Catalogue Of Life Research Articles

Adding Taxonomic Dimensions to the Scientific Names Index in the Biodiversity Heritage Library via Integration with the Catalogue of Life

The most significant specialized and open resource for biodiversity literature is the Biodiversity Heritage Library (BHL). BHL contains more than 200,000 volumes that cover hundreds of years of biological publications. The Catalogue of Life (CoL) is the largest aggregator of global taxonomic information. The Global Names project collaborates with BHL and CoL to create a BHL scientific names index that is continuously improved. The index allows researchers to conveniently find relevant information about any name. Building a scientific names index is challenging because scientific names are quite dynamic and can dramatically change in taxonomic meaning over time. According to our estimates, on average, there are three scientific names per species. Also, a significant number of scientific names have fallen into disuse. For example, approximately 25% of names used in Zoology between 1750–1850 and collected by Charles Sherborn into Index Animalium disappeared from current nomenclatural and taxonomic databases. It is important, therefore, to add "taxonomic intelligence" to BHL names index search and present not only data about a specific name-string but also about all known synonyms so that all relevant information in BHL can be consolidated and conveniently accessed from taxonomic information aggregators like CoL. We developed an open source program "bhlnames", which creates a two-way bridge between the Catalogue of Life and Biodiversity Heritage Library. It provides the location of information in BHL about a taxon, using all names associated with the taxon according to Catalogue of Life synonymy data. Using that information, it attempts to provide CoL with a BHL link to the first descriptions of scientific names in the literature.

Use cases for Taxonomic Name Services

Catalogue of Life Plus (CoL+) was started in 2017 as a collaborative project between the Catalogue of Life (COL), the Global Biodiversity Information Facility (GBIF), Naturalis Biodiversity Center, Barcode of Life Database (BOLD), Biodiversity Heritage Library (BHL), Encyclopedia of Life (EOL), Integrated Taxonomic Information System (ITIS) and representatives from natural history museum collections. The participants jointly recognized a need for the wider biodiversity community to coalesce around common and coordinated approaches for mobilizing and inter-linking biodiversity data and information across a range of scales, themes and types. The Catalogue of Life was identified as being the clear choice to deliver taxonomic services to support these partners. Taxonomic services refer to solutions that address challenges inherent to scientific names: the ubiquitous, and often sole, contextual linkage between a biodiversity data object and the taxon to which it is linked. Without access to expert-mediated taxonomic knowledge, biodiversity data networks risk integrating or delivering biodiversity data that is incomplete or may not make taxonomic sense. As a globally comprehensive and expert-mediated taxonomic resource, the Catalogue of Life is well-positioned to provide the underlying data and services to address these challenges and support a broad community of stakeholders. With financial support from the Netherlands Biodiversity Information Facility, the Netherlands Ministry of Education, Science, and Culture as well as technical support from GBIF, CoL+ represents an effort to stabilize the Catalogue of Life checklist products and refine a roadmap for future services -services that must be informed by the needs of users. The COL+ initiative provides an opportunity to document and understand the requirements of both Col current users and a wider future user base. Key to any expansion is ensuring a clear understanding and the appropriate response to user needs. This includes not only the requirements of "taxonomic data consumer" stakeholders, such as those listed above, but also the needs and motivations of the expert taxonomic community behind the current and future Catalogue of Life. This session will focus on reviewing the user requirements of a diverse community of both taxonomic data producers and consumers and organizing these stories into a set of categories from which we will identify clear and useful tools and services. These will establish the basis for a compelling roadmap for the Catalogue of Life as an enabling foundation to an interlinked and global biodiversity data infrastructure.

The Catalogue of Life Data Package - A new format for exchanging nomenclatural and taxonomic information

The Catalogue of Life Data Package (COLDP) format was developed to overcome limitations existing in currently used formats for sharing taxonomic information, namely Darwin Core Archives (DwC-A) and the Catalogue of Life (CoL) submission format also known as the Annual Checklist Exchange Format (ACEF). The tabular text based format, strongly influenced by DwC-A and ACEF, was designed to work with the Frictionless Data Package specification, but includes support for other well established formats like BibTeX and CSL-JSON for literature citations. It is the recommended exchange format for data published to, and downloaded from, the CoL Clearinghouse.

