scholarly journals The Antarctic Biodiversity Portal, an Online Ecosystem for Linking, Integrating and Disseminating Antarctic Biodiversity Information

2019 ◽  
Vol 3 ◽  
Author(s):  
Yi-Ming Gan ◽  
Maxime Sweetlove ◽  
Anton Van de Putte
Keyword(s):  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
Antarctic Species ◽  
Reference Guide ◽  
Occurrence Data ◽  
Event Based ◽  
The Antarctic ◽  
Global Initiatives ◽  
Sampling Event ◽  
Biodiversity Information

The Antarctic Biodiversity portal (biodiversity.aq) is a gateway to a wide variety of Antarctic biodiversity information and tools. Launched in 2005 as the Scientific Committee on Antarctic Research (SCAR) - Marine Biodiversity Information Network (SCAR-MarBIN, scarmarbin.be) and the Register of Antarctic Marine Species (RAMS, marinespecies.org/rams/), the system has grown in scope from purely marine to include terrestrial information. Biodiversity.aq is a SCAR product, currently supported by Belspo (Belgian Science Policy) as one of the Belgian contributions to the European Lifewatch-European Research Infrastructure Consortium (Lifewatch-ERIC). The goal of Lifewatch is to provide access to: distributed observatories/sensor networks; interoperable databases, existing (data-)networks, using accepted standards; high performance computing (HPC) and grid power, including the use of the state-of-the-art of cloud and big data paradigm technologies; software and tools for visualization, analysis and modeling. Here we provide an overview of the most recent advances in the biodiversity.aq online ecosystem, a number of use cases as well as an overview of future directions. Some of the most notable components are: The Register of Antarctic Species (RAS, ras.biodiversity.aq) is a component of the Lifewatch Taxonomic Backbone and provides an authoritative and comprehensive list of names of marine and terrestrial species in Antarctica and the Southern Ocean. It serves as a reference guide for users to interpret taxonomic literature, as valid names and other names in use are both provided. Integrated Publishing Toolkit (IPT, ipt.biodiversity.aq) allows disseminating Antarctic biodiversity data into global initiatives such as the Ocean Biogeographic Information System (OBIS, obis.org) as Antarctic node of OBIS (Ant-OBIS, also formerly known as SCAR-MarBIN) and the Global Biodiversity Information Facility (GBIF, gbif.org) as Antarctic Biodiversity Information Facility (AntaBIF). Data that can be made available include metadata, species checklists, species occurrence data and more recently, sampling event-based data. Data from these international portals can be accessed through data.biodiversity.aq. The Register of Antarctic Species (RAS, ras.biodiversity.aq) is a component of the Lifewatch Taxonomic Backbone and provides an authoritative and comprehensive list of names of marine and terrestrial species in Antarctica and the Southern Ocean. It serves as a reference guide for users to interpret taxonomic literature, as valid names and other names in use are both provided. Integrated Publishing Toolkit (IPT, ipt.biodiversity.aq) allows disseminating Antarctic biodiversity data into global initiatives such as the Ocean Biogeographic Information System (OBIS, obis.org) as Antarctic node of OBIS (Ant-OBIS, also formerly known as SCAR-MarBIN) and the Global Biodiversity Information Facility (GBIF, gbif.org) as Antarctic Biodiversity Information Facility (AntaBIF). Data that can be made available include metadata, species checklists, species occurrence data and more recently, sampling event-based data. Data from these international portals can be accessed through data.biodiversity.aq. Through SCAR, Biodiversity.aq builds on an international network of expert that provide expert knowledge on taxonomy, species distribution,and ecology. It provides a strong and tested platform for sharing, integrating, discovering and analysing Antarctic biodiversity information originating from a variety of sources into a distributed system.

scholarly journals The Antarctic Biodiversity Portal, an Online Ecosystem for Linking, Integrating and Disseminating Antarctic Biodiversity Information

