Life Science Identifiers Research Articles

Ten years and a million links: building a global taxonomic library connecting persistent identifiers for names, publications and people.

A major gap in the biodiversity knowledge graph is a connection between taxonomic names and the taxonomic literature. While both names and publications often have persistent identifiers (PIDs), such as Life Science Identifiers (LSIDs) or Digital Object Identifiers (DOIs), LSIDs for names are rarely linked to DOIs for publications. This article describes efforts to make those connections across three large taxonomic databases: Index Fungorum, International Plant Names Index (IPNI) and the Index of Organism Names (ION). Over a million names have been matched to DOIs or other persistent identifiers for taxonomic publications. This represents approximately 36% of names for which publication data are available. The mappings between LSIDs and publication PIDs are made available through ChecklistBank. Applications of this mapping are discussed, including a web app to locate the citation of a taxonomic name and a knowledge graph that uses data on researcher ORCID ids to connect taxonomic names and publications to authors of those names.

Ten Years and a Million Links: Building a global taxonomic library connecting persistent identifiers for names (LSIDs), publications (DOIs), and people (ORCIDs)

One thing the field of biodiversity informatics has been very good at is creating databases. However, this success in creation has not been matched by equivalent success in creating deep links between records in those databases. Instead, we create an ever growing number of silos. An obvious route to “silo-breaking” is the shared use of the same persistent identifiers for the same entities across those databases. For example, we have minted millions of Life Science Identifiers (LSIDs) for taxonomic names (which can be resolved at lsid.io), and a growing number of taxonomic papers have Digital Object Identifiers (DOIs), but we lack connections between these two identifiers. In this talk I describe work over the last decade to make these connections between LSIDs and DOIs across three large taxonomic databases: Index Fungorum, International Plant Names Index (IPNI), and the Index to Organism Names (ION) (Page 2023). Over a million names have been matched to DOIs or other persistent identifiers for taxonomic publications (Fig. 1 shows the coverage of publications for animal names). This represents approximately 36% of animal, plant or fungal names for which publication data is available. The mappings between LSIDs and publication persistent identifiers (PIDs) such as DOIs and Wikidata item identifiers, are made available through ChecklistBank (datasets 129659, 164203, 128415), and also archived in Zenodo. By combining these LSID and DOI links with Open Researcher and Contributor ID (ORCIDs) for taxonomists, we can potentially gain insight into who is doing taxonomic research, where they work, and how they are funded. Possible applications of this data are discussed, including a tool to discover the citation for a species name (Species Cite, Fig. 2), using DOI to ORCIDs to discover who is doing taxonomic research, and creating a linked data version of the Catalogue of Life.

Bootstrapping a Biodiversity Knowledge Graph

The "biodiversity knowledge graph" is a nice metaphor for connecting biodiversity data sources, but can we actually build it? Do we have sufficient linked data available? Given that a knowledge graph is an aggregation of data from multiple sources, how do we give those sources credit for that data, and how do we handle changes to that data? Given that the classic interface to a knowledge graph is an intimidatingly empty SPARQL query box, how do we make the knowledge within a graph more accessible? This talk discusses an attempt to build a knowledge graph with an eye on how to maintain the graph in the future. It adopts a model similar to Global Biodiversity Information Facility (GBIF) and CheckListBank where individual data providers make datasets available as independently citable units with Digital Object Identifiers (DOIs). Each dataset comprises linked data in the form of N-triples. To create a knowledge graph we simply download one or more such datasets and add them to a triple store. Each data source is assigned to its own named graph, such that we have provenance for each dataset, and we can update any dataset independently. Furthermore, anyone can build their own knowledge graph by mixing and matching the set of data (people, publications, taxa, etc.) most appropriate to their interests. To bootstrap this approach, exemplar datasets are created based on data harvested from ORCID, Zenodo, and taxonomic name databases. Each demonstration dataset could be replaced in the future by data published directly by those providers. In some cases there are sufficient shared identifiers (such as DOIs and ORCIDs) to form a graph, but taxonomic data typically forms isolated islands. To help the knowledge graph coalesce we need "glue" in the form of datasets that link pairs of different identifiers, such as Life Science Identifiers (LSIDs) for names to DOIs for publications. With the addition of those cross links we can start to generate bibliographies for taxa, discover communities of taxonomic expertise, and more. This model of building a knowledge graph also opens opportunities for smaller, focussed datasets to be added to the graph using the same approach (as set of N-triples archived in an online repository). In order to be useful, a knowledge graph needs to be easy to query and visualise. Simply providing a SPARQL endpoint is unlikely to be enough. As part of this project, I developed a GraphQL interface to the knowledge graph to provide a set of standard queries that can support a simple web interface to the graph. This provides a way to explore the graph as it is being developed, which in turn can highlight gaps in connectivity and coverage that need to be addressed.

