ARPHA-XML is the first publishing platform to support the full manuscript life cycle, from authoring through peer review, publication and dissemination, within a single, XML-based environment. At the core of the ARPHA-XML is the collaborative authoring ARPHA Writing Tool (AWT). ARPHA-XML is the host of the Biodiversity Data Journal, RIO Journal, and others. ARPHA-XML provides several unique services for biodiversity, among many others: 

• Markup of taxon names, treatments, geo-coordinates, collection codes.
• Linking of each taxon name to various world-class biodiversity resources    
• Export of occurrences and taxon treatments into Darwin Core Archive and GBIF.
• Export of articles and separate images to the Biodiversity Literature Repository at Zenodo. 
• Import of data from GBIF, Barcode of Life, iDigBio and PlutoF into manuscripts.    
• Metadata (EML) conversion from GBIF, DataONE and LTER into data paper manuscripts.
• EMBL-ENA metadata conversion into omics data paper manuscripts.

Within  BiCIKL, ARPHA-XML will provide access to semantically enhanced authoring and editorial workflow to further develop, test and implement biodiversity data linking through a next-generation publishing and dissemination process. 

The Botanic Garden and Botanical Museum Berlin (BGBM) of the Freie Universität Berlin (FUB) is a centre of biodiversity research in Europe, housing extensive scientific collections of herbarium specimens as well as one of the world’s largest living plants collections. The BGBM preserves and facilitates access to biodiversity research data. This includes the data generated by the scientific activities of the BGBM itself at collection and taxon level. On the other hand, the BGBM processes data from cooperating scientists and infrastructures that are related to the research priorities of the BGBM. The BGBM is committed to FAIR data principles. It offers IT services for more than 20 partner institutions. The data are processed on the basis of the EDIT Platform for Cybertaxonomy and JACQ  (in cooperation with the Natural History Museum Vienna).

Within BiCIKL there is funding for the support of the following activities:

• Introduction of semantic annotation in collection databases (tools and workflows). We support researchers and institutions in using the developed methods for collection data needed in their research context.
• Support for the introduction of stable IDs for collection items (workflows, software configuration). The BGBM supports collections and researchers in introducing stable identifiers into their data management. This includes the definition of a compatible syntax and the adaptation of the software components.
• Setup of Citizen Science Missions for the transcription of herbarium labels (helpdesk, data imports and exports). The specimens to be processed are bundled in so-called “missions”. We support researchers and institutions in preparing specific herbarium collection objects as missions, and importing them into the “Herbonauten” system as well as exporting the transcribed data for further processing in the respective research context.

The SIB Literature Services (SIBiLS) combines a MEDLINE and PMC mirror, together with specific annotations. It also includes additional contents, such as for instance the ASCO/AACR (American Society of Clinical Oncology/American Association for Cancer Research) proceedings, which are not found in the original PMC (PubMed Central) collection. The library is provided with about 2 billions annotations covering a wide span of named-entities. The platform services are accessible via a generic API, which is used by several community-specific front-ends and portals (neXtProt, Intrinsically Disordered Protein community, etc.). The API is designed to support various biocuration support applications via text mining (triage, information ex- traction, automatic categorization, etc.), see either in a full-automatic mode (e.g. UniProt) or via interactive Graph- ic User Interfaces (e.g. DisProt and neXtProt). A subset of the SIBiLS annotations are integrated into EuropePMC via the SciLit gateway, hosted by the EBI. SIBiLS also provides ETL functionalities to transform JATS compliant documents into BioC, an enhanced XML DTD used to support text mining applications.

The SIBiLS research infrastructure is based on automatic annotation pipelines and semantic search of full-text articles. It provides Transnational Access and a specialized access to PubMedCentral and MEDLINE. Some entity types found in SIBiLS are of particular interest for the biodiversity communities like species, small molecules from ChEBI, molecular functions from the Gene Ontology and gene products from UniProt. Frequently, additional terminologies/vocabularies will be added in the annotation pipeline like.

The European Nucleotide Archive (ENA) is an open, supported platform for the management, sharing, integration, archiving and dissemination of sequence data.

The ENA comprises both the globally comprehensive data resource that preserves the world’s public-domain output of sequence data, and a rich portfolio of tools and services to support the management of sequence data.

As nucleotide sequencing becomes increasingly central to applied areas such as healthcare and environmental sciences, ENA has become a foundation upon which scientific understanding of biological systems may be assembled.

