生物信息学跨学科研究

目的:研究生物信息学起源、发展趋势,与其他学科相互交叉渗透关系的发展及强度。方法:利用美国《科学引文索引》(SCI)数据库web of science,运用文献计量学方法对8种权威生物信息学期刊2001年至2010年于2011年1月15日之前上传至webof science的全部文献进行统计及分析。通过研究生物信息学相关论文的主题分类,被引情况及施引文献的分类,寻找其跨学科的趋势及相关研究领域的进展情况、主要内容。结果:生物信息学的相关文献数在2001-2010间逐年增加,在2009-2010年达到高峰。跨学科领域广泛,并以生物化学、分子生物学、计算生物学、微生物学、数学、统计学等学科为主要交叉学科。各交叉学科与生物信息学之间跨学科研究的文献数也呈逐年递增趋势。结论:生物信息学的跨学科范围广泛,发展迅速。     

A Comprehensive Survey of Retracted Articles from the Scholarly Literature

Background

The number of retracted scholarly articles has risen precipitously in recent years. Past surveys of the retracted literature each limited their scope to articles in PubMed, though many retracted articles are not indexed in PubMed. To understand the scope and characteristics of retracted articles across the full spectrum of scholarly disciplines, we surveyed 42 of the largest bibliographic databases for major scholarly fields and publisher websites to identify retracted articles. This study examines various trends among them.

Results

We found, 4,449 scholarly publications retracted from 1928–2011. Unlike Math, Physics, Engineering and Social Sciences, the percentages of retractions in Medicine, Life Science and Chemistry exceeded their percentages among Web of Science (WoS) records. Retractions due to alleged publishing misconduct (47%) outnumbered those due to alleged research misconduct (20%) or questionable data/interpretations (42%). This total exceeds 100% since multiple justifications were listed in some retraction notices. Retraction/WoS record ratios vary among author affiliation countries. Though widespread, only miniscule percentages of publications for individual years, countries, journals, or disciplines have been retracted. Fifteen prolific individuals accounted for more than half of all retractions due to alleged research misconduct, and strongly influenced all retraction characteristics. The number of articles retracted per year increased by a factor of 19.06 from 2001 to 2010, though excluding repeat offenders and adjusting for growth of the published literature decreases it to a factor of 11.36.

Conclusions

Retracted articles occur across the full spectrum of scholarly disciplines. Most retracted articles do not contain flawed data; and the authors of most retracted articles have not been accused of research misconduct. Despite recent increases, the proportion of published scholarly literature affected by retraction remains very small. Articles and editorials discussing retractions, or their relation to research integrity, should always consider individual cases in these broad contexts. However, better mechanisms are still needed for raising researchers’ awareness of the retracted literature in their field.     

Elementary and middle level biology topics: a content analysis of Science and Children and Science Scope from 1990 to 2014

Science and Children and Science Scope are peer-reviewed science practitioner journals that publish articles for science educators who teach children of ages 5–10 years and 10–13 years, respectively. As such, these articles are a reflection of the science concepts that are being communicated to science educators. This comprehensive literature review was completed to determine the extent to which the articles included in these journals from 1990 to 2014 focused on biology topics, incorporated other non-science subjects and science disciplines, and encouraged inquiry-based learning. The results indicate that out of the 2701 total articles, 557 (21%) focused on biology. The biology topic covered most often by both journals was animals. The biology topics covered least often were fungi, photosynthesis, respiration and viruses. The findings are taken into consideration and the educational implications for the journals and educators are discussed.     

A Simple Semi-Automatic Approach for Land Cover Classification from Multispectral Remote Sensing Imagery

Land cover data represent a fundamental data source for various types of scientific research. The classification of land cover based on satellite data is a challenging task, and an efficient classification method is needed. In this study, an automatic scheme is proposed for the classification of land use using multispectral remote sensing images based on change detection and a semi-supervised classifier. The satellite image can be automatically classified using only the prior land cover map and existing images; therefore human involvement is reduced to a minimum, ensuring the operability of the method. The method was tested in the Qingpu District of Shanghai, China. Using Environment Satellite 1(HJ-1) images of 2009 with 30 m spatial resolution, the areas were classified into five main types of land cover based on previous land cover data and spectral features. The results agreed on validation of land cover maps well with a Kappa value of 0.79 and statistical area biases in proportion less than 6%. This study proposed a simple semi-automatic approach for land cover classification by using prior maps with satisfied accuracy, which integrated the accuracy of visual interpretation and performance of automatic classification methods. The method can be used for land cover mapping in areas lacking ground reference information or identifying rapid variation of land cover regions (such as rapid urbanization) with convenience.     

