Surfacing the deep data of taxonomy

Taxonomic databases are perpetuating approaches to citing literature that may have been appropriate before the Internet, often being little more than digitised 5 × 3 index cards. Typically the original taxonomic literature is either not cited, or is represented in the form of a (typically abbreviated) text string. Hence much of the “deep data” of taxonomy, such as the original descriptions, revisions, and nomenclatural actions are largely hidden from all but the most resourceful users. At the same time there are burgeoning efforts to digitise the scientific literature, and much of this newly available content has been assigned globally unique identifiers such as Digital Object Identifiers (DOIs), which are also the identifier of choice for most modern publications. This represents an opportunity for taxonomic databases to engage with digitisation efforts. Mapping the taxonomic literature on to globally unique identifiers can be time consuming, but need be done only once. Furthermore, if we reuse existing identifiers, rather than mint our own, we can start to build the links between the diverse data that are needed to support the kinds of inference which biodiversity informatics aspires to support. Until this practice becomes widespread, the taxonomic literature will remain balkanized, and much of the knowledge that it contains will linger in obscurity

Taxonomic informatics tools for the electronic nomenclator zoologicus

Author Posting. © Marine Biological Laboratory , 2006. This article is posted here by permission of Marine Biological Laboratory for personal use, not for redistribution. The definitive version was published in Biological Bulletin 210 (2006): 18-24.Given the current trends, it seems inevitable that all biological documents will eventually exist in a digital format and be distributed across the internet. New network services and tools need to be developed to increase retrieval rates for documents and to refine data recovery. Biological data have traditionally been well managed using taxonomic principles. As part of a larger initiative to build an array of names-based network services that emulate taxonomic principles for managing biological information, we undertook the digitization of a major taxonomic reference text, Nomenclator Zoologicus. The process involved replicating the text to a high level of fidelity, parsing the content for inclusion within a database, developing tools to enable expert input into the product, and integrating the metadata and factual content within taxonomic network services. The result is a high-quality and freely available web application (http://uio.mbl.edu/NomenclatorZoologicus/) capable of being exploited in an array of biological informatics services.This work was supported with funding from the Andrew W. Mellon Foundation and GBIF

IRMNG 2006–2016: 10 Years of a Global Taxonomic Database

IRMNG, the Interim Register of Marine and Nonmarine Genera, was commenced in 2006 as an initiative of the Australian OBIS Node (OBIS Australia) following an analysis of the taxonomic names management needs of the Ocean Biogeographic Information System (OBIS). The main objectives were to produce a hierarchical classification of all life, both extant and fossil, to at least generic level (and to species as data were readily available) and to provide a tool to distinguish marine from nonmarine, and extant from fossil taxa. Over its first 10 years of operation IRMNG has acquired almost 487,000 of an estimated 510,000 published genus names (including both valid names and synonyms) in addition to almost 1.8 million species names, of which 1.3 million are considered valid. Throughout this time IRMNG data have been available for public query via a dedicated web interface based at CSIRO in Australia, as well as being supplied as bulk downloads for use by a range of global biodiversity projects. Over the period 2014-2016 responsibility for the system has been passed to the Data Centre Division of the Flanders Marine Institute (VLIZ) in Belgium, which is continuing the maintenance and development of IRMNG at its new web location, www.irmng.org. With its present estimated holdings of >95% of all published genus names (plus associated authorities and years of publication) across all taxonomic domains, including fossil as well as extant taxa, within an internally consistent taxonomic hierarchy, IRMNG is at present uniquely placed to provide an overview of “all life” to at least generic level, to permit the discovery of trends in publication of genera through time, to provide preliminary information on the marine vs. nonmarine and extant vs. fossil status of the taxa concerned, and to generate lists of both unique and non-unique names (homonyms sensu lato) for the benefit of users of biodiversity data

Scientific names of organisms : attribution, rights, and licensing

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Research Notes 7 (2014): 79, doi:10.1186/1756-0500-7-79.As biological disciplines extend into the ‘big data’ world, they will need a names-based infrastructure to index and interconnect distributed data. The infrastructure must have access to all names of all organisms if it is to manage all information. Those who compile lists of species hold different views as to the intellectual property rights that apply to the lists. This creates uncertainty that impedes the development of a much-needed infrastructure for sharing biological data in the digital world. The laws in the United States of America and European Union are consistent with the position that scientific names of organisms and their compilation in checklists, classifications or taxonomic revisions are not subject to copyright. Compilations of names, such as classifications or checklists, are not creative in the sense of copyright law. Many content providers desire credit for their efforts. A ‘blue list’ identifies elements of checklists, classifications and monographs to which intellectual property rights do not apply. To promote sharing, authors of taxonomic content, compilers, intermediaries, and aggregators should receive citable recognition for their contributions, with the greatest recognition being given to the originating authors. Mechanisms for achieving this are discussed

Scientific names of organisms: attribution, rights, and licensing

abstract: Background As biological disciplines extend into the ‘big data’ world, they will need a names-based infrastructure to index and interconnect distributed data. The infrastructure must have access to all names of all organisms if it is to manage all information. Those who compile lists of species hold different views as to the intellectual property rights that apply to the lists. This creates uncertainty that impedes the development of a much-needed infrastructure for sharing biological data in the digital world. Findings The laws in the United States of America and European Union are consistent with the position that scientific names of organisms and their compilation in checklists, classifications or taxonomic revisions are not subject to copyright. Compilations of names, such as classifications or checklists, are not creative in the sense of copyright law. Many content providers desire credit for their efforts. Conclusions A ‘blue list’ identifies elements of checklists, classifications and monographs to which intellectual property rights do not apply. To promote sharing, authors of taxonomic content, compilers, intermediaries, and aggregators should receive citable recognition for their contributions, with the greatest recognition being given to the originating authors. Mechanisms for achieving this are discussed.The electronic version of this article is the complete one and can be found online at: http://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-7-7