ENA sequences will feed into BiCIKL for data integration across taxonomy, biodiversity and the literature. Taxonomic and collections annotations will orient users in data linking; support will be provided for integration of new sequence data.

TreatmentBank (TB) is a service provided by the Swiss Plazi GmbH to  liberate data from within scholarly publications, and convert, enhance, link, store, and disseminate it as findable, accessible, interoperable and reusable (FAIR) data. These data  include taxonomic treatments, treatment citations, figures, tables, material citations and bibliographic reference. The data extraction processes can be highly automated to process entire journal back-issues as well as current publications. A quality control (QC) process as well as manual checks produce data fit to become reference deposits of treatments in BLR, as well as daily uploads of treatment articles data sets to the Global Biodiversity Information Facility (GBIF), with persistent identifiers minted in BLR. Input formats can be printed to born-digital publications. All data are openly accessible in various formats and are searchable. Currently, BLR contains 650,000 treatments extracted from 66,000 articles, 400,000 figures and 1,040,000 material citations.

TB is providing a service for the Transnational Access, developing and improving conversion of PDF publications, and serving as the access point for bidirectional linking to data liberated from literature. TB will provide a search portal to find specimens cited in literature as well as a service to link material citations to other RIs covering taxonomic names, genomics and specimen data.

Meise Botanic Garden is a large traditional botanic garden with all the collections and facilities you might expect from that. We have extensive living collections, both in our outdoor collection and in our large greenhouse complexes. We also have a large herbarium of vascular plants, algae and fungi. In recent years we have undergone a major digitization effort, which means that most of our plant and fungal collections are digitized, most with an accompanying image.

Our research team has a strong taxonomic focus, particularly on tropical Africa and Western Europe, but also works on topics such as evolution, invasive species, crop wild relatives and conservation. Facilities include a seedbank, light and electron microscopy and flow cytometry.

Within BiCIKL we are open to suggestions on how our facilities can be used, however, the semantic annotation of specimens data and the transcription and enrichment of specimen data through our crowdsourcing portal DoeDat.

OpenBiodiv utilizes semantic publishing workflows, text mining, common standards, ontology modelling and graph database technologies to establish a robust infrastructure for creating and managing a Biodiversity Knowledge Graph.

OpenBiodiv encompasses data extracted from full-text article XMLs published by Pensoft and taxonomic treatments extracted by Plazi from journals of other publishers. The data from both sources are converted to RDF and are integrated in a graph database which contains the OpenBiodiv-O ontology and a RDF version of the GBIF taxonomic backbone. OpenBiodiv provides the following services: 

• XML-to-RDF conversion workflow and software for JATS TaxPub XML versions of journal articles
• RDF conversion of taxonomic hierarchies in CSV (example: GBIF taxonomic backbone)
• A triple store of close to one billion triples of facts and metadata extracted from literature
• SPARQL endpoint, accessible for regular queries and federated queries with other domain-specific or generic endpoints
• Predefined SPARQL queries reflecting different research questions. 

Within BiCIKL, OpenBiodiv will be developed to provide a LOD version of data liberated from the literature to make them interoperable with other data infrastructures throughout the biodiversity data life cycle. 

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 and preserve all kinds of digital research artifacts in line with the FAIR principles. Zenodo helps researchers receive credit by making the research results citable, and through OpenAIRE integrates them into existing reporting lines to funding agencies like the European Commission. Hosting more than 350TB of data and 2 million records across 7.000 community collections, Zenodo is a trusted and robust research infrastructure, facilitating the growth of research ecosystems with extensive storage and complex metadata requirements.

PlutoF is an open data management platform for handling different biodiversity data types, including taxon names, specimens, environmental samples, locality data, DNA sequences, laboratory experiments and literature as a linked dataset. The services are used by scientists, labs, institutions, and citizen scientists who focus on taxonomy, ecology, monitoring, conservation, and genetics.

Users can manage datasets through a full data life cycle - from uploading to publishing and archiving in FAIR format. PlutoF follows major data standards developed in this field which allows easy data exports to other repositories and data portals like GBIF, INSDC, etc. It is also possible to publish datasets with DOIs. PlutoF services allow cross-border collaboration and the development of common databases. The services are provided through the EOSC Nordic servers in Estonia and Sweden. Top five most frequent service users are from Estonia, USA, Finland, Germany, and Sweden. ORCID or other social accounts are used to access the infrastructure.

In BiCIKL, PlutoF will be responsible for the implementation of the data management services which are used for the integration and annotation of biological sample, sequence, literature and taxonomic data.