2019 ◽  
Vol 3 ◽  
Author(s):  
Yi-Ming Gan ◽  
Maxime Sweetlove ◽  
Anton Van de Putte
Keyword(s):  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
Antarctic Species ◽  
Reference Guide ◽  
Occurrence Data ◽  
Event Based ◽  
The Antarctic ◽  
Global Initiatives ◽  
Sampling Event ◽  
Biodiversity Information

The Antarctic Biodiversity portal (biodiversity.aq) is a gateway to a wide variety of Antarctic biodiversity information and tools. Launched in 2015 as the Scientific Committee on Antarctic Research (SCAR) - Marine Biodiversity Information Network (SCAR-MarBIN, scarmarbin.be) and the Register of Antarctic Marine Species (RAMS, marinespecies.org/rams/), the system has grown in scope from purely marine to include terrestrial information. Biodiversity.aq is a SCAR product, currently supported by Belspo (Belgian Science Policy) as one of the Belgian contributions to the European Lifewatch-European Research Infrastructure Consortium (Lifewatch-ERIC). The goal of Lifewatch is to provide access to: distributed observatories/sensor networks; interoperable databases, existing (data-)networks, using accepted standards; high performance computing (HPC) and grid power, including the use of the state-of-the-art of cloud and big data paradigm technologies; software and tools for visualization, analysis and modeling. Here we provide an overview of the most recent advances in the biodiversity.aq online ecosystem, a number of use cases as well as an overview of future directions. Some of the most notable components are: The Register of Antarctic Species (RAS, ras.biodiversity.aq) is a component of the Lifewatch Taxonomic Backbone and provides an authoritative and comprehensive list of names of marine and terrestrial species in Antarctica and the Southern Ocean. It serves as a reference guide for users to interpret taxonomic literature, as valid names and other names in use are both provided. Integrated Publishing Toolkit (IPT, ipt.biodiversity.aq) allows disseminating Antarctic biodiversity data into global initiatives such as the Ocean Biogeographic Information System (OBIS, obis.org) as Antarctic node of OBIS (Ant-OBIS, also formerly known as SCAR-MarBIN) and the Global Biodiversity Information Facility (GBIF, gbif.org) as Antarctic Biodiversity Information Facility (AntaBIF). Data that can be made available include metadata, species checklists, species occurrence data and more recently, sampling event-based data. Data from these international portals can be accessed through data.biodiversity.aq. The Register of Antarctic Species (RAS, ras.biodiversity.aq) is a component of the Lifewatch Taxonomic Backbone and provides an authoritative and comprehensive list of names of marine and terrestrial species in Antarctica and the Southern Ocean. It serves as a reference guide for users to interpret taxonomic literature, as valid names and other names in use are both provided. Integrated Publishing Toolkit (IPT, ipt.biodiversity.aq) allows disseminating Antarctic biodiversity data into global initiatives such as the Ocean Biogeographic Information System (OBIS, obis.org) as Antarctic node of OBIS (Ant-OBIS, also formerly known as SCAR-MarBIN) and the Global Biodiversity Information Facility (GBIF, gbif.org) as Antarctic Biodiversity Information Facility (AntaBIF). Data that can be made available include metadata, species checklists, species occurrence data and more recently, sampling event-based data. Data from these international portals can be accessed through data.biodiversity.aq. Through SCAR, Biodiversity.aq builds on an international network of expert that provide expert knowledge on taxonomy, species distribution,and ecology. It provides a strong and tested platform for sharing, integrating, discovering and analysing Antarctic biodiversity information originating from a variety of sources into a distributed system.

scholarly journals SpOccSum: An easy-to-use Python tool to summarize species occurrence data from material examined lists in taxonomic revisions

2019 ◽  
Vol 3 ◽  
Author(s):  
Michael Trizna ◽  
Torsten Dikow
Keyword(s):  
Data Science ◽  
Biodiversity Data ◽  
Species Occurrence ◽  
Global Biodiversity Information Facility ◽  
Seasonal Incidence ◽  
Distribution Maps ◽  
Occurrence Data ◽  
Darwin Core ◽  
Biodiversity Information ◽  
Northern And Southern Hemispheres

