Journal articles: 'Occurrence data portal'

1

Gilbert, Edward, Beckett Sterner, Mark Fisher, et al. "Symbiota Integrations: Exploration of Historical and Current Methods of Data Sharing Across a Decentralized Portal Network and Goals of Extending Interoperability Globally." Biodiversity Information Science and Standards 7 (August 28, 2023): e111680. https://doi.org/10.3897/biss.7.111680.

Full text

Abstract:

Over the last decade, the Symbiota open-source software has been readily available to establish occurrence-based data portals that represent the taxonomic and geographic expertise of a specific community of researchers. Reasons for establishing a data portal vary, but often focus on:data mobilization via the creation of public data access points (e.g., in-house search and export tools, Application Programming Interface (API) access, publication tools pushing data up to aggregators);tools and workflows that support active specimen digitization projectsa method for staging and preparing datasets for analysis to answer specific research questions (e.g., data assessment, correction, augmentation).The software functions as a Content Management System (CMS) allowing any dataset to be collaboratively augmented, modified, and managed online. Currently, the software provides support for over 1000 collection datasets to manage their specimen data directly within a Symbiota portal as a live managed dataset. Portals often include "snapshot" data imported from externally managed systems, which are updated on a regular schedule. Depending on the goals of a project, portals will vary in the composition of live to snapshot collections, though most contain a mixture of both. In this respect, data portals serve as intermediate aggregators, integrating multiple specimen datasets that collectively represent a community-based research perspective.Symbiota portals typically function as mid-level data aggregators that are community driven by a group of researchers with expertise within a specific taxonomic domain. This decentralized approach has been shown to promote the emergence of multiple regionally, taxonomically, or institutionally localized, self-identifying communities of practice. Each community is empowered to control the social and informational design and versioning of their local data infrastructures and signals. The upfront cost of decentralization is more than offset by the long-term benefit of achieving sustained expert engagement, higher-quality data products, and ultimately more societal impact for biodiversity data.In contrast to the vision of pushing data from the source to the global aggregators and ultimately out to the research community, Symbiota records are distributed across a growing array of sub-aggregators. For instance, Arizona State University Vascular Plant Herbarium's specimen data consist of a live managed dataset within SEINet with subsets of their data pushed out to the Portal de Biodiversidad de Guatemala and the Cooperative Taxonomic Resource for American Myrtaceae Symbiota portals as snapshot record sets. Not only does this support research associated with each of the portal communities, it exposes the records to researchers with local and taxonomic expertise to review, correct, and comment on the occurrence data. While the Symbiota portals provide tools for these communities to annotate the distributed snapshot records, the annotations need to be directed back to the source collection. Aside from the technical challenges, there are social negotiations that need to be considered. Collection managers might not want to integrate external edits, or the collection might be understaffed without anyone to approve the information transfer. Issues associated with "round-tripping" back to the source are complicated. Nevertheless, global coordination is feasible through automatable data sharing agreements that enable efficient propagation and translation of biodiversity data across communities.Within this presentation, we will explore ways specimen and annotation data have been shared across the Symbiota portal network, as well as the associated technical and social challenges we have encountered. We will also present recent enhancements in tracking project metadata, data provenance, record annotations, and the establishment of a public API architecture. These developments are leveraged to regulate machine-to-machine annotation propagation to enhance interoperability by providing support for real-time transmission of occurrence annotations across the distributed network of Symbiota portals. By demonstrating methods and challenges associated with data sharing across the Symbiota portal network, we strive to contribute to the global discussion of data sharing, but more importantly, solicit input and direction from the greater community on how we can improve data sharing beyond the Symbiota network.

APA, Harvard, Vancouver, ISO, and other styles

2

Tsiky, Rabetrano. "REBIOMA Data Portal, Tool for Conservation Planning in Madagascar." Biodiversity Information Science and Standards 2 (May 22, 2018): e25864. https://doi.org/10.3897/biss.2.25864.

Full text

Abstract:

Recognizing the abundance and the accumulation of information and data on biodiversity that are still poorly exploited and even unfunded, the REBIOMA project (Madagascar Biodiversity Networking), in collaboration with partners, has developed an online dataportal in order to provide easy access to information and critical data, to support conservation planning and the expansion of scientific and professional activities in Madagascar biodiversity. The mission of the REBIOMA data portal is to serve quality-labeled, up-to-date species occurrence data and environmental niche models for Madagascar's flora and fauna, both marine and terrestrial. REBIOMA is a project of the Wildlife Conservation Society Madagascar and the University of California, Berkeley. REBIOMA serves species occurrence data for marine and terrestrial regions of Madagascar. Following upload, data is automatically validated against a geographic mask and a taxonomic authority. Data providers can decide whether their data will be public, private, or shared only with selected collaborators. Data reviewers can add quality labels to individual records, allowing selection of data for modeling and conservation assessments according to quality. Portal users can query data in numerous ways. One of the key features of the REBIOMA web portal is its support for species distribution models, created from taxonomically valid and quality-reviewed occurrence data. Species distribution models are produced for species for which there are at least eight, reliably reviewed, non-duplicate (per grid cell) records. Maximum Entropy Modeling (MaxEnt for short) is used to produce continuous distribution models from these occurrence records and environmental data for different eras: past (1950), current (2000), and future (2080). The result is generally interpreted as a prediction of habitat suitability. Results for each model are available on the portal and ready for download as ASCII and HTML files. The REBIOMA Data Portal address is http://data.rebioma.net, or visit http://www.rebioma.net for more general information about the entire REBIOMA project.

APA, Harvard, Vancouver, ISO, and other styles

3

Gilbert, Edward, Nico Franz, and Beckett Sterner. "Historical Overview of the Development of the Symbiota Specimen Management Software and Review of the Interoperability Challenges and Opportunities Informing Future Development." Biodiversity Information Science and Standards 4 (September 30, 2020): e59077. https://doi.org/10.3897/biss.4.59077.

Full text

Abstract:

Symbiota (Gries et al. 2014) is an open-source software platform designed to function as a biodiversity Content Management System (CMS) for specimen-based datasets. Primarily in North America though also increasingly on other continents, the Symbiota software platform has risen to prominence in the past ten years as one of the more heavily accessed mid-level aggregation tools for assembling, managing, and distributing datasets associated with biological collections. There are more than 50 public Symbiota portals being managed and promoted by various biodiversity projects and communities. Together, these portals assist in the distribution and mobilization of more than 55 million specimen and 20 million image records associated with hundreds of institutions.The central premise of a standard Symbiota installation is to function as a mini-aggregator capable of integrating multiple occurrence datasets that collectively represent a community-based research data perspective. Datasets are typically limited to geographic and taxonomic scopes that best represent the community of researchers leading the project. Symbiota portals often publish "snapshot records" that originate from external management systems but otherwise align with the portal's community of practice and data focus. Specimen management tools integrated into the Symbiota platform also support the ability to manage occurrence data directly within the portal as "live datasets". The software has become widely adopted as a data management platform. Approximately 550 specimen datasets consisting of more than 14 million specimen records are being directly managed within a portal instance. The appeal of Symbiota as an occurrence management tool is also exemplified by the fact that 18 of the 30 federally funded Thematic Collection Networks (https://www.idigbio.org/content/thematic-collections-networks) have elected to use Symbiota as their central data management system.Symbiota's well-developed data ingestion tools, coupled with the ability to store import profile definitions, allows data snapshots to be partially coordinated with source data managed within a variety of remote systems such as Specify (https://specifysoftware.org), EMu (https://emu.axiell.com), Integrated Publishing Toolkit (IPT, https://gbif.org/ipt) publishers, as well as other Symbiota instances. As with Global Biodiversity Information Facility (GBIF) and Integrated Digitized Biocollections (iDigBio) publishing models, data snapshots are periodically refreshed, based on transfer protocols compliant with Darwin Core (DwC) data exchange standards. The Symbiota data management tools provide the means for the community of experts running the portal to annotate and augment snapshot datasets with the goal of improving the overall fitness-for-use of the aggregated dataset. Even though a data refresh from the source dataset would effectively replace the data improvement with the original flawed data, the system's ability to maintain data versioning of all annotations made within the portal allows data improvements to be reapplied. However, inadequate support for bi-directional data flow between the portal and the source collection effectively isolates the annotations within the portal.On one hand, the mini-aggregator model of Symbiota can be viewed as compounding the further fragmentation of occurrence data. Rather than conforming to the vision of pushing data from the source, to the global aggregators and ultimately the research community, specimen data are being pushed from source collections to a growing array of mini-aggregators. On the other hand, community portals have the ability to incentivize experts and enthusiasts to publish high-quality, "data-intelligent" biodiversity data products with the potential of channeling data improvements back to the source.This presentation will begin with a historical review of the development of the Symbiota model including major shifts in the evolution of the development goals. We will discuss the benefits and shortcomings of the data model and provide a description of schema modifications that are currently in development. We will also discuss the successes and challenges associated with building data commons directly associated with communities of researchers. We will address the software's role in mobilizing occurrence data within North America and the efficacy of adhering to the FAIR use principles of making datasets findable, accessible, interoperable, and reusable (Wilkinson et al. 2016). Finally, we will discuss interoperability developments that we hope will improve the flow of data annotations between decentralized networks of data portals and the original data providers at the source.

APA, Harvard, Vancouver, ISO, and other styles

4

Gouws, Rufus H. "Expanding the data distribution structure." Lexicographica 34, no. 2018 (2019): 225–38. http://dx.doi.org/10.1515/lex-2018-0011.

Full text

Abstract:

AbstractThe transition from printed to online dictionaries demands a re-assessment of and adaptations to dictionary structures. This paper focuses on some aspects of the data distribution structure and the different search positions in dictionaries that can accommodate lexicographic data. It is shown that the traditional search positions should be increased. A dictionary as a whole can be regarded as a search region and a dictionary portal as a search domain. The emergence of dictionary portals compels lexicographers to expand the data distribution structure. The occurrence of dictionaries within a dictionary portal that contains different search regions necessitates the notion of a comprehensive data distribution structure. Further research is needed to investigate the interactive relation between a comprehensive data distribution structure and the access and mediostructure of a dictionary.

APA, Harvard, Vancouver, ISO, and other styles

5

Gouws, Rufus H. "Expanding the data distribution structure." Lexicographica 34, no. 1 (2018): 225–38. http://dx.doi.org/10.1515/lex-2018-340111.