The Distributed System of Scientific Collections (DiSSCo) is a new Research Infrastructure (RI) for Natural Science Collections. The DiSSCo RI works towards the digital unification of all European natural science assets under common curation and access policies and practices and it represents the largest ever formal agreement between natural history museums, botanical gardens and collection-holding universities in the world. 

DiSSCo, currently in the preparation phase, will provide unique access points for integrated data analysis and interpretation through a wide array of services. These services aim to follow the FAIR principles, serve real life needs, and are based on the priorities set by collection providers and a robust base of user stories. One of the services that are currently in operation is the European Loans and Visits System (ELViS). ELViS provides a unified way to request visits, loans and virtual access. Version 1 developed in the SYNTHESYS+ project was used to facilitate the 3rd Transnational Access (to fund short-term research visits to consortium institutions) and the 2nd Virtual Access call (to support digitisation-on-demand requests). 

In BICIKL, DiSSCo will provide Virtual Access services, architectural design for a persistent identifier service, access to FAIR specimen and sample data. These services will be used by users and other infrastructures to enable networks of connected data from the data resources of molecular biology, natural history collections, taxonomy and literature.

LW ERIC is the e-Science European Research Infrastructure for Biodiversity and Ecosystem Research. It provides access to a multitude of datasets, e-Services and tools enabling the construction and operation of Virtual Research Environments (VREs) through innovative technologies, which permit the accelerated capture of data, their analysis and knowledge-based decision-making support for biodiversity and ecosystem management. It can be split into 2 groups of services: BER_e-Infra & BER_VREs.

BER_VREs consists of 3 cutting-edge technologies:

• LifeBlock, a Blockchain technology for transparency and immutability, guaranteeing FAIR-compliant data.
• Tesseract, the technical composability layer to integrate web services, enabling the development of VREs for users to combine and arrange services and software into multiple workflows.
• The Artificial Intelligence virtual laboratory (vLab), an online service allowing users to locate others working on similar subjects and the hubs that link them.

Within BiCiKL, LW ERIC will support virtual access to BER_VREs.

Catalogue of Life (COL) is an international collaboration bringing together the effort and contributions of taxonomists and informaticians from around the world. COL aims to address the needs of researchers, policy-makers, environmental managers and the wider public for a consistent and up-to-date listing of all the world’s known species. COL also supports those who need to manage their own taxonomic information and species lists.

The new Catalogue of Life infrastructure, powered by GBIF infrastructure, consists of three parts:

• The COL public portal facilitates access to the monthly updated COL Checklist, underlying taxonomic databases, and general information on COL;
• ChecklistBank facilitates access to original data sources underlying the COL Checklist, all COL Checklist releases, and assembly tooling for the COL Checklist;
• An API renders all COL Checklist data to ChecklistBank, the COL portal and users, provides persistent name and digital object identifiers, and supports various data standards (e.g. DwC-A, Catalogue of Life Data Package). 

Species 2000 will lead BiCIKL’s WP10 to deliver high-quality virtual access to the taxonomic framework for use by the research infrastructures involved in the BiCIKL project and strengthen linkages with the taxonomic community and taxonomic publishers to ensure the quality of this framework and its trustworthiness. The workflows developed in the Joint Research Activities will be implemented together with GBIF in the new Catalogue of Life (COL) research infrastructure, and especially through COL ChecklistBank. 

LW ERIC is the e-Science European Research Infrastructure for Biodiversity and Ecosystem Research. It provides access to a multitude of datasets, e-Services and tools enabling the construction and operation of Virtual Research Environments (VREs) through innovative technologies, which permit the accelerated capture of data, their analysis and knowledge-based decision-making support for biodiversity and ecosystem management. It can be split into 2 groups of services: BER_e-Infra & BER_VREs.

BER_e-Infra provides web services, applications, software and data, guaranteeing FAIR-compliant data and FAIR(/SHARP)-compliant services, and their integration into workflows and VREs on: taxonomy & classification, phylogenetic algorithms, biogeography, ecology, metabarcoding, genomics and data services.

Within BiCiKL, LW ERIC will support virtual access to BER_e-Infra.

GBIF - the Global Biodiversity Information Facility - 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.

Coordinated through its Secretariat in Copenhagen, the GBIF network of participating countries and organizations, working through participant nodes, provides data-holding institutions around the world with common standards and open-source tools that enable them to share information about where and when species have been recorded. This knowledge derives from many sources, including everything from museum specimens collected in the 18th and 19th century to geotagged smartphone photos shared by amateur naturalists in recent days and weeks.

