Retrieving taxa names from large biodiversity data collections using a flexible matching workflow

In the domain of biological classification there are several taxon name matching services that can search for a species scientific name in a large collection of taxonomic names. Many of these services are available online, and many others run on computers of individual scientists. While these systems may work very well, most suffer from the fact that the list of names used as a reference, and the criteria to decide on a match, are hard-coded in the engine that performs the name matching. In this paper we present BiOnym, a taxon name matching system that separates reference namelists, search criteria and matching engine. The user is offered a choice of several taxonomic reference lists, including the option to upload his/her own list onto the system. Furthermore, BiOnym is a flexible workflow, which embeds and combines techniques using lexical matching algorithms as well as expert knowledge. It is also an open platform allowing developers to contribute with new techniques. In this paper we demonstrate the benefits brought by this approach in terms of the efficiency and effectiveness of the information retrieval process with respect to other solutions.     

North-American Norms for Name Disagreement: Pictorial Stimuli Naming Discrepancies

Pictorial stimuli are commonly used by scientists to explore central processes; including memory, attention, and language. Pictures that have been collected and put into sets for these purposes often contain visual ambiguities that lead to name disagreement amongst subjects. In the present work, we propose new norms which reflect these sources of name disagreement, and we apply this method to two sets of pictures: the Snodgrass and Vanderwart (S&V) set and the Bank of Standardized Stimuli (BOSS). Naming responses of the presented pictures were classified within response categories based on whether they were correct, incorrect, or equivocal. To characterize the naming strategy where an alternative name was being used, responses were further divided into different sub-categories that reflected various sources of name disagreement. Naming strategies were also compared across the two sets of stimuli. Results showed that the pictures of the S&V set and the BOSS were more likely to elicit alternative specific and equivocal names, respectively. It was also found that the use of incorrect names was not significantly different across stimulus sets but that errors were more likely caused by visual ambiguity in the S&V set and by a misuse of names in the BOSS. Norms for name disagreement presented in this paper are useful for subsequent research for their categorization and elucidation of name disagreement that occurs when choosing visual stimuli from one or both stimulus sets. The sources of disagreement should be examined carefully as they help to provide an explanation of errors and inconsistencies of many concepts during picture naming tasks.     

Do we need a Unique Scientist ID for publications in biomedicine?

BACKGROUND: The PubMed database contains nearly 15 million references from more than 4,800 biomedical journals. In general, authors of scientific articles are addressed by their last name and forename initial. DISCUSSION: In general, names can be too common and not unique enough to be search criteria. Today, Ph.D. students, other researchers and women publish scientific work. A person may not only have one name but several names and publish under each name. A Unique Scientist ID could help to address people in peer-to-peer (P2P) networks. As a starting point, perhaps PubMed could generate and manage such a scientist ID. SUMMARY: A Unique Scientist ID would improve knowledge management in science. Unfortunately in some of the publications, and then within the online databases, only one letter abbreviates the author's forename. A common name with only one initial could retrieve pertinent citations, but include many false drops (retrieval matching searched criteria but indisputably irrelevant).     

Young Toddlers’ Word Comprehension Is Flexible and Efficient

Much of what is known about word recognition in toddlers comes from eyetracking studies. Here we show that the speed and facility with which children recognize words, as revealed in such studies, cannot be attributed to a task-specific, closed-set strategy; rather, children’s gaze to referents of spoken nouns reflects successful search of the lexicon. Toddlers’ spoken word comprehension was examined in the context of pictures that had two possible names (such as a cup of juice which could be called “cup” or “juice”) and pictures that had only one likely name for toddlers (such as “apple”), using a visual world eye-tracking task and a picture-labeling task (n = 77, mean age, 21 months). Toddlers were just as fast and accurate in fixating named pictures with two likely names as pictures with one. If toddlers do name pictures to themselves, the name provides no apparent benefit in word recognition, because there is no cost to understanding an alternative lexical construal of the picture. In toddlers, as in adults, spoken words rapidly evoke their referents.     

Review of ‘The Plant List,a working list of all plant species’

The Plant List ( http://www.theplantlist.org/ ) is an on‐line database of plant names that aims to be comprehensive for all described plant species. Version 1 of The Plant List includes 1 040 426 plant name records, of which 298 900 are accepted names. The Plant List is the product of a consortium of the Royal Botanic Gardens, Kew, and the Missouri Botanical Garden. In this review, I evaluate the use of this plant taxonomic database for plant ecologists. The web interface of The Plant List allows a quick search for species names and corresponding synonyms. Moreover, users are able to download search or browse results to compile a customized checklist of plant names. The combination of a straightforward web design and the possibility to download search results provides a valuable resource of plant nomenclature information for a wide range of plant ecologists.     

Motor simulation and the bodily self

Previous studies demonstrated the human ability to implicitly recognize their own body. When submitted to a visual matching task, participants showed the so-called self-advantage, that is, a better performance with self rather than others' body or body parts. Here, we investigated whether the body self-advantage relies upon a motor representation of one's body. Participants were submitted to a laterality judgment of self and others' hands (Experiment 1 and 3), which involves a sensory-motor mental simulation. Moreover, to investigate whether the self-advantage emerges also when an explicit self processing is required, the same participants were submitted to an explicit self-body recognition task (Experiment 2). Participants showed the self-advantage when performing the laterality judgment, but not when self-recognition was explicitly required. Thus, implicit and explicit recognition of the bodily self dissociate and only an implicit recognition of the bodily self, mapped in motor terms, allows the self-advantage to emerge.     

Randomization in the Canadian National Breast Screening Study: a review for evidence of subversion

The authors assess the randomization strategy that had been used in the Canadian National Breast Screening Study (NBSS). Document experts at a private investigation and security company were hired to assist in reviewing instances in which names of subjects were altered in the "allocation books" (the basic instrument used to assign, at random, participants to either the mammography or the usual-care arm). The review was restricted to records from 3 NBSS centres where women assigned to the mammography arm had a distinctly higher (not necessarily significant) number of deaths from breast cancer than those assigned to the usual-care arm, and to records from 2 centres where, for limited periods, administrative problems were reported. In most cases the underlying, original name could be identified. The document experts found no evidence of a deliberate attempt to conceal the alterations. A search of the NBSS database for the underlying and superimposed names revealed that only 1 of the women whose name had been deleted or superimpsed died of breast cancer. She was in the mammography arm. The authors'' thorough review of ways in which the randomization could have been subverted failed to uncover credible evidence of it. They conclude that even if there had been acts of subversion, they could only have been few in number and, given that there was only 1 death from breast cancer in the group reviewed, the alterations could have had only a trivial effect on the study findings as reported in 1992.     

Parents Accidentally Substitute Similar Sounding Sibling Names More Often than Dissimilar Names

When parents select similar sounding names for their children, do they set themselves up for more speech errors in the future? Questionnaire data from 334 respondents suggest that they do. Respondents whose names shared initial or final sounds with a sibling’s reported that their parents accidentally called them by the sibling’s name more often than those without such name overlap. Having a sibling of the same gender, similar appearance, or similar age was also associated with more frequent name substitutions. Almost all other name substitutions by parents involved other family members and over 5% of respondents reported a parent substituting the name of a pet, which suggests a strong role for social and situational cues in retrieving personal names for direct address. To the extent that retrieval cues are shared with other people or animals, other names become available and may substitute for the intended name, particularly when names sound similar.     

Should taxon names be explicitly defined?

Overviews are provided for traditional and phylogenetic nomenclature. In traditional nomenclature, a name is provided with a type and a rank. In the rankless phylogenetic nomenclature, a taxon name is provided with an explicit phylogenetic definition, which attaches the name to a clade. Linnaeus’s approach to nomenclature is also reviewed, and it is shown that, although the current system of nomenclature does use some Linnaean conventions (e.g., certain rank-denoting terms, binary nomenclature), it is actually quite different from Linnaean nomenclature. The primary differences between traditional and phylogenetic nomenclature are reviewed. In phylogenetic nomenclature, names are provided with explicit phylogenetic definitions, whereas in traditional nomenclature names are not explicitly defined. In phylogenetic nomenclature, a name remains attached to a clade regardless of how future changes in phylogeny alter the clade’s content; in traditional nomenclature a name is not “married” to any particular clade. In traditional nomenclature, names must be assigned ranks (an admittedly arbitrary process), whereas in phylogenetic nomenclature there are no formal ranks. Therefore, in phylogenetic nomenclature, the name itself conveys no hierarchical information, and the name conveys nothing regarding set exclusivity. It is concluded that the current system is better able to handle new and unexpected changes in ideas about taxonomic relationships. This greater flexibility, coupled with the greater information content that the names themselves (i.e., when used outside the context of a given taxonomy or phytogeny) provide, makes the current system better designed for use by all users of taxon names.     

Neural Correlates of Own Name and Own Face Detection in Autism Spectrum Disorder

Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition clinically characterized by social interaction and communication difficulties. To date, the majority of research efforts have focused on brain mechanisms underlying the deficits in interpersonal social cognition associated with ASD. Recent empirical and theoretical work has begun to reveal evidence for a reduced or even absent self-preference effect in patients with ASD. One may hypothesize that this is related to the impaired attentional processing of self-referential stimuli. The aim of our study was to test this hypothesis. We investigated the neural correlates of face and name detection in ASD. Four categories of face/name stimuli were used: own, close-other, famous, and unknown. Event-related potentials were recorded from 62 electrodes in 23 subjects with ASD and 23 matched control subjects. P100, N170, and P300 components were analyzed. The control group clearly showed a significant self-preference effect: higher P300 amplitude to the presentation of own face and own name than to the close-other, famous, and unknown categories, indicating preferential attentional engagement in processing of self-related information. In contrast, detection of both own and close-other''s face and name in the ASD group was associated with enhanced P300, suggesting similar attention allocation for self and close-other related information. These findings suggest that attention allocation in the ASD group is modulated by the personal significance factor, and that the self-preference effect is absent if self is compared to close-other. These effects are similar for physical and non-physical aspects of the autistic self. In addition, lateralization of face and name processing is attenuated in ASD, suggesting atypical brain organization.     

The List of Available Names (LAN): A new generation for stable taxonomic names in zoology?

The List of Available Names in Zoology (LAN) is an inventory of names with specific scope in time and content, presented and approved in parts, and constituted as a cumulative index of names available for use in zoological nomenclature. It was defined in Article 79 in the fourth edition of the International Code of Zoological Nomenclature. The LAN is likely to gain importance with the development of the online Official Registry for Zoological Nomenclature (ZooBank) as it is potentially a source of many nomenclaturally certified names. Article 79 describes the deliberative process for adding large numbers of names to the LAN simultaneously, detailing steps and chronology for submission of a candidate Part to the LAN and consideration of a candidate Part by the public and Commission, but it is largely mute about the contents of a candidate Part. It does make clear that a name within the scope of a Part but not on the LAN has no nomenclatural standing, even if it had previously been considered available, thereby preventing long-forgotten names from displacing accepted ones and the accumulation of nomina dubia. Thus, for taxa on the LAN, nomenclatural archaeology – the resurrecting of old unused names to replace by priority names in current usage – will not be worthwhile. Beyond that, it has been unclear if Article 79 is intended to document every available name known within the scope of the Part, or if its intention is to pare the inventory of available names within the scope of the Part. Consideration by the Commission and two committees to deal with the LAN have defined steps to implement Article 79 with the latter intent. Procedures for consideration of a candidate Part are defined in a manual, published as an appendix in this volume.     

Unconscious letter discrimination is enhanced by association with conscious color perception in visual form agnosia

Adaptive behavior guided by unconscious visual cues occurs in patients with various kinds of brain damage as well as in normal observers, all of whom can process visual information of which they are fully unaware [1] [2] [3] [4] [5] [6] [7] [8]. Little is known on the possibility that unconscious vision is influenced by visual cues that have access to consciousness [9]. Here we report a 'blind' letter discrimination induced through a semantic interaction with conscious color processing in a patient who is agnosic for visual shapes, but has normal color vision and visual imagery. In seeing the initial letters of color names printed in different colors, it is normally easier to name the print color when it is congruent with the initial letter of the color name than when it is not [10]. The patient could discriminate the initial letters of the words 'red' and 'green' printed in the corresponding colors significantly above chance but without any conscious accompaniment, whereas he performed at chance with the reverse color-letter mapping as well as in standard tests of letter reading. We suggest that the consciously perceived colors activated a representation of the corresponding word names and their component letters, which in turn brought out a partially successful, unconscious processing of visual inputs corresponding to the activated letter representations.     

The anArchive taxonomic Checklist for Italian botanical data banking and vegetation analysis: Theoretical basis and advantages

In recent years, research in botany was increasingly related with the use of large data-sets and data banks, in order to address emerging issues such as the severe risk of species, habitats and biodiversity loss. In this frame, the anArchive taxonomic Checklist, an online synonymized list of botanical species names, developed to support the botanical data banking and vegetation analysis, is presented and discussed here. The benefits deriving from such a supervised and referenced tool are emphasized. They include the possibility to keep track of old and new species names, pointing out the latest reviewed accepted scientific name and its synonyms, and harmonizing different taxonomic points of view. Furthermore, the list is open access and expert qualified customers can collaborate to its improvement. The basic unit of the taxonomic Checklist is an object including the taxon name at specific or, when present, infraspecific level; the taxonomic frame stops at the level of family and ranks higher than genus are not treated hierarchically. Some technical features, the main taxonomic references and the current state of the art are reported.     

Sex differences in search and gathering skills

The hunter–gatherer theory of sex differences states that female cognition has evolutionarily adapted to gathering and male cognition to hunting. Existing studies corroborate that men excel in hunting-related skills, but there is only indirect support for women excelling in gathering tasks. This study tested if women would outperform men in laboratory-based computer tests of search and gathering skills. In Experiment 1, men found target objects faster and made fewer mistakes than women in a classic visual search study. In Experiment 2, participants gathered items (fruits or letters presented on screen), and again, men performed significantly better. In Experiment 3, participants' incidental learning of object locations in a search experiment was studied, but no statistically significant sex differences were observed. These findings found the opposite of what was expected based on the hypothesis that female cognition has adapted to gathering. Alternative interpretations of the role of object location memory, female gathering roles and the division of labor between the sexes are discussed.     

罂粟正名考

十世纪前罂粟传入中国后,随着岁月的迁移出现了大量的中文名称。其中不少的名称曾作为正名载于古籍。本文讨论了古代罂粟用名的混乱和正名的选用。     

Ostrich,Southern Ostrich or Common Ostrich? The ‘eternal vexed question’ of English bird names and name changes in southern Africa through eight editions of Roberts field guides, 1940–2016

A set of stable simple common bird names helps non-ornithologist birders, who contribute to conservation by visiting protected areas and participating in citizen science projects. Changes in English bird names have caused discomfort in the local birding community, especially those that followed international standardisation of common bird names between 2000 and 2005. To understand the extent and nature of English bird name changes, an analysis was done of all southern African bird names through the eight editions of Roberts Birds of South/Southern Africa field guides published from 1940 to 2016. Of 813 species listed in both the first and the latest of the field guides, 453 (55.7%) had their names changed, among which 108 (13.3%) had changes in both the group name and the species epithet. The greatest single wave of changes (31.4%) occurred in the first ‘Roberts bird guide’ (the seventh field guide) in 2007, following international standardisation. Mean word and syllable counts of bird names also increased significantly in that edition. Name changes were associated with new authorships, taxonomic changes and use of geographic species epithets. There was a trend towards name stability for southern African endemic species. Further name changes should be kept to a minimum, shortening and simplifying wherever possible.     

“Did You Call Me?” 5-Month-Old Infants Own Name Guides Their Attention

An infant's own name is a unique social cue. Infants are sensitive to their own name by 4 months of age, but whether they use their names as a social cue is unknown. Electroencephalogram (EEG) was measured as infants heard their own name or stranger's names and while looking at novel objects. Event related brain potentials (ERPs) in response to names revealed that infants differentiate their own name from stranger names from the first phoneme. The amplitude of the ERPs to objects indicated that infants attended more to objects after hearing their own names compared to another name. Thus, by 5 months of age infants not only detect their name, but also use it as a social cue to guide their attention to events and objects in the world.     

Thermophilic fungi and applied research: a synopsis of name changes and synonymies

The present synopsis reports on taxonomic decisions and name changes introduced in the last decades for a number of thermophilic fungi. Taxa dealt with are those most commonly cited in the literature of fundamental and applied work or concern species having complex taxonomic histories. The definition of a thermophile follows the classificatory scheme elaborated by Cooney & Emerson in 1964. The synopsis provides the latest legal valid names for several thermophiles. Binomials of accepted synonymies are also reported with arguments in favour of these taxonomic decisions. The material of this contribution is a synthetic simplified account of two previous reviews on the taxonomy of thermophilic fungi. The present document aims: (1) to suppress the use of ghost binomials having no status of any kind; (2) to favour the continuous use of the latest legal valid name of a taxon to avoid cases of redundancies by citing binomials of known synonyms. Homogeneity in cited names is a fundamental prerequisite for comparative studies. The synopsis is thus a sound tool for future critical reviews of ecological and of biotechnological interests. The status of over a hundred names are here reviewed. Two additional new synonyms are proposed; these concern Mucor miehei var. minor and Sporotrichum cellulophilum. This revised version was published online in November 2006 with corrections to the Cover Date.     

Gene and protein nomenclature in public databases

Background  

Frequently, several alternative names are in use for biological objects such as genes and proteins. Applications like manual literature search, automated text-mining, named entity identification, gene/protein annotation, and linking of knowledge from different information sources require the knowledge of all used names referring to a given gene or protein. Various organism-specific or general public databases aim at organizing knowledge about genes and proteins. These databases can be used for deriving gene and protein name dictionaries. So far, little is known about the differences between databases in terms of size, ambiguities and overlap.     

Index nominum familiarum plantarum vascularium

A list of 2510 vascular plant family names is provided, valid and not validly published as well as legitimate and not legitimate. Each entry has a full bibliographic reference, nomenclatural status, generic type (when based on a generic name), means of validation, original place of publication for pre-1789 works, isonyms, invalid names proposed prior to a name’s validation, first use of correct orthography (if not given in the original publication), first uses of other orthographic variations, divisional placements of typified names, indication of acceptance in the botanical literature after 1960, and a four-letter abbreviation for the legitimate family name. In addition, nomenclaturally correct, typified names are listed for the ranks of order, superorder, subclass, class, subdivision, division/phylum, and subkingdom (for a total of 753 names), with full bibliographic citations. A similar list of 1569 currently available extant vascular plant family names is also given, of which 960 are considered to be in “current use.” A starting date for all names is assumed to be 4 August 1789 (Jussieu,Generaplantarum). Current difficulties with family nomenclature, and potential changes to bibliographic citations as a result of recently proposed changes to theInternational Code of Botanical Nomenclature, are noted.