Full text

Abstract:

AbstractThe transition from printed to online dictionaries demands a re-assessment of and adaptations to dictionary structures. This paper focuses on some aspects of the data distribution structure and the different search positions in dictionaries that can accommodate lexicographic data. It is shown that the traditional search positions should be increased. A dictionary as a whole can be regarded as a search region and a dictionary portal as a search domain. The emergence of dictionary portals compels lexicographers to expand the data distribution structure. The occurrence of dictionaries within a dictionary portal that contains different search regions necessitates the notion of a comprehensive data distribution structure. Further research is needed to investigate the interactive relation between a comprehensive data distribution structure and the access and mediostructure of a dictionary.

APA, Harvard, Vancouver, ISO, and other styles

6

Lecoq, Marie-Elise, Anne-Sophie Archambeau, Fabien Cavière, Kourouma Koura, Sophie Pamerlon, and Jean Ganglo. "GBIF Benin's Data Portal." Biodiversity Information Science and Standards 2 (May 22, 2018): e25890. http://dx.doi.org/10.3897/biss.2.25890.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

7

Lecoq, Marie-Elise, Anne-Sophie Archambeau, Fabien Cavière, Kourouma Koura, Sophie Pamerlon, and Jean Ganglo. "GBIF Benin's Data Portal." Biodiversity Information Science and Standards 2 (May 22, 2018): e25890. https://doi.org/10.3897/biss.2.25890.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

8

Tsiky, Rabetrano. "REBIOMA Data Portal, Tool for Conservation Planning in Madagascar." Biodiversity Information Science and Standards 2 (May 22, 2018): e25864. http://dx.doi.org/10.3897/biss.2.25864.

Full text

Abstract:

Recognizing the abundance and the accumulation of information and data on biodiversity that are still poorly exploited and even unfunded, the REBIOMA project (Madagascar Biodiversity Networking), in collaboration with partners, has developed an online dataportal in order to provide easy access to information and critical data, to support conservation planning and the expansion of scientific and professional activities in Madagascar biodiversity. The mission of the REBIOMA data portal is to serve quality-labeled, up-to-date species occurrence data and environmental niche models for Madagascar’s flora and fauna, both marine and terrestrial. REBIOMA is a project of the Wildlife Conservation Society Madagascar and the University of California, Berkeley. REBIOMA serves species occurrence data for marine and terrestrial regions of Madagascar. Following upload, data is automatically validated against a geographic mask and a taxonomic authority. Data providers can decide whether their data will be public, private, or shared only with selected collaborators. Data reviewers can add quality labels to individual records, allowing selection of data for modeling and conservation assessments according to quality. Portal users can query data in numerous ways. One of the key features of the REBIOMA web portal is its support for species distribution models, created from taxonomically valid and quality-reviewed occurrence data. Species distribution models are produced for species for which there are at least eight, reliably reviewed, non-duplicate (per grid cell) records. Maximum Entropy Modeling (MaxEnt for short) is used to produce continuous distribution models from these occurrence records and environmental data for different eras: past (1950), current (2000), and future (2080). The result is generally interpreted as a prediction of habitat suitability. Results for each model are available on the portal and ready for download as ASCII and HTML files. The REBIOMA Data Portal address is http://data.rebioma.net, or visit http://www.rebioma.netfor more general information about the entire REBIOMA project.

APA, Harvard, Vancouver, ISO, and other styles

9

Archambeau, Anne-Sophie, Fabien Cavière, Kourouma Koura, Marie-Elise Lecoq, Sophie Pamerlon, and Jean Ganglo. "The Living Atlases community in action: the GBIF Benin data portal." Biodiversity Information Science and Standards 2 (May 21, 2018): e25488. http://dx.doi.org/10.3897/biss.2.25488.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

10

Archambeau, Anne-Sophie, Fabien Cavière, Kourouma Koura, Marie-Elise Lecoq, Sophie Pamerlon, and Jean Ganglo. "The Living Atlases community in action: the GBIF Benin data portal." Biodiversity Information Science and Standards 2 (May 21, 2018): e25488. https://doi.org/10.3897/biss.2.25488.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

11

Silva, Timóteo Monteiro da, Juliana Corrêa dos Santos, Victor Amazonas Viegas Ferreira, Ramos Lorran Alves da Cruz, Wolmar Benjamin Wosiacki, and Marcos Paulo Alves de Sousa. "Data from the ichthyological collection of the Museu Paraense Emílio Goeldi." ZooKeys 687 (August 2, 2017): 89–99. https://doi.org/10.3897/zookeys.687.11233.

Full text

Abstract:

This dataset contains information on the occurrence of Neotropical fishes (Actinopterygii, Chondrichthyes, Sarcopterygii) collected in South America, mostly from the Brazilian Amazon. The ichthyology collections of the Museu Paraense Emílio Goeldi (MPEG: http://www.museu-goeldi.br/) include specimens collected between 1900 and 2014. The dataset is now available for public consultation on the Global Biodiversity Information Facility portal (http://www.gbif.org/dataset/b0059a3a-5cab-4a08-8d14-d92c23378e43), and through Sistema de Informação sobre a Biodiversidade Brasileira (http://gbif.sibbr.gov.br/explorador/pt/recurso/62).

APA, Harvard, Vancouver, ISO, and other styles

12

Grant, Sharon, Kate Webbink, Janeen Jones, Pete Herbst, Robert Zschernitz, and Rusty Russell. "What's Missing From All the Portals?" Biodiversity Information Science and Standards 1 (August 14, 2017): e20236. https://doi.org/10.3897/tdwgproceedings.1.20236.

Full text

Abstract:

At time of writing there are over 784 million occurrence records in the Global Biodiversity Information Facility (GBIF) portal (gbif.org), 106 million on the iDigBio site (idigbio.org); 68 million in the Atlas of Living Australia (ala.org.au) and 20 million in VertNet (vertnet.org). The list of biodiversity aggregators and portals that boast occurrence counts in the millions continues to increase. Combined with sites who gather data their data from outside of the GBIF domain such as The Paleobiology Database, there is compelling evidence that global digitization is starting to illuminate the black hole of biodiversity data held in collections across the world. The visibility and demands on our collective natural history heritage have never been as high, and they are increasingly in the spotlight with both internal and external audiences. Funding sources have moved away from massive "digitization for the sake of digitization" projects and demand much more focused proposals. To compete in this arena, collections staff and researchers must collaborate and mine collections for their strengths and use those to justify efforts. To do this, however, they must have access to information about the non-digitized occurrence level records in the world's holdings. We discuss the potential use of current TDWG standards to allow the capture of existing institutional data about undigitized collections and also those whose records have been marked as environmentally, culturally, or politically sensitive and so must remain digitally dark, so that portals like GBIF can use them in a comparable way as existing occurrence records. Can Darwin Core (with its extensions) together with the Natural Collections Description (draft standard) be used to describe accessions, inventory-level information, and backlog estimates in an efficient and effective way and provide even greater visibility of those undigitized occurrences? In addition, can these data also serve as a means to further refine existing digitized records?

APA, Harvard, Vancouver, ISO, and other styles

13

Leidenberger, Sonja, Martin Käck, Björn Karlsson, and Oskar Kindvall. "The Analysis Portal and the Swedish LifeWatch e-infrastructure for biodiversity research." Biodiversity Data Journal 4 (March 23, 2016): e7644. https://doi.org/10.3897/BDJ.4.e7644.

Full text

Abstract:

During the last years, more and more online portals were generated and are now available for ecologists to run advanced models with extensive data sets. Some examples are the Biodiversity Virtual e-Laboratory (BioVel) Portal (https://portal.biovel.eu) for ecological niche modelling and the Mobyle SNAP Workbench (https://snap.hpc.ncsu.edu) for evolutionary and population genetics analysis. Such portals have the main goal to facilitate the run of advanced models, through access to large-capacity computers or servers. In this study, we present the Analysis Portal (www.analysisportal.se), which is a part of the Swedish LifeWatch e-infrastructure for biodiversity research that combines a variety of Swedish web services to perform different kinds of dataprocessing. For the first time, the Swedish Analysis Portal for integrated analysis of species occurrence data is described in detail. It was launched in 2013 and today, over 60 Million Swedish species observation records can be assessed, visualized and analyzed via the portal. Datasets can be assembled using sophisticated filtering tools, and combined with environmental and climatic data from a wide range of providers. Different validation tools, for example the official Swedish taxon concept database Dyntaxa, ensure high data quality. Results can be downloaded in different formats as maps, tables, diagrams and reports.

APA, Harvard, Vancouver, ISO, and other styles

14

Ainsa, Alice, Sophie Pamerlon, Anne-Sophie Archambeau, Solène Robert, and Rémi Beauvieux. "OpenObs: Living Atlases platform for French biodiversity data." Biodiversity Information Science and Standards 7 (September 7, 2023): e112179. https://doi.org/10.3897/biss.7.112179.

Full text

Abstract:

The OpenObs project, led by Patrinat, was launched in September 2017, and the first version of this tool was released in October 2020. OpenObs is based on the Atlas of Living Australia platform, supported by the Global Biodiversity Information Facility (GBIF) community, particularly the Living Atlases (LA) collective.OpenObs enables the visualization and downloading of observation data on species available in the National Inventory of Natural Heritage (INPN), the national platform of SINP (Information System for the Inventory of Natural Heritage). It provides open access to non-sensitive public data and includes all available observations, whether they are occurrence or synthesis data.As of July 2023, OpenObs has 134,922,015 observation records, and new data is reguarly added (at least twice a year). Furthermore, the project is constantly evolving with new developments planned, such as a user validation interface and new cartographic tools.We will present the architecture of this LA-based national biodiversity portal (Fig. 1), as well as its planned new functionality and development roadmap.

APA, Harvard, Vancouver, ISO, and other styles

15

Prager, Maria, Daniel Lundin, Fredrik Ronquist, and Anders Andersson. "The ASV portal allows for efficient handling of DNA derived data in the Living Atlas." Biodiversity Information Science and Standards 7 (August 7, 2023): e110488. https://doi.org/10.3897/biss.7.110488.

Full text

Abstract:

The Living Atlas platform functions as the national hub for integration of biodiversity data with environmental and contextual information in many countries, but it has had limited functionality for species occurrence data derived from DNA sequences. Meanwhile, molecular methods for species observation, such as metabarcoding of environmental DNA, are becoming increasingly important for documenting the diversity of life. To incorporate this rapidly growing data source into the platform, we developed the Amplicon Sequence Variant (ASV) portal: a web interface for DNA sequence-derived observations in the Living Atlas.We identified three key features that would enhance the utility of the atlas platform for species occurrence data derived from metabarcoding: 1) storage of the processed barcode sequences (ASVs) underlying such occurrences, along with the ability to locate them using sequence alignment search; 2) the option to search for data based on sequencing details, such as target genes and primers; and 3) the possibility to update the taxonomic annotation of observed ASVs as reference databases evolve.In this presentation, we demonstrate how these features have been implemented in the ASV portal, which now operates as a module within the Swedish Biodiversity Data Infrastructure (SBDI). We provide a brief overview of the underlying architecture and its integration with the Living Atlas and Global Biodiversity Information Facility (GBIF) platforms, showcase the online functionality, and conclude by discussing challenges and future development plans.