An Analysis of Peer-Reviewed Scores and Impact Factors with Different Citation Time Windows: A Case Study of 28 Ophthalmologic Journals

Background

An important attribute of the traditional impact factor was the controversial 2-year citation window. So far, several scholars have proposed using different citation time windows for evaluating journals. However, there is no confirmation whether a longer citation time window would be better. How did the journal evaluation effects of 3IF, 4IF, and 6IF comparing with 2IF and 5IF? In order to understand these questions, we made a comparative study of impact factors with different citation time windows with the peer-reviewed scores of ophthalmologic journals indexed by Science Citation Index Expanded (SCIE) database.

Methods

The peer-reviewed scores of 28 ophthalmologic journals were obtained through a self-designed survey questionnaire. Impact factors with different citation time windows (including 2IF, 3IF, 4IF, 5IF, and 6IF) of 28 ophthalmologic journals were computed and compared in accordance with each impact factor’s definition and formula, using the citation analysis function of the Web of Science (WoS) database. An analysis of the correlation between impact factors with different citation time windows and peer-reviewed scores was carried out.

Results

Although impact factor values with different citation time windows were different, there was a high level of correlation between them when it came to evaluating journals. In the current study, for ophthalmologic journals’ impact factors with different time windows in 2013, 3IF and 4IF seemed the ideal ranges for comparison, when assessed in relation to peer-reviewed scores. In addition, the 3-year and 4-year windows were quite consistent with the cited peak age of documents published by ophthalmologic journals.

Research Limitations

Our study is based on ophthalmology journals and we only analyze the impact factors with different citation time window in 2013, so it has yet to be ascertained whether other disciplines (especially those with a later cited peak) or other years would follow the same or similar patterns.

Originality/ Value

We designed the survey questionnaire ourselves, specifically to assess the real influence of journals. We used peer-reviewed scores to judge the journal evaluation effect of impact factors with different citation time windows. The main purpose of this study was to help researchers better understand the role of impact factors with different citation time windows in journal evaluation.     

SCI收录的真菌学核心期刊介绍

以表格的形式汇总介绍了SC I收录的12种真菌学类目核心期刊的英文刊名、中文刊名、出版国和最新影响因子,并详细介绍了这12种期刊的出版周期、出版者、联系地址、最新期刊网址及期刊描述等全方位的期刊信息。期刊描述内容包括：期刊的创刊年以及期刊的发展,期刊刊载的主要内容,网站可免费获取的该刊目次和文摘及全文信息等。     

Impact of Article Language in Multi-Language Medical Journals - a Bibliometric Analysis of Self-Citations and Impact Factor

Background

In times of globalization there is an increasing use of English in the medical literature. The aim of this study was to analyze the influence of English-language articles in multi-language medical journals on their international recognition – as measured by a lower rate of self-citations and higher impact factor (IF).

Methods and Findings

We analyzed publications in multi-language journals in 2008 and 2009 using the Web of Science (WoS) of Thomson Reuters (former Institute of Scientific Information) and PubMed as sources of information. The proportion of English-language articles during the period was compared with both the share of self-citations in the year 2010 and the IF with and without self-citations. Multivariable linear regression analysis was performed to analyze these factors as well as the influence of the journals‘ countries of origin and of the other language(s) used in publications besides English.We identified 168 multi-language journals that were listed in WoS as well as in PubMed and met our criteria. We found a significant positive correlation of the share of English articles in 2008 and 2009 with the IF calculated without self-citations (Pearson r=0.56, p = <0.0001), a correlation with the overall IF (Pearson r = 0.47, p = <0.0001) and with the cites to years of IF calculation (Pearson r = 0.34, p = <0.0001), and a weak negative correlation with the share of self-citations (Pearson r = -0.2, p = 0.009). The IF without self-citations also correlated with the journal‘s country of origin – North American journals had a higher IF compared to Middle and South American or European journals.

Conclusion

Our findings suggest that a larger share of English articles in multi-language medical journals is associated with greater international recognition. Fewer self-citations were found in multi-language journals with a greater share of original articles in English.     

Assessment of transparency indicators across the biomedical literature: How open is open?