Chapter Plant Name Resources

Plant names are the key to communicating and managing information about plants. This paper considers how providers of high quality technical plant name information can better meet the requirements non-botanical audiences who also rely on plant names for elements of their work. The International Plant Name Index, World Checklist of Selected Plant Families and The Plant List are used as examples to illustrate the strengths and weaknesses of plant name resources from a non-expert user’s perspective. The above resources can be thought of as botanists pushing data at audiences. Without closer engagement with users, however, there is a limit to their relevance and impact. The need to cover common names is a frequent criticism of existing resources. The Medicinal Plant Names Services (MPNS, www.kew.org/mpns) is an example of how plant name resources can be adapted to better address the needs of a non-botanical audience. Some of the major challenges are outlined and solutions suggested

Open access to legacy taxonomic literature: Index Animalium & the Biodiversity Heritage Library: open access to legacy literature

pp. 113-12

Taxonomic indexing—extending the role of taxonomy

Author Posting. © Society of Systematic Biologists, 2006. This article is posted here by permission of Society of Systematic Biologists for personal use, not for redistribution. The definitive version was published in Systematic Biology 55 (2006): 367-373, doi: 10.1080/10635150500541680.Taxonomic indexing refers to a new array of taxonomically intelligent network services that use nomenclatural principles and elements of expert taxonomic knowledge to manage information about organisms. Taxonomic indexing was introduced to help manage the increasing amounts of digital information about biology. It has been designed to form a near basal layer in a layered cyberinfrastructure that deals with biological information. Taxonomic Indexing accommodates the special problems of using names of organisms to index biological material. It links alternative names for the same entity (reconciliation), and distinguishes between uses of the same name for different entities (disambiguation), and names are placed within an indefinite number of hierarchical schemes. In order to access all information on all organisms, Taxonomic indexing must be able to call on a registry of all names in all forms for all organisms. NameBank has been developed to meet that need. Taxonomic indexing is an area of informatics that overlaps with taxonomy, is dependent on the expert input of taxonomists, and reveals the relevance of the discipline to a wide audience

MineralSQL : Base de dades web per col·leccions de minerals

Des de ben petit he estat envoltat d'aficionats a l'estudi i el col·leccionisme de minerals. Això m'ha permès conèixer la dificultat que hi ha per gestionar correctament una col·lecció de minerals. L'objectiu d'aquest projecte és establir un sistema de catalogació, inventari i gestió de les col·leccions de mineralogia d'una manera àgil i senzilla. MineralSQL pretén ser el primer gestor per a aficionats a la mineralogia en format web, per poder accedir-hi des de qualsevol lloc en qualsevol moment. Els usuaris disposaran, de manera opcional, d'un espai públic per exposar els seus minerals i, en general, per donar-se a conèixer. També es podran fer cerques incloent resultats dels exemplars de les col·leccions d'altres usuaris, registrar coordenades i visites dels jaciments, poder fer exportacions en diferents formats sobre dades d'un exemplar o la seva localitat de procedència... amb l'objectiu primordial de poder compartir tota aquesta informació. Finalment, el sistema permetrà generar documents que facilitin la gestió de les col·leccions a partir de suports físics, ja sigui generant etiquetes amb informació sobre els exemplars o codis QR que permetin accedir a la fitxa online del mineral des de qualsevol dispositiu.Since l was a child l grow up surrounded by lovers of minerals collecting and their corresponding study. This personal background shows me how difficult is to manage a collection of minerals. The target of this project is to set a new, easy and quick system for cataloging and management of these amateur collections. MineralSQL aims to be the first collection managing software available on-line and focused on mineral collectors. The on-line status will permit the information access everywhere and at any time. MineralSQL will be a place where collectors can share data about their minerals with other people and they also can search information about the specimens or the collections of other users. It will also permit to register coordinates and pictures of mineral localities in different data formats, permitting to share all this information. Finally, the system allows to generate physical documents, those will help to manage the collections, as for example, creating labels with information about the specimen or QR codes permitting the access to the online data from any type of computer device.Desde pequeño he estado rodeado de aficionados al estudio y el coleccionismo de minerales. Esto me ha permitido conocer la dificultad que hay para gestionar correctamente una colección de minerales. El objetivo de este proyecto es establecer un sistema de catalogación, inventario y gestión de las colecciones de mineralogía de una manera ágil y sencilla. MineralSQL pretende ser el primer gestor para aficionados a la mineralogía en formato web, para poder acceder desde cualquier lugar en cualquier momento. Los usuarios dispondrán, de manera opcional, de un espacio público para exponer sus minerales y, en general, para darse a conocer. También se podrán realizar búsquedas incluyendo resultados de los ejemplares de las colecciones de otros usuarios, registrar coordenadas y visitas de los yacimientos, poder hacer exportaciones en diferentes formatos sobre datos de un ejemplar o su localidad de procedencia... con el objetivo primordial de poder compartir toda esta información. Finalmente, el sistema permitirá generar documentos que faciliten la gestión de las colecciones a partir de soportes físicos, ya sea generando etiquetas con información sobre los ejemplares o códigos QR que permitan acceder a la ficha online del mineral desde cualquier dispositivo