Building Large Collections of Chinese and English Medical Terms from Semi-Structured and Encyclopedia Websites

To build large collections of medical terms from semi-structured information sources (e.g. tables, lists, etc.) and encyclopedia sites on the web. The terms are classified into the three semantic categories, Medical Problems, Medications, and Medical Tests, which were used in i2b2 challenge tasks. We developed two systems, one for Chinese and another for English terms. The two systems share the same methodology and use the same software with minimum language dependent parts. We produced large collections of terms by exploiting billions of semi-structured information sources and encyclopedia sites on the Web. The standard performance metric of recall (R) is extended to three different types of Recall to take the surface variability of terms into consideration. They are Surface Recall (), Object Recall (), and Surface Head recall (). We use two test sets for Chinese. For English, we use a collection of terms in the 2010 i2b2 text. Two collections of terms, one for English and the other for Chinese, have been created. The terms in these collections are classified as either of Medical Problems, Medications, or Medical Tests in the i2b2 challenge tasks. The English collection contains 49,249 (Problems), 89,591 (Medications) and 25,107 (Tests) terms, while the Chinese one contains 66,780 (Problems), 101,025 (Medications), and 15,032 (Tests) terms. The proposed method of constructing a large collection of medical terms is both efficient and effective, and, most of all, independent of language. The collections will be made publicly available.     

传粉生物学常用术语释译

A list of common terms in pollination biology was compiled from a large body of literature. For terms with existing Chinese translation, we checked and polished their translation; for those yet without translation, we proposed 本文从大量现有中外文献中分类收集整理了传粉生物学中常见的一些术语, 斟酌了已有的中文译名, 对一些未见中文译名的词语本着望文生义的原则进行了试译, 并对一些重要或易于引起歧义的词语进行了相应的阐明和举例。     

MaSTerClass: a case-based reasoning system for the classification of biomedical terms

MOTIVATION: The sheer volume of textually described biomedical knowledge exerts the need for natural language processing (NLP) applications in order to allow flexible and efficient access to relevant information. Specialized semantic networks (such as biomedical ontologies, terminologies or semantic lexicons) can significantly enhance these applications by supplying the necessary terminological information in a machine-readable form. With the explosive growth of bio-literature, new terms (representing newly identified concepts or variations of the existing terms) may not be explicitly described within the network and hence cannot be fully exploited by NLP applications. Linguistic and statistical clues can be used to extract many new terms from free text. The extracted terms still need to be correctly positioned relative to other terms in the network. Classification as a means of semantic typing represents the first step in updating a semantic network with new terms. RESULTS: The MaSTerClass system implements the case-based reasoning methodology for the classification of biomedical terms.     

Cognitive Aspects of Step- Terms in American Kinship

In this article we extend the study of judged similarity among kinship terms from consanguineal to stepterms. Based on a sample of college students, we present a Euclidean representation of American kinship terms that shows that the distinction between consanguineal terms and step- terms is crucial. This representation matches predictions from the componential analysis paradigm and is shared by respondents of both genders with different ethnicities and first languages spoken. [American kinship, stepfamilies, correspondence analysis, consanguinity]     

Interpretation of Tracer Data: Significance of the Number of Terms in Specific Activity Functions

It has already been shown that the number of pools in an open system in the steady state cannot be determined from the number of exponential terms in the specific activity function of a pool, even if the data were free from experimental error. However, some information is conveyed by the number of exponential terms. The information is different depending upon whether the data are obtained from the pool into which the tracer is introduced or from another pool. In the latter case, the number of exponential terms is shown to indicate the maximum number of intermediate pools involved in the shortest path of transfer of material from the injected pool to the pool in question. With regard to the former case, this paper is restricted to functions with two exponential terms and shows which systems of n pools (n >/= 2) are consistent with such data. Consequently, biexponential experimental curves can be interpreted in terms of models consisting of an unrestricted number of pools in which each pool is defined in terms of fast mixing. The generalization to cases of functions with more than two exponential terms can be carried out in a similar manner.     

