scholarly journals The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 02 - Limoniidae, Pediciidae and Tipulidae

2021 ◽  
Vol 9 ◽  
Author(s):  
Sónia Ferreira ◽  
Pjotr Oosterbroek ◽  
Jaroslav Starý ◽  
Pedro Sousa ◽  
Vanessa Mata ◽  
...  
Keyword(s):  
Species Level ◽  
Dna Barcodes ◽  
Online Database ◽  
Global Biodiversity Information Facility ◽  
Life Data ◽  
Crane Flies ◽  
Collection Data ◽  
Global Biodiversity ◽  
First Time ◽  
Biodiversity Information

The InBIO Barcoding Initiative (IBI) Diptera 02 dataset contains records of 412 crane fly specimens belonging to the Diptera families: Limoniidae, Pediciidae and Tipulidae. This dataset is the second release by IBI on Diptera and it greatly increases the knowledge on the DNA barcodes and distribution of crane flies from Portugal. All specimens were collected in Portugal, including six specimens from the Azores and Madeira archipelagos. Sampling took place from 2003 to 2019. Specimens have been morphologically identified to species level by taxonomists and belong to 83 species in total. The species, represented in this dataset, correspond to about 55% of all the crane fly species known from Portugal and 22% of crane fly species known from the Iberian Peninsula. All DNA extractions and most specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources. Fifty-three species were new additions to the Barcode of Life Data System (BOLD), with another 18 species' barcodes added from under-represented species in BOLD. Furthermore, the submitted sequences were found to cluster in 88 BINs, 54 of which were new to BOLD. All specimens have their DNA barcodes publicly accessible through BOLD online database and its collection data can be accessed through the Global Biodiversity Information Facility (GBIF). One species, Gonomyia tenella (Limoniidae), is recorded for the first time from Portugal, raising the number of crane flies recorded in the country to 145 species.

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 The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Hemiptera 01

2021 ◽  
Vol 9 ◽  
Author(s):  
Pedro Sousa ◽  
José Grosso-Silva ◽  
Rui Andrade ◽  
Cátia Chaves ◽  
Joana Pinto ◽  
...  
Keyword(s):  
Distribution Data ◽  
Dna Barcodes ◽  
Online Database ◽  
Global Biodiversity Information Facility ◽  
Azores Archipelago ◽  
Life Data ◽  
Subspecies Level ◽  
Global Biodiversity ◽  
First Time ◽  
Biodiversity Information

The InBIO Barcoding Initiative (IBI) Hemiptera 01 dataset contains records of 131 specimens of Hemiptera. Most specimens have been morphologically identified to species or subspecies level and represent 88 species in total. The species of this dataset correspond to about 7.3% of continental Portuguese hemipteran species diversity. All specimens were collected in continental Portugal. Sampling took place from 2015 to 2019 and specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources. This dataset increases the knowledge on the DNA barcodes and distribution of 88 species of Hemiptera from Portugal. Six species, from five different families, were new additions to the Barcode of Life Data System (BOLD), with another twenty five species barcodes' added from under-represented taxa in BOLD. All specimens have their DNA barcodes publicly accessible through BOLD online database and the distribution data can be accessed through the Global Biodiversity Information Facility (GBIF). Eutettix variabilis and Fieberiella florii are recorded for the first time for Portugal and Siphanta acuta, an invasive species, previously reported from the Portuguese Azores archipelago, is recorded for the first time for continental Portugal.

scholarly journals The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera

2020 ◽  
Vol 8 ◽  
Author(s):  
Sonia Ferreira ◽  
José Manuel Tierno de Figueroa ◽  
Filipa Martins ◽  
Joana Verissimo ◽  
Lorenzo Quaglietta ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Freshwater Ecosystems ◽  
Distribution Data ◽  
Dna Barcodes ◽  
Limited Information ◽  
Online Database ◽  
Global Biodiversity Information Facility ◽  
Life Data ◽  
Biodiversity Information ◽  
Comprehensive Reference

