Summary of recent systems of angiosperm classification

Seven recently established (2007 – 2010) systems of classification for flowering plants (Magnoliidae or angiosperms) are uniformly arranged in a linear fashion to allow ready comparisons with an eighth proposed anew here. Uniform names and orthography are used throughout with author abbreviations; however, the choice of names above the rank of family are not standardised as rules of priority do not apply. Full bibliographic information is not given but is available both in print and online. The numbers of names per rank for each system is given. Two previously unpublished names recognised by Takhtajan in 2009, Aextoxicales and Polypremaceae, are validated. In addition nine suborder and two family names are established: Alseuosmiineae, Campynematineae, Crossosomatineae, Geissolomatineae, Mazaceae, Proteineae, Rehmanniaceae, Rutineae, Sarraceniineae, Simmondsiineae, and Smilacineae.     

Proposed nomenclature for human butyrylcholinesterase genetic variants identified by DNA sequencing

1. New information identifying nucleotide alterations of human butyrylcholinesterase allows the use of more specific nomenclature for the variants commonly known as atypical, fluoride, silent, and K variant. 2. In addition to suggesting a system of trivial names and abbreviations, we provide a list of formal names that follow the guidelines of the Committee for Human Gene Nomenclature. 3. It is suggested that formal names be included in publications whenever possible.     

Specific epithets of the flowering plants of central French Guiana

The epithets of the flowering plants of central French Guiana are classified into derivation categories. Specific epithets of the flowering plants of central French Guiana refer mostly to shapes (274 species), persons (252), places (212), appearance (146), and size (140). These categories account for 55% of names given to the plants of this flora. The most prolific publishers of names for the flora of central French Guiana are Aublet and Linnaeus, who were respectively the authors of 177 and 110 of the names of species (15% of the total) found in the flora of central French Guiana. Although many of the species names, such as those relating to place and person, are easy to categorize, many others are open to different interpretations. Specific epithets with different orthographies derived from Guiana or Guyana are discussed. In addition, problems in the use of diacritical marks and inconsistencies with spacing between the abbreviations of given names and surnames of authors of plant names are noted.     

PNAD-CSS: a workbench for constructing a protein name abbreviation dictionary

MOTIVATION: Since their initial development, integration and construction of databases for molecular-level data have progressed. Though biological molecules are related to each other and form a complex system, the information is stored in the vast archives of the literature or in diverse databases. There is no unified naming convention for biological object, and biological terms may be ambiguous or polysemic. This makes the integration and interaction of databases difficult. In order to eliminate these problems, machine-readable natural language resources appear to be quite promising. We have developed a workbench for protein name abbreviation dictionary (PNAD) building. RESULTS: We have developed PNAD Construction Support System (PNAD-CSS), which offers various convenient facilities to decrease the construction costs of a protein name abbreviation dictionary of which entries are collected from abstracts in biomedical papers. The system allows the users to concentrate on higher level interpretation by removing some troublesome tasks, e.g. management of abstracts, extracting protein names and their abbreviations, and so on. To extract a pair of protein names and abbreviations, we have developed a hybrid system composed of the PROPER System and the PNAD System. The PNAD System can extract the pairs from parenthetical-paraphrases involved in protein names, the PROPER System identified these paris, with 98.95% precision, 95.56% recall and 97.58% complete precision. AVAILABILITY: PROPER System is freely available from http://www.hgc.inc.u-tokyo.ac.jp/service/tooldoc /KeX/intro.html. The other software are also available on request. Contact the authors. CONTACT: mikio@ims.u-tokyo.ac.jp     

Index of new names of syntaxa published in 1993

The present work collects the new names of syntaxa (in the sense of the Code of Phytosociological Nomenclature,Barkman et al. 1986) above subassociation rank found in the literature received by the Library of the Conservatoire Botanique in Geneva. For the year 1993, 1028 names have been listed and the validity of each one is considered in relation to the Code of Phytosociological Nomenclature. Two names are given in addition to the Index 1992 (Theurillat & Moravec 1995).     

Index of new names of syntaxa published in 1991

This Index collects the new names of syntaxa (in the sense of the Code of Phytosociological Nomenclature,Barkman et al. 1986) above subassociation rank found in the literature received by the Library of the Conservatoire Botanique in Geneva. For the year 1991 591 names have been listed. Each one is accompanied by an appreciation about its validity with respect to the Code of Nomenclature. 25 names are given in addition to the Indexes 1988, 1989 and 1990 (Theurillat & Moravec 1991, 1992, 1993).     

Index of new names of syntaxa published in 1992

The present work collects the new names of syntaxa (in the sense of the Code of Phytosociological Nomenclature,Barkman et al. 1986) above subassociation, rank found in the literature received by the Library of the Conservatoire et Jardin botaniques in Geneva. For the year 1992, 658 names have been listed. For each one of them, an appreciation about its validity is given relating to the Code of Phytosociological Nomenclature. Fifteen names are given in addition to the Indexes 1987, 1990 and 1991 (Theurillat & Moravec 1990, 1993, 1994).     