A glossary of scientific terms used in the Russian-language literature on parasitic and blood-sucking arthropods

The glossary includes the major terms and concepts most often used in the Russian literature on parasitology and medico-veterinary entomology. Each term is explained, and some are supplemented with more common English equivalents. The glossary covers only the common terms and does not include those referring to very specific topics and concepts; the names of arthropod taxa and morphological terms are also not included. The list of terms is by no means a comprehensive glossary and is not supposed to be a normative edition.     

The importance of transport processes and spatial gradients on in situ estimates of lake metabolism

We measured spatial gradients of dissolved oxygen in a eutrophic reservoir from repeated transects over a 5-day period. The equation typically used to compute lake metabolism was extended to the full advection?Cdiffusion?Creaction equation, which includes transport terms. These transport terms were computed and found to be of similar magnitude to the rate of change of dissolved oxygen. We demonstrate that neglecting transport terms in this reservoir could lead to over-estimates in net ecosystem production calculations in the surface layer of up to 100%. We advocate the calculation of nondimensional Peclet and Damkohler numbers in future studies to assist in determining the importance of transport terms on lake metabolism estimates.     

A review of terminology on aggregation patterns in bonobos (Pan paniscus)

We review terms that describe the levels of group structure in Pan paniscus.We discuss points of confusion that result from unclear definition of terms, which could lead to inaccurate intra- and interspecific comparisons. We recommend terms that are applicable to captive populations.     

Differentiable, multi-dimensional, knowledge-based energy terms for torsion angle probabilities and propensities

Rotatable torsion angles are the major degrees of freedom in proteins. Adjacent angles are highly correlated and energy terms that rely on these correlations are intensively used in molecular modeling. However, the utility of torsion based terms is not yet fully exploited. Many of these terms do not capture the full scale of the correlations. Other terms, which rely on lookup tables, cannot be used in the context of force-driven algorithms because they are not fully differentiable. This study aims to extend the usability of torsion terms by presenting a set of high-dimensional and fully-differentiable energy terms that are derived from high-resolution structures. The set includes terms that describe backbone conformational probabilities and propensities, side-chain rotamer probabilities, and an elaborate term that couples all the torsion angles within the same residue. The terms are constructed by cubic spline interpolation with periodic boundary conditions that enable full differentiability and high computational efficiency. We show that the spline implementation does not compromise the accuracy of the original database statistics. We further show that the side-chain relevant terms are compatible with established rotamer probabilities. Despite their very local characteristics, the new terms are often able to identify native and native-like structures within decoy sets. Finally, force-based minimization of NMR structures with the new terms improves their torsion angle statistics with minor structural distortion (0.5 A RMSD on average). The new terms are freely available in the MESHI molecular modeling package. The spline coefficients are also available as a documented MATLAB file.     

A review of terminology on aggregation patterns in bonobos (Pan paniscus)

We review terms that describe the levels of group structure in Pan paniscus.We discuss points of confusion that result from unclear definition of terms, which could lead to inaccurate intra- and interspecific comparisons. We recommend terms that are applicable to captive populations.     

Evaluation and Cross-Comparison of Lexical Entities of Biological Interest (LexEBI)

Motivation

Biomedical entities, their identifiers and names, are essential in the representation of biomedical facts and knowledge. In the same way, the complete set of biomedical and chemical terms, i.e. the biomedical “term space” (the “Lexeome”), forms a key resource to achieve the full integration of the scientific literature with biomedical data resources: any identified named entity can immediately be normalized to the correct database entry. This goal does not only require that we are aware of all existing terms, but would also profit from knowing all their senses and their semantic interpretation (ambiguities, nestedness).

Result

This study compiles a resource for lexical terms of biomedical interest in a standard format (called “LexEBI”), determines the overall number of terms, their reuse in different resources and the nestedness of terms. LexEBI comprises references for protein and gene entries and their term variants and chemical entities amongst other terms. In addition, disease terms have been identified from Medline and PubmedCentral and added to LexEBI. Our analysis demonstrates that the baseforms of terms from the different semantic types show only little polysemous use. Nonetheless, the term variants of protein and gene names (PGNs) frequently contain species mentions, which should have been avoided according to protein annotation guidelines. Furthermore, the protein and gene entities as well as the chemical entities, both do comprise enzymes leading to hierarchical polysemy, and a large portion of PGNs make reference to a chemical entity. Altogether, according to our analysis based on the Medline distribution, 401,869 unique PGNs in the documents contain a reference to 25,022 chemical entities, 3,125 disease terms or 1,576 species mentions.

