scholarly journals The Living Atlases Community in Action: Sharing Species Pages through the Atlas of Living Costa Rica

2018 ◽  
Vol 2 ◽  
pp. e25990 ◽  
Author(s):  
Manuel Vargas ◽  
María Mora ◽  
William Ulate ◽  
José Cuadra
Keyword(s):  
Costa Rica ◽  
Conservation Status ◽  
Biological Species ◽  
Costa Rican ◽  
Biodiversity Informatics ◽  
Global Biodiversity Information Facility ◽  
Data Portal ◽  
Access To Data ◽  
Biodiversity Information ◽  
Occurrence Records

The Atlas of Living Costa Rica (http://www.crbio.cr/) is a biodiversity data portal, based on the Atlas of Living Australia (ALA), which provides integrated, free, and open access to data and information about Costa Rican biodiversity in order to support science, education, and conservation. It is managed by the Biodiversity Informatics Research Center (CRBio) and the National Biodiversity Institute (INBio). Currently, the Atlas of Living Costa Rica includes nearly 8 million georeferenced species occurrence records, mediated by the Global Biodiversity Information Facility (GBIF), which come from more than 900 databases and have been published by research centers in 36 countries. Half of those records are published by Costa Rican institutions. In addition, CRBio is making a special effort to enrich and share more than 5000 species pages, developed by INBio, about Costa Rican vertebrates, arthropods, molluscs, nematodes, plants and fungi. These pages contain information elements pertaining to, for instance, morphological descriptions, distribution, habitat, conservation status, management, nomenclature and multimedia. This effort is aligned with collaboration established by Costa Rica with other countries such as Spain, Mexico, Colombia and Brazil to standarize this type of information through Plinian Core (https://github.com/PlinianCore), a set of vocabulary terms that can be used to describe different aspects of biological species. The Biodiversity Information Explorer (BIE) is one of the modules made available by ALA which indexes taxonomic and species content and provides a search interface for it. We will present how CRBio is implementing BIE as part of the Atlas of Living Costa Rica in order to share all the information elements contained in the Costa Rican species pages.

scholarly journals The conservation status of Costa Rican velvet worms (Onychophora)

2018 ◽  
Author(s):  
Bernal Morera-Brenes ◽  
Julian Monge-Najera ◽  
Paola Carrera-Mora
Keyword(s):  
Costa Rica ◽  
National Parks ◽  
Video Game ◽  
Conservation Status ◽  
Natural Habitat ◽  
Biological Species ◽  
Costa Rican ◽  
Private Land ◽  
Land Protection ◽  
Velvet Worms

Charismatic species, like the panda, play an important role in conservation, and velvet worms arguably are charismatic worms. Thanks to their extraordinary hunting mechanism, they have inspired from a female metal band in Japan, to origami worms in Russia and video game monsters in the USA. Objective: To assess their conservation status in Costa Rica. Methods: we located all collection records of the 29 known species from the Onychophora Database in the map of the Costa Rican Conservation Network. Results: We found that seven species are protected inside forest reserves, five in Protected Zones, four in Wildlife Refuges, two in National Parks and one, Principapillatus hitoyensis, in a strictly pristine Biological Reserve. The largest species in the world, Peripatus solorzanoi, occurs both inside a Forest Reserve and in protected private land. Protection inside Costa Rican nature areas is enforced year round by personnel that includes armed guards, and is supported by educational programs in surrounding communities. Twelve species have not been found in protected areas, but in Costa Rica, all biological species, named and unnamed, are protected by law and cannot be legally collected, or exported, without technically issued permits. Conclusion: Like in the only other country with similar information (New Zealand), the conservation of onychophorans seems to be of least concern for at least two thirds of the known species. Epiperipatus isthmicola, recently rediscovered after a century of absence in collections, can be considered Threatened because nearly all of its natural habitat has now been covered by a city.

scholarly journals The Living Atlases community in action: the GBIF Benin data portal

2018 ◽  
Vol 2 ◽  
pp. e25488
Author(s):  
Anne-Sophie Archambeau ◽  
Fabien Cavière ◽  
Kourouma Koura ◽  
Marie-Elise Lecoq ◽  
Sophie Pamerlon ◽  
...  
Keyword(s):  
African Country ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
Capacity Enhancement ◽  
Support Programme ◽  
Data Portal ◽  
Global Biodiversity ◽  
The University ◽  
Biodiversity Information ◽  
Occurrence Records

