COL and GBIF have united their capabilities to make ChecklistBank, a publishing platform and repository focused on taxonomic checklist and nomenclatural datasets including TreatmentBank datasets, classifications, species hypotheses, (M)OTUs and BINs from e.g. Barcode of Life, NCBI Taxonomy/ENA, UNITE/PlutoF. Data and tooling are also used to create custom taxonomic data products by COL and GBIF.
ChecklistBank is open for others to add and use. It generates a standardised interpretation of data. Tooling is offered for matching and search for name usages across different datasets (checklists) and to compare name usages between datasets through stable name usage identifiers. All datasets can be searched, browsed, downloaded or accessed programmatically via the ChecklistBank API.
The e-Biodiversity matching services, in short e-Biodiv, are a set of services and Graphic User Interfaces to support the linking of specimen and material citation data. These pairs are based on material citations in GBIF mediated by Plazi and discovered by applying the clustering algorithm in GBIF.
LifeBlock is a service developed by LifeWatch ERIC that provides federated search and semantic search on any of the research infrastructures. The user can search and then store the results in a dedicated account that preserves the traceability of all the information management following FAIR principles. LifeBlock can search both metadata and data. Additionally, advanced users can create their own applications and implement them to manage the information retrieved.
OpenBiodiv offers a broad biodiversity-related querying system answering open-ended queries based on the data extracted and converted to RDF from Pensoft journals and Plazi’s taxon treatments. Data can be explored in four different ways: General search, SPARQL, User applications and API. OpenBiodiv can discover hidden links within biodiversity data (e.g. between authors, taxa, sequences, material citations, publications and others) and can guide research into how data is used in scholarly articles.
PlutoF offers a third-party curation service to improve the quality of public DNA sequences and their source metadata (e.g., on material source, geolocation and habitat, taxonomic identifications, interacting taxa, literature, etc.) In collaboration with EMBL-EBI, improved or corrected annotations on INSD sequences in PlutoF are fed back to primary repositories through operating the ELIXIR Contextual Data ClearingHouse. Searching and browsing of third-party annotations introduced by the UNITE Community can be done via RESTful API or using search interfaces of PlutoF and UNITE.
A custom search engine to explore biodiversity literature alongside biomedical biomedicallogical literature (e.g., PMC, MEDLINE). The service provides access to Pazi’s taxonomic treatments in JATS/TaxPub formats. Based on the SIB Literature Services (SIBiLS), all contents have been semantically enriched with several domain-specific onto-terminologies (e.g. NCBI Taxonomy, Open Tree of Life, Gene Ontology) to enable users to author semantically enhanced queries. Inspired by the “One Health” recommendations of WHO, the service is enhancing the coverage of PubMed Central by integrating a growing collection of Open Access full-text publications in biodiversity related fields, such as ecology and taxonomy. The data are distributed under CC-BY licences in BioC formats.
The biotic interactions browser searches the literature to identify pairs of species that could have a biotic relationship. Each identified interaction is accompanied by one or several relevant passages extracted from the scientific literature. With this tool, users can discover new biotic interactions and understand how they are established.
The SIBiLS SPARQL endpoint allows to run SPARQL queries on a subset of annotated PMC publications. The textual content and structure (title, sections, paragraphs, etc.) is described as well as a list of named entities (multidimensional concepts) found and located in the full text of the publications. The ontology used to describe the publications can be found here. The triple store contains a sample of 3000 publications at the moment. The content of the triple store will be extended in the future and include alternate publication sources as well.
Synospecies is using published taxonomic treatment citations to represent the history of taxonomic names. A visualisation provides an overview of the history and a SPARQL endpoint is available for exploration. The data is provided by TreatmentBank and is available as RDF.
TreatmentBank provides an access point to explore and discover data liberated from publications, and to bidirectional links created by the deposition of data to respective services (Catalogue of Life / ChecklistBank; GBIF; ENA; Zenodo (Biodiversity Literature Service)
ARPHA Writing Tool 2.0 (AWT 2.0) is an XML-based, WYSIWYG (What-You-See-Is-What-You-Get) authoring tool, which allows co-authors and collaborators to work conveniently together on manuscripts before submission to a journal. To ensure interoperability and prompt re-use of data after publication, the tool relies on semantic enhancements and PIDs, vocabularies and ontologies.
To cater for the specifics of biodiversity publications, AWT 2.0 supports various domain-specific workflows, including data import and export, as well as bi-directional links with leading aggregators, e.g. GBIF, BOLD, INSDC, Catalogue of Life, ChecklistBank, TreatmentBank, BHL, Biodiversity Literature Repository, BiodiversityPMC (SiBILS) and others.
Nanopublications allow researchers to ‘fragment’ their most important scientific findings into ‘pixels of knowledge’, where each assertion becomes findable, accessible, interoperable and reusable (FAIR). Nanopublications can also be used to annotate existing publications or other online resources.
The Nanopublications-for-Biodiversity workflow and templates support various associations, such as those between organisms, between taxa, between taxa and environments, between organisms and nucleotide sequences amongst others. To do this, the domain-specific workflow and templates rely on community-agreed and widely used standards and persistent identifiers and API services from the likes of ChecklistBank, Catalogue of Life, GBIF, GenBank/ENA, BOLD, Darwin Core, ZooBank, Index Fungorum, MycoBank, IPNI and TreatmentBank.
Nanopublications can be published in association to a manuscript in BDJ, as standalone publications related to any other article or online resource or as annotation to any article published on ARPHA.
Nanopublications-for-Biodiversity is a collaboration project between Pensoft and Knowledge Pixels AG using the Nanodash tool.
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