Show Me The Data: An Evaluation Of Data Access In The JRS Grant Portfolio

In order to be useful for biodiversity conservation and sustainable development, biodiversity information must be not only available, but also accessible.The JRS Biodiversity Foundation contracted an independent study to assess the level to which data produced by JRS-funded projects were discoverable online, and the ease with which those data could be viewed or downloaded. Only about half of the expected data products were viewable or discoverable online, and in many cases data were not clearly connected with project results. Data accessibility was not dependent on the country in which the project was located, and hasn't changed over time. Interviews with grantees helped to identify challenges to and enabling conditions for creating sharable data products. JRS is actively responding to the findings of this study through new planning tools to support future grantees and a data sharing policy that explicitly supports open access to data and data publication to well-recognized and secure repositories

Ciencia ciudadana y datos de biodiversidad: ¿qué datos importan? ¿cómo los anoto?

La Ciencia Ciudadana es una fuente muy importante de datos de biodiversidad. Personas alrededor de todo el mundo capturan datos de ocurrencia de especies que son fundamentales para comprender el estado y dinámica de las poblaciones y para planificar la toma de decisiones, en cuanto a manejo y protección de la biodiversidad. Sin embargo, no todos los datos adquiridos de esta forma son utilizables.Facultad de Informátic

Datos de biodiversidad, estándar Darwin Core y ciencia ciudadana: una trilogía dorada

Ciencia ciudadana: contribución activa de los ciudadanos a la ciencia con su esfuerzo intelectual o dando soporte al conocimiento, proveyendo datos experimentales o equipos a los investigadores.Facultad de Informátic

ARTHROPOD PREY AVAILABILITY AND BREEDING OF THE THREATENED STRANGE‐TAILED TYRANT (ALECTRURUS RISORA)

ABSTRACT ∙ The Strange‐tailed Tyrant (Alectrurus risora) is an insectivorous flycatcher (Tyrannidae) endemic to the natural tall grasslands of northern Argentina and southern Paraguay. Alectrurus risora has a polygynous mating system and the abundance of arthropods could be a major factor determining the establishment of male breeding territories and the extent of the breeding season, which is shorter than in most other reported tyrant flycatchers. To investigate this hypothesis, we examined the abundance of arthropods in upland and lowland breeding habitats. Upland habitats seem to be preferred for breeding, and usually harbour more nests. Data from one year showed that, for both grasslands, the beginning of the breeding season coincides with a greater availability of arthropods, and that the short reproductive season of A. risora coincides with a general lower availability of prey during February and March in the year we conducted the study. In upland territories, males attracted more females and had more active nests than males holding territories in lowland grasslands. However, the abundance and biomass of total arthropods and of potential prey were higher in lowland than in upland grasslands, with the exception of the abundance of Orthoptera, which was higher in upland habitat and could represent one of the major prey items. Therefore, we conclude that 1) female preference for males in upland grasslands cannot be explained by higher arthropod prey availability, and 2) the availability of arthropod prey may be important in determining the extent of the breeding season, although further, multiannual studies are required to corroborate this hypothesis. RESUMEN ∙ Disponibilidad de artrópodos presa asociados a territorios de reproducción de un ave en peligro de extinción, el Yetapá de Collar (Alectrurus risora) El Yetapá de Collar (Alectrurus risora) es un tiránido insectívoro endémico de los pastizales altos naturales del norte de Argentina y sur de Paraguay, que posee una temporada reproductiva más corta que aquella reportada para la mayoría de los tiránidos. Alectrurus risora posee un sistema de apareamiento poligínico, y la abundancia de artrópodos podría representar un factor determinante en el establecimiento de los territorios de los machos y en la duración de la temporada reproductiva. Con el fin de investigar esta hipótesis examinamos la abundancia de artrópodos en hábitats reproductivos de pastizales altos y bajos. Los pastizales altos parecen ser más utilizados durante la época reproductiva y usualmente albergan un mayor número de nidos activos. Los datos de un año de muestreo mostraron que el inicio de la temporada reproductiva coincide con el pico de abundancia de artrópodos en ambos pastizales, y que su corta duración coincide, para el área en estudio durante el año analizado, con una menor disponibilidad de presas durante los meses de febrero y marzo. En los territorios ubicados en el pastizal alto los machos atrajeron más hembras y tuvieron más nidos activos que en los territorios de pastizal bajo. Sin embargo, la abundancia y biomasa de artrópodos totales y de presas potenciales fueron mayores en el pastizal bajo, con la excepción de la abundancia de Orthoptera, que podría representar uno de los tipos principales de presa. A partir de estos resultados, concluimos que 1) la preferencia de las hembras por machos en el pastizal alto no puede ser explicada por una mayor disponibilidad de artrópodos presa, y 2) la disponibilidad de artrópodos presa podría representar un factor importante en la determinación de la extensión de la temporada reproductiva, pero se requieren estudios adicionales, plurianuales, para corroborar esta hipótesis.