Meeting In-Between: Moving beyond the buzz, bottlenecks, and bubble to collaboratively develop digitization tooling

Specimen digitization software and tooling is moving well past its third decade of development, yet in many ways new tools have yet to leapfrog or overcome the initial innovation realized years ago. Here I argue that a biodiversity informatics bubble has emerged, creating demands of digitization tools that are not always in line with the requirements of physical specimen curators (or others doing actual science). Pressuring tools to keep up with concepts that have emerged from this bubble, for example Life Science Identifiers (LSIDs), and its parallels in the tech industry, for example microservices, has detracted from advancements that could be made with respect to day-to-day workflows and practices of the curators themselves. These advances in turn might provide a more enjoyable, intuitive, and ultimately sustainable foundation perhaps more immune to inevitable bubble bursts, hype-based derailments, and changes in scientific goals. How then should development proceed? We can observe that existing digitization software largely fits into two sides of the spectrum: commercial monoliths like EMu and "home-grown" efforts, e.g. Specify, Arctos, and Symbiota. I argue the latter are much more in-tune with user needs, because they were first built by the users themselves. Our approach, therefore, should be to go back to the well, the curator, the digitizer, the student hourly, and the person who has to fulfill requests of those using the physical collection itself, and seek their needs, and understand their experiences. With this understanding in place, i.e., a solid user-interface/experience foundation, we can build out tooling (and standards) that developers will want to utilize in their own software. These arguments and ideas are contextualized against TaxonWorks (http://taxonworks.org) and the experiences of the five collections now using it to digitize collections to illustrate their shortcomings and potentialities.

A new genus for the freshwater crab Potamonemus asylos Cumberlidge, 1993, (Brachyura: Potamoidea: Potamonautidae) from Cameroon, Central Africa, with a key to the genera of the Potamonautinae

ABSTRACTBuea gen. nov. is established to accommodate the freshwater crab Potamonemus asylos, from south-western Cameroon, Central Africa. This new genus is defined based on molecular evidence combined with morphological characters of the mandible and the first and second gonopods. Buea asylos comb. nov. is endemic to Cameroon, and is here compared with, and distinguished from, other freshwater crabs occurring in that country. Buea gen. nov. is the fifth freshwater crab genus known from Cameroon. The removal of P. asylos from Potamonemus leaves this genus with two species, P. mambilorum and P. sachsi, both of which are illustrated here and compared with the new genus. An amended key to the Potamonautinae genera is provided.Zoobank ID (LSID)This published work and the nomenclatural acts it contains have been registered in ZooBank, the online registration system for the ICZN. The ZooBank Life Science Identifiers (LSIDs) can be resolved and the associated information viewed through any standard web browser by appending the LSID to the prefix http://zoobank.org/.urn:lsid:zoobank.org:pub:5EA7E3A7-D890-45DF-B9E1-8C22131B8DF8

