scholarly journals GBIF Benin's Data Portal

2018 ◽  
Vol 2 ◽  
pp. e25890
Author(s):  
Marie-Elise Lecoq ◽  
Anne-Sophie Archambeau ◽  
Fabien Cavière ◽  
Kourouma Koura ◽  
Sophie Pamerlon ◽  
...  
Keyword(s):  
Information Technologies ◽  
Geographic Area ◽  
Transfer Of Knowledge ◽  
Global Biodiversity Information Facility ◽  
Capacity Enhancement ◽  
Support Programme ◽  
Data Portal ◽  
The University ◽  
Different Levels ◽  
Biodiversity Information

GBIF Benin, hosted at the University of Abomey-Calavi, has published more than 338,000 occurrence records in 87 datasets and checklists. It has been a Global Biodiversity Information Facility (GBIF) node since 2004 and is a leader in several projects from the Biodiversity Information for Development (BID) programme. GBIF facilitates collaboration between nodes at different levels through its Capacity Enhancement Support Programme (CESP) [https://www.gbif.org/programme/82219/capacity-enhancement-support-programme]. One of the actions included in the CESP guidelines is called ‘Mentoring activities’. Its main goal is the transfer of knowledge between partners such as information, technologies, experience, and best practices. Sharing architecture and development is the key solution to solve some technical challenges or impediments (hosting, staff turnover, etc.) that GBIF nodes could face. The Atlas of Living Australia (ALA) team developed a functionality called ‘data hub’. It gives the possibility to create a standalone website with a dedicated occurrence search engine that seeks among a range of data (e.g. specific genus, geographic area). In 2017, GBIF Benin and GBIF France wanted to strengthen their partnership and started a CESP project. One of the core objectives of this project is the creation of the Atlas of Living Benin using ALA modules. GBIF France developers, with the help of the GBIF Benin team, are in the process of configuring a data hub that will give access to Beninese data only, while at the same time Atlas of Living France will give access to French data only. Both data portals will use the same back end, therefore the same databases. Benin is the first African GBIF node to implement this kind of infrastructure. On this poster, we will present the Atlas of Living Benin specific architecture and how we have managed to distinguish data coming from Benin and coming from France.

scholarly journals Three Portals, One Infrastructure: How to manage information with ALA tools

2019 ◽  
Vol 3 ◽  
Author(s):  
Fabien Cavière ◽  
Anne-Sophie Archambeau ◽  
Raoufou Radji ◽  
Christian Ahadji ◽  
Sophie Pamerlon
Keyword(s):  
Information Technologies ◽  
Its Region ◽  
Geographic Area ◽  
Transfer Of Knowledge ◽  
Global Biodiversity Information Facility ◽  
Support Programme ◽  
Management Procedure ◽  
The Creation ◽  
The University ◽  
Biodiversity Information

GBIF Togo, hosted at the University of Lomé, has published more than 62,200 occurrence records from 37 datasets and checklists. As a node participant of Global Biodiversity Information Facility (GBIF) since 2011, it has participated actively in several projects including the Biodiversity Information for Development (BID) programme. GBIF facilitates collaboration between nodes at different levels through its Capacity Enhancement Support Programme (CESP). One of the actions included in the CESP guidelines is called ‘Mentoring activities’. Its main goal is the transfer of knowledge between partners, such as information, technologies, experience, and best practices. Sharing architecture and development is the key solution to solving some the technical challenges and impediments (e.g. hosting, staff turnover, etc.) that GBIF nodes occasionally face. The Atlas of Living Australia (ALA) team have developed a feature called ‘data hub’, which allows the creation of a standalone website with a dedicated occurrence search engine that supports data discovery (e.g. specific genus, geographic area) published by particular GBIF nodes. In 2017, a CESP project between the GBIF Benin and the GBIF France led to the creation of a new portal: Atlas of Living Beninises. This portal shared the same back-end database as the Atlas of Living France portal, while at the same time, each portal displayed and managed information relevant only to its region. In 2018, another CESP project between GBIF France and GBIF Togo shared the same goal as the previous one: implement a new Atlas of Living Australia portal for Togo. This goal will be fulfilled using a similar implementation as the previous project: a shared back-end and different front-end. Togo will be the second African GBIF node to implement this kind of infrastructure. This poster will highlight the architecture specific to the Atlas of Living Togo, and present the management procedure that distinguishes data coming from the three different countries.