Recent concerns about the reproducibility of science have led to several calls for more open and transparent research practices and for the monitoring of potential improvements over time. However, with tens of thousands of new biomedical articles published per week, manually mapping and monitoring changes in transparency is unrealistic. We present an open-source, automated approach to identify 5 indicators of transparency (data sharing, code sharing, conflicts of interest disclosures, funding disclosures, and protocol registration) and apply it across the entire open access biomedical literature of 2.75 million articles on PubMed Central (PMC). Our results indicate remarkable improvements in some (e.g., conflict of interest [COI] disclosures and funding disclosures), but not other (e.g., protocol registration and code sharing) areas of transparency over time, and map transparency across fields of science, countries, journals, and publishers. This work has enabled the creation of a large, integrated, and openly available database to expedite further efforts to monitor, understand, and promote transparency and reproducibility in science.

This study uses novel open source automated tools to monitor transparency across all 2.75 million open access articles on PubMed Central, discovering that different disciplines, journals and publishers abide by principles of transparency to varying degrees over time.     

Three options for citation tracking: Google Scholar,Scopus and Web of Science

Background

Researchers turn to citation tracking to find the most influential articles for a particular topic and to see how often their own published papers are cited. For years researchers looking for this type of information had only one resource to consult: the Web of Science from Thomson Scientific. In 2004 two competitors emerged – Scopus from Elsevier and Google Scholar from Google. The research reported here uses citation analysis in an observational study examining these three databases; comparing citation counts for articles from two disciplines (oncology and condensed matter physics) and two years (1993 and 2003) to test the hypothesis that the different scholarly publication coverage provided by the three search tools will lead to different citation counts from each.

Methods

Eleven journal titles with varying impact factors were selected from each discipline (oncology and condensed matter physics) using the Journal Citation Reports (JCR). All articles published in the selected titles were retrieved for the years 1993 and 2003, and a stratified random sample of articles was chosen, resulting in four sets of articles. During the week of November 7–12, 2005, the citation counts for each research article were extracted from the three sources. The actual citing references for a subset of the articles published in 2003 were also gathered from each of the three sources.

Results

For oncology 1993 Web of Science returned the highest average number of citations, 45.3. Scopus returned the highest average number of citations (8.9) for oncology 2003. Web of Science returned the highest number of citations for condensed matter physics 1993 and 2003 (22.5 and 3.9 respectively). The data showed a significant difference in the mean citation rates between all pairs of resources except between Google Scholar and Scopus for condensed matter physics 2003. For articles published in 2003 Google Scholar returned the largest amount of unique citing material for oncology and Web of Science returned the most for condensed matter physics.

Conclusion

This study did not identify any one of these three resources as the answer to all citation tracking needs. Scopus showed strength in providing citing literature for current (2003) oncology articles, while Web of Science produced more citing material for 2003 and 1993 condensed matter physics, and 1993 oncology articles. All three tools returned some unique material. Our data indicate that the question of which tool provides the most complete set of citing literature may depend on the subject and publication year of a given article.

     

Impact factor of Revista Iberoamericana de Micología

The impact factor is a bibliometric indicator published annually in the Journal Citation Reports, and widely regarded as a quality ranking of the journals included in this database. The problem with this indicator is that the impact factor of several journals not listed in the Science Citation Index database is largely unknown. The aim of this study was to analyze the 2001 national and international impact factor of Revista Iberoamericana de Micología. The National impact factor of Revista Iberoamericana de Micología was obtained by adding the number of cites in 2001 from a total of 87 Spanish medical journals of greater scientific quality. Also, bibliographical references from Spanish journals indexed in the 2001 Journal Citation reports database have been included to determine the international impact factor of this analyzed journal. Revista Iberoamericana de Micología received a total of 62 cites from published articles in 1999 to 2001, coming from 20 different journals, being their self-citation index 10.1%. The journal with the highest number of cites to Revista Iberoamericana de Micología was Journal of Clinical Microbiology, with 12 cites (19.3%). According to this findings the national and international impact factor of Revista Iberoamericana de Micología was 0.266 and 0.606, respectively. The impact factor of Revista Iberoamericana de Micología, although not included in the Science Citation Index database, was higher than other Journal Citation Reports. Moreover, Revista Iberoamericana de Micología received most of its citations from high impact factor journals included in the Journal Citation Reports database. These data support the international recognition of the scientific level of the journal.     