The LifeWatch Taxonomic Backbone: Connecting information on taxonomy, biogeography, literature, traits and genomics

The Flanders Marine Institute (VLIZ) is responsible for the set-up of the LifeWatch Taxonomic Backbone (LW-TaxBB), as a central part of the European LifeWatch Infrastructure. The LW-TaxBB aims to (virtually) bring together different component databases and data systems, all of them related to taxonomy, biogeography, ecology, genetics and literature. By doing so, the LW-TaxBB standardises species data and integrates biodiversity data from different repositories and operating facilities and is the driving force behind the species information services of the Belgian LifeWatch.be e-Lab and the Marine Virtual Research Environment that are being developed. The mission of LifeWatch is to advance biodiversity research and to provide major contributions to address the big environmental challenges, such as knowledge-based solutions for environmental managers in the field of conservation or dealing with long-standing ecological questions that could so far not be addressed due to a lack of data or a lack of good and easy access to data. This is being achieved by giving access to data and information through a single infrastructure which (virtually) brings together a large range and variety of datasets, services and tools. Scientists can use these tools and services to construct so-called Virtual Research Environments (VREs), where they are able to address specific questions related to biodiversity research, including e.g. topics related to conservation. They are not only offered an environment with unlimited computer and data storage capacity, but there is also transparency at all stages of the research process and the generic application of the e-infrastructure opens the door towards more inter- and multidisciplinary research. The LW-TaxBB – virtually - brings together different component databases and data systems, dealing with five major components: (1) taxonomy, through regional, national, European, global and thematic databases, (2) biogeography, based on databases dealing with species occurrences, (3) ecology, in the form of species-specific traits, (4) genetics and (5) literature, by linking all available information to the relevant sources and through tools that can intelligently search this literature. The LifeWatch Taxonomic Backbone is a two-way street: besides using the tools and functionalities it is offering – which are often developed based on identified needs within the scientific community -, scientists can also contribute themselves to make it more complete. Feedback on all available data and information (e.g. taxonomy and traits) is highly appreciated and communicated with the experts involved in the different component databases. All distribution information collected by individual scientists can become part of the biogeographic component of this backbone, by contributing occurrence data to the system. Through the LW-TaxBB, users benefit in several ways, amongst others by: Easy access to data and information to a variety of resources The opportunity to quality control their own data, by cross-checking with data available through the LW-TaXBB Free and easy access to a wide range of data services and web services Possibility to combine available services into workflows, and link several systems together Easy access to data and information to a variety of resources The opportunity to quality control their own data, by cross-checking with data available through the LW-TaXBB Free and easy access to a wide range of data services and web services Possibility to combine available services into workflows, and link several systems together Major components of the LW-TaxBB are – amongst others - the World Register of Marine Species (WoRMS) and the European node of the Ocean Biogeographic Information System (EurOBIS). WoRMS is an authoritative classification and catalogue of marine names currently containing 233,275 accepted marine species. EurOBIS publishes distribution data on marine species, collected within European marine waters or collected by European researchers outside European marine waters and currently contains 24.8 million distribution records. Both these systems have a strong link and collaboration agreements with international initiatives such as e.g. the Catalogue of Life (CoL), the Ocean Biogeographic Information System (OBIS) and the Global Biodiversity Information System (GBIF) and aim to collaborate with other ESFRIs such as DiSSCO and ELIXIR.

