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EXPLORE Infrastructures & Organisations

Explore (meta)data, tools and services offered by the participating Research Infrastructures and Network Organisations

 

Please contact the service provider directly if you have any questions or comments

Name of the infrastructure: ARPHA-XML

Supporting organisation: Pensoft Publishers

Brief description:  Full-featured publishing platform supporting the full manuscript life cycle: authoring, peer review, publication and dissemination, with the ARPHA Writing Tool (AWT) at the core of it. The host of the Biodiversity Data Journal, RIO Journal, and others. 

Data types: Published information on specimens, sequences, taxon names, taxonomic treatments, bibliographies, and others. 

Services: ARPHA-XML provides services to researchers and journals, including several unique services for biodiversity: import, exchange and semantic enrichment of data in an entirely XML-based environment.

Website: https://arphahub.com

API: https://arphahub.com/about/OAI-PMH  

Name of the infrastructure: International Barcode of Life (iBOL)

Supporting organisation: Centre for Biodiversity Genomics

Brief description: A global network to deliver reference data and tools for sequence-based species identification using DNA barcodes.

Data types: Specimens, sequences, molecular OTUs, images

Services: DNA barcode reference data, cross-walk of scientific names to moleular OTUs (BINs), identification from DNA barcodes

Website: https://boldsystems.org/
API: Documentation: http://v4.boldsystems.org/index.php/api_home   

Name of the infrastructure: Biodiversity Heritage Library (BHL)

Supporting organisation: Smithsonian Libraries and Archives

Brief description: BHL provides free access to nearly 300,000 volumes (over 60.5 million pages), from the 15th-21st centuries. Content includes public domain content as well as in-copyright materials made available through permission from rights holders.

Data types: Names, bibliographies, articles, full-text, PDFs

names, taxonomic treatments, persons, articles, bibliographies, and others. 

Services: Citable bibliography references to taxonomic information; downloadable PDFs; bibliographic DOIs.

Website: https://www.biodiversitylibrary.org/
API: Available APIs listed on this page

BLR

Name of the infrastructure: Biodiversity Literature Repository

Supporting organisation: Plazi 

Brief description: BHL provides findable, accessible, interoperable and reusable data liberated from scientific publications, with an emphasis on taxonomic treatments and figures with rich metadata.

Data types: Articles, treatments, figures accessible in JSON, HTML, PDF, PNG

Services: search and retrieval service 

Website: http://plazi.org/blr/ 

API: https://developers.zenodo.org/ 

BGBM-FUB

Name of the infrastructure: Herbarium B

Supporting organisation: Botanic Garden Berlin, Freie Universität Berlin

Brief description: The Botanic Garden Berlin is a centre of biodiversity research facilitating access to biodiversity data including data generated by the BGBM and data from cooperating scientists and infrastructures. The BGBM is committed to FAIR principles and provides services for 20 partner institutions.

Data types: Both living and preserved collections of plants, algae and fungi. Multimedia.

Services:

Website: https://www.bo.berlin/

API: (via JACQ) https://services.jacq.org/jacq-services/rest/JACQscinames/description.html

Name of the infrastructure: Catalogue of Life & ChecklistBank

Supporting organisation: Species 2000

Brief description: COL aims to deliver a consistent and up-to-date listing of all the world’s known species; the COL Checklist. ChecklistBank, developed by GBIF and COL, is a publishing platform and data infrastructure for taxonomic and nomenclatural datasets.

Data types: taxonomic checklists, nomenclature datasources literature references, type specimens, species descriptions/treatments, OTUs

Services: DOIs for COL Checklist releases, taxon name identifiers, transformation into data standards (e.g. DwC-A, ColDP, DOT, Newick); tools to share, discover, analyse, compare and download taxonomic datasets

Websites: Catalogue of Life & ChecklistBank
API: https://api.checklistbank.org

Name of the infrastructure: Distributed System of Scientific Collections (DiSSCo)

Supporting organisation: Naturalis Biodiversity Center

Brief description:  A World-class RI for integrated access to natural science collections in Europe that unifies all European natural science assets under common curation and access policies and practices. 

Data types: FAIR Digital Objects serialised as JSON and JSON-LD for Digital Specimens and related objects such as Media objects, Annotations, Facilities and Agents.