Data standardization of plant-pollinator interactions

Background Animal pollination is an important ecosystem function and service, ensuring both the integrity of natural systems and human well-being. Although many knowledge shortfalls remain, some high-quality data sets on biological interactions are now available. The development and adoption of standards for biodiversity data and metadata has promoted great advances in biological data sharing and aggregation, supporting large-scale studies and science-based public policies. However, these standards are currently not suitable to fully support interaction data sharing. Results Here we present a vocabulary of terms and a data model for sharing plant–pollinator interactions data based on the Darwin Core standard. The vocabulary introduces 48 new terms targeting several aspects of plant–pollinator interactions and can be used to capture information from different approaches and scales. Additionally, we provide solutions for data serialization using RDF, XML, and DwC-Archives and recommendations of existing controlled vocabularies for some of the terms. Our contribution supports open access to standardized data on plant–pollinator interactions. Conclusions The adoption of the vocabulary would facilitate data sharing to support studies ranging from the spatial and temporal distribution of interactions to the taxonomic, phenological, functional, and phylogenetic aspects of plant–pollinator interactions. We expect to fill data and knowledge gaps, thus further enabling scientific research on the ecology and evolution of plant–pollinator communities, biodiversity conservation, ecosystem services, and the development of public policies. The proposed data model is flexible and can be adapted for sharing other types of interactions data by developing discipline-specific vocabularies of terms

Data standardization of plant-pollinator interactions

Background: Animal pollination is an important ecosystem function and service, ensuring both the integrity of natural systems and human well-being. Although many knowledge shortfalls remain, some high-quality data sets on biological interactions are now available. The development and adoption of standards for biodiversity data and metadata has promoted great advances in biological data sharing and aggregation, supporting large-scale studies and science-based public policies. However, these standards are currently not suitable to fully support interaction data sharing. Results: Here we present a vocabulary of terms and a data model for sharing plant–pollinator interactions data based on the Darwin Core standard. The vocabulary introduces 48 new terms targeting several aspects of plant–pollinator interactions and can be used to capture information from different approaches and scales. Additionally, we provide solutions for data serialization using RDF, XML, and DwC-Archives and recommendations of existing controlled vocabularies for some of the terms. Our contribution supports open access to standardized data on plant–pollinator interactions. Conclusions: The adoption of the vocabulary would facilitate data sharing to support studies ranging from the spatial and temporal distribution of interactions to the taxonomic, phenological, functional, and phylogenetic aspects of plant–pollinator interactions. We expect to fill data and knowledge gaps, thus further enabling scientific research on the ecology and evolution of plant–pollinator communities, biodiversity conservation, ecosystem services, and the development of public policies. The proposed data model is flexible and can be adapted for sharing other types of interactions data by developing discipline-specific vocabularies of terms.Fil: Salim, José A. Universidade de Sao Paulo; BrasilFil: Saraiva, Antonio M.. Universidade de Sao Paulo; BrasilFil: Zermoglio, Paula Florencia. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Patagonia Norte. Instituto de Investigaciones En Recursos Naturales, Agroecologia y Desarrollo Rural. - Universidad Nacional de Rio Negro. Instituto de Investigaciones En Recursos Naturales, Agroecologia y Desarrollo Rural.; ArgentinaFil: Agostini, Kayna. Universidade Federal do São Carlos; BrasilFil: Wolowski, Marina. Universidade Federal de Alfenas; BrasilFil: Drucker, Debora P.. Empresa Brasileira de Pesquisa Agropecuaria (embrapa);Fil: Soares, Filipi M.. Universidade de Sao Paulo; BrasilFil: Bergamo, Pedro J.. Jardim Botânico do Rio de Janeiro; BrasilFil: Varassin, Isabela G.. Universidade Federal do Paraná; BrasilFil: Freitas, Leandro. Jardim Botânico do Rio de Janeiro; BrasilFil: Maués, Márcia M.. Empresa Brasileira de Pesquisa Agropecuaria (embrapa);Fil: Rech, Andre R.. Universidade Federal dos Vales do Jequitinhonha e Mucuri; BrasilFil: Veiga, Allan K.. Universidade de Sao Paulo; BrasilFil: Acosta, Andre L.. Instituto Tecnológico Vale; BrasilFil: Araujo, Andréa C. Universidade Federal do Mato Grosso do Sul; BrasilFil: Nogueira, Anselmo. Universidad Federal do Abc; BrasilFil: Blochtein, Betina. Pontificia Universidade Católica do Rio Grande do Sul; BrasilFil: Freitas, Breno M.. Universidade Estadual do Ceará; BrasilFil: Albertini, Bruno C.. Universidade de Sao Paulo; BrasilFil: Maia Silva, Camila. Universidade Federal Rural Do Semi Arido; BrasilFil: Nunes, Carlos E. P.. University of Stirling; BrasilFil: Pires, Carmen S. S.. Empresa Brasileira de Pesquisa Agropecuaria (embrapa);Fil: Dos Santos, Charles F.. Pontificia Universidade Católica do Rio Grande do Sul; BrasilFil: Queiroz, Elisa P.. Universidade de Sao Paulo; BrasilFil: Cartolano, Etienne A.. Universidade de Sao Paulo; BrasilFil: de Oliveira, Favízia F. Universidade Federal da Bahia; BrasilFil: Amorim, Felipe W.. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Fontúrbel, Francisco E.. Pontificia Universidad Católica de Valparaíso; ChileFil: da Silva, Gleycon V.. Ministério da Ciência, Tecnologia, Inovações. Instituto Nacional de Pesquisas da Amazônia; BrasilFil: Consolaro, Hélder. Universidade Federal de Catalão; Brasi