Index of new names of syntaxa published in 1988

The present work collects the new names of syntaxa (in the sense of the Code of Phytosociological Nomenclature,Barkman et al. 1986) above subassociation rank found in the literature received by the Library of the Conservatoire Botanique in Geneva. For the year 1988, 297 names have been listed. For each one of them, an appreciation about its validity is given relating to the Code of Nomenclature. 17 names are given in addition to the Index 1987 (Theurillat etMoravec 1990).     

Index of new names of syntaxa published in 1994

The present work collects the new names of syntaxa (in the sense of the Code of phytosociological nomenclature,Barkman et al. 1986) above subassociation rank found in the literature received by the Library of the Conservatoire Botanique in Geneva. For the year 1994 851 names were listed corresponding to 34 classes, 55 orders, 2 suborders, 128 alliances, 29 suballiances, and 603 associations. For each of them, an assessment of its validity is given relating to the Code of Phytosociological Nomenclature. 72 names are given to add to the Indices 1991, 1992, 1993 (Theurillat & Moravec 1994, 1995, 1996).     

中国植物分类学者姓名拼写的讨论与建议

在汉语拼音方案未正式推行前, 近代较早的文献书籍里对中国植物分类学者姓名的记载以威妥玛拼音为主, 同时混杂其他拼音形式, 另外存在诸多以缩写方式记录人名的情况。在进行近当代中国植物学的文献阅读、资料查询以及文献引证时, 多样化的人名拼写与缩写方式在一定程度上造成了困扰与混乱。本文简述了中国植物分类学发展初期主要用于人名地名的拼写系统, 以近当代中国植物学相关研究者的姓名索引为基础数据, 结合国内外的植物学相关网站及数据库, 整理出了较完整的早期中国植物分类学家姓名拼写的信息对照表。基于历史数据和当下应用实例, 归纳了中国植物分类学者姓名拼写多样现象的类型及其原因。过去及当代国内外在拼写中国人名上存在的问题有: (1)历史记载中写法不规范现象; (2)不同拼音形式的识别与使用混乱现象; (3)现代拼写在姓与名的顺序、拼音大小写、双名连接以及缩写上不统一现象。最后, 我们提出了关于中国植物分类学者姓名拼写与引用的建议。     

Index of new names of syntaxa published in 1989

The present work collects the new names of syntaxa (in the sense of the Code of Phytosociological Nomenclature,Barkman et al. 1986) above subassociation rank found in the literature received by the Library of the Conservatoire Botanique in Geneva. For the year 1989, 588 names have been listed. For each one of them, an appreciation about its validity is given relating to the Code of Nomenclature. 15 names are given in addition to the “Index 1987” (Theurillat etMoravec 1990) and 53 to the “Index 1988” (Theurillat etMoravec 1991).     

Consensus International Council for Commonality in Blood Banking Automation–International Society for Cell & Gene Therapy statement on standard nomenclature abbreviations for the tissue of origin of mesenchymal stromal cells

The Cellular Therapy Coding and Labeling Advisory Group of the International Council for Commonality in Blood Banking Automation and the International Society for Cell & Gene Therapy mesenchymal stromal cell (MSC) committee are providing specific recommendations on abbreviating tissue sources of culture-adapted MSCs. These recommendations include using abbreviations based on the ISBT 128 terminology model that specifies standard class names to distinguish cell types and tissue sources for culture-adapted MSCs. Thus, MSCs from bone marrow are MSC(M), MSCs from cord blood are MSC(CB), MSCs from adipose tissue are MSC(AT) and MSCs from Wharton's jelly are MSC(WJ). Additional recommendations include using these abbreviations through the full spectrum of pre-clinical, translational and clinical research for the development of culture-adapted MSC products. This does not apply to basic research focused on investigating the developmental origins, identity or functionalities of endogenous progenitor cells in different tissues. These recommendations will serve to harmonize nomenclature in describing research and development surrounding culture-adapted MSCs, many of which are destined for clinical and/or commercial translation. These recommendations will also serve to align research and development efforts on culture-adapted MSCs with other cell therapy products.     

A proposed nomenclature for bile acids.

A proposal is made for a system of nomenclature of the more common unconjugated and conjugated bile acids. Acceptable trivial names for bile acids are tabulated, and guidelines are proposed for using these existing trivial names as roots to create acceptable semi-systematic names for other bile acids, as well as for new natural bile acids that will be discovered in the future. The term alpha-hyocholic is recommended to replace hyocholic, and beta-hyocholic to replace omega-muricholic. The term murideoxycholic acid is recommended for 3 alpha,6 beta-dihydroxy-5 beta-cholan-24-oic acid. Proposals are also made for bile acids with epimeric hydroxy groups, for unsaturated bile acids, and for bile acids with oxo- and/or hydroxy-oxo- substituents on the nucleus and/or on the side chain. For conjugated bile acids, the term "aminoacyl amidates" is recommended to replace "amidates" for bile acids conjugated in N-acyl linkage with amino acids. Nomenclature for other types of conjugates (sulfates, glucuronides, glucosides) is included as well as abbreviations. It is recommended that the historic tradition of naming a newly discovered bile acid after the species from which it was isolated be abandoned, and that in the future such a bile acid should be named using the principles contained in this paper.     

