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
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/
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:
- Specimen portal via JACQ (https://www.jacq.org/)
- Herbonauten (https://www.herbonauten.de/
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:
- Specimen portal (https://www.botanicalcollections.be/#/en/home)
- Living collections (https://www.botanicalcollections.be/#/en/search/living-collection)
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
Name of the infrastructure: OpenBiodiv
Supporting organisation: Pensoft Publishers
Brief description: A biodiversity knowledge graph encompassing Linked Open Data extracted from literature by Pensoft and Plazi and converted to RDF following the OpenBiodiv-O ontology.
Data types: RDF triples on specimens, sequences, taxon names, taxonomic treatments, persons, articles, bibliographies, and others.
Services: XML-to-RDF conversion, SPARQL endpoint, search engine, user-oriented applications for literature exploration.
Website: https://openbiodiv.net
SPARQL endpoint: http://graph.openbiodiv.net/
Name of the infrastructure: PlutoF
Supporting organisation: University of Tartu
Brief description: PlutoF provides online services to manage biological data fully integrated and ready for analyses. Users can manage datasets through a full data life cycle - from uploading to publishing and archiving in FAIR format.
Data types: taxon names, taxon hypotheses, specimens, DNA sequences, samples, traits, observations, locality data, references.
Services: data management, data publishing in GBIF, INSDC, Datacite DOI, data export and import, collection management, molecular laboratory.
Website: https://plutof.ut.ee
Name of the infrastructure: SIBiLS (Swiss Institute of Bioinformatics Literature Services Services and HES-SO/HEG Genève)
Supporting organisation: Swiss Institute of Bioinformatics Text Mining group
Brief description: SIBiLS provide holistic access to the biological and biodiversity literature (e.g. PMC, MEDLINE, TreatmentBank): all articles are semantically enriched with reference terminologies and the resource is freely accessible via REST APIs.
Data types: biomedical articles and material citations with annotations in JSON/JATS/BioC, queries in Lucene syntax and search results in Elasticsearch ’s JSON.
Services: literature retrieval engine.
Website: https://candy.hesge.ch/SIBiLS
API: https://candy.text-analytics.ch/SIBiLS/MEDLINE/search.jsp
Name of the infrastructure: TreatmentBank
Supporting organisation: Plazi
Brief description: TreatmentBank is a service liberating data from scientific publications to make the data imprisoned in publications widely accessible, citable and enriched with links to cited specimen, taxonomic and genomic data.
Data types: Articles, treatments, figures accessible in JSON, HTML, PDF, PNG.
Services: data conversion, FAIRization, linking, dissemination, search and retrieval service of data liberated from scientific publications.
Website: https://treatmentbank.org/
API: https://tb.plazi.org/GgServer/srsStats (treatment data); https://tb.plazi.org/GgServer/dioStats (article data)
Name of the infrastructure: World Register of Marine Species (WoRMS)
Supporting organisation: Flanders Marine Institute
Brief description: WoRMS aims to provide an authoritative and comprehensive classification and catalogue of marine names, including information on synonymy, type locality, general distribution, ecological traits and images. Its content is being controlled by experts.
Data types: taxon names, taxonomic classification, distributions, notes, attributes, images
Services: RESTful service, SOAP service, R packages, several applications for content exploration
Website: https://www.marinespecies.org
API: WoRMS REST webservice - https://www.marinespecies.org/rest/
Name of the infrastructure: Zenodo
Supporting organisation: CERN
Brief description: Zenodo is a general-purpose repository for the long tail of research, developed and hosted at CERN. It eliminates barriers and enables researchers across all disciplines to share, preserve, cite, and discover all kinds of digital research artefacts in line with the FAIR principles.
Data types: No restrictions on data types. Currently, hosting mainly taxonomic treatments, and other related content coming from literature extraction (through Plazi).
Services: user-oriented (UIs) and machine-oriented (APIs) application for data deposition.
Website: https://zenodo.org
API: https://zenodo.org/api (docs: http://developers.zenodo.org)
Name of the Infrastructure: Biodiversity Information Standards (TDWG)
Supporting organisation: International Taxonomic Databases Working Group (TDWG)
Brief Description: Biodiversity Information Standards (TDWG) creates, maintains, evolves, and promotes open, community-driven standards to enable sharing and use of biodiversity data for all. Our vision seeks to realise open, free, and interconnected biodiversity knowledge. Much of the data being linked through the BKH use standards and standard data packages developed by the international TDWG community. In addition to our website, you can find us on Slack, on Twitter @tdwg, and on FB.