Atlas of Living Australia (ALA) (https://www.ala.org.au/) is the Global Biodiversity Information Facility (GBIF) node of Australia. They developed an open and free platform for sharing and exploring biodiversity data. All the modules are publicly available for reuse and customization on their GitHub account (https://github.com/AtlasOfLivingAustralia). GBIF Benin, hosted at the University of Abomey-Calavi, has published more than 338 000 occurrence records from 87 datasets and 2 checklists. Through the GBIF Capacity Enhancement Support Programme (https://www.gbif.org/programme/82219/capacity-enhancement-support-programme), GBIF Benin, with the help of GBIF France, is in the process of deploying the Beninese data portal using the GBIF France back-end architecture. GBIF Benin is the first African country to implement this module of the ALA infrastructure. In this presentation, we will show you an overview of the registry and the occurrence search engine using the Beninese data portal. We will begin with the administration interface and how to manage metadata, then we will continue with the user interface of the registry and how you can find Beninese occurrences through the hub.

scholarly journals The Conservation Status of Costa Rican Velvet Worms (Onychophora)

2018 ◽  
Author(s):  
Bernal Morera ◽  
Julian Monge-Najera ◽  
Paola Carrera Mora
Keyword(s):  
Costa Rica ◽  
National Parks ◽  
Video Game ◽  
Conservation Status ◽  
Natural Habitat ◽  
Biological Species ◽  
Costa Rican ◽  
Private Land ◽  
Land Protection ◽  
Velvet Worms

ABSTRACT: Charismatic species, like the panda, play an important role in conservation, and velvet worms arguably are charismatic worms. Thanks to their extraordinary hunting mechanism, they have inspired from a female metal band in Japan, to origami worms in Russia and video game monsters in the USA. Objective: To assess their conservation status in Costa Rica. Methods: we located all collection records of the 29 known species from the Onychophora Database in the map of the Costa Rican Conservation Network. Results: We found that seven species are protected inside forest reserves, five in Protected Zones, four in Wildlife Refuges, two in National Parks and one, Principapillatus hitoyensis, in a strictly pristine Biological Reserve. The largest species in the world, Peripatus solorzanoi, occurs both inside a Forest Reserve and in protected private land. Protection inside Costa Rican nature areas is enforced year round by personnel that includes armed guards, and is supported by educational programs in surrounding communities. Twelve species have not been found in protected areas, but in Costa Rica, all biological species, named and unnamed, are protected by law and cannot be legally collected, or exported, without technically issued permits. Conclusion: Like in the only other country with similar information (New Zealand), the conservation of onychophorans seems to be of least concern for at least two thirds of the known species. Epiperipatus isthmicola, recently rediscovered after a century of absence in collections, can be considered Threatened because nearly all of its natural habitat has now been covered by a city.

scholarly journals Contribution to a reference library of DNA barcodes for Colombian freshwater fishes

2021 ◽  
Author(s):  
Manuela Mejía Estrada ◽  
Luz Fernanda Jiménez-Segura ◽  
Iván Soto Calderón
Keyword(s):  
Dna Sequences ◽  
Freshwater Fishes ◽  
Dna Barcodes ◽  
Reference Library ◽  
Global Biodiversity Information Facility ◽  
The World ◽  
Poecilia Sphenops ◽  
Key Indicators ◽  
Biodiversity Information ◽  
Occurrence Records

The Barcoding was proposed motivated by the mismatch between the low number of taxonomists that contrasts with the large number of species, the method requires the construction of reference collections of DNA sequences that represent existing biodiversity. Freshwater fishes are key indicators for understanding biogeography around the world. Colombia with 1610 species of freshwater fishes is the second richest country in the world in this group. However, genetic information of the species continues to be limited, the contribution to a reference library of DNA barcodes for Colombian freshwater fishes highlights the importance of biological collections and seeks to strengthen inventories and taxonomy of such collections in future studies. This dataset contributes to the knowledge on the DNA barcodes and occurrence records of 96 species of Freshwater fishes from Colombia. The species represented in this dataset correspond to an addition to BOLD public databases of 39 species. Forty-nine specimens were collected in Atrato bassin and 708 in Magdalena-Cauca bassin during the period of 2010 to 2020, two species (Loricariichthys brunneus and Poecilia sphenops) are considered exotic to the Atrato, Cauca and Magdalena basins and four species (Oncorhynchu mykiss, Oreochromis niloticus, Parachromis friedrichsthalii and Xiphophorus helleri) are exotic to Colombian hydrogeographic regions. All specimens are deposited in the CIUA collection at University of Antioquia and 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 Mobilizing Data from Taxonomic Literature for an Iconic Species (Dinosauria, Theropoda, Tyrannosaurus rex)