Taxonomic revisions contain crucial biodiversity data in the material examined sections for each species. In entomology, material examined lists minimally include the collecting locality, date of collection, and the number of specimens of each collection event. Insect species might be represented in taxonomic revisions by only a single specimen or hundreds to thousands of specimens. Furthermore, revisions of insect genera might treat small genera with few species or include tens to hundreds of species. Summarizing data from such large and complex material examined lists and revisions is cumbersome, time-consuming, and prone to errors. However, providing data on the seasonal incidence, abundance, and collecting period of species is an important way to mobilize primary biodiversity data to understand a species’s occurrence or rarity. Here, we present SpOccSum (Species Occurrence Summary)—a tool to easily obtain metrics of seasonal incidence from specimen occurrence data in taxonomic revisions. SpOccSum is written in Python (Python Software Foundation 2019) and accessible through the Anaconda Python/R Data Science Platform as a Jupyter Notebook (Kluyver et al. 2016). The tool takes a simple list of specimen data containing species name, locality, date of collection (preferably separated by day, month, and year), and number of specimens in CSV format and generates a series of tables and graphs summarizing: number of specimens per species, number of specimens collected per month, number of unique collection events, as well as earliest, and most recent collecting year of each species. number of specimens per species, number of specimens collected per month, number of unique collection events, as well as earliest, and most recent collecting year of each species. The results can be exported as graphics or as csv-formatted tables and can easily be included in manuscripts for publication. An example of an early version of the summary produced by SpOccSum can be viewed in Tables 1, 2 from Markee and Dikow (2018). To accommodate seasonality in the Northern and Southern Hemispheres, users can choose to start the data display with either January or July. When geographic coordinates are available and species have widespread distributions spanning, for example, the equator, the user can itemize particular regions such as North of Tropic of Cancer (23.5˚N), Tropic of Cancer to the Equator, Equator to Tropic of Capricorn, and South of Tropic of Capricorn (23.5˚S). Other features currently in development include the ability to produce distribution maps from the provided data (when geographic coordinates are included) and the option to export specimen occurrence data as a Darwin-Core Archive ready for upload to the Global Biodiversity Information Facility (GBIF).

scholarly journals DiSSCo, iDigBio and the Future of Global Collaboration

2019 ◽  
Vol 3 ◽  
Author(s):  
Gil Nelson ◽  
Deborah L Paul
Keyword(s):  
Working Group ◽  
Application Programming Interface ◽  
The United States ◽  
Common Source ◽  
Data Generation ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
Data Accessibility ◽  
The Us ◽  
Biodiversity Information

Integrated Digitized Biocollections (iDigBio) is the United States’ (US) national resource and coordinating center for biodiversity specimen digitization and mobilization. It was established in 2011 through the US National Science Foundation’s (NSF) Advancing Digitization of Biodiversity Collections (ADBC) program, an initiative that grew from a working group of museum-based and other biocollections professionals working in concert with NSF to make collections' specimen data accessible for science, education, and public consumption. The working group, Network Integrated Biocollections Alliance (NIBA), released two reports (Beach et al. 2010, American Institute of Biological Sciences 2013) that provided the foundation for iDigBio and ADBC. iDigBio is restricted in focus to the ingestion of data generated by public, non-federal museum and academic collections. Its focus is on specimen-based (as opposed to observational) occurrence records. iDigBio currently serves about 118 million transcribed specimen-based records and 29 million specimen-based media records from approximately 1600 datasets. These digital objects have been contributed by about 700 collections representing nearly 400 institutions and is the most comprehensive biodiversity data aggregator in the US. Currently, iDigBio, DiSSCo (Distributed System of Scientific Collections), GBIF (Global Biodiversity Information Facility), and the Atlas of Living Australia (ALA) are collaborating on a global framework to harmonize technologies towards standardizing and synchronizing ingestion strategies, data models and standards, cyberinfrastructure, APIs (application programming interface), specimen record identifiers, etc. in service to a developing consolidated global data product that can provide a common source for the world’s digital biodiversity data. The collaboration strives to harness and combine the unique strengths of its partners in ways that ensure the individual needs of each partner’s constituencies are met, design pathways for accommodating existing and emerging aggregators, simultaneously strengthen and enhance access to the world’s biodiversity data, and underscore the scope and importance of worldwide biodiversity informatics activities. Collaborators will share technology strategies and outputs, align conceptual understandings, and establish and draw from an international knowledge base. These collaborators, along with Biodiversity Information Standards (TDWG), will join iDigBio and the Smithsonian National Museum of Natural History as they host Biodiversity 2020 in Washington, DC. Biodiversity 2020 will combine an international celebration of the worldwide progress made in biodiversity data accessibility in the 21st century with a biodiversity data conference that extends the life of Biodiversity Next. It will provide a venue for the GBIF governing board meeting, TDWG annual meeting, and the annual iDigBio Summit as well as three days of plenary and concurrent sessions focused on the present and future of biodiversity data generation, mobilization, and use.