Catalogue of Life Plus: A collaborative project to complete the checklist of the world's species

Although the Catalogue of Life (CoL) continues to expand, its coverage is still far from complete, with several important megadiverse groups mostly lacking. Additionally, some segments of the Catalogue require major work to resolve synonymy or to incorporate recent names. As a result, key infrastructures that seek to organise data on the species of the world or particular regions (including GBIF, EOL, BHL and BOLD, among others) are unable to use CoL as a complete checklist of the world's species. It has become common for such platforms to augment CoL with automatically constructed arrangements of additional names and taxa to ensure that all species can be placed in a common framework. Since these efforts usually depend on algorithmic interpretation of text strings, the results are variable and lead in some cases to undesirable results. There is no easy way for all of these infrastructures to fix these issues in a consistent and interoperable way. Accordingly, Catalogue of Life Plus (CoL+) was started in 2017 as a collaborative project between the Catalogue of Life, the Global Biodiversity Information Facility, Naturalis Biodiversity Center and other partners, with financial support from the Netherlands Biodiversity Information Facility and the Netherlands Ministry of Education, Science, and Culture. CoL+ seeks to replace existing disconnected efforts with a shared, extended catalogue and to complete coverage of expert-reviewed names without sacrificing quality. The project aims to create an open, shared, and sustainable consensus taxonomy to serve the proper linking of data with in and between biodiversity information initiatives. The goals for the CoL+ project are to build a new infrastructure for the Catalogue of Life that: Extends and enriches the catalogue with more taxonomic sources to create a larger pool of scientific names, where feasible fill taxonomic gaps, and provide other enrichments with linkages to literature and references Replaces the current GBIF Backbone Taxonomy Separates names and taxonomy with different identifiers and authorities for names and taxa for better reuse Provides avenues for (infrastructural) support to the completion and strengthening of taxonomic and nomenclature content authorities Extends and enriches the catalogue with more taxonomic sources to create a larger pool of scientific names, where feasible fill taxonomic gaps, and provide other enrichments with linkages to literature and references Replaces the current GBIF Backbone Taxonomy Separates names and taxonomy with different identifiers and authorities for names and taxa for better reuse Provides avenues for (infrastructural) support to the completion and strengthening of taxonomic and nomenclature content authorities Specifically the project will establish a clearinghouse for taxonomy and nomenclature and rebuild all existing infrastructure of the Catalogue of Life including webservices, the portal and the software for the assembly of the catalogue and its editorial work.

Supporting 21st Century Taxonomy and Society Through Collaborative Cataloguing of the World's Species

Biological sciences have for more than 250 years depended on the nomenclatural system established by Carl Linnaeus to assign names to the world's species. These names can be considered to be a pre-digital effort to associate species, as key biological concepts, with globally unique identifiers. All sciences and all other human endeavours that relate to biological organisms have depended on this system to enable international communication and connect essential knowledge for taxonomy, conservation, agriculture, pest and disease management, trade and many other fields. Unfortunately, the scale and complexity both of life on earth and of the continued efforts by taxonomists to describe the millions of species on earth have prevented subsequent Linnaeus' followers from attempting to deliver a comprehensive catalogue of named species. Instead, many millions of names have been published throughout a vast and disconnected multilingual literature. Experts studying particular groups of organisms are likely to be familiar with the history of naming for their species of interest, but the dream of a fully interconnected naming system has remained elusive. In the last 25 years, major efforts have sought to address this need by assisting experts in collating the scattered information on scientific names and organising it in a consistent way. Most significantly, Species 2000, working in partnership with the Integrated Taxonomic Information System (ITIS), has led development of the Catalogue of Life (CoL). CoL is the most comprehensive and authoritative global index of species currently available. It consists of a single integrated species checklist and taxonomic hierarchy. The Catalogue holds essential information on the names, relationships and distributions of over 1.8 million species. This figure continues to rise as information is compiled from diverse sources around the world. However, CoL is still far from complete, with several important megadiverse groups mostly lacking. Additionally, some segments of the Catalogue require major work to resolve synonymy or to incorporate recent names. As a result, there is still no complete checklist of the world's species. Recognising the important role and efforts of many others that are aligned with this vision, including the existing nomenclatural databases (IPNI, Index Fungorum, ZooBank, etc.), other significant international checklist initiatives (especially WoRMS and World Flora Online) and many regional and national checklist databases (some with official status within national regulations), it is clear that a more collaborative model is needed to accelerate completion of this global catalogue. The benefits from achieving this will be significant, reducing wasted efforts in repeated databasing of the same core information on names and species, maximising the benefits from contributions of taxonomists and others to improve coverage and completeness, offering confidence to researchers and to data infrastructures in interpretation of all scientific names, facilitating community discussion and assessment of divergent perspectives on species classification, and providing a framework for documentation and communication of information on biogrography, species traits and interactions, conservation status, etc. In particular, the global information resource and national versions should be complementary and all products should benefit equally from new additions and corrections. Likewise relevant experts should be empowered to contribute freely to maintaining and improving this critical biodiversity data infrastructure. Achieving these goals will require innovative tools and community models that enable the international taxonomic community to contribute their expertise efficiently and ensure that information entered is never lost, only improved. This session is to refine this vision and contribute to planning for a comprehensive collaborative taxonomic catalogue.