An Analysis of Citizen Science Based Research: Usage and Publication Patterns

The use of citizen science for scientific discovery relies on the acceptance of this method by the scientific community. Using the Web of Science and Scopus as the source of peer reviewed articles, an analysis of all published articles on “citizen science” confirmed its growth, and found that significant research on methodology and validation techniques preceded the rapid rise of the publications on research outcomes based on citizen science methods. Of considerable interest is the growing number of studies relying on the re-use of collected datasets from past citizen science research projects, which used data from either individual or multiple citizen science projects for new discoveries, such as for climate change research. The extent to which citizen science has been used in scientific discovery demonstrates its importance as a research approach. This broad analysis of peer reviewed papers on citizen science, that included not only citizen science projects, but the theory and methods developed to underpin the research, highlights the breadth and depth of the citizen science approach and encourages cross-fertilization between the different disciplines.     

Scientific publications of Costa Rica in Science Citation Index bibliometric analysis of the period 1999-2001

This study analyzed the publications of authors from Costa Rican institutions that were included in the Science Citation Index (SCI) during 1999-2001. Out of the 722 references detected, distributed in 328 journals, 90.7% corresponded to original research articles. The total productivity figures showed a moderately increasing trend, both in absolute and population-adjusted terms, in concordance with previous data recorded for the period 1980-1998. The contribution of Revista de Biología Tropical to these figures corresponded to 10.0%, 8.9%, and 19.1%, for the years 1999, 2000, and 2001, respectively. The subject distribution of articles followed a similar pattern to that described for 1980-1998, with a predominance of biomedical (33.3%) and biological (27.5%) sciences, followed by agronomical (15.5%) sciences, chemistry (13.6%), physics (5.0%), geological sciences (3.6%), and mathematics (1.5%). Citation analyses for individual publications (up to July 15, 2002) revealed that only 45.2% of the articles had been cited at least once. The ten most cited references were analyzed, varying from 26 to 114 citations. The average citation per article was 2.60, and the average number of authors per article was 2.92. In agreement with data from 1980-1998, the University of Costa Rica appeared as the institution with highest productivity of SCI publications during 1999-2001, with a contribution of 50.0%. The percentage of publications performed without the participation of foreign co-authors showed a change in its decreasing trend of 1980-1998, stabilizing near the range of 25-30% during the period 1999-2001.     

The effect of an imprecise map on interval mapping QTLs

The statistical analysis of quantitative trait locus (QTL) experiments relies on the use of a linkage map of the markers genotyped. Such a map is, at best, a good estimate of the true map. Resources might be diverted into developing better marker maps or improved maps become available after the analysis, raising concerns over the original analysis. It is therefore important to understand the sensitivity of QTL analysis to map inaccuracy. We have used simulation methods to investigate the consequences of an incorrect map on the results of a QTL analysis using interval mapping. Backcross data sets were generated with a particular map and then analysed with both the correct map and incorrect maps. If the incorrect maps maintained the true linkage groups (i.e. no markers were incorrectly assigned to another linkage group), the accuracy of the map had little or no impact on the ability to detect QTLs, the true significance levels of the tests or the relative placement of QTLs. When a marker was incorrectly placed on another linkage group, there was a small increase in the level of the test. After adjusting for this increase, there was a decrease in power to detect a QTL near the misplaced marker. This decrease was of a similar magnitude to that found when using a single-marker analysis compared with interval mapping. These results mean that QTL analyses can proceed without the need for very accurate marker maps, and that estimated QTL positions can be translated onto updated maps without the need for reanalysis.     

Object-oriented image analysis to extract landscape elements in urban fringes, Central Japan

A method enabling the object-oriented image analysis of landscape elements incorporating topographic data was designed and tested on a Japanese countryside target area. IKONOS data (four multispectral bands with a spatial resolution of 4 m and a panchromatic band with a spatial resolution of 1 m) acquired on 23 April 2001 were used. Definiens v.5 software (Definiens AG, München, Germany) was employed for the classification. The initial segmentation was multiresolution and bottom-up, and each segment identified was considered to be one object. Two classifications employing the same landscape elements and ground truth data were implemented. One classification adopted an object-based image analysis classification method based on spectral characteristics; the other utilized an object-oriented image analysis (OOIA) that allows for a suitable scale parameter to be selected independently for each landscape element. In addition, topographic data derived from field surveys (walking surveys) and topographic maps were used to create a topographic database delineating the boundary between valley bottoms and the adjacent slopes (elevation: about 10 m). These data were then integrated into the OOIA analysis. The accuracies of the two classifications were assessed by comparing the results to a master landscape map produced directly from aerial photographs and on-site observations. The object-oriented method using the topographic data resulted in a higher overall kappa coefficients (0.63–0.47) than the object-based method. These results indicate that object-oriented image analysis of very high resolution data used in combination with topographic data can be an effective tool for landscape classification in Japan, where historical land-use patterns have resulted in finely dissected landscapes.     