scholarly journals Completeness of Digital Accessible Knowledge of the Plants of Ghana

2016 ◽  
Vol 11 ◽  
Author(s):  
Alex Asase ◽  
A. Townsend Peterson
Keyword(s):  
Geographic Distance ◽  
Northern Ghana ◽  
Biodiversity Informatics ◽  
Primary Research ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
Herbarium Data ◽  
Research Grade ◽  
Biodiversity Information

Providing comprehensive, informative, primary, research-grade biodiversity information represents an important focus of biodiversity informatics initiatives. Recent efforts within Ghana have digitized >90% of primary biodiversity data records associated with specimen sheets in Ghanaian herbaria; additional herbarium data are available from other institutions via biodiversity informatics initiatives such as the Global Biodiversity Information Facility. However, data on the plants of Ghana have not as yet been integrated and assessed to establish how complete site inventories are, so that appropriate levels of confidence can be applied. In this study, we assessed inventory completeness and identified gaps in current Digital Accessible Knowledge (DAK) of the plants of Ghana, to prioritize areas for future surveys and inventories. We evaluated the completeness of inventories at ½° spatial resolution using statistics that summarize inventory completeness, and characterized gaps in coverage in terms of geographic distance and climatic difference from well-documented sites across the country. The southwestern and southeastern parts of the country held many well-known grid cells; the largest spatial gaps were found in central and northern parts of the country. Climatic difference showed contrasting patterns, with a dramatic gap in coverage in central-northern Ghana. This study provides a detailed case study of how to prioritize for new botanical surveys and inventories based on existing DAK.

scholarly journals R Python, and Ruby clients for GBIF species occurrence data

2017 ◽  
Author(s):  
Scott A Chamberlain ◽  
Carl Boettiger
Keyword(s):  
Programming Languages ◽  
Significant Contribution ◽  
Species Occurrence ◽  
Global Biodiversity Information Facility ◽  
Occurrence Data ◽  
Research Questions ◽  
Global Biodiversity ◽  
Number Of Individuals ◽  
Biodiversity Information ◽  
Programmatic Access

Background. The number of individuals of each species in a given location forms the basis for many sub-fields of ecology and evolution. Data on individuals, including which species, and where they're found can be used for a large number of research questions. Global Biodiversity Information Facility (hereafter, GBIF) is the largest of these. Programmatic clients for GBIF would make research dealing with GBIF data much easier and more reproducible. Methods. We have developed clients to access GBIF data for each of the R, Python, and Ruby programming languages: rgbif, pygbif, gbifrb. Results. For all clients we describe their design and utility, and demonstrate some use cases. Discussion. Programmatic access to GBIF will facilitate more open and reproducible science - the three GBIF clients described herein are a significant contribution towards this goal.

scholarly journals What You Probably Didn't Know about Biodiversity Information Serving Our Nation (BISON) 