2019 ◽  
Vol 3 ◽  
Author(s):  
Jeremy Miller ◽  
Yanell Braumuller ◽  
Puneet Kishor ◽  
David Shorthouse ◽  
Mariya Dimitrova ◽  
...  
Keyword(s):  
Global Biodiversity Information Facility ◽  
Museum Exhibits ◽  
The Public ◽  
The Past ◽  
Biodiversity Knowledge ◽  
Informatics Infrastructure ◽  
The Subject ◽  
The Impact ◽  
Biodiversity Information ◽  
Occurrence Records

A vast amount of biodiversity data is reported in the primary taxonomic literature. In the past, we have demonstrated the use of semantic enhancement to extract data from taxonomic literature and make it available to a network of databases (Miller et al. 2015). For technical reasons, semantic enhancement of taxonomic literature is most efficient when customized according to the format of a particular journal. This journal-based approach captures and disseminates data on whatever taxa happen to be published therein. But if we want to extract all treatments on a particular taxon of interest, these are likely to be spread across multiple journals. Fortunately, the GoldenGATE Imagine document editor (Sautter 2019) is flexible enough to parse most taxonomic literature. Tyrannosaurus rex is an iconic dinosaur with broad public appeal, as well as the subject of more than a century of scholarship. The Naturalis Biodiversity Center recently acquired a specimen that has become a major attraction in the public exhibit space. For most species on earth, the primary taxonomic literature contains nearly everything that is known about it. Every described species on earth is the subject of one or more taxonomic treatments. A taxon-based approach to semantic enhancement can mobilize all this knowledge using the network of databases and resources that comprise the modern biodiversity informatics infrastructure. When a particular species is of special interest, a taxon-based approach to semantic enhancement can be a powerful tool for scholarship and communication. In light of this, we resolved to semantically enhance all taxonomic treatments on T. rex. Our objective was to make these treatments and associated data available for the broad range of stakeholders who might have an interest in this animal, including professional paleontologists, the curious public, and museum exhibits and public communications personnel. Among the routine parsing and data sharing activities in the Plazi workflow (Agosti and Egloff 2009), taxonomic treatments, as well as cited figures, are deposited in the Biodiversity Literature Repository (BLR), and occurrence records are shared with the Global Biodiversity Information Facility (GBIF). Treatment citations were enhanced with hyperlinks to the cited treatment on TreatmentBank, and specimen citations were linked to their entries on public facing collections databases. We used the OpenBiodiv biodiversity knowledge graph (Senderov et al. 2017) to discover other taxa mentioned together with T. rex, and to create a timeline of T. rex research to evaluate the impact of individual researchers and specimen repositories to T. rex research. We contributed treatment links to WikiData, and queried WikiData to discover identifiers to different platforms holding data about T. rex. We used bloodhound-tracker.net to disambiguate human agents, like collectors, identifiers, and authors. We evaluate the adequacy of the fields currently available to extract data from taxonomic treatments, and make recommendations for future standards.

scholarly journals An audit of some processing effects in aggregated occurrence records

ZooKeys ◽  
2018 ◽  
Vol 751 ◽  
pp. 129-146 ◽  
Author(s):  
Robert Mesibov
Keyword(s):  
Data Loss ◽  
Global Biodiversity Information Facility ◽  
Australian Museum ◽  
Darwin Core ◽  
Species Groups ◽  
Processing Effects ◽  
Global Biodiversity ◽  
Name Changes ◽  
Biodiversity Information ◽  
Occurrence Records

A total of ca 800,000 occurrence records from the Australian Museum (AM), Museums Victoria (MV) and the New Zealand Arthropod Collection (NZAC) were audited for changes in selected Darwin Core fields after processing by the Atlas of Living Australia (ALA; for AM and MV records) and the Global Biodiversity Information Facility (GBIF; for AM, MV and NZAC records). Formal taxon names in the genus- and species-groups were changed in 13–21% of AM and MV records, depending on dataset and aggregator. There was little agreement between the two aggregators on processed names, with names changed in two to three times as many records by one aggregator alone compared to records with names changed by both aggregators. The type status of specimen records did not change with name changes, resulting in confusion as to the name with which a type was associated. Data losses of up to 100% were found after processing in some fields, apparently due to programming errors. The taxonomic usefulness of occurrence records could be improved if aggregators included both original and the processed taxonomic data items for each record. It is recommended that end-users check original and processed records for data loss and name replacements after processing by aggregators.

