Novos registros da avifauna relacionada a áreas úmidas em Itajaí/SC, Sul do Brasil

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.

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.

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.

Data Auditing, Cleaning and Quality Assurance Workflows from the Experience of a Scholarly Publisher

Natural history collections (NHC) worldwide contain vast amount of valuable data that can be used to answer a wide range of questions by exploring biodiversity and natural resources records, having an immense potential to contribute to science, policy making and legislating, and to public scientific awareness. Likewise, the development and increase of global and regional biodiversity digital databases (e.g., Global Biodiversity Information Facility - GBIF; Fauna Europaea; Naturdata, etc.), scientific literature and all digital information regarding biodiversity, ecological areas and climate records comprise a huge amount of primary and processed digital ecological data (DED) accessible globally that can be readily used, at no cost, and integrated to further study e.g. biodiversity changes, ecological processes, natural habitat distribution, prioritizing ecosystem management and conservation actions, etc. Marine invertebrate biodiversity contributes to the structure and stability of ecosystem processes such as productivity, ecological networks, as well as nutrient and biogeochemical cycling having also an economic importance as a food source for local populations. Mangroves and seagrasses encompass ecological and socio-economic relevance as they have a preponderant role in marine and coastal ecosystem biodiversity and functioning providing a vast number of goods and services to local populations. Although generally pristine, mangroves and seagrasses in Africa are extremely vulnerable to the increased migration of rural populations to urban coastal areas and to extreme climate events. As a result, human activities such as construction, agriculture and food harvesting, provoke habitat degradation and biodiversity loss which will have further devastating consequences. The degradation and unsustainable use of these ecosystems have major drawbacks to the elimination of extreme poverty because this is one of the key factors that drive environmental degradation and biodiversity loss. The main goal of this work is to use NHC and digital repositories data (including scientific literature) to assess how biodiversity loss and habitat degradation affect ecosystem functioning and services provided by marine invertebrate communities of mangroves and seagrass meadows in the West and East African coast, using the case study of Mozambique and Príncipe’s Island. These will lead to the construction of a comprehensive dataset, an ecological model and a framework adapted to marine invertebrate biodiversity from Mozambique’s (MZ) and São Tomé and Príncipe’s (STP) mangroves and seagrasses as tools:1) integrate and disseminate marine invertebrate biodiversity data gathered along a spatio-temporal scale; 2) compare marine invertebrate assemblies from pristine and impacted habitats in African countries and predict the progress of these communities to habitat degradation and biodiversity loss; and 3) manage ecosystem functioning and services delivered by marine invertebrate assemblages under anthropogenic and environmental pressure scenarios. Specifically this project intends to: compile and integrate the available information contained in NHC and DED to develop a comprehensive spatio-temporal dataset on marine invertebrate biodiversity (e.g. species, number of individuals, local of occurrence and georeferencing, date of collection/observation), as well as mangroves and seagrasses distribution along the Mozambique’s and Príncipe’s coasts; assess different indexes of invertebrate marine biodiversity, biodiversity and habitat spatio-temporal distribution; develop an ecological network approach to assess the functional links of marine invertebrate communities within the studied habitats, and to refine their role in ecosystem functioning, as well as ecosystem services (ES) provided by marine invertebrates in mangroves and seagrasses from MZ and STP; construct a model to evaluate the ecological responses of mangrove and seagrass invertebrate communities to habitat degradation and biodiversity loss and to predict multi-dimensional (spatial, temporal, and social) trade-offs in local/regional ecosystem services along a spatio-temporal gradient; develop a practical framework to manage and preserve ecosystem functioning and services delivered by mangrove and seagrass marine invertebrates under a global change scenario. compile and integrate the available information contained in NHC and DED to develop a comprehensive spatio-temporal dataset on marine invertebrate biodiversity (e.g. species, number of individuals, local of occurrence and georeferencing, date of collection/observation), as well as mangroves and seagrasses distribution along the Mozambique’s and Príncipe’s coasts; assess different indexes of invertebrate marine biodiversity, biodiversity and habitat spatio-temporal distribution; develop an ecological network approach to assess the functional links of marine invertebrate communities within the studied habitats, and to refine their role in ecosystem functioning, as well as ecosystem services (ES) provided by marine invertebrates in mangroves and seagrasses from MZ and STP; construct a model to evaluate the ecological responses of mangrove and seagrass invertebrate communities to habitat degradation and biodiversity loss and to predict multi-dimensional (spatial, temporal, and social) trade-offs in local/regional ecosystem services along a spatio-temporal gradient; develop a practical framework to manage and preserve ecosystem functioning and services delivered by mangrove and seagrass marine invertebrates under a global change scenario.