Options to Apply the IGSN Model to Biodiversity Data

For more than a decade, the biodiversity informatics community has recognised the importance of stable resolvable identifiers to enable unambiguous references to data objects and the associated concepts and entities, including museum/herbarium specimens and, more broadly, all records serving as evidence of species occurrence in time and space. Early efforts built on the Darwin Core institutionCode, collectionCode and catalogueNumber terms, treated as a triple and expected to uniquely to identify a specimen. Following review of current technologies for globally unique identifiers, TDWG adopted Life Science Identifiers (LSIDs) (Pereira et al. 2009). Unfortunately, the key stakeholders in the LSID consortium soon withdrew support for the technology, leaving TDWG committed to a moribund technology. Subsequently, publishers of biodiversity data have adopted a range of technologies to provide unique identifiers, including (among others) HTTP Universal Resource Identifiers (URIs), Universal Unique Identifiers (UUIDs), Archival Resource Keys (ARKs), and Handles. Each of these technologies has merit but they do not provide consistent guarantees of persistence or resolvability. More importantly, the heterogeneity of these solutions hampers delivery of services that can treat all of these data objects as part of a consistent linked-open-data domain. The geoscience community has established the System for Earth Sample Registration (SESAR) that enables collections to publish standard metadata records for their samples and for each of these to be associated with an International Geo Sample Number (IGSN http://www.geosamples.org/igsnabout). IGSNs follow a standard format, distribute responsibility for uniqueness between SESAR and the publishing collections, and support resolution via HTTP URI or Handles. Each IGSN resolves to a standard metadata page, roughly equivalent in detail to a Darwin Core specimen record. The standardisation of identifiers has allowed the community to secure support from some journal publishers for promotion and use of IGSNs within articles. The biodiversity informatics community encompasses a much larger number of publishers and greater pre-existing variation in identifier formats. Nevertheless, it would be possible to deliver a shared global identifier scheme with the same features as IGSNs by building off the aggregation services offered by the Global Biodiversity Information Facility (GBIF). The GBIF data index includes normalised Darwin Core metadata for all data records from registered data sources and could serve as a platform for resolution of HTTP URIs and/or Handles for all specimens and for all occurrence records. The most significant trade-off requiring consideration would be between autonomy for collections and other publishers in how they format identifiers within their own data and the benefits that may arise from greater consistency and predictability in the form of resolvable identifiers.

How Aphia—The Platform behind Several Online and Taxonomically Oriented Databases—Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics

The Aphia platform is an infrastructure designed to capture taxonomic and related data and information, and includes an online editing environment. The latter allows easy access to experts so they can update the content of the database in a timely fashion. Aphia is the core platform that underpins the World Register of Marine Species (WoRMS) and its more than 80 related global, regional and thematic species databases, but it also allows the storage of non-marine data. The content of Aphia can be consulted online, either by individual users or via machine-to-machine interactions. Aphia uses unique and stable identifiers for each available name in the database through the use of Life Science Identifiers (LSIDs). The system not only allows the storage of accepted and unaccepted names, but it also documents the relationships between names. This makes it a very powerful tool for taxonomic quality control, and also allows the linking of different pieces of information through scientific names, both within the Aphia platform and in relation to externally hosted databases. Through these LSIDs, Aphia has become an important player in the field of (marine) biodiversity informatics, allowing interactions between its own taxonomic data and e.g., biogeographic databases. Some applications in the field of biodiversity informatics encompass the coupling of species traits and taxonomy, as well as the creation of diverse, expert validated data products that can be used by policy makers, for example. Aphia also supplies (part of) its content to other data integrators and the infrastructure can be used to host orphan databases in danger of being lost.