The use of DNA barcoding allows unprecedented advances in biodiversity assessments and monitoring schemes of freshwater ecosystems; nevertheless, it requires the construction of comprehensive reference collections of DNA sequences that represent the existing biodiversity. Plecoptera are considered particularly good ecological indicators and one of the most endangered groups of insects, but very limited information on their DNA barcodes is available in public databases. Currently, less than 50% of the Iberian species are represented in BOLD. The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera dataset contains records of 71 specimens of Plecoptera. All specimens have been morphologically identified to species level and belong to 29 species in total. This dataset contributes to the knowledge on the DNA barcodes and distribution of Plecoptera from the Iberian Peninsula and it is one of the IBI database public releases that makes available genetic and distribution data for a series of taxa. The species represented in this dataset correspond to an addition to public databases of 17 species and 21 BINs. Fifty-eight specimens were collected in Portugal and 18 in Spain during the period of 2004 to 2018. All specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources and their DNA barcodes are publicly available in the Barcode of Life Data System (BOLD) online database. The distribution dataset can be freely accessed through the Global Biodiversity Information Facility (GBIF).

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/.

scholarly journals Die Global Biodiversity Information Facility (GBIF) - Struktur, Aufgaben und Ziele.

2005 ◽  
Vol 55 (2) ◽  
pp. 421-431
Author(s):  
Joachim Holstein ◽  
Christoph L. Häuser
Keyword(s):  
International Cooperation ◽  
Global Biodiversity Information Facility ◽  
Collection Data ◽  
Global Biodiversity ◽  
Biodiversity Information

Die Global Biodiversity Information Facility (GBIF) wurde nach über dreijähriger Vorarbeit des Megascience Forum der OECD im Frühjahr 2001 mit dem Ziel gegründet, wissenschaftliche Daten und Informationen zur Biodiversität über des Internet frei verfügbar und zur besseren Nutzung zu verknüpfen. Im Rahmen einer weltweiten Forschungskooperation wird GBIF von derzeit 47 Staaten und 29 internationalen Organisationen als Mitgliedern getragen, die sich alle zur freien Bereitstellung digitaler Biodiversitätsdaten nach gemeinsamen Standards über eigene, dafür selbst einzurichtende Datenknoten verpflichtet haben. Das internationale Vorhaben wird durch einen Aufsichtsrat mit Vertretern aller Mitgliedsstaaten und –organisationen geleitet, dessen Arbeit durch mehrere Komitees und Ausschüsse unterstützt wird. Das seit 2002 in Kopenhagen, Dänemark, angesiedelte GBIF-Sekretariat betreibt den Aufbau des internationalen GBIF Portals (www.gbif.net) und unterstützt koordinierend die Aktivitäten der einzelnen Mitglieder, die sich auf vier Programmbereiche erstrecken: Standardisierung und Verknüpfung von Datenbanken (DADI), Digitalisierung von Daten zu Sammlungsobjekten (DIGIT), Katalog der bekannten Organismennamen (ECAT), sowie Ausbildung und Öffentlichkeitsarbeit (OCB). Für die deutsche Beteiligung an GBIF wurden mit Unterstützung der Bundesregierung (BMBF) sieben Datenknoten an verschiedenen Forschungsinstitutionen aufgebaut, deren Zuständigkeit sich auf unterschiedliche Organismengruppen erstreckt: 1. Insekten (Wirbellose 1) am Staatlichen Museum für Naturkunde Stuttgart; 2. terrestrische Wirbellose (Wirbellose 2) an der Zoologischen Staatssammlung München; 3. marine Wirbellose (Wirbellose 3) am Forschungsinstitut und Naturmuseum Senckenberg in Frankfurt/Main; 4. Wirbeltiere am Zoologischen Forschungsinstitut und Museum Alexander Koenig in Bonn; 5. Pflanzen am Botanischen Garten und Botanischen Museum Berlin; 6. Pilze an der Botanischen Staatssammlung München; 7. Mikroorganismen an der Deutschen Sammlung für Mikroorganismen und Zellkulturen in Braunschweig. Die aufgrund ihrer fachlich unterschiedlichen Ausrichtung innerhalb der einzelnen Knoten zur Erfassung von Sammlungsdaten verwendeten, verschiedenen Datenbankprogramme werden kurz angeführt.StichwörterBiodiversity information, international cooperation, internet, database, collection data, GBIF node.

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.

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