APA, Harvard, Vancouver, ISO, and other styles

16

Ko, Jerome Chie-Jen, Huiling Chang, Yihong Chang, et al. "Will a Local Portal using Global Data Encourage the Mainstreaming of Biodiversity Informatics in Asia? In Taiwan, We Say Yes." Biodiversity Information Science and Standards 7 (September 6, 2023): e112176. https://doi.org/10.3897/biss.7.112176.

Full text

Abstract:

Five years ago, the value of biodiversity open data was scarcely recognized in Taiwan. This posed a significant challenge to the Taiwan Biodiversity Infomation Facility (TaiBIF), our national node of the Global Biodiversity Information Facility (GBIF), in its sustained efforts to enhance data publishing capacities. Notably, non-academic entities, both governmental and industrial, were reluctant to invest resources in data management and publication, questioning the benefits beyond purely research-oriented returns.At the time, Taiwan had fewer than a million published records domestically, while GBIF held around 3 million occurrence records for Taiwan, largely unused by local users. We speculated that this discrepancy in data usage stemmed from three factors: (1) lack of species names in the local language within the occurrence data, (2) missing locally important species attributes, such as conservation status and national red list categories, and (3) absence of a culturally relatable local portal promoting biodiversity data usage.To address these issues, we launched the Taiwan Biodiversity Network (TBN) website in 2018, localizing global data from GBIF and integrating missing information from local data sources. Collaborating with wildlife illustrators, we designed a user-friendly data interface to lessen the system's technical or academic barriers. This effort led to a doubling of website visitors and data download requests annually, and in recent years, biodiversity open data has become a vital component in environmental impact assessments. This upward trend heightened the recognition of the value of biodiversity open data, inciting organizations, such as initially data-conservative government agencies and private sectors with no obligatory data-sharing, to invest in data management and mobilization. This advancement also catalyzed the formation of the Taiwan Biodiversity Information Alliance (TBIA), actively promoting cross-organizational collaborations on data integration.Today, Taiwan offers more than 19 million globally accessible occurrence records and data for more than 28,000 species. While the surge in data volume can certainly be credited to the active local citizen science community, we believe the expanded coverage of species and data types is a result of a growing community supportive of biodiversity open data. This was made possible by the establishment of a local portal that effectively bridged the gap between global data and local needs. We hope our experience will motivate other Asian countries to create analogous local portals using global open data sources like GBIF, illustrating the value of biodiversity open data to decision-makers and overcoming resource limitations that impede investments in biodiversity informatics.

APA, Harvard, Vancouver, ISO, and other styles

17

Elliott, Michael, Manuel Luciano, and Jose Fortes. "Integrating Large Language Models and the iDigBio Portal for Conversational Data Exploration and Retrieval." Biodiversity Information Science and Standards 8 (November 26, 2024): e142696. https://doi.org/10.3897/biss.8.142696.

Full text

Abstract:

The advent of cloud-based large language model (LLM) services such as ChatGPT (Generative Pre-Trained Transformer) has given rise to a wide array of novel artificial intelligence (AI) applications. In particular, LLMs have been used to power AI assistants that serve as intermediaries between human users and online web services, namely, web-based application programming interfaces (web APIs). These AI assistants allow users to make requests in natural language to initiate complex processes, ranging from searching a database to making a reservation.We are exploring the development of AI assistants that can intelligently search for and process species occurrence data served by the Integrated Digitized Biocollections (iDigBio) Portal. Though the portal already provides a human-friendly search interface, it is tailored for a very particular use case: finding and inspecting records that match the user's search parameters. However, the underlying iDigBio APIs that power the search interface offer direct access to biodiversity data and metadata that can support a wider range of applications. An LLM-powered AI assistant with access to such APIs has the potential to redefine how researchers discover and interact with scientific data by 1) allowing users to interact with scientific databases using natural language, 2) serving as a single unifying interface for many different use cases, and 3) enhancing the user's experience with AI insights that are backed by citable, curated data.Fig. 1 demonstrates a prototype chatbot we have developed, which interfaces with the iDigBio Portal. The chatbot uses OpenAI's GPT-4 to understand user requests and call the appropriate APIs as needed. It currently has access to the following iDigBio APIs:The Search API allows the chatbot to perform the same search functions as the portal search interface. The results of the search can be observed by either directly calling the API from the user's web browser, opening the existing portal search interface with generated search parameters, or visualizing the geographic distribution of matched records on an interactive map.The Download API allows the chatbot to package search results as a Darwin Core Archive to be delivered by email.The Summary API allows the chatbot to collect statistics across all of iDigBio's data, such as a breakdown of record counts for unique species reported within a particular geographic region.Because the chatbot is intended for use by researchers, transparency is critical. When responding to user requests, LLMs often include their own internalized knowledge—which may be unreliable but difficult to verify—or make up information entirely. Thus, it must be abundantly clear how the chatbot forms its responses, in particular how the LLM interprets user requests and how it queries external APIs, such that users may independently assess the correctness of the chatbot's actions and link its conclusions back to data. The approach we adopted for the design of our prototype is illustrated in Fig. 2; whenever the chatbot initiates a data retrieval or analysis process, a detailed log of that process is embedded in the conversation, including the sequence of actions taken and their inputs and outputs.The chatbot's behavior is tightly controlled by the rigid use of specialized AI agents with expert-defined validators (Fig. 3). Importantly, we do not allow the LLM to respond freely to user requests; rather, we use a fixed set of AI agents that are specialized to produce structured outputs that follow strict schema as enforced by the agent's assigned validator. An orchestrator agent is responsible for deciding which agent is most appropriate to handle each request. If no agent is chosen, the system does not attempt to answer the user's request.As a prototype, the functionality of the chatbot is currently limited to the few illustrative use cases we have outlined. However, as the system is incrementally refined and expanded, we envision the single chatbot interface to be of interest to both the general public and researchers alike. For the general public, it may be a useful tool to learn about biodiversity in their local community and around the world. Meanwhile, researchers may find the chatbot useful for quickly navigating and exploring iDigBio's hosted data and APIs. The prototype is hosted online at chat.acis.ufl.edu with source code in GitHub.

APA, Harvard, Vancouver, ISO, and other styles

18

Novotný, Petr, Stefan Seifert, Martin Rohn, Wolfgang Diewald, Milan Štech, and Dagmar Triebel. "Software infrastructure and data pipelines established for technical interoperability within a cross-border cooperation for the flora of the Bohemian Forest." Biodiversity Data Journal 10 (October 14, 2022): e87254. https://doi.org/10.3897/BDJ.10.e87254.

Full text

Abstract:

The timely and geographical resolutions, as well as the quantity and taxon concepts of records on the occurrence of plants near national borders is often ambiguous. This is due to the regional focus and different approaches of the contributing national and regional databases and networks of the neighbouring countries. Careful data transformation between national data providers is essential for understanding distribution patterns and its dynamics for organisms in areas along the national borders. Sharing occurrence data through the international data aggregator Global Biodiversity Information Facility (GBIF) is also complicated and has to consider that the underlying taxonomic concept and geographic information system of each single GBIF dataset might be different. In addition, some regional data providers have a restrictive (non-cc) licensing policy which does not allow data publication via the GBIF network. Therefore, it is necessary to investigate new ways to make data fit for use for a better and comprehensive understanding of the Flora of the Bohemian Forest.In this paper, we present a bilateral technical interoperability solution for vascular plant occurrence data for the area between the Czech Republic and Bavaria. We describe the initial state of data providers in both countries and the factual and technical challenges in finding a sustainable concept to establish mutual data sharing. The resulting solution for a functional infrastructure and an agreed data pipeline is described in a step-by-step approach. The new distributed infrastructure allows botanists and other stakeholders from both countries to work within the cross-border context of historical and current plants' distribution.

APA, Harvard, Vancouver, ISO, and other styles

19

Schmider-Martínez, Andreas, Claudia Maturana, Yarleth Poveda, et al. "Laevilacunaria (Mollusca, Gastropoda) in the Southern Ocean: A comprehensive occurrence dataset." Biodiversity Data Journal 11 (October 9, 2023): e111982. https://doi.org/10.3897/BDJ.11.e111982.

Full text

Abstract:

The present dataset is a compilation of georeferenced occurrences of the littorinid genus Laevilacunaria Powell, 1951 (Mollusca, Gastropoda) in the Southern Ocean. Occurrence data were obtained from field expeditions (Antarctic and sub-Antarctic sampling) between 2015 and 2022, together with a review of published literature including records from 1887 to 2022. Three Laevilacunaria species have been recorded from the Southern Ocean: Laevilacunaria bennetti, L. antarctica and L. pumilio.The present dataset includes 75 occurrences, representing the most exhaustive database of this Antarctic and sub-Antarctic littorinid genus. The publication of this data paper was funded by the Belgian Science Policy Office (BELSPO, contract n°FR/36/AN1/AntaBIS) in the Framework of EU-Lifewatch as a contribution to the SCAR Antarctic biodiversity portal (biodiversity.aq).

APA, Harvard, Vancouver, ISO, and other styles

20

Onyango, Vonwicks C., Kenneth H. Makokha, Samuel M. Gachie, Boniface Mutiso, Nicholas M. Mutuma, and Paul M. Kamau. "Morbid Obesity Associated with Non-Alcoholic Fatty Liver Disease and Complicated by Severe Non-Cirrhotic Portal Hypertension: A Case Report from Rural Kenya." American Journal of Medical Science and Innovation 2, no. 2 (2023): 57–60. http://dx.doi.org/10.54536/ajmsi.v2i2.1907.

Full text

Abstract:

Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease and is closely linked with obesity and metabolic syndrome. Portal hypertension in NAFLD typically occurs in the cirrhotic phase of the disease and may present with esophageal varices, splenomegaly with splenic sequestration syndrome, ascites, and features of liver failure. However, recent experimental and clinical data show the occurrence of portal hypertension in NAFLD in the absence of fibrosis or cirrhosis. We present such a clinical case from rural Kenya in this study with the literature review that proposes novel mechanisms for such non-cirrhotic portal hypertension in NAFLD.