Addendum to ‘Revision of the Late Jurassic teleosaurid genus Machimosaurus (Crocodylomorpha, Thalattosuchia)’

This addendum is to ensure that the ICZN (International Commission on Zoological Nomenclature) Code criteria for the availability of new nomenclatural acts are satisfied. In our original publication [1], the newly established taxon Machimosaurus buffetauti was not named in accordance with the ICZN Code, specifically it failed to fulfil Article 8.5.3. This addendum, being a ‘corrigendum’ in the sense of the Glossary of the Code, should be consulted alongside the original publication [1]. However, it is this addendum that fulfils the ICZN Code criteria for establishing the name M. buffetauti . As such, the date of publication and nominal authority of that nomenclatural act is the date that this addendum has been published. This addendum fulfils Article 8.5.3 of the ICZN Code, namely to ‘be registered in the Official Register of Zoological Nomenclature (ZooBank) (see Article 78.2.4)’. Thus, we have officially registered the new nomenculatural act M. buffetauti (in addition to registering the genus, type species and the publication establishing them). Note that at present (14/Jan/2015), ZooBank only accepts new names, as other nomenclatural acts (such as amendment of spellings) are not currently supported. As such, Machimosaurus is currently registered under Madrimosaurus (see [1] for details). Below are the resultant LSIDs (Life Science Identifiers), and we provide an updated Systematic Palaeontology section from Young et al . [1] thus ensuring M. buffetauti sp. nov. is now a valid name. In addition to being registered with ZooBank, and having the LSIDs recorded within, the electronic edition of this work was published in a journal with an ISSN, and has been archived and is available from the following digital repositories: CLOCKSS and PORTICO. Institutional abbreviations. DFMMh, Dinosaurier-Freilichtmuseum Munchehagen, Lower Saxony, Germany; GPIT, Palaontologische Sammlung der …

Making species checklists understandable to machines - a shift from relational databases to ontologies.

BackgroundThe scientific names of plants and animals play a major role in Life Sciences as information is indexed, integrated, and searched using scientific names. The main problem with names is their ambiguous nature, because more than one name may point to the same taxon and multiple taxa may share the same name. In addition, scientific names change over time, which makes them open to various interpretations. Applying machine-understandable semantics to these names enables efficient processing of biological content in information systems. The first step is to use unique persistent identifiers instead of name strings when referring to taxa. The most commonly used identifiers are Life Science Identifiers (LSID), which are traditionally used in relational databases, and more recently HTTP URIs, which are applied on the Semantic Web by Linked Data applications.ResultsWe introduce two models for expressing taxonomic information in the form of species checklists. First, we show how species checklists are presented in a relational database system using LSIDs. Then, in order to gain a more detailed representation of taxonomic information, we introduce meta-ontology TaxMeOn to model the same content as Semantic Web ontologies where taxa are identified using HTTP URIs. We also explore how changes in scientific names can be managed over time.ConclusionsThe use of HTTP URIs is preferable for presenting the taxonomic information of species checklists. An HTTP URI identifies a taxon and operates as a web address from which additional information about the taxon can be located, unlike LSID. This enables the integration of biological data from different sources on the web using Linked Data principles and prevents the formation of information silos. The Linked Data approach allows a user to assemble information and evaluate the complexity of taxonomical data based on conflicting views of taxonomic classifications. Using HTTP URIs and Semantic Web technologies also facilitate the representation of the semantics of biological data, and in this way, the creation of more “intelligent” biological applications and services.Electronic supplementary materialThe online version of this article (doi:10.1186/2041-1480-5-40) contains supplementary material, which is available to authorized users.

Algal taxonomy: a road to nowhere?

The widespread view of taxonomy as an essentially retrogressive and outmoded science unable to cope with the current biodiversity crisis stimulated us to analyze the current status of cataloguing global algal diversity. Contrary to this largely pessimistic belief, species description rates of algae through time and trends in the number of active taxonomists, as revealed by the web resource AlgaeBase, show a much more positive picture. More species than ever before are being described by a large community of algal taxonomists. The lack of any decline in the rate at which new species and genera are described, however, is indicative of the large proportion of undiscovered diversity and bears heavily on any prediction of global algal species diversity and the time needed to catalogue it. The saturation of accumulation curves of higher taxa (family, order, and classes) on the other hand suggest that at these taxonomic levels most diversity has been discovered. This reasonably positive picture does not imply that algal taxonomy does not face serious challenges in the near future. The observed levels of cryptic diversity in algae, combined with the shift in methods used to characterize them, have resulted in a rampant uncertainty about the status of many older species. As a consequence, there is a tendency in phycology to move gradually away from traditional names to a more informal system whereby clade-, specimen- or strain-based identifiers are used to communicate biological information. Whether these informal names for species-level clades represent a temporary situation stimulated by the lag between species discovery and formal description, or an incipient alternative or parallel taxonomy, will be largely determined by how well we manage to integrate historical collections into modern taxonomic research. Additionally, there is a pressing need for a consensus about the organizational framework to manage the information about algal species names. An eventual strategy should preferably come out of an international working group that includes the various databases as well as the various phycological societies. In this strategy, phycologists should link up to major international initiatives that are currently being developed, such as the compulsory registration of taxonomic and nomenclatural acts and the introduction of Life Science Identifiers.