The Catalogue of Life: Assembling data into a global taxonomic checklist

Producing a global taxonomic checklist of all species is essential for indexing biodiversity data, and for providing the basic knowledge needed to study, manage, and conserve biological diversity. The Catalogue of Life (CoL) aims to provide a global taxonomic checklist of all species, and includes 1.9 million species names in the 2019 annual edition. The task of assembling data into CoL is complex and requires reformatting data, quality assurance testing, and collaborating with data providers to resolve detected taxonomic conflicts. Global Species Databases (GSDs) are submitted in a wide variety of data formats to CoL by hundreds of taxonomic experts and institutions. Submitted data are reformatted to a standard data submission format: CoL Standard Dataset (ACEF), DarwinCore, or CoLDP. A series of standardized data integrity checks are run to detect and resolve frequently occurring data quality problems including character encoding corruption, non-Latin characters in scientific names, missing parents, duplicated and homonymic names within the GSD and among other GSDs, split taxonomic groups that have been assigned to multiple parent taxa, and other issues. The process and challenges of assembling data into the Catalogue of Life, and future directions of the project in migrating to CoL+ infrastructure will be discussed.

Mangal: An open infrastructure for ecological interactions

Interactions among species is at the heart of ecology. Despite their importance, studying ecological interactions remains difficult due to the lack of standard information and the disparity of formats in which ecological interactions are stored (Poisot et al. 2015). Historically, ecologists have used matrices to store interactions, which tend to easily decontextualize interactions from fieldwork when metadata is missing. To overcome these limitations, we designed Mangal - a global ecological interactions database - which serialize ecological interaction matrices into nodes (e.g. taxon, individuals or population) and edges. This database offers the opportunity to store information on traits, environment and homogenized taxonomy through unique taxonomic identifiers such as Encyclopedia of Life (EOL), Catalogue of Life (COL), Global Biodiversity Information Facility (GBIF) and Integrated Taxonomic Information System (ITIS). Here, we present the new release of Mangal including more than 120,000 interactions, 1,300 networks from 172 scientific publications distributed across the globe. We explore the content, illustrate case studies and present templates in order to contribute to this open infrastructure. For this purpose, we developed and maintained two packages/clients from popular scientific languages: R and Julia to facilitate data access, curation and network deposits on the database (Source code).

Catalogue of Life Plus: innovating the CoL systems as a foundation for a clearinghouse for names and taxonomy

In 2015, the global biodiversity information initiatives Biodiversity Heritage Library (BHL), Barcode of Life Data systems (BoLD), Catalogue of Life (CoL), Encyclopedia of Life (EOL), and the Global Biodiversity Information Facility (GBIF) took the first step to work on the idea for building a single shared authoritative nomenclature and taxonomic foundation that could be used as a backbone to order and connect biodiversity data across various domains. At present, the Catalogue of Life is being used by BHL, BoLD, EOL, and GBIF, but each extend the CoL with additional data to meet the specific backbone services required. The goal of the CoL+ project is to innovate the CoL systems by developing a new information technology infrastructure that includes both the current Catalogue of Life and a provisional Catalogue of Life (replacing the current GBIF backbone taxonomy), separates scientific names and taxonomic concepts with associated unique identifiers, and provides some (infrastructural) support for taxonomic and nomenclatural content authorities to finish their work. The project’s specific objectives are to establish a clearinghouse covering scientific names across all life; provide a single taxonomic view grounded in the consensus classification of the Catalogue of Life along with candidate taxonomic sources, show differences between sources, and provide an avenue for feedback to content authorities while allowing the broader community to contribute, and establish a partnership and governance, allowing a continuing commitment after the project’s end for a clearinghouse infrastructure and its associated components, including a roadmap for future developments of the infrastructure. establish a clearinghouse covering scientific names across all life; provide a single taxonomic view grounded in the consensus classification of the Catalogue of Life along with candidate taxonomic sources, show differences between sources, and provide an avenue for feedback to content authorities while allowing the broader community to contribute, and establish a partnership and governance, allowing a continuing commitment after the project’s end for a clearinghouse infrastructure and its associated components, including a roadmap for future developments of the infrastructure. As result of the project we expect to have a shared information space for names and taxonomy between the Catalogue of Life, nomenclator content authorities (e.g. IPNI, ZooBank) and several global biodiversity information initiatives.