The Open Biodiversity Knowledge Management (eco-)System: Tools and Services for Extraction, Mobilization, Handling and Re-use of Data from the Published Literature

Culturally diverse expert teams have yet to bring comprehensive linguistic diversity to intergovernmental ecosystem assessments

The global effort to digitize biodiversity occurrence data from collections, museums and other institutions has stimulated the development of important tools to improve the knowledge and conservation of biodiversity. The Global Biodiversity Information Facility (GBIF) enables and opens access to biodiversity data of 321 million of records, from 379 host institutions. Neotropical bats are a highly diverse and specialized group, and the geographic information about them is increasing since few years ago, but there are a few reports about this topic. The aim of this study was to analyze the number of digital records in GBIF of Neotropical bats with distribution in 21 American countries, evaluating their nomenclatural and geographical consistence at scale of country. Moreover, we evaluated the gaps of information on 1 degrees latitude x 1 degrees longitude grids cells. There were over 1/2 million records, but 58% of them have no latitude and longitude data; and 52% full fit nomenclatural and geographic evaluation. We estimated that there are no records in 54% of the analyzed area; the principal gaps are in biodiversity hotspots like the Colombian and Brazilian Amazonia and Southern Venezuela. In conclusion, our study suggests that available data on GBIF have nomenclatural and geographic biases. GBIF data represent partially the bat species richness and the main gaps in information are in South America.

In the current information environment, libraries need to leverage on the latest digital technologies as well as the traditional paper technologies towards building practical digital libraries and electronic information systems. Digital libraries built exclusively out of nascent electronic publications such as e-journals, e-books, e-reference works (Web-based training programs, computer-based training programs, etc.), digital scholarly works (monographs, etc. in the public domain) and digitized documents conforming to standard digital formats are proving to be an uphill and unfinished task. Perhaps this could be the major reason why the start-success-finish ratio of most of the digital library initiatives, particularly initiated by isolated/individual libraries, is still left at alarmingly low numbers. We find the motivational and emotional bonding among the stakeholders melting down eventually as the digital library development process gets fired up. There are a host of problems the enthusiastic library fraternity face in their digital library development endeavours starting from copyright issues, technology complexities, infrastructure threats, diverse publication types, multiplicity of digital object formats and above all the publishers’ stringent policies and monopolies. It is therefore essential that the libraries adopt necessary strategies towards developing digital libraries from the lessons learnt. The monolithic and all-in-one-container approach is no longer feasible and no more advocated. It is imperative on the part of the information professional to have a componentized and a multi-system approach to knowledge technologies and information management. Seamless aggregation and meticulous integration of diverse datastreams, embracing the print as well as the electronic information, is the most appropriate strategy to be adopted and applied. This paper shares Indian Institute of Management Kozhikode's experience in creating a state-of-art digital library information system by seamlessly integrating and aggregating the print as well as the diverse and distributed digital content penetrating into its knowledge domain. The paper highlights significant features of IIMK's digital information system—the content aggregation and the content integration strategies we adopted for designing a scholarship Web portal and developing a digital library using the ‘Greenstone’ open source digital library software. The paper also highlights the role of libraries in promoting open access by setting up scholarly institutional repositories (IR). In summary, today's digital library information system is to be seen from a much wider and more holistic perspective, and provided with a much broadened meaning to hold and put together all the print, digital and electronic information available and accessible to the library.

A crucial component of the analysis of shotgun proteomics datasets is the search engine, an algorithm that attempts to identify the peptide sequence from the parent molecular ion that produced each fragment ion spectrum in the dataset. There are many different search engines, both commercial and open source, each employing a somewhat different technique for spectrum identification. The set of high-scoring peptide-spectrum matches for a defined set of input spectra differs markedly among the various search engine results; individual engines each provide unique correct identifications among a core set of correlative identifications. This has led to the approach of combining the results from multiple search engines to achieve improved analysis of each dataset. Here we review the techniques and available software for combining the results of multiple search engines and briefly compare the relative performance of these techniques.