Correction: Oldest Known Pantherine Skull and Evolution of the Tiger

The electronic version of this document does not represent a published work according to the International Code of Zoological Nomenclature (ICZN), and hence the nomenclatural acts contained in the electronic version are not available under that Code from the electronic edition. Therefore, a separate edition of this document was produced by a method that assures numerous identical and durable copies, and those copies were simultaneously obtainable for the purpose of providing a public and permanent scientific record, in accordance with Article 8.1 of the Code on December 14th, 2011. The separate print-only edition is available on request from PLoS by sending a request to PLoS ONE, 1160 Battery Street, Suite 100, San Francisco, CA 94111, USA along with a check for $10 (to cover printing and postage) payable to Public Library of Science. In addition, this published work and the nomenclatural acts it contains have been registered in ZooBank, the proposed online registration system for the ICZN. The ZooBank LSIDs (Life Science Identifiers) can be resolved and the associated information viewed through any standard web browser by appending the LSID to the prefix http://zoobank.org/. The LSID for this publication is: (urn:lsid:zoobank.org:act:A7A75025-5E17-4CAA-B6FE-400301F8A57D).

ZooKeys 150: Three and a half years of innovative publishing and growth.

On the 28th of November 2011, the open access journal ZooKeys published its 150th issue – an excellent occasion for the Editorial team to evaluate the journal’s development and its position among systematic biology journals worldwide. From the very beginning, ZooKeys was designed as an innovative journal aiming at developing new methods of publication and dissemination of taxonomy information, including publishing of atomized, semantically enhanced automated exports to global data aggregators, such as Encyclopedia of Life (EOL), the Global Biodiversity Information Facility (GBIF), Plazi, Species-ID and others. Since its launch on the 4th of July 2008, the journal provided registration of all new taxa and authors in ZooBank on a mandatory basis and continues to include their Life Science Identifiers (LSID) in the published articles (Penev et al. 2008). Also since its first issue, ZooKeys made it a routine practice of supplying all new taxa to the Encyclopedia of Life through XML mark up. In the subsequent years, the journal joined GBIF and the Taxonomic Databases Working Group (TDWG) in the development of common data publishing standards and workflows. In 2009, ZooKeys initiated several pilot projects thereby setting foundations of semantic tagging of, and enhancements to, biodiversity articles using the TaxPub XML ZooKeys 150: 5–14 (2011)

Changes to publication requirements made at the XVIII International Botanical Congress in Melbourne - what does e-publication mean for you?