EDIT Platform Web Services in the Biodiversity Infrastructure Landscape

The EDIT Platform for Cybertaxonomy is a standards based suite of software components supporting the taxonomic research workflow from field work to publication in journals and dynamic web portals (FUB, BGBM 2011). The underlying Common Data Model (CDM) covers the main biodiversity informatics foci such as names, classifications, descriptions, literature, multimedia, literature as well as specimens and observations and their derived objects. Today, more than 30 instances of the platform are serving data to the international biodiversity research communities. An often overlooked feature of the platform is its well defined web service layer which provides capable functions for machine access and integration into the growing service-based biodiversity informatics landscape (FUB, BGBM 2010). All platform instances have a pre-installed and open service layer serving three different use cases: The CDM REST API provides a platform independent RESTful (read-only) interface to all resources represented in the CDM. In addition, a set of portal services have been designed to meet the special functional requirements of CDM data portals and their advanced navigation capabilities. While the "raw" REST API has already all functions for searching and browsing the entire information space spanned by the CDM, the integration of CDM services into external infrastructures and workflows requires an additional set of streamlined service endpoints with a special focus on documentation and version stability. To this end, the platform provides a set of "catalogue services" with optimized functions for (fuzzy) name, taxon, and occurrence data searches (FUB, BGBM 2013, FUB, BGBM 2014). A good example for the integration of EDIT platform catalogue services into broader workflows is the "Taxonomic Data Refinement Workflow" implemented in the context of the EU 7th Framework Program Project BioVeL (Hardisty et al. 2016). The workflow uses the service layer of an EDIT Platform based instance of the Catalogue of Life (CoL) for resolving taxonomic discrepancies between specimen datasets (Mathew et al. 2014). The same service is also part of the Unified Taxonomic Information Service (UTIS) providing an easy-to-use interface for running simultaneous searches across multiple taxonomic checklists (FUB, BGBM 2016).

Challenges with using names to link digital biodiversity information.

The need for a names-based cyber-infrastructure for digital biology is based on the argument that scientific names serve as a standardized metadata system that has been used consistently and near universally for 250 years. As we move towards data-centric biology, name-strings can be called on to discover, index, manage, and analyze accessible digital biodiversity information from multiple sources. Known impediments to the use of scientific names as metadata include synonyms, homonyms, mis-spellings, and the use of other strings as identifiers. We here compare the name-strings in GenBank, Catalogue of Life (CoL), and the Dryad Digital Repository (DRYAD) to assess the effectiveness of the current names-management toolkit developed by Global Names to achieve interoperability among distributed data sources. New tools that have been used here include Parser (to break name-strings into component parts and to promote the use of canonical versions of the names), a modified TaxaMatch fuzzy-matcher (to help manage typographical, transliteration, and OCR errors), and Cross-Mapper (to make comparisons among data sets). The data sources include scientific names at multiple ranks; vernacular (common) names; acronyms; strain identifiers and other surrogates including idiosyncratic abbreviations and concatenations. About 40% of the name-strings in GenBank are scientific names representing about 400,000 species or infraspecies and their synonyms.

A higher level classification of all living organisms.