2019 ◽  
Vol 3 ◽  
Author(s):  
Gerald Guala
Keyword(s):  
The United States ◽  
Species Occurrence ◽  
Global Biodiversity Information Facility ◽  
Exact Role ◽  
Occurrence Data ◽  
The Us ◽  
Significant Augmentation ◽  
The Relationship ◽  
Biodiversity Information

Biodiversity Information Serving Our Nation (BISON - bison.usgs.gov) is the US Node application for the Global Biodiversity Information Facility (GBIF) and the most comprehensive source of species occurrence data for the United States of America. It currently contains more than 460 million records and provides significant augmentation and integration of US occurrence data in terrestrial, marine and freshwater systems. Publicly released in 2013, BISON has generated a large community of stakeholders and they have passed on a lot of questions over the years through email ([email protected]), presentations and other means. In this presentation, some of the most common questions will be addressed in detail. For example: why all BISON data isn't in GBIF; how is BISON different from GBIF; what is the relationship between BISON and other US providers to GBIF; and what is the exact role of the Integrated Taxonomic Information System (ITIS - www.itis.gov) in BISON.

scholarly journals Unlocking the Entomological Collection of the Natural History Museum of Maputo, Mozambique

2021 ◽  
Vol 9 ◽  
Author(s):  
Domingos Sandramo ◽  
Enrico Nicosia ◽  
Silvio Cianciullo ◽  
Bernardo Muatinte ◽  
Almeida Guissamulo
Keyword(s):  
Natural History ◽  
Crucial Role ◽  
Development Programme ◽  
Natural History Museum ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
History Museum ◽  
Data Portal ◽  
Global Biodiversity ◽  
Biodiversity Information

The collections of the Natural History Museum of Maputo have a crucial role in the safeguarding of Mozambique's biodiversity, representing an important repository of data and materials regarding the natural heritage of the country. In this paper, a dataset is described, based on the Museum’s Entomological Collection recording 409 species belonging to seven orders and 48 families. Each specimen’s available data, such as geographical coordinates and taxonomic information, have been digitised to build the dataset. The specimens included in the dataset were obtained between 1914–2018 by collectors and researchers from the Natural History Museum of Maputo (once known as “Museu Alváro de Castro”) in all the country’s provinces, with the exception of Cabo Delgado Province. This paper adds data to the Biodiversity Network of Mozambique and the Global Biodiversity Information Facility, within the objectives of the SECOSUD II Project and the Biodiversity Information for Development Programme. The aforementioned insect dataset is available on the GBIF Engine data portal (https://doi.org/10.15468/j8ikhb). Data were also shared on the Mozambican national portal of biodiversity data BioNoMo (https://bionomo.openscidata.org), developed by SECOSUD II Project.

scholarly journals Harvestmen occurrence database (Arachnida, Opiliones) of the Museu Paraense Emílio Goeldi, Brazil

2019 ◽  
Vol 7 ◽  
Author(s):  
Valéria da Silva ◽  
Manoel Aguiar-Neto ◽  
Dan Teixeira ◽  
Cleverson Santos ◽  
Marcos de Sousa ◽  
...  
Keyword(s):  
Public Consultation ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
The Third ◽  
The World ◽  
Northern Brazil ◽  
Global Biodiversity ◽  
The Government ◽  
Biodiversity Information ◽  
Brazilian Biodiversity