APA, Harvard, Vancouver, ISO, and other styles

21

Martin-Cabrera, Patricia, Fabien Lombard, Jean-Olivier Irisson, et al. "Coordinating Efforts to Define Marine Plankton Imagery Data and Metadata Best Practices and Standards." Biodiversity Information Science and Standards 4 (September 29, 2020): e58932. https://doi.org/10.3897/biss.4.58932.

Full text

Abstract:

"Imagery data" can be referred as qualitative and quantitative information from a collection of images. Imaging systems are used more and more frequently in the marine domain to generate huge amounts of imagery data. For example, automatic image classification is used to determine the abundance, size and biomass of plankton communities. In addition, the recent advances of imaging sensors and the growing datasets, highlight the importance of the management and storage capacity of these data. Thus, establishing data standards, optimized data flows and quality control procedures will promote the ability to make these datasets findable, accessible, interoperable and reusable (FAIR principles).At the moment, there are a number of online open-access databases that collect marine biodiversity data, such as the Ocean Biodiversity Information System (OBIS), and more specialized in plankton observations such as the COPEPOD for plankton biomass and ECOTAXA for taxonomic annotation of plankton images. However, they currently lack relevant standards to link metadata of the images.International biodiversity data standards, such as Darwin Core (DwC), are already widely used in OBIS and the Global Biodiversity Information Facility (GBIF). OBIS, has recently adopted the OBIS-ENV-DATA, a format that follows the DwC-Archive (DwC-A) standard, consisting of a DwC Event table in combination with an Occurrence an extended Measurement or Fact table. This structure enables the linkage of quantitative and qualitative properties to both sampling events and species occurrences. It also includes additional fields for property standardization, such as the BODC (British Oceanographic Data Centre) controlled vocabularies, the World Register of Marine Species (WoRMS), which provides crucial quality control support for taxonomic data, and Marine Regions, a database that provides standardized marine georeferenced place names and areas. However, there are no clear guidelines on how to include imagery metadata and derived data in OBIS-ENV-DATA.During this TDWG 2020 symposium, we would like to present and discuss our ongoing work to establish best practices and standardized protocols for imaging data and metadata acquired by a large spectrum of bio-optic sensors. Furthermore, we highlight how the integration of the metadata will flow to existing biodiversity data portals, the European EMODnet Biology portal, (EurOBIS) and OBIS.

APA, Harvard, Vancouver, ISO, and other styles

22

Ivanova, Natalya V., and Maxim P. Shashkov. "Biodiversity databases in Russia: towards a national portal." Arctic Science 3, no. 3 (2017): 560–76. http://dx.doi.org/10.1139/as-2016-0050.

Full text

Abstract:

Russia holds massive biodiversity data accumulated in botanical and zoological collections, literature publications, annual reports of natural reserves, nature conservation, and monitoring study project reports. While some data have been digitized and organized in databases or spreadsheets, most of the biodiversity data in Russia remain dormant and digitally inaccessible. Concepts of open access to research data is spreading, and the lack of data publishing tradition and of use of data standards remain prominent. A national biodiversity information system is lacking and most of the biodiversity data are not available or the available data are not consolidated. As a result, Russian biodiversity data remain fragmented and inaccessible for researchers. The majority of Russian biodiversity databases do not have web interfaces and are accessible only to a limited numbers of researchers. The main reason for lack of access to these resources relates to the fact that the databases have previously been developed only as a local resource. In addition, many sources have previously been developed in the desktop database environments mainly using MS Access and, in some cases, earlier DBMS for DOS, i.e., file-server system, which does not have the functionality to create access to records through a web interface. Among the databases with a web interface, a few information systems have interactive maps with the species occurrence data and systems allowing registered users to upload data. It is important to note that the conceptual structures of these databases were created without taking into account modern standards of the Darwin Core; furthermore, some data sources were developed prior to the first work version of the Darwin Core release in 2001. Despite the complexity and size of the biodiversity data landscape in Russia, the interest in publishing data through international biodiversity portals is increasing among Russian researchers. Since 2014, institutional data publishers in Russia have published about 140 000 species occurrences through gbif.org. The increase in data publishing activity calls for the creation of a GBIF node in Russia, aiming to support Russian biodiversity experts in international data work.

APA, Harvard, Vancouver, ISO, and other styles

23

Khalid, Rabia, Nighat Jamal, Sara Mannan, Ghulam Jaffar, Waheed Ali Mirbahar, and Asmat Ullah Khan. "Frequency and Characteristic of Portal Hypertensive Gastropathy in Liver Cirrhosis Patients." Pakistan Journal of Medical and Health Sciences 16, no. 1 (2022): 687–89. http://dx.doi.org/10.53350/pjmhs22161687.

Full text

Abstract:

Introduction: Portal hypertensive gastropathy is a term applied to the typical appearance of the mucosa of stomach consisting of a mosaic-like diffuse and reticular cobblestone pattern of gastric mucosal layer secondary to increased blood pressure in the portal vein. Objective: To determine the occurrence and characteristic of portal hypertensive gastropathy in patients with liver cirrhosis Methodology: This study was descriptive cross-sectional piloted at the department of Medicine, Hayatabad medical complex Peshawar for duration of six months from November 2020 to May 2021. A total of 158 patients were observed in our study. All the data was entered and analyzed in SPSS version 21. Results: In our study portal Hypertensive Gastropathy was observed in 34(21.5%) cirrhosis patients while it was not observed in 124(78.5%) patients. Based on the class of portal hypertensive gastropathy, severe and mild types were observed in 43(27.2%) and 115(72.8%) patients respectively. Conclusion: In our study portal hypertensive gastropathy was observed in 34(21.5%) cirrhotic patients, amongst these 27.2% were severe and 72.8% were mild types. In cirrhotic and portal hypertensive gastropathy patients, these findings might have major therapeutic implications. Keywords: Frequency; Portal Hypertensive Gastropathy, Liver cirrhosis

APA, Harvard, Vancouver, ISO, and other styles

24

Cavière, Fabien, Anne-Sophie Archambeau, Raoufou Radji, Christian Ahadji, and Sophie Pamerlon. "Three Portals, One Infrastructure: How to manage information with ALA tools." Biodiversity Information Science and Standards 3 (July 17, 2019): e38318. https://doi.org/10.3897/biss.3.38318.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

25

Wang, Xiaojun, Jason Knoft, Darren Ficklin, Nelson Rios, and Henry Bart. "HydroClim Data Portal: Cyberinfrastructure for providing high-resolution GIS modeled streamflow and water temperature data to researchers." Biodiversity Information Science and Standards 5 (September 20, 2021): e75269. https://doi.org/10.3897/biss.5.75269.

Full text

Abstract:

Freshwater ecosystems play a key role in sustaining aquatic biodiversity. However, human alterations to watersheds and climate change are reducing critical habitat and the viability of populations of many aquatic species. The environmental changes have also had significant adverse impacts on water temperatures and streamflow. The changes in temperature and precipitation forecast over the next century are expected to affect the freshwater ecosystems and their biodiversity to an even greater extent than in the past. The aims of the HydroClim project are to provide openly accessible data on two key measures of stream conditions in the United States (US) and Canada for use in research, to increase public understanding of issues involving water resources, and to provide training opportunities for scientists who will be responsible for the conservation of freshwater biodiversity in the future.The project has used contemporary air temperature and precipitation data and future climate data from multiple Global Climate Model scenarios to generated high-resolution, spatially explicit, monthly streamflow and water temperature data for all watersheds across the US and Canada from 1950–2099 through multiple Soil and Water Assessment Tool (SWAT) hydrologic models. This presentation describes a cyberinfrastructure we developed for hosting the HydroClim data, consisting of a relational database and a web-based data portal that allows scientists to query and download the data. We have imported almost 1.9 billion HydroClim data records into the system. At the time of this submission, 1.3 billion records of historical data and predicted streamflow and water temperature model data are available in the HydroClim data portal for 26 watersheds in the United States. The HydroClim data are also being integrated with fish occurrence data from Fishnet 2, via the Fishnet 2 API (Application Programming Interface), which provides occurence data records for over 4.1 million species lots representing over 40 million specimens in ichthyological research collections.Our plan is to extract and merge environmental data from Hydroclim API, with fish occurrences containing geospatial information from the Fishnet 2 API, displaying the integrated data on web-based interactive hydrological maps in different time-series, and providing a tool for visualizing ecosystem diversity. The combined Hydroclim and Fishnet2 data can be used for ecological niche modeling applications, such as predicting the future distribution of threatened and endangered freshwater fish species. I will describe the cyberinfrastructure of HydroClim data portal and some of the ways the data can be used in biodiverisity research in the future.

APA, Harvard, Vancouver, ISO, and other styles

26

Perez, Perez Ruben, Joana Beja, Leen Vandepitte, et al. "EMODnet Biology: Unlocking European marine biodiversity data." Biodiversity Information Science and Standards 7 (September 8, 2023): e112147. https://doi.org/10.3897/biss.7.112147.

Full text

Abstract:

EMODnet Biology (hosted and coordinated by the Flanders Marine Institute (VLIZ)) is one of the seven themes within the European Marine Observation and Data network (EMODnet). The EMODnet Biology consortium aims to facilitate the accessibility and usage of marine biodiversity data. With the principle of "collect once, use many times" at its core, EMODnet Biology fosters collaboration across various sectors, including research, policy-making, industry, and individual citizens, to enhance knowledge sharing and inform decision-making.EMODnet Biology focuses on providing free and open access to comprehensive historical and recent data on the occurrence of marine species and their traits in all European regional seas. It achieves this through partnerships and collaboration with diverse international initiatives, such as the World Register of Marine Species (WoRMS), Marine Regions and the European node of the Ocean Biodiversity Information System (EurOBIS) among others. By promoting the usage of the Darwin Core Standard (Wieczorek et al. 2012), EMODnet Biology fosters data interoperability and ensures seamless integration with wider networks such as the Global Biodiversity Information Facility (GBIF) and the Ocean Biodiversity Information System (OBIS), serving as a significant data provider of the latter, as it is responsible for most of its data generated in Europe.Since its inception, EMODnet Biology has undertaken actions covering various areas, includingproviding access to marine biological data with spatio-temporal, taxonomic, environmental- and sampling-related information among others;developing an exhaustive data quality control tool based on the Darwin Core standard, the British Oceanographic Data Centre and Natural Environment Research Council Vocabulary Server (BODC NVS2) parameters and other controlled vocabularies used;creating and providing training courses to guide data providers;performing gap analyses to identify data quality and coverage shortcomings;creating and publishing marine biological distribution maps for various species or species groups; andinteracting with international and European initiatives, projects and organizations.Furthermore, EMODnet Biology contributes to the overall EMODnet initiative, which covers multidisciplinary data and products. Thanks to the use of standard protocols and tools across disciplines, EMODnet Biology products can contribute to multidisciplinary analysis of pressures and impacts on key marine species and habitats, and, lastly, support a better management and planning of the maritime space.In conclusion, EMODnet Biology plays a pivotal role in biodiversity informatics by providing users with a wealth of accessible and reusable marine biodiversity data and products. Its collaborative approach, extensive partnerships, and adherence to the FAIR (Findable, Accessible, Interoperable, Reusable) data principles (Wilkinson et al. 2016) as well as to the Infrastructure for Spatial Information in Europe (INSPIRE) metadata technical guidelines (European Commission Joint Research Centre 2013) and the Open Geospatial Consortium (OGC) standards make it a valuable resource for advancing knowledge, informing policies, and supporting sustainable management of marine ecosystems.