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 Implementing GBIF Pipelines in the Atlas of Living Australia: The first step towards alignment and further collaboration

2021 ◽  
Vol 5 ◽  
Author(s):  
Javier Molina ◽  
Peggy Newman ◽  
David Martin ◽  
Vicente Ruiz Jurado
Keyword(s):  
Management Systems ◽  
Records Management ◽  
Global Biodiversity Information Facility ◽  
Operation Costs ◽  
Operational Costs ◽  
Development Teams ◽  
Infrastructure Project ◽  
Data Ingestion ◽  
Biodiversity Information ◽  
Occurrence Records

The Global Biodiversity Information Facility (GBIF) and the Atlas of Living Australia (ALA) are two leading infrastructures serving the biodiversity community. In 2020, the ALA’s occurrence records management systems reached end of life after more than 10 years of operation, and the ALA embarked on a project to replace them. Significant overlap exists in the function of the ALA and GBIF data ingestion pipeline systems. Instead of the ALA developing new systems from scratch, we initiated a project to better align the two infrastructures. The collaboration brings benefits such as the improved reuse of modules and an overall reduction in development and operation costs. The ALA recently replaced its occurrence ingestion system with GBIF pipelines infrastructure and shared code. This is the first milestone of the broader ALA’s Core Infrastructure Project and some of the benefits from it are a more reliable, performant and scalable system, proven by the ability to ingest more and larger datasets while at the same time reducing infrastructure operational costs by more than 40% compared to the previous system. The new system is a key building block for an improved ingestion framework that is being developed within the ALA. The collaboration between the ALA and GBIF development teams will result in more consistent outputs from their respective processing pipelines. It will also allow the broader collective expertise of both infrastructure communities to inform future development and direction. The ALA’s adoption of GBIF pipelines will pave the way for the Living Atlases community to adopt GBIF systems and also contribute to them. In this talk we will introduce the project, share insights on how both the teams from the GBIF and the ALA worked together and finally we will delve into details about the technical implementation and benefits.

scholarly journals Towards a Post-Graduate Level Curriculum for Biodiversity Informatics. Perspectives from the Global Biodiversity Information Facility (GBIF) Community

2021 ◽  
Vol 9 ◽  
Author(s):  
Fatima Parker-Allie ◽  
Francisco Pando ◽  
Anders Telenius ◽  
Jean Ganglo ◽  
Danny Vélez ◽  
...  
Keyword(s):  
Biological Data ◽  
Initial Assessment ◽  
Biodiversity Informatics ◽  
Global Biodiversity Information Facility ◽  
Policy Makers ◽  
Academic Teaching ◽  
E Learning ◽  
Learning Platforms ◽  
Global Biodiversity ◽  
Biodiversity Information

Biodiversity informatics is a new and evolving field, requiring efforts to develop capacity and a curriculum for this field of science. The main objective was to summarise the level of activity and the efforts towards developing biodiversity informatics curricula, for work-based training and/or academic teaching at universities, taking place within the Global Biodiversity Information Facility (GBIF) countries and its associated network. A survey approach was used to identify existing capacities and resources within the network. Most of GBIF Nodes survey respondents (80%) are engaged in onsite training activities, with a focus on work-based professionals, mostly researchers, policy-makers and students. Training topics include data mobilisation, digitisation, management, publishing, analysis and use, to enable the accessibility of analogue and digital biological data that currently reside as scattered datasets. An initial assessment of academic teaching activities highlighted that countries in most regions, to varying degrees, were already engaged in the conceptualisation, development and/or implementation of formal academic programmes in biodiversity informatics, including programmes in Benin, Colombia, Costa Rica, Finland, France, India, Norway, South Africa, Sweden, Taiwan and Togo. Digital e-learning platforms were an important tool to help build capacity in many countries. In terms of the potential in the Nodes network, 60% expressed willingness to be recruited or commissioned for capacity enhancement purposes. Contributions and activities of various country nodes across the network have been highlighted and a working curriculum framework has been defined.

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.

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