Index of new names of syntaxa published in 1990

The present work collects the new names of syntaxa (in the sense of the Code of Phytosociological Nomenclature,Barkman et al. 1986) above subassociation rank found in the literature received by the Library of the Conservatoire Botanique in Geneva. For the year 1990 454 names have been listed. For each one of them, a first appreciation about its validity is given relating to the Code of Nomenclature. 8 names are given in addition to the Index 1987 (Theurillat andMoravec 1990), 9 to the Index 1988 (Theurillat andMoravec 1991) and 4 to Index 1989 (Theurillat andMoravec 1992).     

Index of new names of syntaxa published in 1987

The present work collects the new names of syntaxa (in the sense of the Code of Phytosociological Nomenclature,Barkman et al. 1986) above subassociation rank found in the literature received by the Library of the Conservatoire Botanique in Geneva. For the year 1987, 460 names have been listed. For each one of them, an appreciation about its validity is given relating to the Code of Nomenclature.     

Morpheme Matching Based Text Tokenization for a Scarce Resourced Language

Text tokenization is a fundamental pre-processing step for almost all the information processing applications. This task is nontrivial for the scarce resourced languages such as Urdu, as there is inconsistent use of space between words. In this paper a morpheme matching based approach has been proposed for Urdu text tokenization, along with some other algorithms to solve the additional issues of boundary detection of compound words, affixation, reduplication, names and abbreviations. This study resulted into 97.28% precision, 93.71% recall, and 95.46% F1-measure; while tokenizing a corpus of 57000 words by using a morpheme list with 6400 entries.     

ADAM: another database of abbreviations in MEDLINE

MOTIVATION: Abbreviations are an important type of terminology in the biomedical domain. Although several groups have already created databases of biomedical abbreviations, these are either not public, or are not comprehensive, or focus exclusively on acronym-type abbreviations. We have created another abbreviation database, ADAM, which covers commonly used abbreviations and their definitions (or long-forms) within MEDLINE titles and abstracts, including both acronym and non-acronym abbreviations. RESULTS: A model of recognizing abbreviations and their long-forms from titles and abstracts of MEDLINE (2006 baseline) was employed. After grouping morphological variants, 59 405 abbreviation/long-form pairs were identified. ADAM shows high precision (97.4%) and includes most of the frequently used abbreviations contained in the Unified Medical Language System (UMLS) Lexicon and the Stanford Abbreviation Database. Conversely, one-third of abbreviations in ADAM are novel insofar as they are not included in either database. About 19% of the novel abbreviations are non-acronym-type and these cover at least seven different types of short-form/long-form pairs. AVAILABILITY: A free, public query interface to ADAM is available at http://arrowsmith.psych.uic.edu, and the entire database can be downloaded as a text file.     

MBA: a literature mining system for extracting biomedical abbreviations

Background  

The exploding growth of the biomedical literature presents many challenges for biological researchers. One such challenge is from the use of a great deal of abbreviations. Extracting abbreviations and their definitions accurately is very helpful to biologists and also facilitates biomedical text analysis. Existing approaches fall into four broad categories: rule based, machine learning based, text alignment based and statistically based. State of the art methods either focus exclusively on acronym-type abbreviations, or could not recognize rare abbreviations. We propose a systematic method to extract abbreviations effectively. At first a scoring method is used to classify the abbreviations into acronym-type and non-acronym-type abbreviations, and then their corresponding definitions are identified by two different methods: text alignment algorithm for the former, statistical method for the latter.     

Names in Gnaphalium, Xeranthemum and Helichrysum published between 1753 and 1800

All the names published under the genera Gnaphalium, Xeranthemum and Helichrysum in the period 1753–1800 are listed and up-to-date determinations are given. Appendices deal with: the specimens preserved in the Linnaean herbarium; the plants illustrated in Burman's Rariorum Africanarum Plantarum decades and the nomenclature of a number of species that needed clarification.     

Resolving abbreviations to their senses in Medline

MOTIVATION: Biological literature contains many abbreviations with one particular sense in each document. However, most abbreviations do not have a unique sense across the literature. Furthermore, many documents do not contain the long forms of the abbreviations. Resolving an abbreviation in a document consists of retrieving its sense in use. Abbreviation resolution improves accuracy of document retrieval engines and of information extraction systems. RESULTS: We combine an automatic analysis of Medline abstracts and linguistic methods to build a dictionary of abbreviation/sense pairs. The dictionary is used for the resolution of abbreviations occurring with their long forms. Ambiguous global abbreviations are resolved using support vector machines that have been trained on the context of each instance of the abbreviation/sense pairs, previously extracted for the dictionary set-up. The system disambiguates abbreviations with a precision of 98.9% for a recall of 98.2% (98.5% accuracy). This performance is superior in comparison with previously reported research work. AVAILABILITY: The abbreviation resolution module is available at http://www.ebi.ac.uk/Rebholz/software.html.