APA, Harvard, Vancouver, ISO, and other styles

27

Penev, Lyubomir, Terry Erwin, Jeremy Miller, Vishwas Chavan, Tom Moritz, and Charles Griswold. "Publication and dissemination of datasets in taxonomy: ZooKeys working example." ZooKeys 11, no. 11 (2009): 1–8. https://doi.org/10.3897/zookeys.11.210.

Full text

Abstract:

A concept for data publication and semantic enhancements proposed by ZooKeys and applied in the milestone paper of Miller et al. (2009) is described. For the first time in systematic zoology, an unique combination of data publication and semantic enhancements is applied within the mainstream process of journal publishing, to demonstrate how: (1) All primary biodiversity data underlying a taxonomic monograph are published as a dataset under a separate DOI within the paper; (2) The occurrence dataset is discoverable and accessible through GBIF data portal (data.gbif.org) simultaneously with the publication; (3) Occurrence dataset is published as a KML file under a distinct DOI to provide an interactive experience in Google Earth; (4) All new taxa (42) are registered at ZooBank during the publication process (mandatory for ZooKeys); (5) All new taxa (42) are provided to Encyclopedia of Life through XML mark up on the day of publication (mandatory for ZooKeys). It is proposed to clearly distinguish between static and dynamic datasets in the way they are published, preserved and cited.

APA, Harvard, Vancouver, ISO, and other styles

28

dos, Remedios Nick, Marie-Elise Lecoq, David Martin, and Sophia Ratcliffe. "The Living Atlases community in action: the NBN Atlas Spatial Portal and "Explore Your Region" module." Biodiversity Information Science and Standards 2 (May 21, 2018): e25486. https://doi.org/10.3897/biss.2.25486.

Full text

Abstract:

Atlas of Living Australia (ALA) (https://www.ala.org.au/) is the Global Biodiversity Information Facility (GBIF) node of Australia. Since 2010, they have developed and improved a platform for sharing and exploring biodiversity information. All the modules are publicly available for reuse and customization on their GitHub account (https://github.com/AtlasOfLivingAustralia). The National Biodiversity Network, a registered charity, is the UK GBIF node and has been sharing biodiversity data since 2000. They published more than 79 million occurrences from 818 datasets. In 2016, they launched the NBN Atlas Scotland (https://scotland.nbnatlas.org/) based on the Atlas of Living Australia infrastructure. Since then, they released the NBN Atlas (https://nbnatlas.org/), the NBN Atlas Wales (https://wales.nbnatlas.org/) and soon the NBN Atlas Isle of Man. In addition to the occurrence/species search engine and the metadata registry, they put in place several tools that help users to work with data published in the network: the spatial portal and "explore your region" module. Both elements are based on Atlas of Living Australia developments. Because the Atlas of Living Australia platform is really powerful an reusable, we want to show you these two applications used to make geographical analyses. In order to perform this, we will present you the specificities of each component by giving examples of some functionalities.

APA, Harvard, Vancouver, ISO, and other styles

29

GAMA, Maria Carolina Feres de Lima Rocha, Eleonora Druve Tavares FAGUNDES, Thaís Costa Nascentes QUEIROZ, Adriana Teixeira RODRIGUES, Luiza Caroline VIEIRA, and Alexandre Rodrigues FERREIRA. "PREDICTIVE FACTORS OF MORBIDITY ASSOCIATED WITH ESOPHAGEAL VARICEAL BLEEDING IN CHILDREN WITH PORTAL HYPERTENSION." Arquivos de Gastroenterologia 60, no. 2 (2023): 247–56. http://dx.doi.org/10.1590/s0004-2803.202302023-37.

Full text

Abstract:

ABSTRACT Background: Most data on the natural history of portal hypertension come from studies in adults. The morbidity rate of upper gastrointestinal bleeding (UGIB) in children with portal hypertension has not been systematically characterized. Objective: To describe the morbidity and mortality of UGIB in pediatric patients with portal hypertension and identify predictive factors for the occurrence of its main complications. Methods: This retrospective study included pediatric patients with cirrhotic portal hypertension or with extrahepatic portal vein obstruction (EHPVO). Mortality and UGIB complications within a period of up to 6 weeks of the bleeding were investigated. To determine the predictive factors of morbidity, a multivariate analysis was performed using logistic regression; all results were considered significant at P<0.05. Results: A total of 86 patients (51.2% with EHPVO and 48.8% with cirrhosis) had 174 bleeding events. Ascites was the most common complication (43.1% of all cases), being more prevalent in patients with cirrhosis (P<0.001). Cirrhosis was a predictor of the occurrence of any morbidity (OR 20.3). The need for blood transfusion was predictor of at least one complication (OR 5.8), ascites (OR 7.2) and infections (OR 3.8) in the general group and at least one complication (OR 11.3) and ascites (OR 5.8) in cirrhotic patients. The need for expansion was a predictor of any morbidity (OR 4.6) and infections (OR 3.9) in the general group, in addition to being predictor of infection in cirrhotic patients (OR 5.4). There were no deaths from UGIB in the six weeks post-bleeding. Conclusion: The study showed the relevance of morbidity after UGIB in pediatric patients with portal hypertension, especially in those with cirrhosis. The patients with hemodynamic instability requiring blood transfusion or expansion on admission are at increased risk of complications related to upper gastrointestinal bleeding and should be closely monitored.

APA, Harvard, Vancouver, ISO, and other styles

30

Dema, Sangay, Choki Gyeltshen, Thomas Vattakaven, and Prabhakar Rajagopal. "Development of a National Repository for Aquatic Biodiversity in Bhutan." Proceedings of TDWG 1 (September 5, 2017): e20809. https://doi.org/10.3897/tdwgproceedings.1.20809.

Full text

Abstract:

In response to a request from the Royal Government of Bhutan, the World Bank commissioned a study on the sustainable development of hydropower in Bhutan. The study identified loss and decline of aquatic biodiversity as one of the major potential environmental impacts of hydropower development in Bhutan. Access to information on aquatic biodiversity is of utmost importance in planning and designing of new hydropower projects in Bhutan. This data is essential for planners to avoid, minimize and effectively mitigate potential adverse impacts on aquatic biodiversity. However, access to this information is not easy. With the objective of making aquatic biodiversity data accessible, key stakeholders within Bhutan have taken the initiative to create and maintain a national data repository for aquatic biodiversity within the country. An inventory and gap analysis of aquatic biodiversity data in Bhutan was done to summarize the available data and information on aquatic biodiversity, stakeholder meetings were held to obtain feedback for the repository and a plan of action has been formulated for creating the repository. Bhutan already maintains a rich biodiversity information repository - the Bhutan Biodiversity Portal (BBP, http://biodiversity.bt/), under the aegis of the National Biodiversity Centre (NBC), Ministry of Agriculture and Forests, Serbithang, Thimphu. The platform is powered by the open source Biodiversity Informatics Platform that also powers the India Biodiversity Portal (IBP) and a portal on Weed Identification and Knowledge in the Western Indian Ocean (WIKWIO). Additional data fields and functionality were identified to extend the functionality of BBP to cover the needs of the stakeholders. Primarily, interfaces will be built to upload already available datasets on organisms that have been surveyed and identified, as well as newer aquatic biodiversity data that will be generated by surveys and monitoring in future. The portal will facilitate upload of data that captures observed characteristics, e.g., life stage, body size, reproductive state; environmental variables of the locality of occurrence; and other sampling data such as sampling gear and mode of observation. It will also enhance species knowledge by adding the ability to link existing species pages with international databases such as IUCN and FishBase, as well as fields to store voucher specimen details and ecological status. All tabular data that is added will be synchronised to either standard observation fields, custom observation fields that are relevant to aquatic biodiversity or to species traits. Data that cannot be categorised under any of the above will stored as key value pairs. The data upload module will have metadata marked up to the Ecological Metadata Language (EML) metadata specification and data will be available for exchange using the Darwin Core (DwC) standards. The platform will be enabled with an enhanced search and serve function through easy-to-use query panels. Uploaded data will be aggregated and visualised on the portal along spatial, temporal and taxonomic axes. Furthermore, it will be available for stakeholders to download under Creative Commons licences for further processing and planning. The creation of the repository will be complemented by training the stakeholders in data curation and developing a campaign to build awareness of the portal within the community of stakeholders. The establishment of this repository will provide a guide to conserve aquatic biodiversity, maintain ecosystem functioning, and protect livelihoods and food security dependent upon aquatic biodiversity. It will also contribute to the open source biodiversity informatics platform and be available to all other instances of the portal. This will help in enriching the functions of the open source platform and provide value to conservation of biodiversity in other areas of the world.

APA, Harvard, Vancouver, ISO, and other styles

31

Gan, Yi-Ming, Maxime Sweetlove, and de Putte Anton Van. "The Antarctic Biodiversity Portal, an Online Ecosystem for Linking, Integrating and Disseminating Antarctic Biodiversity Information." Biodiversity Information Science and Standards 3 (June 18, 2019): e37182. https://doi.org/10.3897/biss.3.37182.

Full text

Abstract:

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. 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.

APA, Harvard, Vancouver, ISO, and other styles

32

Gan, Yi-Ming, Maxime Sweetlove, and de Putte Anton Van. "The Antarctic Biodiversity Portal, an Online Ecosystem for Linking, Integrating and Disseminating Antarctic Biodiversity Information." Biodiversity Information Science and Standards 3 (July 17, 2019): e37501. https://doi.org/10.3897/biss.3.37501.

Full text

Abstract:

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. 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.

APA, Harvard, Vancouver, ISO, and other styles

33

Waller, John. "Data Location Quality at GBIF." Biodiversity Information Science and Standards 3 (June 13, 2019): e35829. https://doi.org/10.3897/biss.3.35829.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

34

Ainsa, Alice, Sophie Pamerlon, Anne-Sophie Archambeau, Rémi Beauvieux, Raoufou Radji, and Hervé Chevillotte. "Regional Data Platform of West and Central African Herbaria." Biodiversity Information Science and Standards 7 (September 7, 2023): e112180. https://doi.org/10.3897/biss.7.112180.