Services: digital specimens, collection management systems integration, PID infrastructure, unified curation and annotation system, digitisation services integration, unified loans and visits system, DO APIs. 

Website: https://dissco.eu, https://dissco.tech/,
API: RESTful JSON based: https://sandbox.dissco.tech/api/swagger-ui/index.html#/

Name of the infrastructure: European Nucleotide Archive (ENA)

Supporting organisation: European Molecular Biology Laboratories - European Bioinformatics Institute (EMBL-EBI)

Brief description: The European Nucleotide Archive (ENA) is an open, supported platform for the management, sharing, integration, archiving, and dissemination of sequence data. This authoritative nucleotide sequence repository comprises the European node of the INSDC. 

Data types: projects, samples, read data, sequences, assemblies and other analyses, taxon names 

Services: ENA Browser, Metadata Search, Taxonomy services, Webin Submission Portal, Helpdesk services, support documentation, RESTful APIs 

Website: https://www.ebi.ac.uk/ena

API: Discovery API: https://www.ebi.ac.uk/ena/portal/api; Retrieval API:  https://www.ebi.ac.uk/ena/browser/api/; ENA taxonomy: https://www.ebi.ac.uk/ena/taxonomy/rest/#/; Source Attribute Helper API: https://www.ebi.ac.uk/ena/sah/api/; Cross References API: https://www.ebi.ac.uk/ena/xref/rest/

Name of the infrastructure: Europe PMC

Supporting organisation: European Molecular Biology Laboratories - European Bioinformatics Institute (EMBL-EBI)

Brief description: Europe PMC is a global, free, life sciences literature repository that provides comprehensive access to life sciences literature (research articles and preprints) from trusted sources. It is partnered with PubMed and PubMed Central.

Data types: literature 

Services: Europe PMC has built tools and services on top of the literature indexed:

Website: https://europepmc.org/

API: Articles RESTful API: https://europepmc.org/RestfulWebService; Annotations API: https://europepmc.org/AnnotationsApi; Grants RESTful (Grist) API: https://europepmc.org/GristAPI

Name of the infrastructure: Global Biodiversity Information Facility

Supporting organisation: Global Biodiversity Information Facility

Brief description: GBIF is an international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth. 

Data types: occurrences, specimens, observations, eDNA, sequences, taxon names, taxonomies, collection catalogue, images, literature, training materials. 

Services: portal, Cloud-based downloads, search engine, RESTful JSON based API, taxonomic comparisons, collection catalogue. 

Website: https://www.gbif.org/

API: RESTful JSON based: https://api.gbif.org/v1/

Name of the infrastructure: GGBN

Supporting organisation: Botanic Garden Berlin, Freie Universität Berlin

Brief description: GGBN is an international network of institutions that share an interest in long-term preservation of genomic samples representing the diversity of non-human life on Earth. GGBN provides a platform for biodiversity biobanks worldwide to harmonise exchange and use of material in accordance with national and international legislation and conventions.

Data types: Tissue/DNA samples, links to voucher specimens

Services: GGBN Data Portal, GGBN Document Library

Website: https://www.ggbn.org/

Name of the infrastructure: LifeWatch ERIC
Supporting organisation: LifeWatch ERIC
Brief description: LifeWatch ERIC provides access to a multitude of datasets, webservices and other research resources, allowing the accelerated capture of data, their analysis and support for knowledge-based decision-making for biodiversity & ecosystem management.
Data types: occurrences, observations, eDNA, sequences, taxon names, taxonomies, images, training materials. 
Services: portal, Cloud-based downloads, search engine, RESTful JSON based API, web services on all levels of biodiversity, organised in thematic services, workflows and virtual research environments (VREs).
Website: lifewatch.eu
API: RESTful JASON APIs available at: https://trainingcatalogue.lifewatch.eu/site/api

Name of the infrastructure: BR Herbarium

Supporting organisation: Meise Botanic Garden, Meise, Belgium

Brief description: A large botanic garden with all the collections and facilities you might expect from that. Large living collections both outdoor and in greenhouses. A large herbarium of plants, algae and fungi most of which has been digitised, most with an image.

Data types: Both living and preserved collections of plants, algae and fungi 

Services:

Website: https://www.plantentuinmeise.be/en/

API: The data are accessible through the dataset published to GBIF https://www.gbif.org/dataset/b740eaa0-0679-41dc-acb7-990d562dfa37