Satellite remote sensing of wetlands

To conserve and manage wetland resources, it is important to inventoryand monitor wetlands and their adjacent uplands. Satellite remote sensing hasseveral advantages for monitoring wetland resources, especially for largegeographic areas. This review summarizes the literature on satellite remotesensing of wetlands, including what classification techniques were mostsuccessful in identifying wetlands and separating them from other land covertypes. All types of wetlands have been studied with satellite remote sensing.Landsat MSS, Landsat TM, and SPOT are the major satellite systems that have beenused to study wetlands; other systems are NOAA AVHRR, IRS-1B LISS-II and radarsystems, including JERS-1, ERS-1 and RADARSAT. Early work with satellite imageryused visual interpretation for classification. The most commonly used computerclassification method to map wetlands is unsupervised classification orclustering. Maximum likelihood is the most common supervised classificationmethod. Wetland classification is difficult because of spectral confusion withother landcover classes and among different types of wetlands. However,multi-temporal data usually improves the classification of wetlands, as doesancillary data such as soil data, elevation or topography data. Classifiedsatellite imagery and maps derived from aerial photography have been comparedwith the conclusion that they offer different but complimentary information.Change detection studies have taken advantage of the repeat coverage andarchival data available with satellite remote sensing. Detailed wetland maps canbe updated using satellite imagery. Given the spatial resolution of satelliteremote sensing systems, fuzzy classification, subpixel classification, spectralmixture analysis, and mixtures estimation may provide more detailed informationon wetlands. A layered, hybrid or rule-based approach may give better resultsthan more traditional methods. The combination of radar and optical data providethe most promise for improving wetland classification.     

A geospatial approach to monitoring impervious surfaces in watersheds using Landsat data (the Mondego Basin,Portugal as a case study)

The urbanization of watersheds is a highly dynamic global phenomenon that must be monitored. With consequences for the environment, the population, and the economy, accurate products at adequate spatial and temporal resolutions are required and demanded by the science community and stakeholders alike. To address these needs, a new Impervious Surface Area (ISA) product was created for a Portuguese Watershed (Mondego river) from Landsat data (a combination of leaf-on multispectral bands, derived products, and NDVI time series), using Regression Tree Models (RTM). The product provides 30-m spatial resolution ISA estimates (0–100%) with a Mean Average Error (MAE) of 1.6% and Root Mean Square Error (RMSE) of 5.5%.A strategy to update the baseline product was tested in earlier imagery (2001 and 2007) for a subset of the watershed. Instead of updating the baseline product, the strategy seeks to identify stable training samples and remove those where change was detected in a time series of Change Vector Analysis (CVA). The stable samples were then used to create new ISA models using RTM. The updated maps were similar to the original product in terms of accuracy metrics (MAE: 2001: 2.6%; 2007:3.6%).The products and methodology offer a new perspective on the urban development of the watershed, at a scale previously unavailable. It can also be replicated elsewhere at a low cost, leveraging the growing Landsat data archive, and provide timely information on relevant land cover metrics to the scientific community and stakeholders.     

Past and present forest vegetation in NE Slovenia derived from old maps

Abstract. Using old military and cadastral maps and modern vegetation maps, the changes in land use over the past 230 yr were followed. The following maps were used: the military map from the second half of the 18th century, the cadastral map of the ‘Economic cadastral survey for regulation of land taxes’ from the first half of the 19th century, and a field map made in the 1980s. A vegetation map of the area was made on the basis of satellite images. We used basic classification techniques combined with extensive field inspections and aerial photographs. The output of this procedure was verified in the field. Additionally, a comparison of statistical data about land use categories is presented. It was established that the last remaining areas of inundated riverine forest disappeared 200 yr ago, and since then only minor changes in land use have occurred.     

Updated geographic range maps for giraffe,Giraffa spp., throughout sub‐Saharan Africa,and implications of changing distributions for conservation

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Public sphere and the sustainability of the bioinformatics promise

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