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 Living Atlases community in action: general introduction

2018 ◽  
Vol 2 ◽  
pp. e25487
Author(s):  
Marie-Elise Lecoq ◽  
Anne-Sophie Archambeau ◽  
Fabien Cavière ◽  
David Martin ◽  
Nick dos Remedios
Keyword(s):  
Training Session ◽  
Technical Documentation ◽  
Community Members ◽  
General Introduction ◽  
Global Biodiversity Information Facility ◽  
Capacity Enhancement ◽  
Support Programme ◽  
Work Done ◽  
Biodiversity Information ◽  
New Infrastructure

Atlas of Living Australia (ALA) (https://www.ala.org.au/) is the Global Biodiversity Information Facility (GBIF) node of Australia. In 2010, they launched an open and free platform for sharing and exploring biodiversity data. Thanks to this new infrastructure, they have been able to drastically increase the number of occurrences published through the GBIF.org . In order to help other GBIF nodes or institutions, they made all of their modules publicly available for reuse and customization through GitHub (https://github.com/AtlasOfLivingAustralia). Since 2013, the community created by developers interested by ALA tools, organized, with the help of GBIF, 8 technical workshops around the world. These workshops helped the launch of at least 13 data portals. The last training session, funded through the GBIF Capacity Enhancement Support Programme (https://www.gbif.org/programme/82219/capacity-enhancement-support-programme), was been attended by 23 participants from 19 countries on 6 continents. Moreover, on the new GBIF website, a section has been dedicated to this programme (https://www.gbif.org/programme/82953/living-atlases), the Living Atlases community official website has been launched in 2017 (https://living-atlases.gbif.org) and the technical documentation has been improved and translated in several languages. All of these achievements would not have been possible without a huge effort from the ALA developer community. After a brief introduction of the Living Atlases community, we will present you the work done by ALA to simplify the process of getting a living atlas up and running. We will also show you how ALA developers managed to help the community members to create their own version by performing simple HTML/CSS customizations.

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 Data Location Quality at GBIF

2019 ◽  
Vol 3 ◽  
Author(s):  
John Waller
Keyword(s):  
Data Quality ◽  
Open Data ◽  
R Package ◽  
Large Network ◽  
Global Biodiversity Information Facility ◽  
Quality Issue ◽  
Data Portal ◽  
Quality Issues ◽  
Data Location ◽  
Biodiversity Information

I will cover how the Global Biodiversity Information Facility (GBIF) handles data quality issues, with specific focus on coordinate location issues, such as gridded datasets (Fig. 1) and country centroids. I will highlight the challenges GBIF faces identifying potential data quality problems and what we and others (Zizka et al. 2019) are doing to discover and address them. GBIF is the largest open-data portal of biodiversity data, which is a large network of individual datasets (> 40k) from various sources and publishers. Since these datasets are variable both within themselves and dataset-to-dataset, this creates a challenge for users wanting to use data collected from museums, smartphones, atlases, satellite tracking, DNA sequencing, and various other sources for research or analysis. Data quality at GBIF will always be a moving target (Chapman 2005), and GBIF already handles many obvious errors such as zero/impossible coordinates, empty or invalid data fields, and fuzzy taxon matching. Since GBIF primarily (but not exclusively) serves lat-lon location information, there is an expectation that occurrences fall somewhat close to where the species actually occurs. This is not always the case. Occurrence data can be hundereds of kilometers away from where the species naturally occur, and there can be multiple reasons for why this can happen, which might not be entirely obvious to users. One reasons is that many GBIF datasets are gridded. Gridded datasets are datasets that have low resolution due to equally-spaced sampling. This can be a data quality issue because a user might assume an occurrence record was recorded exactly at its coordinates. Country centroids are another reason why a species occurrence record might be far from where it occurs naturally. GBIF does not yet flag country centroids, which are records where the dataset publishers has entered the lat-long center of a country instead of leaving the field blank. I will discuss the challenges surrounding locating these issues and the current solutions (such as the CoordinateCleaner R package). I will touch on how existing DWCA terms like coordinateUncertaintyInMeters and footprintWKT are being utilized to highlight low coordinate resolution. Finally, I will highlight some other emerging data quality issues and how GBIF is beginning to experiment with dataset-level flagging. Currently we have flagged around 500 datasets as gridded and around 400 datasets as citizen science, but there are many more potential dataset flags.