Limitations in Global Information on Species Occurrences

The collaboration between LifeWatch ERIC and DiSSCo (Distributed System of Scientific Collections), both pan-European research infrastructures focusing on biodiversity, can be achieved in a number of ways. The direct initiation of this collaboration can be carried out through their joint support to GBIF (Global Biodiversity Information Facility). This approach will facilitate meeting GBIF’s overall objective stated as: “Connecting data and expertise: a new alliance for biodiversity knowledge” (Hobern and Miller 2019). LifeWatch ERIC supports GBIF in a collaborative way by integrating and providing e-Services according to Global Biodiversity Informatics Outlook (GBIO) Framework objectives (Fig. 1), particularly suitable for the Understanding focus area. This concentrates on building modeled representations of biodiversity patterns and properties, based on any possible evidence, using the following components: Multiscale species modelling; Trends and predictions; Modelling biological systems; Visualization and dissemination; Prioritizing new data capture. Multiscale species modelling; Trends and predictions; Modelling biological systems; Visualization and dissemination; Prioritizing new data capture. In this regard, and during the 2nd Global Biodiversity Information Conference, LifeWatch ERIC actively participated in one of the four parallel working groups reviewing different components from the GBIO framework. Each component was selected to capture information on a broad range of different challenges and opportunities. At the same event, DiSSCo mainly focused on the Data layer, as the main provider of data and other types of collections resources in Europe. The Evidence layer is the fertile interface to develop sound synergies for collaboration by both research infrastructures in order to support GBIF through the development of 3 concrete activities: Participation in the co-design, development and deployment of a multi-purpose Virtual Research Environment (VRE) to support DiSSCo, specifically by integrating the collections e-Services and by engaging the various communities of practice; Participation in the co-design and co-implementation of relevant e-Services in LifeBlock (LifeWatch ERIC blockchain-based technology platform); The active participation of DiSSCo for integrating collections data: DiSSCo is one of the main resources needed for the integration of GLOBIS-B GLOBal Infrastructures for Supporting Biodiversity work on Essential Biodiversity Variables (EBVs) (Kissling et al. 2018). Thus, EBVs together with species traits will be integrated into LifeBlock platform in order to feed Ecosystem Services needed to further support Biodiversity Ecosystem Services VRE provided by LifeWatch ERIC distributed e-Infrastructure. Participation in the co-design, development and deployment of a multi-purpose Virtual Research Environment (VRE) to support DiSSCo, specifically by integrating the collections e-Services and by engaging the various communities of practice; Participation in the co-design and co-implementation of relevant e-Services in LifeBlock (LifeWatch ERIC blockchain-based technology platform); The active participation of DiSSCo for integrating collections data: DiSSCo is one of the main resources needed for the integration of GLOBIS-B GLOBal Infrastructures for Supporting Biodiversity work on Essential Biodiversity Variables (EBVs) (Kissling et al. 2018). Thus, EBVs together with species traits will be integrated into LifeBlock platform in order to feed Ecosystem Services needed to further support Biodiversity Ecosystem Services VRE provided by LifeWatch ERIC distributed e-Infrastructure.

