Dataset Information

A common registration-to-publication automated pipeline for nomenclatural acts for higher plants (International Plant Names Index, IPNI), fungi (Index Fungorum, MycoBank) and animals (ZooBank).

ABSTRACT: Collaborative effort among four lead indexes of taxon names and nomenclatural acts (International Plant Name Index (IPNI), Index Fungorum, MycoBank and ZooBank) and the journals PhytoKeys, MycoKeys and ZooKeys to create an automated, pre-publication, registration workflow, based on a server-to-server, XML request/response model. The registration model for ZooBank uses the TaxPub schema, which is an extension to the Journal Tag Publishing Suite (JATS) of the National Library of Medicine (NLM). The indexing or registration model of IPNI and Index Fungorum will use the Taxonomic Concept Transfer Schema (TCS) as a basic standard for the workflow. Other journals and publishers who intend to implement automated, pre-publication, registration of taxon names and nomenclatural acts can also use the open sample XML formats and links to schemas and relevant information published in the paper.

SUBMITTER: Penev L

PROVIDER: S-EPMC4741224 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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A common registration-to-publication automated pipeline for nomenclatural acts for higher plants (International Plant Names Index, IPNI), fungi (Index Fungorum, MycoBank) and animals (ZooBank).

Penev Lyubomir L Paton Alan A Nicolson Nicola N Kirk Paul P Pyle Richard L RL Whitton Robert R Georgiev Teodor T Barker Christine C Hopkins Christopher C Robert Vincent V Biserkov Jordan J Stoev Pavel P

ZooKeys 20160107 550

Collaborative effort among four lead indexes of taxon names and nomenclatural acts (International Plant Name Index (IPNI), Index Fungorum, MycoBank and ZooBank) and the journals PhytoKeys, MycoKeys and ZooKeys to create an automated, pre-publication, registration workflow, based on a server-to-server, XML request/response model. The registration model for ZooBank uses the TaxPub schema, which is an extension to the Journal Tag Publishing Suite (JATS) of the National Library of Medicine (NLM). Th ...[more]

PMID: 26877662

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Project description:As a service to taxonomists and ecologists using names in the well-known and species-rich ship-fouling serpulid genus Hydroides we present an update of all 107 non-synonymised scientific names, with additional information on Hydroides nomenclature, original names, etymologies, and type localities derived from original literature, and in accord with the World Register of Marine Species (WoRMS) database. An update is needed because the gender of genus Hydroides has from 1 January 2000 reverted to the original feminine, due to a change in the wording of International Code of Zoological Nomenclature which was overlooked at that time, and is contrary to the usage in practice of Hydroides as masculine which had started about 1992, although Code-required from the 1960s. We match 31 further original names of current WoRMS subjective junior synonyms to each non-synonymised name, and also report on the world distribution of the genus as illustrated by type localities of the valid names. We include notes on seven species inquirenda. The correct rendering is given of six names that have been altered for gender agreement for the first time herein. Hydroides gottfriedinom. n. replaces junior homonym Hydroides rostrata Pillai, 1971. Currently there are 41 non-synonymised species-group names in Hydroides which should be gender invariant, and 23 names which would only change if moved to a neuter genus; the remaining 43 names are fully gender variable. Place-names (23), and personal names (16) make up more than a third (36%) of the species names, with most of the remainder (68) being descriptive of species character states, usually of operculum morphology (54). All species, except Hydroides norvegica (63°N), have type localities in shallow-water coastal locations in temperate to tropical waters below latitude 44°, with the highest number of new species (54) from the adjoining Western Pacific and Indian Ocean areas. The other concentration of new species (31) are those first found on the Pacific and Atlantic coasts of North America and in the Caribbean.

Project description:BackgroundClinicalTrials.gov is a publicly accessible, Internet-based registry of clinical trials managed by the US National Library of Medicine that has the potential to address selective trial publication. Our objectives were to examine completeness of registration within ClinicalTrials.gov and to determine the extent and correlates of selective publication.Methods and findingsWe examined reporting of registration information among a cross-section of trials that had been registered at ClinicalTrials.gov after December 31, 1999 and updated as having been completed by June 8, 2007, excluding phase I trials. We then determined publication status among a random 10% subsample by searching MEDLINE using a systematic protocol, after excluding trials completed after December 31, 2005 to allow at least 2 y for publication following completion. Among the full sample of completed trials (n = 7,515), nearly 100% reported all data elements mandated by ClinicalTrials.gov, such as intervention and sponsorship. Optional data element reporting varied, with 53% reporting trial end date, 66% reporting primary outcome, and 87% reporting trial start date. Among the 10% subsample, less than half (311 of 677, 46%) of trials were published, among which 96 (31%) provided a citation within ClinicalTrials.gov of a publication describing trial results. Trials primarily sponsored by industry (40%, 144 of 357) were less likely to be published when compared with nonindustry/nongovernment sponsored trials (56%, 110 of 198; p<0.001), but there was no significant difference when compared with government sponsored trials (47%, 57 of 122; p = 0.22). Among trials that reported an end date, 75 of 123 (61%) completed prior to 2004, 50 of 96 (52%) completed during 2004, and 62 of 149 (42%) completed during 2005 were published (p = 0.006).ConclusionsReporting of optional data elements varied and publication rates among completed trials registered within ClinicalTrials.gov were low. Without greater attention to reporting of all data elements, the potential for ClinicalTrials.gov to address selective publication of clinical trials will be limited. Please see later in the article for the Editors' Summary.

Dataset Information

A common registration-to-publication automated pipeline for nomenclatural acts for higher plants (International Plant Names Index, IPNI), fungi (Index Fungorum, MycoBank) and animals (ZooBank).

Publications

A common registration-to-publication automated pipeline for nomenclatural acts for higher plants (International Plant Names Index, IPNI), fungi (Index Fungorum, MycoBank) and animals (ZooBank).

Similar Datasets

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