scholarly journals No one-size-fits-all solution to clean GBIF

2020 ◽  
Author(s):  
Alexander Zizka ◽  
Fernanda Antunes Carvalho ◽  
Alice Calvente ◽  
Mabel Rocio Baez-Lizarazo ◽  
Andressa Cabral ◽  
...  
Keyword(s):  
Urban Areas ◽  
Geographic Area ◽  
Strict Sense ◽  
Global Biodiversity Information Facility ◽  
Marine Animals ◽  
Conservation Assessments ◽  
Richness Patterns ◽  
Taxonomic Groups ◽  
Biodiversity Information ◽  
Occurrence Records

ABSTRACTSpecies occurrence records provide the basis for many biodiversity studies. They derive from georeferenced specimens deposited in natural history collections and visual observations, such as those obtained through various mobile applications. Given the rapid increase in availability of such data, the control of quality and accuracy constitutes a particular concern. Automatic filtering is a scalable and reproducible means to identify potentially problematic records and tailor datasets from public databases such as the Global Biodiversity Information Facility (GBIF; www.gbif.org), for biodiversity analyses. However, it is unclear how much data may be lost by filtering, whether the same filters should be applied across all taxonomic groups, and what the effect of filtering is on common downstream analyses. Here, we evaluate the effect of 13 recently proposed filters on the inference of species richness patterns and automated conservation assessments for 18 Neotropical taxa, including terrestrial and marine animals, fungi, and plants downloaded from GBIF. We find that a total of 44.3% of the records are potentially problematic, with large variation across taxonomic groups (25 - 90%). A small fraction of records was identified as erroneous in the strict sense (4.2%), and a much larger proportion as unfit for most downstream analyses (41.7%). Filters of duplicated information, collection year, and basis of record, as well as coordinates in urban areas, or for terrestrial taxa in the sea or marine taxa on land, have the greatest effect. Automated filtering can help in identifying problematic records, but requires customization of which tests and thresholds should be applied to the taxonomic group and geographic area under focus. Our results stress the importance of thorough recording and exploration of the meta-data associated with species records for biodiversity research.

scholarly journals Revitalization of the University of Iowa's Bird Egg Collection after 100 Years of Dormancy

2018 ◽  
Vol 2 ◽  
pp. e26529
Author(s):  
Cody Crawford ◽  
Cindy Opitz ◽  
Trina Roberts
Keyword(s):  
Undergraduate Students ◽  
Web Application ◽  
Easy Access ◽  
Global Biodiversity Information Facility ◽  
University Of Iowa ◽  
Museum Staff ◽  
Global Biodiversity ◽  
The University ◽  
Private Collections ◽  
Biodiversity Information