Data standardization of plant–pollinator interactions

Background: Animal pollination is an important ecosystem function and service, ensuring both the integrity of natural systems and human well-being. Although many knowledge shortfalls remain, some high-quality data sets on biological interactions are now available. The development and adoption of standards for biodiversity data and metadata has promoted great advances in biological data sharing and aggregation, supporting large-scale studies and science-based public policies. However, these standards are currently not suitable to fully support interaction data sharing. Results: Here we present a vocabulary of terms and a data model for sharing plant–pollinator interactions data based on the Darwin Core standard. The vocabulary introduces 48 new terms targeting several aspects of plant–pollinator interactions and can be used to capture information from different approaches and scales. Additionally, we provide solutions for data serialization using RDF, XML, and DwC-Archives and recommendations of existing controlled vocabularies for some of the terms. Our contribution supports open access to standardized data on plant–pollinator interactions. Conclusions: The adoption of the vocabulary would facilitate data sharing to support studies ranging from the spatial and temporal distribution of interactions to the taxonomic, phenological, functional, and phylogenetic aspects of plant–pollinator interactions. We expect to fill data and knowledge gaps, thus further enabling scientific research on the ecology and evolution of plant–pollinator communities, biodiversity conservation, ecosystem services, and the development of public policies. The proposed data model is flexible and can be adapted for sharing other types of interactions data by developing discipline-specific vocabularies of termsinfo:eu-repo/semantics/publishedVersio

Unlocking Inventory Data Capture, Sharing and Reuse: The Humboldt Extension to Darwin Core

Biodiversity inventories, i.e., recording multiple species at a specific place and time, are routinely performed and offer high-quality data for characterizing biodiversity and its change. Digitization, sharing and reuse of incidental point records (i.e., records that are not readily associated with systematic sampling or monitoring, typically museum specimens and many observations from citizen science projects) has been the focus for many years in the biodiversity data community. Only more recently, attention has been directed towards mobilizing data from both new and longstanding inventories and monitoring efforts. These kinds of studies provide very rich data that can enable inferences about species absence, but their reliability depends on the methodology implemented, the survey effort and completeness. The information about these elements has often been regarded as metadata and captured in an unstructured manner, thus making their full use very challenging.Unlocking and integrating inventory data requires data standards that can facilitate capture and sharing of data with the appropriate depth. The Darwin Core standard (Wieczorek et al. 2012) currently enables reporting some of the information contained in inventories, particularly using Darwin Core Event terms such as samplingProtocol, sampleSizeValue, sampleSizeUnit, samplingEffort. However, it is limited in its ability to accommodate spatial, temporal, and taxonomic scopes, and other key aspects of the inventory sampling process, such as direct or inferred measures of sampling effort and completeness. The lack of a standardized way to share inventory data has hindered their mobilization, integration, and broad reuse. In an effort to overcome these limitations, a framework was developed to standardize inventory data reporting: Humboldt Core (Guralnick et al. 2018). Humboldt Core identified three types of inventories (single, elementary, and summary inventories) and proposed a series of terms to report their content. These terms were organized in six categories: dataset and identification; geospatial and habitat scope; temporal scope; taxonomic scope; methodology description; and completeness and effort. While originally planned as a new TDWG standard and being currently implemented in Map of Life (https://mol.org/humboldtcore/), ratification was not pursued at the time, thus limiting broader community adoption.In 2021 the TDWG Humboldt Core Task Group was established to review how to best integrate the terms proposed in the original publication with existing standards and implementation schemas. The first goal of the task group was to determine whether a new, separate standard was needed or if an extension to Darwin Core could accommodate the terms necessary to describe the relevant information elements. Since the different types of inventories can be thought of as Events with different nesting levels (events within events, e.g., plots within sites), and after an initial mapping to existing Darwin Core terms, it was deemed appropriate to start from a Darwin Core Event Core and build an extension to include Humboldt Core terms. The task group members are currently revising all original Humboldt Core terms, reformulating definitions, comments, and examples, and discarding or adding new terms where needed. We are also gathering real datasets to test the use of the extension once an initial list of revised terms is ready, before undergoing a public review period as established by the TDWG process.Through the ratification of Humboldt Core as a TDWG extension, we expect to provide the community with a solution to share and use inventory data, which improves biodiversity data discoverability, interoperability and reuse while lowering the reporting burden at different levels (data collection, integration and sharing)