Changes to the International Code of Botanical Nomenclature are decided upon every six years at Nomenclature Sections associated with International Botanical Congresses (IBC). The XVIII IBC was held in Melbourne, Australia; the Nomenclature Section met on 18–22 July 2011 and its decisions were accepted by the Congress at its plenary session on 30 July. Several important changes were made to the Code as a result of this meeting that will affect publication of new names. Two of these changes will come into effect on 1 January 2012, some months before the Melbourne Code is published. Electronic material published online in Portable Document Format (PDF) with an International Standard Serial Number (ISSN) or an International Standard Book Number (ISBN) will constitute effective publication, and the requirement for a Latin description or diagnosis for names of new taxa will be changed to a requirement for a description or diagnosis in either Latin or English. In addition, effective from 1 January 2013, new names of organisms treated as fungi must, in order to be validly published, include in the protologue (everything associated with a name at its valid publication) the citation of an identifier issued by a recognized repository (e.g. MycoBank). Draft text of the new articles to do with publication is provided and best practice is outlined. © The Authors. Journal compilation © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 167, 133–136. To encourage dissemination of the changes made to the International Code of Nomenclature for algae, fungi, and plants, this article will be published in BMC Evolutionary Biology, Botanical Journal of the Linnean Society, Brittonia, Cladistics, MycoKeys, Mycotaxon, New Phytologist, North American Fungi, Novon, Opuscula Philolichenum, PhytoKeys, Phytoneuron, Phytotaxa, Plant Diversity and Resources, Systematic Botany and Taxon.

Revision of the stiletto fly genera Acupalpa Kröber and Pipinnipons Winterton (Diptera, Therevidae, Agapophytinae) using cybertaxonomic methods, with a key to Australasian genera.

Australian stiletto flies of the sister-genera Acupalpa Kröber, 1912 and Pipinnipons Winterton, 2001 (Diptera: Therevidae: Agapophytinae) are revised. Twelve new species of Acupalpa are described, while Acupalpa imitans (White, 1915), comb. n. is transferred from Pipinnipons and Acupalpa albimanis (Kröber, 1914), comb. n. is transferred from Ectinorhynchus Macquart as a senior synonym of Acupalpa pollinosa Mann. The total number of species of Acupalpa is therefore increased to 19: Acupalpa albimanis (Kröber), comb. n., Acupalpa albitarsa Mann, Acupalpa boharti sp. n., Acupalpa divisa (Walker), Acupalpa dolichorhyncha sp. n., Acupalpa glossa sp. n., Acupalpa imitans (White), comb. n., Acupalpa irwini Winterton, Acupalpa melanophaeos sp. n., Acupalpa miaboolya sp. n., Acupalpa minuta sp. n., Acupalpa minutoides sp. n., Acupalpa notomelas sp. n., Acupalpa novayamarna sp. n., Acupalpa rostrata Kröber, Acupalpa semirufa Mann, Acupalpa westralica sp. n., Acupalpa yalgoo sp. n. and Acupalpa yanchep sp. n. Three new species of Pipinnipons are described, increasing the total number of species to five: Pipinnipons chauncyvallis sp. n., Pipinnipons fascipennis (Kröber), Pipinnipons kampmeierae sp. n., Pipinnipons kroeberi Winterton, and P. sphecoda sp. n. Pipinnipons and Acupalpa are rediagnosed in light of the new species presented herein and revised keys to species are included. A dichotomous key to genera of Australasian Therevidae is included. As an empirical example of cybertaxonomy, taxonomic descriptions were composed using a character matrix developed in Lucid Builder (in Structured Descriptive Data (SDD) format) to generate natural language descriptions supplemented by online specimen and image databases. Web resources are provided throughout the document including: a) links to high resolution colour images of all species on Morphbank, b) registration of authors, publications, taxon names and other nomenclatural acts in Zoobank, with assignment of Life Science Identifiers (LSIDs) for each, c) links to Genbank accession records for DNA sequences, and d) assignment of LSIDs to specimen records with links to respective records in an online Therevidae specimen database.