Conclusion

LexEBI delivers the complete biomedical and chemical Lexeome in a standardized representation (http://www.ebi.ac.uk/Rebholz-srv/LexEBI/). The resource provides the disease terms as open source content, and fully interlinks terms across resources.     

Definition and Classification of Manufacturing Flexibility Types and Measures

Flexibility is one of the most sought-after properties in modern manufacturing systems. Despite this interest, flexibility remains poorly understood in theory and poorly utilized in practice. One reason for this is the lack of general agreement on how to define flexibility: over 70 terms (types and measures) can be found in the literature. This paper concerns developing a framework and classification scheme for use in defining and classifying the various terms regarding flexibility found in manufacturing. The framework consists of six attributes: level of manufacturing requirements specification, manufacturing system specification, manufacturing environment specification, flexibility dimension, flexibility measurement approach, and time frame. A six-field hybrid classification scheme is developed based on this framework. The framework serves as a guide for developing new flexibility terms, whereas the classification scheme provides a mechanism for summarizing the important aspects of and assumptions behind a given term. The approach is demonstrated by using the classification scheme to classify over 50 existing flexibility terms. The results indicate that the classification scheme is an effective tool to aid in understanding different flexibility terms and how they compare to one another. At the same time, the difficulty of the classification exercise indicates the need for a suitable framework when defining such terms.     

Biological nomenclature terms for facilitating communication in the naming of organisms

A set of terms recommended for use in facilitating communication in biological nomenclature is presented as a table showing broadly equivalent terms used in the traditional Codes of nomenclature. These terms are intended to help those engaged in naming across organism groups, and are the result of the work of the International Committee on Bionomenclature, whose aim is to promote harmonisation and communication amongst those naming life on Earth.     

Cost analysis of arterial branching in the cardiovascular systems of man and animals

A new scheme is presented whereby data on arterial branching can be interpreted in terms of direct cost to the physiological system. The scheme makes it possible to assess, at a glance, the true degree of optimality of an arterial network. Departure from optimality is indicated in terms of cost, rather than in terms of the difference between theoretical and measured branching angles. The scheme is applied to several groups of biological data and new conclusions are reached with regard to their degrees of optimality.     

Role of microglia in CNS inflammation

There is increasing confusion about the meaning of the terms inflammation, neuroinflammation, and microglial inflammation. We aim in this review to achieve greater clarity regarding these terms, which are essential for our understanding of the role of microglia in CNS inflammatory conditions. The important concept of sterile inflammation is explained against the backdrop of classical inflammation, and its key differences from what researchers refer to when they use the terms neuroinflammation and microglial inflammation are illustrated. We propose to replace the term "neuroinflammation" with "microglial activation" or "CNS pseudo-inflammation", if microglial activation does not suffice. In addition, we recommend abandoning the terms "microglial inflammation" and "inflamed microglia" because of the lack of a clear concept behind them.     

GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns

GO-Module is a web-accessible synthesis and visualization tool developed for end-user biologists to greatly simplify the interpretation of prioritized Gene Ontology (GO) terms. GO-Module radically reduces the complexity of raw GO results into compact biomodules in two distinct ways, by (i) constructing biomodules from significant GO terms based on hierarchical knowledge, and (ii) refining the GO terms in each biomodule to contain only true positive results. Altogether, the features (biomodules) of GO-Module outputs are better organized and on average four times smaller than the input GO terms list (P = 0.0005, n = 16). AVAILABILITY: http://lussierlab.org/GO-Module.     

On the terms in the International Code of Botanical Nomenclature

The most recent edition of the International Code of Botanical Nomenclature (Vienna Code) has superseded all previous editions. One of the notable changes in the Vienna Code is that it contains a glossary of nomenclatural terms defined and used in the Code. It has been made clear that the glossary of these terms is an integral part of the Code. This paper presents a Chinese translation of the definitions of the nomenclatural terms in the Code.