Building community-specific standards and vocabularies: prospects and challenges for linking to the broader community - The SINP Case

Biodiversity data may come from myriad sources. From data capture in the field through digitization processes, each source may choose distinctive ways to capture data. When it comes to sharing data more broadly at national or regional levels, it is imperative that data is presented in ways that encourage understanding both by humans and machines, allowing aggregation and serving the data back to the community. This implies two levels of agreement, one at a structural level, where data is organized under certain terms or fields, and another related to the actual values contained in such fields. Since its ratification in 2009, the Darwin Core standard Wieczorek et al. (2012) has been increasingly used across the community to respond to the first need, providing a relatively simple means to organize shared data. Nonetheless, despite its broad acceptance, efforts to develop different standards to answer the same problems are not uncommon among some stakeholders, and may introduce yet another issue: reconciling the data shared under different standards. The second level of agreement, at the value level, constitutes a much more complex issue, partly given the nature of biodiversity data and partly due to social constraints. Many potential, partial solutions involving the development of dictionaries and controlled vocabularies are found scattered across the community. As the lack of homogeneity renders data less discoverable (Zermoglio et al. 2016) and therefore less usable for research and decision making, there exists a growing need for unifying such efforts. As part of the Biodiversity Information System on Nature and Landscapes (SINP), the French National Museum of Natural History was appointed to develop biodiversity data exchange standards, with the goal of sharing French marine and terrestrial data at the national level, meeting national and European requirements (e.g., the European INSPIRE Directive European Commission 2017). The French data providers include a broad range of people with diverse backgrounds. While some stakeholders can provide data under very specific constraints and formats, others lack the capabilities or resources to do so. The variability in the data provided therefore extends through both the structure and the value levels. In order to integrate the data in a coherent national system, a dedicated working group was assembled, mobilizing a range of biodiversity stakeholders and experts. Existing standards were compared, existing vocabularies gathered and compiled for review by experts, and then presented to the working group. As a result, a set of terms and associated controlled vocabularies was established. Finally, the set was released to the public to test and amended as needed. The results of the French initiative proved useful to compile and share data at the national level, bringing together data providers that otherwise would have been excluded. However, at a global scale, it faces some challenges that still need to be fully addressed. For instance, the standards created do not have an exact correspondence with Darwin Core, and so a complex mapping is required in order to integrate the data with that of the rest of the community. A serious mapping effort is being carried out as the national standards progress and has already rendered good results (Jomier and Pamerlon 2016). Regardless of the problems that remain to be solved, some lessons can be learnt from this effort. Getting actively involved in the broader, global community can help identify available tools, resources and expertise, and avoid repeated efforts that can be costly and time-consuming. Furthermore, re-using elements that already have been proven to work, prevents the need for reconciliations and makes data integration easier. With the ultimate goal of making biodiversity data readily available, these lessons should be kept in mind for future initiatives

Translating TDWG Controlled Vocabularies

Users may be more likely to understand and utilize standards if they are able to read labels and definitions of terms in their own languages. Increasing standards usage in non-English speaking parts of the world will be important for making biodiversity data from across the globe more uniformly available. For these reasons, it is important for Biodiversity Information Standards (TDWG) to make its standards widely available in as many languages as possible. Currently, TDWG has six ratified controlled vocabularies*1, 2, 3, 4, 5, 6 that were originally available only in English. As an outcome of this workshop, we have made term labels and definitions in those vocabularies available in the languages of translators who participated in its sessions. In the introduction, we reviewed the concept of vocabularies, explained the distinction between term labels and controlled value strings, and described how multilingual labels and definitions fit into the standards development process. The introduction was followed by working sessions in which individual translators or small groups working in a single language filled out Google Sheets with their translations. The resulting translations were compiled along with attribution information for the translators and made freely available in JavaScript Object Notation (JSON) and comma separated values (CSV) formats.*