We present a dataset with information from the Opiliones collection of the Museu Paraense Emílio Goeldi, Northern Brazil. This collection currently has 6,400 specimens distributed in 13 families, 30 genera and 32 species and holotypes of four species: Imeri ajuba Coronato-Ribeiro, Pinto-da-Rocha & Rheims, 2013, Phareicranaus patauateua Pinto-da-Rocha & Bonaldo, 2011, Protimesius trocaraincola Pinto-da-Rocha, 1997 and Sickesia tremembe Pinto-da-Rocha & Carvalho, 2009. The material of the collection is exclusive from Brazil, mostly from the Amazon Region. The dataset is now available for public consultation on the Sistema de Informação sobre a Biodiversidade Brasileira (SiBBr) (https://ipt.sibbr.gov.br/goeldi/resource?r=museuparaenseemiliogoeldi-collection-aracnologiaopiliones). SiBBr is the Brazilian Biodiversity Information System, an initiative of the government and the Brazilian node of the Global Biodiversity Information Facility (GBIF), which aims to consolidate and make primary biodiversity data available on a platform (Dias et al. 2017). Harvestmen or Opiliones constitute the third largest arachnid order, with approximately 6,500 described species. Brazil is the holder of the greatest diversity in the world, with more than 1,000 described species, 95% (960 species) of which are endemic to the country. Of these, 32 species were identified and deposited in the collection of the Museu Paraense Emílio Goeldi.

scholarly journals Integrating ABCD and DarwinCore: Toward a better foundation for biodiversity information standards

2019 ◽  
Vol 3 ◽  
Author(s):  
Stanley Blum ◽  
Katharine Barker ◽  
Steven J Baskauf ◽  
Walter G. Berendsohn ◽  
Pier Luigi Buttigieg ◽  
...  
Keyword(s):  
Conceptual Modeling ◽  
Data Representation ◽  
Scientific Data ◽  
Formal Ontology ◽  
Basic Formal Ontology ◽  
Global Biodiversity Information Facility ◽  
Ontology Language ◽  
Occurrence Data ◽  
Knowledge Organization System ◽  
Biodiversity Information

For the last 15 years, Biodiversity Information Standards (TDWG) has recognized two competing standards for organism occurrence data, ABCD (Access to Biological Collections Data; Holetschek et al. 2012) and DarwinCore (Wieczorek et al. 2012). These two representations emerged from contrasting strategies for mobilizing information about organism occurrences (also commonly called species occurrence data). ABCD was capable of representing details of more kinds of information, but was necessarily more complicated. DarwinCore, on the other hand, was simpler but more limited in its ability to represent data of different kinds and formats. TDWG endorsed both standards because the different projects and communities that generated them remained dedicated to their different strategies and tool sets, and the Global Biodiversity Information Facility (GBIF) developed the ability to integrate data published in either standard. Since their inceptions, DarwinCore and ABCD have become more similar. DarwinCore has gotten more complicated through the addition of terms and has begun to assign terms to classes. ABCD is now expressed in RDF (Resource Description Framework), potentially enabling re-use of terms with alternative structures among classes. At the same time, methodologies for conceptual modeling and representing complex scientific data have continued to evolve. In particular, a suite of modeling and data representation methods related to linked data and the semantic web, i.e., RDF, SKOS (Simple Knowledge Organization System), and OWL (web Ontology Language), promise to make it easier for us to reconcile shared concepts among different representations or schemas. A mapping between ABCD 2.1 and DarwinCore has existed since before 2005.*1 ABCD 3.0 and DarwinCore are both now represented in RDF. In addition, the BioCollections Ontology (BCO) covers many of the shared concepts and is derived from the Basic Formal Ontology (BFO), an upper level ontology that has oriented many other biomedical ontologies. Reconciling ABCD and DarwinCore through alignment with BCO (in the OBO Foundry; Smith et al. 2007) would better connect TDWG standards to other domains in biology. We appreciate that many working scientists and data managers perceive ontologies as overly complicated. To mitigate the steep learning curve associated with ontologies, we expect to create simpler application profiles or schemas to guide and serve narrower communities of practice within the wider biodiversity domain. We also plan to integrate the current work of the Taxonomic Names and Concepts Interest Group and thereby eliminate the redundancy between DarwinCore and Taxonomic Concepts Transfer Schema (TCS; Kennedy et al. 2006). At the time of this writing, we have only agreements from the authors (i.e., conveners of relevant TDWG Interest Groups and other key stakeholders) to collaborate in pursuit of these common goals. In this presentation we will give a more detailed description of our objectives and products, the methods we are using to achieve them, and our progress to date.

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