Full text

Abstract:

In April 2021, a Biodiversity Information for Development (BID) project was launched to deliver a regional data platform of West and Central African herbaria, which just concluded in April 2023. A dataset containing 168,545 herbarium specimens from 6 different countries: Togo, Gabon, Ivory Coast, Benin, Guinea Conakry and Cameroon, is now visible on the Global Biodiversity Information Facility (GBIF) website and will be regularly updated. A checklist datatset (Radji 2023a) and an occurrence dataset (Radji 2023b) obtained from herbarium parts are also available on GBIF.In addition, a Living Atlases portal for herbaria in West and Central Africa has been created to allow users to search, display, filter, and download these data. This application reuses open source modules developed by the Atlas of Living Australia (ALA) community (Morin et al. 2021).In addition to that, the RIHA platform (Réseau Informatique des Herbiers d'Afrique / Digital Network of African Herbaria) enables herbarium administrators to manage their own data. Thanks to all these tools, the workflow (Fig. 1) for data publication on GBIF is carried out regularly and easily and the addition of new member herbaria from West and Central Africa can be easily incorporated.

APA, Harvard, Vancouver, ISO, and other styles

35

Brosens, Dimitri, Francois Vankerkhoven, David Ignace, et al. "FORMIDABEL: The Belgian Ants Database." ZooKeys 306 (June 3, 2013): 59–70. https://doi.org/10.3897/zookeys.306.4898.

Full text

Abstract:

FORMIDABEL is a database of Belgian Ants containing more than 27.000 occurrence records. These records originate from collections, field sampling and literature. The database gives information on 76 native and 9 introduced ant species found in Belgium. The collection records originated mainly from the ants collection in Royal Belgian Institute of Natural Sciences (RBINS), the ‘Gaspar’ Ants collection in Gembloux and the zoological collection of the University of Liège (ULG). The oldest occurrences date back from May 1866, the most recent refer to August 2012. FORMIDABEL is a work in progress and the database is updated twice a year.The latest version of the dataset is publicly and freely accessible through this url: http://ipt.biodiversity.be/resource.do?r=formidabel. The dataset is also retrievable via the GBIF data portal through this link: http://data.gbif.org/datasets/resource/14697A dedicated geo-portal, developed by the Belgian Biodiversity Platform is accessible at: http://www.formicidae-atlas.bePurpose: FORMIDABEL is a joint cooperation of the Flemish ants working group “Polyergus” (http://formicidae.be) and the Wallonian ants working group “FourmisWalBru” (http://fourmiswalbru.be). The original database was created in 2002 in the context of the preliminary red data book of Flemish Ants (Dekoninck et al. 2003). Later, in 2005, data from the Southern part of Belgium; Wallonia and Brussels were added. In 2012 this dataset was again updated for the creation of the first Belgian Ants Atlas (Figure 1) (Dekoninck et al. 2012). The main purpose of this atlas was to generate maps for all outdoor-living ant species in Belgium using an overlay of the standard Belgian ecoregions. By using this overlay for most species, we can discern a clear and often restricted distribution pattern in Belgium, mainly based on vegetation and soil types.

APA, Harvard, Vancouver, ISO, and other styles

36

Huq, Moeen Ul, Aymen Jamal, Muhammad Zain Akhtar, Ammarah Tassudaq, Muhammad Faisal Bacha, and Tahir Mukhtar Sayed. "Prevalence of Portal Vein Thrombosis in Budd-Chiari Syndrome Patients." Pakistan Journal of Medical and Health Sciences 17, no. 1 (2023): 619–21. http://dx.doi.org/10.53350/pjmhs2023171619.

Full text

Abstract:

Background and Aim: Thrombosis of the portal vein or obstruction of the hepatic venous outflow tract is the cause of portal vein thrombosis (PVT) and Budd-Chiari syndrome (BCS). Patients with PVT may experience a shorter survival rate compared to those without. The present study aimed to determine the portal vein thrombosis occurrence in Budd-Chiari syndrome patients. Patients and Methods: This cross-sectional study was conducted on 46 Budd-Chiari syndrome patients in Gastroenterology department of DHQ Teaching Hospital and Mufti Mahmood Memorial Hospital, Dera Ismail Khan from November 2021 to October 2022. Written informed consent was taken from each individual. Doppler ultrasonography (colored-pulsed) was used to confirm the PVT and BCS cases. Clinical data, laboratory findings, and radiological data were recorded. SPSS version 26 was used for data analysis. Results: The overall mean age of the BCS patients was 28.34±4.6 years. The prevalence of portal vein thrombosis in BCS patients was 12.8% (n=6). Of the total cases, the incidence of chronic and acute BCS presentation was 42 (91.3%) and 4 (8.7%) respectively. The most prevalent symptoms of BCS were abdominal pain and abdominal enlargement in 38 (82.6%) and 41 (89.1%) respectively. Hepatomegaly and ascites were most prevalent clinical signs found in 36 (78.3%) and 37 (80.4%) respectively. The incidence of esophageal varices, gastric extension, and fundal varices were 32 (69.6%), 4 (8.7%), and 2 (4.3%) respectively. About 21 (45.7%) cases had Portal hypertensive gastropathy (PHG). Conclusion: A higher incidence of PVT was observed in the present study than previously reported. Sociodemographic data and underlying etiology of BCS were not significantly different between patients with and without PVT. Those with PVT were more likely to experience hepatic tenderness, increased white blood cells, and increased direct bilirubin. PVT and other patients had similar Doppler ultrasound findings. Keywords: Portal vein thrombosis, Prevalence, Budd-Chiari syndrome

APA, Harvard, Vancouver, ISO, and other styles

37

Kalina, Irina E., Yulia D. Sokolova, Alexey V. Shevchuk, and Oleg S. Mariev. "SPECIFIC FEATURES OF IDENTIFYING MAJOR ECONOMIC DEVELOPMENT TRENDS IN RUSSIA BASED ON STRUCTURAL TOPIC MODELLING METHOD." SOFT MEASUREMENTS AND COMPUTING 6, no. 67 (2023): 12–24. http://dx.doi.org/10.36871/2618-9976.2023.06.002.

Full text

Abstract:

This paper assesses the degree of news coverage by topic by applying structural topic modelling. The preliminary stage involves the computeraided gathering and systematisation of information from the Lenta.ru online news portal, converting words into a single form, and cleaning the text data from stopwords. The method of structural thematic modelling (STM) was used in this study, which made it possible to identify the 25 most popular topics for publication on the news portal and to determine the frequency of occurrence of the words in the subject and their uniqueness. Correlation and regression analyses indicated the correlation of the topics under study and the change in the degree of coverage of the topics over time.

APA, Harvard, Vancouver, ISO, and other styles

38

Smirnova, Larissa, Patricia Mergen, Quentin Groom, et al. "Data sharing tools adopted by the European Biodiversity Observation Network Project." Research Ideas and Outcomes 2 (May 31, 2016): e9390. https://doi.org/10.3897/rio.2.e9390.

Full text

Abstract:

A fundamental constituent of a biodiversity observation network is the technological infrastructure that underpins it. The European Biodiversity Network project (EU BON) has been working with and improving upon pre-existing tools for data mobilization, sharing and description. This paper provides conceptual and practical advice for the use of these tools. We review tools for managing metadata, occurrence data, and ecological data and give detailed description of these tools, their capabilities and limitations. This is followed by recommendations on their deployment and possible future enhancements. This is done from the perspective of the needs of the biodiversity observation community with a view to the development of a unified user interface to these data – the European Biodiversity Portal (EBP). We described the steps taken to develop, adapt, deploy and test these tools. This document also gives an overview of the objectives that still need to be achieved and challenges to be addressed for the remainder of the project.

APA, Harvard, Vancouver, ISO, and other styles

39

Hovstad, Knut Anders, Stein Hoem, Eveliina Kallioniemi, et al. "Developing and Maintaining a National Biodiversity Data Infrastructure – An example from Norway." Biodiversity Information Science and Standards 6 (September 7, 2022): e94078. https://doi.org/10.3897/biss.6.94078.

Full text

Abstract:

Biodiversity data infrastructures are fundamental to halting the ongoing loss of species and habitats. Here we provide an overview of the national biodiversity data infrastructure developed and implemented in Norway by The Norwegian Biodiversity Information Centre (NBIC). Key elements and properties of this infrastructure are highlighted and directions for future development are outlined.The overarching objective for the infrastructure is to make data on habitats and species in Norway available for policy and decision makers, researchers and the general public. Here we will focus on data on species and their distribution. The infrastructure is built as a modular system but with a high level of integration between the components. NBIC has the main responsibility for developing and managing the infrastructure in collaboration with natural history museums, research organizations, private companies and non-governmental organizations (NGOs), including the Norwegian node of the Global Biodiversity Information Facility (GBIF). The infrastructure includes a citizen science portal that gives both amateurs and professionals the possibility to report species sightings. The data from this portal together with data from natural history museums and other data providers are then made available though the Species Map Service website. The infrastructure also includes the Norwegian taxonomic backbone database and a trait bank that is under development. The trait bank is planned to contain both ecological traits but also other information about species such as Red List status. The infrastructure builds on a few simple principles. The exchange of data is based on the Darwin Core Standard and its extensions, or other open data standards. Each data owner is responsible for quality control, secure storage and management of their own data. The data owners publish the data using the Integrated Publishing Toolkit (IPT) developed by GBIF. NBIC then harvests all observations with spatial coordinates that fall within Norway and adds information about, for example, status on the Norwegian Red List before the data are made available in the map. The core parts of the infrastructure only handle data that are open and adhere to the FAIR principles, i.e. that the data are Findable, Accessible, Interoperable, and available for Reuse. An important exception to this principle is observations of threatened species that are particularly vulnerable to human disturbance. Sensitive data are managed in a separate, secure system and with a restricted access portal for data viewing.Data in the Species Map Service are also available through a public API, which can be used to harvest and import the data or subsets of it into other systems and services. To give an example, the forestry industry integrates data on Red Listed species into their planning systems tools and has even an option to display a subset of species occurrences on their forestry machine computers.NBIC has in cooperation with NGOs established a system in which experts validate observations that are reported through the citizen science portal. As it is not possible to validate all observations, species of particular interest for environmental management and conservation are given priority. A future solution could be to develop a system that can identify observations with a low likelihood of being correct using, for example, statistical models that describe the likelihood of an occurrence in a given space and environment. If photos are available, image recognition based on machine learning can be used to spot species that are likely to be misidentified. It is also possible/conceivable to use a more heuristic approach based on an ontology for organisms and ecological traits (for example, "this is a fish, fish are always aquatic organisms, this observation was made on dry land and is thus unlikely to be true"). The development of improved tools and systems to improve data quality is a major task for future development of the infrastructure.In Norway, spatial planning processes and decisions are required to integrate information made available through the infrastructure. If new information about the occurrence of Red Listed species or other species of special interest for environmental management and conservation are discovered through the planning process, the developer is responsible for archiving these observations in a publicly available database.Key factors for the success of the biodiversity data infrastructure described here are: (i) the close cooperation between NBIC, data providers, NGO's and data users, (ii) the modularity of the infrastructure, (iii) the use of open and flexible standards for data exchange, and (iv) the integration of the infrastructure in the legal framework for spatial planning requiring that data from e.g., environmental impact assessments are made available through the infrastructure.