In BiCIKL, GBIF leads WP 2 and is also involved in several other work packages across the entire project. The main work focuses on the Coordination and interoperability of infrastructures through policies, standards, guidelines, defining and co-designing the Biodiversity Knowledge Hub (BKH) and ensuring its hosting and sustainability beyond the project end, development of landscaping analysis and knowledge of interactions, and engagement of overall data integration topics to deliver a trusted taxonomic framework/extending CoL work through novel methods for data linking. GBIF will also provide Virtual Access through the GBIF research infrastructure.

The Biodiversity Literature Repository (BLR) is a research infrastructure (RI) comprising the BLR Community on Zenodo at the European Center for Nuclear Research (CERN), and services to search and retrieve the data (Ocellus, Zenodeo API, BLR website). BLR’s focus is on biodiversity data liberated from scholarly publications, and it  uses custom metadata linking to external vocabularies covering the needs of the biodiversity community. This includes taxonomic treatment or figures as well as the deposit of the original article annotated with metadata describing the data contained in the articles itself, as well as related identifiers for figures and and treatments therein. The main data import is through TreatmentBank or via publishers such as Pensoft. With over 650,000 deposits, BLR is the single largest community in Zenodo. It’s data is widely reused, for example by the Global Biodiversity Information Facility (GBIF). All data in BLR is published under the CC0 Public Domain Dedication, remaining free for anyone to use, anywhere, for any purpose.

BLR’s role in BiCIKL is to provide long-term virtual access to data liberated from scientific literature, as well as to data liberated through transnational access.

Europe PMC is an open science platform that enables access to a worldwide collection of life science publications and preprints from trusted sources around the globe.

Europe PMC is developed by EMBL-EBI. It is a partner of PubMed Central and a repository of choice for many international science funders.

Free, transparent, and community-driven, Europe PMC is your gateway to life science research.

Europe PMC will provide a key literature data into BiCIKL to support data linking. The resource's text mining programmes and tools will provide specific discoverability of literature of relevance to particular taxonomic groups or molecular data sets.

The Biodiversity Heritage Library (BHL) is the world’s largest open access digital library for biodiversity literature and archives.

BHL operates as a worldwide consortium of natural history, botanical, research, and national libraries that digitize the natural history literature in their collections and make it freely available as part of a global “biodiversity community.”

BHL provides free access to over 200,000 volumes (over 59 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.

BHL works with the taxonomic community, publishers, bioinformaticians, and others to develop tools and services to facilitate greater access, interoperability, and reuse of content and data. BHL provides data exports and APIs to allow users to download content, harvest source data files, and reuse materials for research purposes. Through taxonomic intelligence tools developed by Global Names Architecture, BHL indexes the taxonomic names throughout the collection, allowing researchers to locate publications about specific taxa.

BHL is a supporter of BiCKL, supplying data from historical and current literature for reuse. 

The Global Genome Biodiversity Network 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 from across the world to:

• Collaborate to ensure consistent quality standards for DNA and tissue collections,
• Improve best practices for the preservation and use of such collections and
• Harmonize exchange and use of material in accordance with national and international legislation and conventions.

Its infrastructure consists of

• Data portal and API, enabling relationships and links between voucher specimens, tissue/DNA samples and INSDC records
• GGBN Data Standard (to be used with ABCD or DarwinCore)
• GGBN Document Library (Alfresco)

Its main role within BiCIKL (WP7 and WP8) is to develop best practices and tools in order to enable and improve linkages between INSDC records and underlying biological material and vice versa.

The International Barcode of Life (iBOL) Consortium brings together scientists and research organisations in more than 45 countries with a shared interest in developing DNA-based species identification systems. iBOL promotes the capture of short sequences known as DNA barcodes and maintains BOLD (Barcode of Life Data Systems) as the reference database for these barcodes. Closely related barcodes are clustered and assigned a Barcode Index Number (BIN). Sequences from curated specimens enable many of these BINs to be associated with named species. As new specimens are sequenced, more of the BINs will be identified. The BIN system supports identification of DNA from any source, including specimens of all life stages, gut contents, soil, water and other environmental samples. High-throughput sequencing platforms allow large numbers of species to be diagnosed from a single sample, a process known as metabarcoding.

iBOL will contribute to BiCIKL through access to the tools and data associated with BOLD, working to enhance the linkages between barcode sequences and the specimens from which they were derived and to support integration of BOLD BINs into the taxonomic framework developed by Species 2000 and other BiCIKL partners.