Identifying and relating biological concepts in the Catalogue of Life

BackgroundIn this paper we describe our experience of adding globally unique identifiers to the Species 2000 and ITIS Catalogue of Life, an on-line index of organisms which is intended, ultimately, to cover all the world's known species. The scientific species names held in the Catalogue are names that already play an extensive role as terms in the organisation of information about living organisms in bioinformatics and other domains, but the effectiveness of their use is hindered by variation in individuals' opinions and understanding of these terms; indeed, in some cases more than one name will have been used to refer to the same organism. This means that it is desirable to be able to give unique labels to each of these differing concepts within the catalogue and to be able to determine which concepts are being used in other systems, in order that they can be associated with the concepts in the catalogue. Not only is this needed, but it is also necessary to know the relationships between alternative concepts that scientists might have employed, as these determine what can be inferred when data associated with related concepts is being processed. A further complication is that the catalogue itself is evolving as scientific opinion changes due to an increasing understanding of life.ResultsWe describe how we are using Life Science Identifiers (LSIDs) as globally unique identifiers in the Catalogue of Life, explaining how the mapping to species concepts is performed, how concepts are associated with specific editions of the catalogue, and how the Taxon Concept Schema has been adopted in order to express information about concepts and their relationships. We explore the implications of using globally unique identifiers in order to refer to abstract concepts such as species, which incorporate at least a measure of subjectivity in their definition, in contrast with the more traditional use of such identifiers to refer to more tangible entities, events, documents, observations, etc.ConclusionsA major reason for adopting identifiers such as LSIDs is to facilitate data integration. We have demonstrated the incorporation of LSIDs into the Catalogue of Life, in a manner consistent with the biodiversity informatics community's conventions for LSID use. The Catalogue of Life is therefore available as a taxonomy of organisms for use within various disciplines, including biomedical research, by software written with an awareness of these conventions.

Fast, linked, and open – the future of taxonomic publishing for plants: launching the journal PhytoKeys

The paper describes the focus, scope and the rationale of PhytoKeys, a newly established, peer-reviewed, open-access journal in plant systematics. PhytoKeys is launched to respond to four main challenges of our time: (1) Appearance of electronic publications as amendments or even alternatives to paper publications; (2) Open Access (OA) as a new publishing model; (3) Linkage of electronic registers, indices and aggregators that summarize information on biological species through taxonomic names or their persistent identifiers (Globally Unique Identifiers or GUIDs; currently Life Science Identifiers or LSIDs); (4) Web 2.0 technologies that permit the semantic markup of, and semantic enhancements to, published biological texts. The journal will pursue cutting-edge technologies in publication and dissemination of biodiversity information while strictly following the requirements of the current International Code of Botanical Nomenclature (ICBN).

Correction: Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology

The following subsection should be added beneath the Methods subsection Terminology: Nomenclatural Acts The electronic version of this document does not represent a published work according to the International Code of Zoological Nomenclature (ICZN), and hence the nomenclatural acts contained herein are not available under that Code from the electronic edition. A separate edition of this document was produced by a method that assures numerous identical and durable copies, and those copies were simultaneously obtainable (from May 21st 2009) for the purpose of providing a public and permanent scientific record, in accordance with Article 8.1 of the Code. The separate print-only edition is available on request from PLoS by sending a request to PLoS ONE, 185 Berry Street, Suite 3100, San Francisco, CA 94107, USA along with a check for $10 (to cover printing and postage) payable to Public Library of Science. In addition, this published work and the nomenclatural acts it contains have been retrospectively registered in ZooBank (http://www.zoobank.org/) , the proposed online registration system for the ICZN. The ZooBank LSIDs (Life Science Identifiers) can be resolved and the associated information viewed through any standard web browser by appending the LSID to the prefix http://zoobank.org/. The LSID for this publication is: urn:lsid:zoobank.org:pub:0357A28C-0547-4423-8E5C-A069128DF888 The LSIDs for the Nomenclature Acts are: Darwinius urn:lsid:zoobank.org:act:117EE2BF-DCAD-4311-973A-91366AB04003 D. masillae urn:lsid:zoobank.org:act:C246EC77-E90B-4FB4-B6CB-ADB473A40320

Revision of the stiletto fly genus Neodialineura Mann (Diptera: Therevidae): an empirical example of cybertaxonomy