APA, Harvard, Vancouver, ISO, and other styles

40

Hartini, Tin, and Fajar Ramdani Piernawan. "Analyzing Adaptation of MNC Portal Indonesia Internship Students in Facing Culture Shock." Paradigma 21, no. 2 (2024): 441–53. http://dx.doi.org/10.33558/paradigma.v21i2.9956.

Full text

Abstract:

College students who undergo internship activities often experience culture shock due to entering a new environment that has cultural differences with their home culture. Culture shock can cause a variety of reactions, including discomfort with the new environment. Intercultural communication, as an interaction between individuals who come from different cultural backgrounds can be an important element in overcoming this problem. The research method is a qualitative research method with a descriptive approach. Data collection research methods with five informants and one key informant through interviews and documentation. The data analysis techniques used are data reduction, data presentation and conclusions. The data validity used is source triangulation. The results of this study indicate the occurrence of culture shock experienced by several internship students at MNC Portal Indonesia in four stages of cultural adaptation, namely honeymoon, frustration, readjustment and resolution. Differences in lifestyles, ways of communication, as well as responsibilities and targets achieved in the work that resulted in internship students experiencing culture shock while doing internships at MNC Portal Indonesia. However, interns choose to survive and face all the conditions that exist, so that all interns are able to adapt to the new environment, and get benefits after doing an internship at MNC Portal Indonesia.

APA, Harvard, Vancouver, ISO, and other styles

41

Shao, Ruoyang, Zhiwei Li, Jitao Wang, et al. "Hepatic venous pressure gradient-guided laparoscopic splenectomy and pericardial devascularisation versus endoscopic therapy for secondary prophylaxis for variceal rebleeding in portal hypertension (CHESS1803): study protocol of a multicenter randomised controlled trial in China." BMJ Open 10, no. 6 (2020): e030960. http://dx.doi.org/10.1136/bmjopen-2019-030960.

Full text

Abstract:

IntroductionGastro-oesophageal variceal bleeding is one of the most common and severe complications with high mortality in cirrhotic patients who developed portal hypertension. Hepatic venous pressure gradient (HVPG) is a globally recommended golden standard for the portal pressure assessment and an HVPG ≥16 mm Hg indicates a higher risk of death and rebleeding. This study aims to compare the effectiveness and safety of splenectomy and pericardial devascularisation (laparoscopic therapy) plus propranolol and endoscopic therapy plus propranolol for variceal rebleeding in cirrhotic patients with HVPG between 16 and 20 mm Hg.Methods and analysisThis is a multicenter, randomised, controlled clinical trial. Participants will be 1:1 assigned randomly into either laparoscopic or endoscopic groups. Forty participants whose transjugular HVPG lies between 16 and 20 mm Hg with a history of gastro-oesophageal variceal bleeding will be recruited from three sites in China. Participants will receive either endoscopic therapy plus propranolol or laparoscopic therapy plus propranolol. The primary outcome measure will be the occurrence of gastro-oesophageal variceal rebleeding. Secondary outcome measures will include overall survival, occurrence of hepatocellular carcinoma, the occurrence of venous thrombosis, the occurrence of adverse events, quality of life and tolerability of treatment. Outcome measures will be evaluated at baseline, 12 weeks, 24 weeks, 36 weeks, 48 weeks and 60 weeks. Multivariate COX regression model will be introduced for analyses of occurrence data and Kaplan-Meier analysis with the log-rank test for intergroup comparison.Ethics and disseminationEthical approval was obtained from all three participating sites. Primary and secondary outcome data will be submitted for publication in peer-reviewed journals and widely disseminated.Trial registration numberNCT03783065; Pre-results.Trial statusRecruitment for this study started in December 2018 while the first participant was randomised in January 2019. Recruitment is estimated to stop in October 2019.

APA, Harvard, Vancouver, ISO, and other styles

42

Voroniak, D. I., O. S. Godik, I. V. Kolomoiets, and O. G. Dubrovin. "Efficacy of the staged endoscopic ligature of the varicose veins in children, suffering portal hypertension." Klinicheskaia khirurgiia 86, no. 10 (2019): 24–27. http://dx.doi.org/10.26779/2522-1396.2019.10.24.

Full text

Abstract:

Objective. To estimate the efficacy of first procedure of endoscopic ligature for the varicose esophageal veins in children, suffering portal hypertension in accordance to data of endoscopic examination. Materials and methods. Endoscopic ligature of the varicose esophageal veins was performed in 24 patients, suffering portal hypertension, aiming at prophylaxis of hemorrhage from the varicose veins. Results. Reduction of the varicose veins degree after first ligature procedure was observed in 14 (58.33%) children, eradication of the varicose veins - in 5 (20.83%) of them. In 1 (4.17%) patient a complication (hemorrhage) have occurred in a moment of a ligature application. In 2 (8.33%) patients a hemorrhage from the varicose veins of stomach have occurred. Conclusion. Endoscopic ligature constitutes a secure and effective prophylactic method for hemorrhage from the esophageal varicose in children, suffering portal hypertension, and permits to control the varicose degree on stages of the portal hypertension treatment. Even after first procedure of endoscopic ligature the esophageal varicose degree have had reduced at average (p < 0.05). After endoscopic ligature the hemorrhage occurrence risk have reduced: p=0.05, and the risks ratio constitutes 0.14 (95% CI 0.04-0.56).

APA, Harvard, Vancouver, ISO, and other styles

43

Shashkov, Maxim, Natalya Ivanova, and Sergey Ermolov. "Filling Gaps in Earthworm Digital Diversity in Northern Eurasia from Russian-language Literature." Biodiversity Information Science and Standards 7 (September 20, 2023): e112957. https://doi.org/10.3897/biss.7.112957.

Full text

Abstract:

Data availability for certain groups of organisms (ecosystem engineers, invasive or protected species, etc.) is important for monitoring and making predictions in changing environments. One of the most promising directions for research on the impact of changes is species distribution modelling. Such technologies are highly dependent on occurrence data of high quality (Van Eupen et al. 2021). Earthworms (order Crassiclitellata) are a key group of organisms (Lavelle 2014), but their distribution around the globe is underrepresented in digital resources. Dozens of earthworm species, both widespread and endemic, inhabit the territory of Northern Eurasia (Perel 1979), but extremely poor data on them is available through global biodiversity repositories (Cameron 2018). There are two main obstacles to data mobilisation. Firstly, studies of the diversity of earthworms in Northen Eurasia have a long history (since the end of the nineteenth century) and were conducted by several generations of Soviet and Russian researchers. Most of the collected data have been published in "grey literature", now stored only in a few libraries. Until recently, most of these remained largely undigitised, and some are probably irretrievably lost. The second problem is the difference in the taxonomic checklists used by Soviet and European researchers. Not all species and synonyms are included in the GBIF (Global Biodiversity Information Facility) Backbone Taxonomy. As a result, existing earthworm species distribution models (Phillips 2019) potentially miss a significant amount of data and may underestimate biodiversity, and predict distributions inaccurately. To fill this gap, we collected occurrence data from the Russian language literature (published by Soviet and Russian researchers) and digitised species checklists, keeping the original scientific names.To find relevant literature, we conducted a keyword search for "earthworms" and "Lumbricidae" through the Russian national scientific online library eLibrary and screened reference lists from the monographs of leading Soviet and Russian soil zoologist Tamara Perel (Vsevolodova-Perel 1997, Perel 1979). As a result, about 1,000 references were collected, of which 330 papers had titles indicating the potential to contain data on earthworm occurrences. Among these, 219 were found as PDF files or printed papers. For dataset compilation, 159 papers were used; the others had no exact location data or duplicated data contained in other papers. Most of the sources were peer-reviewed articles (Table 1). A reference list is available through Zenodo (Ivanova et al. 2023).The earliest publication we could find dates back to 1899, by Wilhelm Michaelsen. The most recent publication is 2023. About a third of the sources were written by systematists Iosif Malevich and Tamara Perel. Occurrence data were extracted and structured according to the Darwin Core standard (Wieczorek et al. 2012). During the data digitisation process, we tried to include as much primary information as possible. Only one tenth of the literature occurrences contained the geographic coordinates of locations provided by the authors. The remaining occurrences were manually georeferenced using the point-radius method (Wieczorek et al. 2010).The resulting occurrence dataset Earthworm occurrences from Russian-language literature (Shashkov et al. 2023) was published through the Global Biodiversity Information Facility portal. It contains 5304 occurrences of 117 species from 27 countries (Fig. 1).To improve the GBIF Backbone Taxonomy, we digitised two catalogues of earthworm species published for the USSR (Perel 1979) and Russian Federation (Vsevolodova-Perel 1997) by Tamara Perel. Based on these monographs, three checklist datasets were published through GBIF (Shashkov 2023b, 124 records; Shashkov 2023c, 87 records; Shashkov 2023a, 95 records). Now we work towards including these names in the GBIF Backbone so that all species names can be matched and recorded exactly as mentioned in papers published by Soviet and Russian researchers.

APA, Harvard, Vancouver, ISO, and other styles

44

Grillo, Marco, Guido Bonello, Matteo Cecchetto, et al. "Planktonic, benthic and sympagic copepods collected from the desalination unit of Mario Zucchelli Research Station in Terra Nova Bay (Ross Sea, Antarctica)." Biodiversity Data Journal 12 (March 11, 2024): e119633. https://doi.org/10.3897/BDJ.12.e119633.