The University of Iowa Museum of Natural History's egg collection spans many avian orders, 6 continents, and over 160 years. However, this collection of approximately 17,000 egg specimens has remained disorganized and underutilized for most of its history. Only in 2017 did the museum begin taking significant steps toward organizing the eggs, cataloging them, and making them and their data available for researchers. Like many museum egg collections, ours is composed mostly of donated private collections originally collected, purchased, or traded between 1870 and 1910, and with variable amounts of data associated with individual specimens. Since the time the eggs were collected, most of them have been separated from the cards on which collectors stored their data. Much of the current project revolves around reuniting eggs and data cards. We have scanned over 2,000 egg cards, crowdsourced transcriptions of the handwriting, verified the accuracy of each transcription, and added the scans and transcriptions to our database for easy access by museum staff and volunteers. We are using the egg cards, any data written on the eggs, and many books and websites to match eggs with egg cards and integrate the data into our database. The eggs are then placed in new cabinets and relabelled with newly generated database information. Each egg set will be photographed and georeferenced if possible, using the GEOLocate web application. At the end of this project, these specimen records will be integrated into biodiversity repositories such as GBIF (Global Biodiversity Information Facility), Integrated Digitized Biocollections (iDigBio), and VertNet, so they can be downloaded and used by researchers globally, as our bird, mammal and insect collections already are. Most of the work is carried out by a team of volunteers and interns, usually undergraduate students, without whom this project would not be possible at its current pace.

scholarly journals A reference library for the identification of Canadian invertebrates: 1.5 million DNA barcodes, voucher specimens, and genomic samples

2019 ◽  
Author(s):  
Jeremy R. deWaard ◽  
Sujeevan Ratnasingham ◽  
Evgeny V. Zakharov ◽  
Alex V. Borisenko ◽  
Dirk Steinke ◽  
...  
Keyword(s):  
Land Surface ◽  
Animal Species ◽  
Sequence Data ◽  
Dna Barcodes ◽  
Reference Library ◽  
Global Biodiversity Information Facility ◽  
Dna Sequence Data ◽  
Voucher Specimens ◽  
Data Portal ◽  
Biodiversity Information

AbstractThe reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet’s land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.

scholarly journals Reviving a Dormant Collection: Updating the Invertebrate Zoology Collection at the University of Kansas Biodiversity Institute for Future Use and Accessibility

2018 ◽  
Vol 2 ◽  
pp. e26716
Author(s):  
Vanessa Delnavaz ◽  
Kirsten Jensen ◽  
Kaylee Herzog
Keyword(s):  
The United States ◽  
Future Research ◽  
University Of Kansas ◽  
Global Biodiversity Information Facility ◽  
Label Data ◽  
Research Activities ◽  
The Caribbean ◽  
The University ◽  
Biodiversity Information ◽  
Invertebrate Zoology

The Invertebrate Zoology Collection at the University of Kansas (KU) Biodiversity Institute is one of KU’s smaller collections, with just over 2,000 lots. Its taxonomic strength are hexacorallians (Cnidaria: Anthozoa) from across the globe. Holdings also include earthworms primarily from Southeast Asia and the Caribbean, as well as crayfish and molluscs from the United States, notably from Kansas. The collection has seen little loan activity over the past decade, in part due to the fact that collection records are not digitally available. Moreover, the collection has been virtually untouched for several years as research activities on hexacorallians has ceased following curator retirement. In an initial inventory, physical holdings were checked against original catalog data, while simultaneously re-curating to ensure proper storage containers and maximal levels of either ethanol or formalin. Preliminary comparison of the catalogued data with original and secondary label data housed with the specimens suggest that across these sources, the captured and entered data is somewhat inconsistent and incomplete. In an attempt to remedy such issues, the next phase of the project will involve digitally capturing label data to verify collection information. Once the data has been validated, the working data in spreadsheet format will be imported into Specify, and published to a list of aggregators including Global Biodiversity Information Facility (GBIF), Integrated Digitized Biocollections (iDigBio), Biodiversity Information Serving Our Nation (BISON), and Ocean Biogeographic Information System (OBIS), for visibility and use outside of KU. The hope through such efforts is an accessible and easily searchable collection that is properly preserved for future research.

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.

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