Data types: data standards for natural science collections, taxonomic data, observations, genomic data, trait data, media data, geospatial data, citizen science, remote monitoring, data quality, api standards, attribution standards
Services: TDWG communities of expertise https://www.tdwg.org/community/; TDWG Standards https://www.tdwg.org/standards/
Website: https://www.tdwg.org
CETAF
Name of the Infrastructure: Consortium of European Taxonomic Facilities, CETAF
Supporting organisation:Consortium of European Taxonomic Facilities, CETAF
Brief Description: CETAF is a network of 71 research institutions holding collections that represent more than 80% of the world's bio- and geodiversity. It serves as a knowledge and expertise exchange platform for researchers from a wide variety of scientific disciplines.
Data types: natural science collections, taxonomic expertise, research facilities, institutional.
Services: Distributed European School of Taxonomy (DEST) platform; CETAF Registry of Collections and Expertise
Website: https://cetaf.org/
Explore (meta)data, tools and services offered by the participating Research Infrastructures organised by category: Specimens, Sequences, Taxon names and Literature
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: 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: OpenBiodiv
Supporting organisation: Pensoft Publishers
Brief description: A biodiversity knowledge graph encompassing Linked Open Data extracted from literature by Pensoft and Plazi and converted to RDF following the OpenBiodiv-O ontology.
Data types: RDF triples on specimens, sequences, taxon names, taxonomic treatments, persons, articles, bibliographies, and others.
Services: XML-to-RDF conversion, SPARQL endpoint, search engine, user-oriented applications for literature exploration.
Website: https://openbiodiv.net
SPARQL endpoint: http://graph.openbiodiv.net/
Name of the infrastructure: TreatmentBank
Supporting organisation: Plazi
Brief description: TreatmentBank is a service liberating data from scientific publications to make the data imprisoned in publications widely accessible, citable and enriched with links to cited specimen, taxonomic and genomic data.
Data types: Articles, treatments, figures accessible in JSON, HTML, PDF, PNG.
Services: data conversion, FAIRization, linking, dissemination, search and retrieval service of data liberated from scientific publications.
Website: https://treatmentbank.org/
API: https://tb.plazi.org/GgServer/srsStats (treatment data); https://tb.plazi.org/GgServer/dioStats (article data)
Name of the infrastructure: World Register of Marine Species (WoRMS)
Supporting organisation: Flanders Marine Institute
Brief description: WoRMS aims to provide an authoritative and comprehensive classification and catalogue of marine names, including information on synonymy, type locality, general distribution, ecological traits and images. Its content is being controlled by experts.
Data types: taxon names, taxonomic classification, distributions, notes, attributes, images
Services: RESTful service, SOAP service, R packages, several applications for content exploration
Website: https://www.marinespecies.org
API: WoRMS REST webservice - https://www.marinespecies.org/rest/
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: OpenBiodiv
Supporting organisation: Pensoft Publishers
Brief description: A biodiversity knowledge graph encompassing Linked Open Data extracted from literature by Pensoft and Plazi and converted to RDF following the OpenBiodiv-O ontology.
Data types: RDF triples on specimens, sequences, taxon names, taxonomic treatments, persons, articles, bibliographies, and others.
Services: XML-to-RDF conversion, SPARQL endpoint, search engine, user-oriented applications for literature exploration.
Website: https://openbiodiv.net
SPARQL endpoint: http://graph.openbiodiv.net/
Name of the infrastructure: PlutoF
Supporting organisation: University of Tartu
Brief description: PlutoF provides online services to manage biological data fully integrated and ready for analyses. Users can manage datasets through a full data life cycle - from uploading to publishing and archiving in FAIR format.
Data types: taxon names, taxon hypotheses, specimens, DNA sequences, samples, traits, observations, locality data, references.
Services: data management, data publishing in GBIF, INSDC, Datacite DOI, data export and import, collection management, molecular laboratory.
Website: https://plutof.ut.ee
Name of the infrastructure: TreatmentBank
Supporting organisation: Plazi
Brief description: TreatmentBank is a service liberating data from scientific publications to make the data imprisoned in publications widely accessible, citable and enriched with links to cited specimen, taxonomic and genomic data.
Data types: Articles, treatments, figures accessible in JSON, HTML, PDF, PNG
Services: data conversion, FAIRization, linking, dissemination, search and retrieval service of data liberated from scientific publications
Website: https://treatmentbank.org/
API: https://tb.plazi.org/GgServer/srsStats (treatment data); https://tb.plazi.org/GgServer/dioStats (article data)
Name of the infrastructure: World Register of Marine Species (WoRMS)
Supporting organisation: Flanders Marine Institute
Brief description: WoRMS aims to provide an authoritative and comprehensive classification and catalogue of marine names, including information on synonymy, type locality, general distribution, ecological traits and images. Its content is being controlled by experts.
