates an ensemble of machine-learning algorithms (Random Forest, Boosted Regression Trees, K-Nearest Neighbors and AdaBoost) stacked together as a meta-model to produce the final risk map at 1 km2 resolution (Fig. 1). Risk maps are generated automatically for standard Intergovernmental Panel on Climate Change (IPCC) greenhouse gas emission scenarios and are accompanied by maps illustrating the confidence of each individual prediction across space, thus enabling the intuitive visualization and understanding of how the confidence of the model varies across space and scenario (Fig. 2). The effects of sampling bias are accounted for by providing options to: use the sampling effort of the higher taxon the modelled species belongs to (e.g., vascular plants), and to thin species occurrences. use the sampling effort of the higher taxon the modelled species belongs to (e.g., vascular plants), and to thin species occurrences. The risk maps generated by our workflow are defensible and repeatable and provide forecasts of alien species distributions under further climate change scenarios. They can be used to support risk assessments and guide surveillance efforts on alien species in Europe. The detailied modeling framework and code are available on GitHub: https://github.com/trias-project.

Development and Deployment of an Ethnobotanical and Phytochemical Knowledge Database of Malaysia

2013 ◽  
Vol 64 (2) ◽  
Author(s):  
Shakina Mohd Talkah ◽  
Iylia Zulkiflee ◽  
Mohd Shahir Shamsir
Keyword(s):  
Scientific Literature ◽  
Pharmaceutical Compounds ◽  
South East Asia ◽  
Online Database ◽  
Global Biodiversity Information Facility ◽  
Knowledge Database ◽  
Global Biodiversity ◽  
Digital Knowledge ◽  
Biodiversity Information ◽  
Scientific Name

Currently, all the information regarding ethnobotanical, phytochemical and pharmaceutical information of South East Asia are scattered over many different publications, depositories and databases using various digital and analogue formats. Although there are taxonomic databases of medicinal plants, they are not linked to phytochemical and pharmaceutical information which are often resides in scientific literature. We present Phyknome; an ethnobotanical and phytochemical database with more than 22,000 species of ethnoflora of Asia. The creation of this database will enable a biotechnology researcher to seek and identify ethnobotanical information based on a species’ scientific name, description and phytochemical information. It is constructed using a digitization pipeline that allow high throughput digitization of archival data, an automated dataminer to mine for pharmaceutical compounds information and an online database to integrated these information. The main functions include an automated taxonomy, bibliography and API interface with primary databases such as Global Biodiversity Information Facility (GBIF). We believe that Phyknome will contribute to the digital knowledge ecosystem to elevate access and provide tools for ethnobotanical research and contributes to the management, assessment and stewardship of biodiversity. The database is available at http://mapping.fbb.utm.my/phyknome/.

Sign in / Sign up

Export Citation Format

Share Document