We present a consensus classification of life to embrace the more than 1.6 million species already provided by more than 3,000 taxonomists’ expert opinions in a unified and coherent, hierarchically ranked system known as the Catalogue of Life (CoL). The intent of this collaborative effort is to provide a hierarchical classification serving not only the needs of the CoL’s database providers but also the diverse public-domain user community, most of whom are familiar with the Linnaean conceptual system of ordering taxon relationships. This classification is neither phylogenetic nor evolutionary but instead represents a consensus view that accommodates taxonomic choices and practical compromises among diverse expert opinions, public usages, and conflicting evidence about the boundaries between taxa and the ranks of major taxa, including kingdoms. Certain key issues, some not fully resolved, are addressed in particular. Beyond its immediate use as a management tool for the CoL and ITIS (Integrated Taxonomic Information System), it is immediately valuable as a reference for taxonomic and biodiversity research, as a tool for societal communication, and as a classificatory “backbone” for biodiversity databases, museum collections, libraries, and textbooks. Such a modern comprehensive hierarchy has not previously existed at this level of specificity.

Protecting biodiversity and promoting sustainable development: in memory of the releasing of Catalogue of Life China 2015 and China Biodiversity Red List on the International Day for Biological Diversity 2015

2015年5月22日是第22个＂国际生物多样性日＂,主题是＂生物多样性促进可持续发展＂,体现了从保护生物多样性出发,促进生物资源永续利用和社会可持续发展的思想。即日,环境保护部与中国科学院在北京联合发布了《中国生物物种名录2015版》和《中国生物多样性红色名录·脊椎动物卷》。生物圈是一个相互关联的功能整体,生物物种的分布和迁徙没有国界,局部的污染和生物多样性变化将影响整个生物圈。

The LifeWatch approach to the exploration of distributed species information.

This paper introduces a new method of automatically extracting, integrating and presenting information regarding species from the most relevant online taxonomic resources. First, the information is extracted and joined using data wrappers and integration solutions. Then, an analytical tool is used to provide a visual representation of the data. The information is then integrated into a user friendly content management system. The proposal has been implemented using data from the Global Biodiversity Information Facility (GBIF), the Catalogue of Life (CoL), the World Register of Marine Species (WoRMS), the Integrated Taxonomic Information System (ITIS) and the Global Names Index (GNI). The approach improves data quality, avoiding taxonomic and nomenclature errors whilst increasing the availability and accessibility of the information.

As in other taxa, relatively fewer beetles are being described by an increasing number of authors: response to Löbl and Leschen

As in other taxa, relatively fewer beetles are being described by an increasing number of authors: response to <scp>L</scp>öbl and <scp>L</scp>eschen

An appraisal of megascience platforms for biodiversity information

The megascience platforms Biodiversity Heritage Library (BHL), Catalogue of Life (CoL), Encyclopedia of Life (EOL), Global Biodiversity Information Facility (GBIF), International Barcode of Life (iBOL), International Nucleotide Sequence Database Collaboration (INSDC) and JSTOR Plant Science, all belong to a group of global players that harvest, process, repurpose and provide biodiversity data on all kinds of organisms. Each of these platforms primarily focus on one data domain, for instance, taxonomy and classification, occurrence, morphology, ecology, and molecular data.The present contribution describes aspects of processing and provision of biological research data on these platforms, focusing on the technical implementation of data exchange, copyright issues, and data sharing policies as well as their implications for data custodians, owners, providers, and publishers. With the exception of JSTOR Plant Science, most international initiatives seek long-term business models and funding mechanisms to provide online data openly and free of charge. For example, currently GBIF depends on governmental commitments for its funding, and CoL is financed by EU or national grants, as well as being based on Species 2000, a British non-for-profit company, and ITIS. These business models are compared with that of JSTOR Plant Science, the commercial portal of the Global Plant Initiative (GPI). All initiatives currently meet challenges of sustainability with regard to data curation as well as software development for maintaining the complexity of their services. All platforms discussed here also harvest and provide mycological and lichenological research data.

Catalogue of life could become reality

Catalogue of life could become reality