The endemic Australian genus Neodialineura Mann is revised to include 13 species. Three species are previously described: N. nitens (White) and N. saxatilis (White) from southern mainland Australia and Tasmania, and N. striatithorax Mann from eastern Australia. Ten species are described as new, including N. ataxia sp. nov., N. atmis sp. nov., N. bagdad sp. nov, N. bifaria sp. nov., N. litura sp. nov., N. polygramma sp. nov., N. signum sp. nov., N. spinosa sp. nov., N. tessella sp. nov. and N. trichidion sp. nov. This revision serves as an empirical example for modernising the process of documenting global biodiversity by making taxonomic description and key development more efficient by avoiding redundancy in data handling and using digital media. Complete taxonomic descriptions were generated using online specimen and image databases, and a character matrix in Structured Descriptive Data (SDD) format developed in Lucid Builder to simultaneously generate natural language descriptions and an interactive key. Numerous web resources are provided with taxonomic descriptions throughout the document including: a) links to archived images of all species on Morphbank, b) registration of authors, publications, taxon names and other nomenclatural acts in Zoobank, with assignment of Life Science Identifiers (LSIDs) for each, c) links to Genbank accession records for DNA sequences, and d) assignment of LSIDs to specimen records with links to respective records in an online Therevidae specimen database. Colour images of male and female specimens of all Neodialineura species are included, along with a traditional dichotomous key to species.

Taxonomic information exchange and copyright: the Plazi approach.

BackgroundA large part of our knowledge on the world's species is recorded in the corpus of biodiversity literature with well over hundred million pages, and is represented in natural history collections estimated at 2 – 3 billion specimens. But this body of knowledge is almost entirely in paper-print form and is not directly accessible through the Internet. For the digitization of this literature, new territories have to be chartered in the fields of technical, legal and social issues that presently impede its advance. The taxonomic literature seems especially destined for such a transformation.DiscussionPlazi was founded as an association with the primary goal of transforming both the printed and, more recently, "born-digital" taxonomic literature into semantically enabled, enhanced documents. This includes the creation of a test body of literature, an XML schema modeling its logic content (TaxonX), the development of a mark-up editor (GoldenGATE) allowing also the enhancement of documents with links to external resources via Life Science Identifiers (LSID), a repository for publications and issuance of bibliographic identifiers, a dedicated server to serve the marked up content (the Plazi Search and Retrieval Server, SRS) and semantic tools to mine information. Plazi's workflow is designed to respect copyright protection and achieves extraction by observing exceptions and limitations existent in international copyright law.ConclusionThe information found in Plazi's databases – taxonomic treatments as well as the metadata of the publications – are in the public domain and can therefore be used for further scientific research without any restriction, whether or not contained in copyrighted publications.

ZooBank: Developing a nomenclatural tool for unifying 250 years of biological information

Nomenclature represents the backbone upon which virtually all biological information is organized. However, the practice of zoological nomenclature has changed relatively little since its start in 1758. As modern technology changes the paradigm under which modern scientists exchange information, there is increasing need to capitalize on these same technologies to fortify nomenclature. ZooBank has been proposed as the official registry of names and nomenclatural acts, in zoology, as well as associated published works and their authors, and type specimens. Having a coordinated registry of zoological names, integrated with the existing Code of Zoological Nomenclature, will allow increased efficiency of communication among biologists, and enhanced stability of names. Such a registry would encompass two distinct realms, each with their own set of challenges. Retrospective registration involves the monumental task of aggregating and validating two and a half centuries of existing names, whereas prospective registration must be tightly integrated with the future paradigm in which scientific names are created and managed under new models of publication. The prototype of ZooBank has been hosted at Bishop Museum during its initial development phase. Following the lead of standard-setting bodies in biodiversity informatics, Life Science Identifiers (LSIDs) have been selected for use as the globally unique identifiers for ZooBank registration entries. The first ZooBank LSIDs were issued on January 1 st , 2008, and included five new fish species described in a work published that same day, as well as all 4,819 names established in the 10 th Edition of Linnaeus’ Systema Naturae. Three alternate scenarios for implementing mandatory registration in ZooBank have been articulated, each incorporating different degrees of coordination between published works and registration events. A robust discussion involving a broad spectrum of practicing zoological taxonomists is required over the next several years to define the specific implementation aspects of ZooBank.