As one of the first advocates of open access and open data in the field of biodiversity publishiing, Pensoft has adopted a multiple data publishing model, resulting in the ARPHA-BioDiv toolbox (Penev et al. 2017). ARPHA-BioDiv consists of several data publishing workflows and tools described in the Strategies and Guidelines for Publishing of Biodiversity Data and elsewhere: Data underlying research results are deposited in an external repository and/or published as supplementary file(s) to the article and then linked/cited in the article text; supplementary files are published under their own DOIs and bear their own citation details. Data deposited in trusted repositories and/or supplementary files and described in data papers; data papers may be submitted in text format or converted into manuscripts from Ecological Metadata Language (EML) metadata. Integrated narrative and data publishing realised by the Biodiversity Data Journal, where structured data are imported into the article text from tables or via web services and downloaded/distributed from the published article. Data published in structured, semanticaly enriched, full-text XMLs, so that several data elements can thereafter easily be harvested by machines. Linked Open Data (LOD) extracted from literature, converted into interoperable RDF triples in accordance with the OpenBiodiv-O ontology (Senderov et al. 2018) and stored in the OpenBiodiv Biodiversity Knowledge Graph. Data underlying research results are deposited in an external repository and/or published as supplementary file(s) to the article and then linked/cited in the article text; supplementary files are published under their own DOIs and bear their own citation details. Data deposited in trusted repositories and/or supplementary files and described in data papers; data papers may be submitted in text format or converted into manuscripts from Ecological Metadata Language (EML) metadata. Integrated narrative and data publishing realised by the Biodiversity Data Journal, where structured data are imported into the article text from tables or via web services and downloaded/distributed from the published article. Data published in structured, semanticaly enriched, full-text XMLs, so that several data elements can thereafter easily be harvested by machines. Linked Open Data (LOD) extracted from literature, converted into interoperable RDF triples in accordance with the OpenBiodiv-O ontology (Senderov et al. 2018) and stored in the OpenBiodiv Biodiversity Knowledge Graph. The above mentioned approaches are supported by a whole ecosystem of additional workflows and tools, for example: (1) pre-publication data auditing, involving both human and machine data quality checks (workflow 2); (2) web-service integration with data repositories and data centres, such as Global Biodiversity Information Facility (GBIF), Barcode of Life Data Systems (BOLD), Integrated Digitized Biocollections (iDigBio), Data Observation Network for Earth (DataONE), Long Term Ecological Research (LTER), PlutoF, Dryad, and others (workflows 1,2); (3) semantic markup of the article texts in the TaxPub format facilitating further extraction, distribution and re-use of sub-article elements and data (workflows 3,4); (4) server-to-server import of specimen data from GBIF, BOLD, iDigBio and PlutoR into manuscript text (workflow 3); (5) automated conversion of EML metadata into data paper manuscripts (workflow 2); (6) export of Darwin Core Archive and automated deposition in GBIF (workflow 3); (7) submission of individual images and supplementary data under own DOIs to the Biodiversity Literature Repository, BLR (workflows 1-3); (8) conversion of key data elements from TaxPub articles and taxonomic treatments extracted by Plazi into RDF handled by OpenBiodiv (workflow 5). These approaches represent different aspects of the prospective scholarly publishing of biodiversity data, which in a combination with text and data mining (TDM) technologies for legacy literature (PDF) developed by Plazi, lay the ground of an entire data publishing ecosystem for biodiversity, supplying FAIR (Findable, Accessible, Interoperable and Reusable data to several interoperable overarching infrastructures, such as GBIF, BLR, Plazi TreatmentBank, OpenBiodiv and various end users.

Every five years the Global Biodiversity Information Facility (GBIF) reevaluates its work in an updated Strategic Framework. The latest was recently approved and will be in effect 2023–2027. In responding to our Governing Board and network expectations to accelerate data mobilization and capacity enhancement to improve science for research and policy relevance, the new Framework specifically responds to the biodiversity crisis in its Vision, Mission and Values statements. In addition to the successful national data mobilization framework, GBIF is developing thematic data use cases to accelerate towards the goals set forth in the Framework's priority areas. The thematic data mobilization will identify critical data gaps in areas of research and policy importance and work with new communities to mobilize this data into the GBIF network. Additionally, we will work with user communities to facilitate and track data use. These thematic topics will include areas of interest to global policy initiatives, such as human health, invasive species, agricultural biodiversity, eDNA and others. Aligned with this work is the enhancement of the GBIF Data Model, based on DwC, to better integrate data from diverse sources. We expect that this advancement will encourage the publishing of more and diverse data types that can be used to improve science for research and policy relevance of GBIF-mediated data. In order to accomplish this ambitious Strategic Framework, GBIF will also need to evolve how we operate. The pandemic has taught us that virtual interactions are positive, but have limits. We are developing a more distributed workforce and importantly expanding collaborations, such as with the Atlas of Living Australia, Biodiversity Information Standards (TDWG), and the Catalogue of Life on joint infrastructure and models. These alliances build interoperability, enlarge and improve data mobilization and use, and quicken knowledge growth to strengthen the entire biodiversity knowledge network to meet our critical needs.

Editor's SummaryThough natural history collections are long established and numerous, data on biodiversity is sparse, poorly developed, inconsistent and rarely digitally preserved, and their providers are often inaccessible. The Global Biodiversity Information Facility (GBIF) and the Taxonomic Databases Working Group (TDWG) for Biodiversity Information Standards are leading efforts to overcome such barriers. The GBIF has collected over 200 million records formally describing natural history specimens from hundreds of sources, while also serving the rapidly growing online community of amateur field observers. The two organizations face challenges arising from ambiguity of taxonomic names and the need to make voluminous and critical historical collections available and to develop standard metadata vocabularies that can be understood and used by all. The combination of science informatics tools, including a robust vocabulary and linked data conventions, with a networked, active user community will enable effective biodiversity data management over the long term.