Full text

Abstract:

Distributional data on planktonic, benthic and sympagic copepods collected in the framework of the XXXIVth Expeditions of the Italian National Antarctic Programme (PNRA) to the Ross Sea sector from 2018–2019 are here provided. These occurrences correspond to specimens collected from the 25 μm filters used in the desalination plant of the Italian research station "Mario Zucchelli" (MZS), located in the Terra Nova Bay area (TNB; Ross Sea, Antarctica). This dataset is a contribution to the Antarctic Biodiversity Portal, the thematic Antarctic node for both the Ocean Biogeographic Information System (AntOBIS) and the Global Biodiversity Information Facility Antarctic Biodiversity Information Facility (ANTABIF). The dataset was uploaded and integrated with the SCAR-AntOBIS database (the geospatial component of SCAR-MarBIN). Please follow the guidelines from the SCAR Data Policy (ISSN 1998-0337) when using the data. If you have any questions regarding this dataset, please contact us via the contact information provided in the metadata or via data-biodiversity-aq@naturalsciences.be. Issues with the dataset can be reported at the biodiversity-aq GitHub project.We describe the diversity of marine copepods Terra Nova Bay sampled by the filters installed in the desalination unit (DU) of the Italian research station "Mario Zucchelli" described in recent work. The opening of the intake pipe of the DU is positioned at a depth of 4 m and allowed a total of 2,116 specimens to be sampled and recognised. In addition, new occurrence records of copepod genera and species are reported in the same zone. We provide an overview of the marine copepod diversity reported for TNB. The total of 2,116 individuals corresponds to 14 genera and 15 species and is represented by 136 occurrence records in this dataset. Around 52% of the total number of species are new records for the TNB area. The publication of this data paper was funded by the Belgian Science Policy Office (BELSPO, contract n°FR/36/AN1/AntaBIS) in the Framework of EU-Lifewatch as a contribution to the SCAR Antarctic biodiversity portal (biodiversity.aq).

APA, Harvard, Vancouver, ISO, and other styles

45

Lepoint, Gilles, André Heughebaert, and Loïc N. Michel. "Epiphytic bryozoans on Neptune grass – a sample-based data set." ZooKeys 606 (July 21, 2016): 1–10. https://doi.org/10.3897/zookeys.606.8238.

Full text

Abstract:

Background The seagrass Posidonia oceanica L. Delile, commonly known as Neptune grass, is an endemic species of the Mediterranean Sea. It hosts a distinctive and diverse epiphytic community, dominated by various macroalgal and animal organisms. Mediterranean bryozoans have been extensively studied but quantitative data assessing temporal and spatial variability have rarely been documented. In Lepoint et al. (2014a, b) occurrence and abundance data of epiphytic bryozoan communities on leaves of P. oceanica inhabiting Revellata Bay (Corsica, Mediterranean Sea) were reported and trophic ecology of Electra posidoniae Gautier assessed. New information Here, metadata information is provided on the data set discussed in Lepoint et al. (2014a) and published on the GBIF portal as a sampling-event data set: http://ipt.biodiversity.be/resource?r=ulg_bryozoa&v=1.0). The data set is enriched by data concerning species settled on Posidonia scales (dead petiole of Posidonia leaves, remaining after limb abscission).

APA, Harvard, Vancouver, ISO, and other styles

46

Lecoq, Marie-Elise, Fabien Cavière, and Régine Vignes-Lebbe. "Living Atlases: tips and advices." Biodiversity Information Science and Standards 1 (August 14, 2017): e20252. https://doi.org/10.3897/tdwgproceedings.1.20252.

Full text

Abstract:

Atlas of Living Australia (ALA), Australian node of the Global Biodiversity Information Facility (GBIF), provides information on all the known species in Australia. Since 2010, ALA has developed an open source framework providing different tools to help users from various sectors. The ALA technical team, with the help of GBIF, has reorganized the architecture of ALA tools into several modules to help other institutions to re-use the code. The three first sessions of this workshop focuses on data indexation, occurrence search engine and metadata registry. The last session delves into more technical subjects with hands-on demonstration of installing an instance of the portal (also known as ALA-demo*1) using Ansible scripts. In addition to this, sharing of experience regarding the customization of data portals and building a name indexer using national checklists will be covered. Finally, we will present others modules such as ALA4R*2, project allowing R users to access data and resources hosted by a platform based on ALA, or Image service*3, tiling and image repository tool.

APA, Harvard, Vancouver, ISO, and other styles

47

Pravitasari, Ratna Adelia. "Correlation between Ascites and Total Lymphocyte Count with Occurrence of Hepatic Encephalopathy in Liver Cirrhosis Patients." Jurnal Kedokteran Brawijaya 31, no. 4 (2021): 3. http://dx.doi.org/10.21776/ub.jkb.2021.031.04.3.

Full text

Abstract:

Hepatic encephalopathy (HE) is brain dysfunction manifested as a broad spectrum of neuropsychiatric abnormalities caused by hepatic insufficiency or portosystemic shunting due to portal hypertension. Portal hypertension in liver cirrhosis also causes ascites, as the most common clinical manifestation. Further, immune dysfunction, one of which is decreased total lymphocyte count (TLC), happens at liver cirrhosis, which triggers the systemic inflammatory response. This systemic inflammatory response plays a role in HE. Objective of this study is to know the correlation between ascites and TLC with occurence of HE in liver cirrhosis patient. This study was conducted by retrospective cohort design in Saiful Anwar Hospital. Determination of sample amount at this study used total sampling method. Hepatic encephalopathy diagnosis was based on West Haven Criteria. Ascites was determined by physical examination and/or abdominal ultasonography. Total lymphocyte count data was taken from medical record, with complete blood count examination used XS-800i hematology analyzer machine. Data were analyzed using a logistic regression test, with p&lt;0.05 was considered significant and Confidence Interval (CI) 95%. Seventy-eight liver cirrhosis patients were observed using a retrospective cohort method regarding the HE occurrence, and physical examination for ascites and laboratory examination were performed. The statistical analysis result of the correlation between ascites and HE is significant with an odds ratio of 5.108 and CI of 1.36-19.25. On the other hand, TLC has no significant correlation with the occurrence of HE. Based on this analysis result, it is concluded that ascites has a correlation with HE, but TLC does not.

APA, Harvard, Vancouver, ISO, and other styles

48

Primignani, Massimo, Giulia Tosetti, and Anna Maria Ierardi. "Approach to different thrombolysis techniques and timing of thrombolysis in the management of portal vein thrombosis in cirrhotic patients." Journal of Translational Internal Medicine 11, no. 3 (2023): 198–202. http://dx.doi.org/10.2478/jtim-2023-0113.

Full text

Abstract:

Abstract Thrombolysis is not currently recommended in cirrhotic patients with acute portal vein thrombosis (PVT) in most guidelines, because of the exceedingly limited data and the perceived high risk of bleeding adverse events. However, in the few studies including patients with cirrhosis, the rate of success was high and that of adverse events was similar in patients with or without cirrhosis. Hence, thrombolysis might be a rescue therapeutic option in patients with cirrhosis and acute, symptomatic thrombosis of the portal venous system, unresponsive to anticoagulation, provided a suitable timing is kept, less than 30 days and, if possible, less than 14 days from the acute onset of portal vein thrombosis. In this review perspective article, I discuss the several potential approaches of thrombolysis, either local or systemic, alone or combined with mechanical procedures for thrombus removal, or as a complement to Transjugular Intrahepatic Portosystemic Shunt placement, with a focus on the more suitable timing of thrombolysis. However, the very limited available data preclude from performing firm recommendations, and decision to carry out thrombolysis must take into account both the occurrence of major contraindications and the current critical clinical setting. In the next future, large high-quality multicentre studies will hopefully be able to settle more firm indications and preferable techniques.

APA, Harvard, Vancouver, ISO, and other styles

49

dos Remedios, Nick, Marie-Elise Lecoq, David Martin, and Sophia Ratcliffe. "The Living Atlases community in action: the NBN Atlas Spatial Portal and “Explore Your Region” module." Biodiversity Information Science and Standards 2 (May 21, 2018): e25486. http://dx.doi.org/10.3897/biss.2.25486.

Full text

Abstract:

Atlas of Living Australia (ALA) (https://www.ala.org.au/) is the Global Biodiversity Information Facility (GBIF) node of Australia. Since 2010, they have developed and improved a platform for sharing and exploring biodiversity information. All the modules are publicly available for reuse and customization on their GitHub account (https://github.com/AtlasOfLivingAustralia). The National Biodiversity Network, a registered charity, is the UK GBIF node and has been sharing biodiversity data since 2000. They published more than 79 million occurrences from 818 datasets. In 2016, they launched the NBN Atlas Scotland (https://scotland.nbnatlas.org/) based on the Atlas of Living Australia infrastructure. Since then, they released the NBN Atlas (https://nbnatlas.org/), the NBN Atlas Wales (https://wales.nbnatlas.org/) and soon the NBN Atlas Isle of Man. In addition to the occurrence/species search engine and the metadata registry, they put in place several tools that help users to work with data published in the network: the spatial portal and "explore your region" module. Both elements are based on Atlas of Living Australia developments. Because the Atlas of Living Australia platform is really powerful an reusable, we want to show you these two applications used to make geographical analyses. In order to perform this, we will present you the specificities of each component by giving examples of some functionalities.

APA, Harvard, Vancouver, ISO, and other styles

50

Rosenfeld, Sebastian, Claudia Maturana, Melisa Gañan, et al. "Revealing the hidden biodiversity of Antarctic and the Magellanic Sub-Antarctic Ecoregion: A comprehensive study of aquatic invertebrates from the BASE Project." Biodiversity Data Journal 11 (August 17, 2023): e108566. https://doi.org/10.3897/BDJ.11.e108566.

Full text

Abstract:

Antarctica, its outlying archipelagoes and the Magellanic Subantarctic (MSA) ecoregion are amongst the last true wilderness areas remaining on the planet. Therefore, the publication, citation and peer review of their biodiversity data are essential. The new Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), a Chilean scientific initiative funded by the National Agency of Research and Innovation, contributes 770 new records of aquatic invertebrates as a point of reference for present-day biodiversity research at these latitudes.The occurrence dataset presented here has never been released before and is the result of the systematic recording of occurrences of several taxa across the Antarctic, Subantarctic and Magellanic Subantarctic ecoregions. We collected data from marine and freshwater invertebrates across numerous samplings from 2008 to 2023. From the 770 occurrences, we identified 160 taxa, 125 at species level and 35 at the genus level. The database has been registered in the Global Biodiversity Information Facility (GBIF). The publication of this data paper was funded by the Belgian Science Policy Office (BELSPO, contract n°FR/36/AN1/AntaBIS) in the Framework of EU-Lifewatch as a contribution to the SCAR Antarctic biodiversity portal (biodiversity.aq)

APA, Harvard, Vancouver, ISO, and other styles

Journal articles on the topic 'Occurrence data portal'

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles