Quirks of dye nomenclature. 12. Victoria’s rainbow

ABSTRACT

The identities of 18 dyes whose names begin with “Victoria” are described using their chemical structures, names and numerical identifiers. All are synthetic dyes originally synthesized in Germany during the late 19^th century as colorants for textiles. Brief manufacturing details are included. All the colors of the rainbow are represented except indigo. Unusual properties including explosive tendency or toxicity are noted. Some of the applications as stains and for food coloring, anti-obesity medication and pigments for ball pen inks also are discussed     

A century of community ecology: How much progress?

Much of the apparent progress in community ecology amounts to little more than re-inventing the wheel, albeit with technical improvements. Many central ideas in the field were stated by A.K. Cajander at the turn of the century. Thereafter, community ecology has moved back and forth between competition-centered and individualistic views of community structure. The chief problems have probably been inappropriate methodology (lack of rigorous formulation and/or critical experimental testing of theories) and a tendency to work only on subcommunities that are delimited by taxonomic criteria. Although these problems are beginning to be remedied, a new one has emerged: ignorance of history and a tendency to re-invent old ideas under new, flashy names. This problem is potentially as dangerous as the old ones and must be tackled by improving our first-hand contact with the classics in our field.     

Taxonomic identity and typification of selected names of North American Potamogetonaceae

Most names in North American Potamogetonaceae have not been typified. Details of typifications are given for 72 names based on North American material published in the genus Potamogeton mainly by North American botanists. All names are reviewed for their nomenclatural validity and legitimacy, and interpreted taxonomically. Holotypes are indicated for 31 names and previously declared lectotypes or neotypes are listed for eight names. Lectotypes are designated for 24 previously untypified names and step-2 lectotypifications are proposed for three names that were based on heterogeneous material. Type material for three Rafinesque names and one proposed by Wood have not been located. An annotated list provides collection data, type status, homotypic synonyms, and currently accepted names. Two names are excluded from Potamogeton, being based on species of Myriophyllum (Haloragaceae).     

苦苣苔科植物学名种加词的问题

苦苣苔科植物是个研究活跃的类群,近年来随着新类群的报道和分类系统的变动,在该科的分类学研究中,出现了不少学名的种加词的性和属名不一致或出现拼写错误的情况,虽然这些错误不影响该名称的合格发表,但还是有必要根据《国际藻类、菌物和植物命名法规》进行改正。该文就苦苣苔科植物中属名以-stigma结尾的学名、属名以-cheilos结尾的学名、根据属名词尾不容易判断出性别的学名、拼写错误的名称等问题进行了分析,并对13个不符合法规的名称予以改正。此外,还就苦苣苔科植物学名的合格发表和规范使用进行了讨论。     

A Provisional List of Common Names for Australian Butterflies

A provisional list of common names for the known species of Australian butterflies is presented, and the advantages of producing such a set of standard common names discussed. the criteria and methodology on which the names are based are detailed and instances in which terms should be avoided itemised. All previously used names are reviewed and current or traditional names considered; where possible, traditional names were given highest priority. Group names have been standardised at the higher taxonomic levels (i.e. genus, tribe, subfamily etc.). Problems faced in compiling the list are discussed and comments on the suitability of the proposed names invited.     

冬虫夏草无性型研究概况*

文献调查结果表明与冬虫夏草有关的无性型菌种已报道有22个学名,涉及13个属。针对这些名称上存在的命名问题本文展开了讨论,并评述了不同名称与冬虫夏草的关系及其有关菌种的研究进展。在已报道的分离菌种中,作为新种正式描述的名称有8个,其中6个为合格发表,其余2个未能满足名称合格发表的条件;还有4个名称在文献中作为新种提到,但没有合格发表的出处,也有一例只提到名称而无其他要素;另有5个名称则只有属名,尚未鉴定到种的水平。中国被毛孢为多个独立的研究证明为冬虫夏草的无性型,还有3个无性型名称已被证明不可能是冬虫夏草的无性型。其他无性型名称与冬虫夏草的关系有待进一步验证。文中对与冬虫夏草有关的菌种定名、无性型分离和验证方法、复无性型现象,以及有关学名问题作了讨论。     

Are species names proper names?

The nature of species names has been a source of controversy, and has played a role in developing ideas about the status of species, such as the species‐as‐individuals hypothesis. Some argue that species names are Millian proper names: names that have no meaning. Others have countered that species names are Millian general names that have stipulative definitions. Here I argue that species names belong to neither category. In particular, unlike Millian proper names, species names have unique referents and are connotative. Further, species names are names of intension that, unlike Millian general names, refer to specific collective entities. Because species names have unique properties not associated with Millian general or proper names, but recognizing the similarity to proper names in most respects, I propose that they be categorized as extra‐proper names.
     

NetiNeti: discovery of scientific names from text using machine learning methods

ABSTRACT: BACKGROUND: A scientific name for an organism can be associated with almost all biological data. Name identification is an important step in many text mining tasks aiming to extract useful information from biological, biomedical and biodiversity text sources. A scientific name acts as an important metadata element to link biological information. RESULTS: We present NetiNeti (Name Extraction from Textual Information-Name Extraction for Taxonomic Indexing), a machine learning based approach for recognition of scientific names including the discovery of new species names from text that will also handle misspellings, OCR errors and other variations in names. The system generates candidate names using rules for scientific names and applies probabilistic machine learning methods to classify names based on structural features of candidate names and features derived from their contexts. NetiNeti can also disambiguate scientific names from other names using the contextual information. We evaluated NetiNeti on legacy biodiversity texts and biomedical literature (MEDLINE). NetiNeti performs better (precision = 98.9 % and recall = 70.5 %) compared to a popular dictionary based approach (precision = 97.5 % and recall = 54.3 %) on a 600-page biodiversity book that was manually marked by an annotator. On a small set of PubMed Central's full text articles annotated with scientific names, the precision and recall values are 98.5 % and 96.2 % respectively. NetiNeti found more than 190,000 unique binomial and trinomial names in more than 1,880,000 PubMed records when used on the full MEDLINE database. NetiNeti also successfully identifies almost all of the new species names mentioned within web pages. Additionally, we present the comparison results of various machine learning algorithms on our annotated corpus. Naive Bayes and Maximum Entropy with Generalized Iterative Scaling (GIS) parameter estimation are the top two performing algorithms. CONCLUSIONS: We present NetiNeti, a machine learning based approach for identification and discovery of scientific names. The system implementing the approach can be accessed at http://namefinding.ubio.org.     

Generation of a large gene/protein lexicon by morphological pattern analysis

The identification of gene/protein names in natural language text is an important problem in named entity recognition. In previous work we have processed MEDLINE documents to obtain a collection of over two million names of which we estimate that perhaps two thirds are valid gene/protein names. Our problem has been how to purify this set to obtain a high quality subset of gene/protein names. Here we describe an approach which is based on the generation of certain classes of names that are characterized by common morphological features. Within each class inductive logic programming (ILP) is applied to learn the characteristics of those names that are gene/protein names. The criteria learned in this manner are then applied to our large set of names. We generated 193 classes of names and ILP led to criteria defining a select subset of 1,240,462 names. A simple false positive filter was applied to remove 8% of this set leaving 1,145,913 names. Examination of a random sample from this gene/protein name lexicon suggests it is composed of 82% (+/-3%) complete and accurate gene/protein names, 12% names related to genes/proteins (too generic, a valid name plus additional text, part of a valid name, etc.), and 6% names unrelated to genes/proteins. The lexicon is freely available at ftp.ncbi.nlm.nih.gov/pub/tanabe/Gene.Lexicon.     

The species of Hymenoptera described by Linnaeus in the genera Sphex, Chrysis, Vespa, Apis and Mutilla

Data are presented on the type-material representing the species described by Linnaeus in his genera Sphex, Chrysis, Vespa, Apis and Mutilla , The names here considered total 158; six are currently applied in the Hymenoptera Parasitica. Of the balance of 147, three are emendations and five are unavailable homonyms or names proposed in the synonymy of other species. Fifteen Linnaean names are here placed as synonyms. One name is attributed to an author other than Linnaeus, and live names remain species incertae sedis. The remainder, 118, are applied as valid names in die Hymenoptera Aculeata. Holotype specimens in London, Uppsala or Stockholm represent 60 names; 55 names are based on lectotype specimens of which 49 are here designated, two by other authors. One name is represented by a neotype specimen in Lund, and one by a lectotype figure. One non-aculeate species is based on syntypes. Specimens appear to be lost with respect to 25 names; three specimens in Uppsala may be the holotypes of a further three species.
Eight new combinations are made, and twelve new synonyms established; three further new combinations and three further new synonymies are suggested. A systematically arranged summary of species treated and of nomenclatural changes made is given. Nomenclatural changes affecting non-Linnaean names are included where relevant; lectotypes are designated for two non-Linnaean species.     

化石植物中文名的现状、问题与建议

化石植物的中文名, 即化石植物学名的中文译名, 在古植物学、植物演化生物学专业领域和科学普及等方面起着重要的作用。然而, 长期以来对化石植物中文名重视程度不够且拟订时缺乏统一的标准, 导致各种文本中化石植物的中文名比较混乱, 不利于古植物学知识的传播及科学普及。本文通过统计中文古植物学综合性文献和教材中的化石植物中文名, 梳理出化石植物中文名拟订方面出现的一些包括同物异中文名、中文名重名、音译拗口和存在生僻字的使用等常见问题。针对这些问题, 本文提出应尽快制定出一套规范统一的化石植物中文名拟定方案, 编写和出版化石植物拉汉词典及相应网络查询系统等, 从而统一和规范化石植物的中文名, 同时也可为化石动物中文名的拟订方案提供相关参考。     

与日本有关的一些原核微生物种属的规范和分类

以地理位置和人名命名是原核微生物命名中最常见的方式之一。基于中日(东亚汉语圈)同文,从拉丁文转译时,错译和/或误译涉及日本和琉球的菌名是不允许的。本文初步介绍一些涉及日本和琉球地名、机构和人名的原核微生物,提出了机构简写的中文规范命名,指出日本有优势的领域如放线菌研究,从打破文化隔阂的角度,藉此加强中日微生物领域的交流与合作。     

THE ENGLISH NAMES OF THE AFROTROPICAL NIGHTJARS (CAPRIMULGIDAE)

Jackson, H. D. 1993. The English names of the Afrotropical nightjars (Caprimulgidae). Ostrich 64: 148–159.

At least 172 different English names have been used on the nightjars of Africa and its related islands, including Madagascar. A review of the literature chronicles the name changes within each species. Problems created by some duplication and transposition of names between species are discussed. A key to all the names is provided by an alphabetical list cross referenced to the species concerned. The orthography of names is discussed and it is recommended that all animal names be capitalized and freed of unnecessary hyphens. The nightjar names used in The Birds of Africa are accepted as the standard to be followed subject to a few changes.     

中国药用真菌名录及部分名称的修订

近年来,我国对药用真菌的研究和利用越来越重视,相关报道逐年增加。针对有些种类鉴定有误、拉丁学名使用没有严格遵守最新国际植物命名法规、命名人缩写不规范等问题,作者系统考证了我国药用真菌的名称,共收录473种,对每种名称按新近的研究成果和最新命名法规(维也纳法规)进行了订正,对过去的错误报道或不存在的名称进行了修正,将曾报道的、但应作为其他种的同物异名者列在其正名之后,所有名称定名人的缩写全部按国际植物命名法规的要求加以规范化。每种名称之后还列举了该种的主要药用功能或价值,并引证了主要参考文献。     

麻黄属的属下名称问题

统计麻黄属属下名称33个,其中包括13个合法名称,19个不合格发表的名称和1个晚出同名。     

Relationships among given names in the Scilly Isles

The pseudo-genetic analysis of given names shows that, in the Scilly Isles, coefficients of relationship of first names are similar on St Mary's, the Outer Isles, and in the total sample of 5666 individuals married there in two and a half centuries. Comparable coefficients of relationship of a sample of 1658 given names in marriages in England and Wales in 1975 are considerably smaller, but similar within and between districts. The coefficients of relationship of given names on the Scilly Isles decreases during the 19th and especially the 20th centuries in parallel with decreases in random relationship from surnames. The genetic versus cultural-linguistic factors cannot be distinguished in the temporal variation in names, but the geographic differentiation virtually always reported in surnames is not present in these examples of given names and the geographic pattern in the surnames thus seems to result from the hereditary aspect of surnames. This result supports the validity of use of surnames in models of human genetic geography.     

Local names for vascular plants in the John Crow mountains,Jamaica

Local names of vascular plants, accompanied by botanical specimens, were collected in the John Crow Mountains, Portland Parish, Jamaica. Each of the names was volunteered by one local informant; many were independently corroborated by others. We recorded 91 names of forest trees and shrubs, 20 names of climbers, and 33 names of other plants. The uneven distribution of local names among different categories of plants is discussed. The names are mostly of English origin, with a scattering from Spanish, Amerindian and West African languages. Many names are not listed in the standard floras; 20 names are apparently hitherto unrecorded in print. The same name was often found to be applied to a different species from the usage given in the floras, showing the variation in vernacular names from one part of the island to another.     

对中国植物名称引入世界语的商榷

<正> 笔者在《世界语词源结构略析》一文中,曾提到中国植物名称引入世界语的问题,将另作论述。本文就是笔者根据近年来对千余种植物名称,就英、日、俄、拉及世界语等语种,进行文献调研,挑选其中约二百个中国常见植物的名称反复考察,发现在大多数资源植物中,几乎有一半属于药用植物。而它们的名称,近年来随着我国科技成果的推广,已经按汉语拼音在世界各国广泛应用,另有部分植物名称早年已为国外引用,至今仍在使用的。尚有部分在学名中有中国或中国某地方名的音译。对于这些植物名称引入世界语的问题,笔者在此提出个人的一些见解。