Data types: taxon names, taxonomic classification, distributions, notes, attributes, images
Services: RESTful service, SOAP service, R packages, several applications for content exploration
Website: https://www.marinespecies.org
API: WoRMS REST webservice - https://www.marinespecies.org/rest/
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: Consortium of European Taxonomic Facilities, CETAF
Supporting organisation: Consortium of European Taxonomic Facilities, CETAF
Brief Description: CETAF is a network of 71 research institutions holding collections that represent more than 80% of the world's bio- and geodiversity. It serves as a knowledge and expertise exchange platform for researchers from a wide variety of scientific disciplines.
Data types: natural science collections, taxonomic expertise, research facilities, institutional.
Services: Distributed European School of Taxonomy (DEST) platform; CETAF Registry of Collections and Expertise
Website: https://cetaf.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: 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: 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: OpenBiodiv
Supporting organisation: Pensoft Publishers
Brief description: A biodiversity knowledge graph encompassing Linked Open Data extracted from literature by Pensoft and Plazi and converted to RDF following the OpenBiodiv-O ontology.
Data types: RDF triples on specimens, sequences, taxon names, taxonomic treatments, persons, articles, bibliographies, and others.
Services: XML-to-RDF conversion, SPARQL endpoint, search engine, user-oriented applications for literature exploration.
Website: https://openbiodiv.net
SPARQL endpoint: http://graph.openbiodiv.net/
Name of the infrastructure: TreatmentBank
Supporting organisation: Plazi
Brief description: TreatmentBank is a service liberating data from scientific publications to make the data imprisoned in publications widely accessible, citable and enriched with links to cited specimen, taxonomic and genomic data.
Data types: Articles, treatments, figures accessible in JSON, HTML, PDF, PNG.
Services: data conversion, FAIRization, linking, dissemination, search and retrieval service of data liberated from scientific publications.
Website: https://treatmentbank.org/
API: https://tb.plazi.org/GgServer/srsStats (treatment data); https://tb.plazi.org/GgServer/dioStats (article data)
Name of the infrastructure: World Register of Marine Species (WoRMS)
Supporting organisation: Flanders Marine Institute
Brief description: WoRMS aims to provide an authoritative and comprehensive classification and catalogue of marine names, including information on synonymy, type locality, general distribution, ecological traits and images. Its content is being controlled by experts.
Data types: taxon names, taxonomic classification, distributions, notes, attributes, images
Services: RESTful service, SOAP service, R packages, several applications for content exploration
Website: https://www.marinespecies.org
API: WoRMS REST webservice - https://www.marinespecies.org/rest/
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/
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
Name of the infrastructure: OpenBiodiv
Supporting organisation: Pensoft Publishers
Brief description: A biodiversity knowledge graph encompassing Linked Open Data extracted from literature by Pensoft and Plazi and converted to RDF following the OpenBiodiv-O ontology.
Data types: RDF triples on specimens, sequences, taxon names, taxonomic treatments, persons, articles, bibliographies, and others.
Services: XML-to-RDF conversion, SPARQL endpoint, search engine, user-oriented applications for literature exploration.
Website: https://openbiodiv.net
SPARQL endpoint: http://graph.openbiodiv.net/
Name of the infrastructure: SIBiLS (Swiss Institute of Bioinformatics Literature Services Services and HES-SO/HEG Genève)
Supporting organisation: Swiss Institute of Bioinformatics Text Mining group
Brief description: SIBiLS provide holistic access to the biological and biodiversity literature (e.g. PMC, MEDLINE, TreatmentBank): all articles are semantically enriched with reference terminologies and the resource is freely accessible via REST APIs.
Data types: biomedical articles and material citations with annotations in JSON/JATS/BioC, queries in Lucene syntax and search results in Elasticsearch ’s JSON.
Services: literature retrieval engine.
Website: https://candy.hesge.ch/SIBiLS
API: https://candy.text-analytics.ch/SIBiLS/MEDLINE/search.jsp
Name of the infrastructure: TreatmentBank
Supporting organisation: Plazi
Brief description: TreatmentBank is a service liberating data from scientific publications to make the data imprisoned in publications widely accessible, citable and enriched with links to cited specimen, taxonomic and genomic data.
Data types: Articles, treatments, figures accessible in JSON, HTML, PDF, PNG.
Services: data conversion, FAIRization, linking, dissemination, search and retrieval service of data liberated from scientific publications.
Website: https://treatmentbank.org/
API: https://tb.plazi.org/GgServer/srsStats (treatment data); https://tb.plazi.org/GgServer/dioStats (article data)
Name of the infrastructure: World Register of Marine Species (WoRMS)
Supporting organisation: Flanders Marine Institute
Brief description: WoRMS aims to provide an authoritative and comprehensive classification and catalogue of marine names, including information on synonymy, type locality, general distribution, ecological traits and images. Its content is being controlled by experts.
Data types: taxon names, taxonomic classification, distributions, notes, attributes, images
Services: RESTful service, SOAP service, R packages, several applications for content exploration
Website: https://www.marinespecies.org
API: WoRMS REST webservice - https://www.marinespecies.org/rest/