Biodiversity Informatics最新文献_第5页

Character Selection During Interactive Taxonomic Identification: “Best Characters” 交互分类鉴定中的性状选择:“最佳性状”

Biodiversity Informatics Pub Date : 2014-03-27 DOI: 10.17161/BI.V9I1.4611

N. Talent, R. Dickinson, T. Dickinson

{"title":"Character Selection During Interactive Taxonomic Identification: “Best Characters”","authors":"N. Talent, R. Dickinson, T. Dickinson","doi":"10.17161/BI.V9I1.4611","DOIUrl":"https://doi.org/10.17161/BI.V9I1.4611","url":null,"abstract":"Software interfaces for interactive multiple-entry taxonomic identification (polyclaves) sometimes provide a “best character” or “separation” coefficient, to guide the user to choose a character that could most effectively reduce the number of identification steps required. The coefficient could be particularly helpful when difficult or expensive tasks are needed for forensic identification, and in very large databases, uses that appear likely to increase in importance. Several current systems also provide tools to develop taxonomies or single-entry identification keys, with a variety of coefficients that are appropriate to that purpose. For the identification task, however, information theory neatly applies, and provides the most appropriate coefficient. To our knowledge, Delta-Intkey is the only currently available system that uses a coefficient related to information theory, and it is currently being reimplemented, which may allow for improvement. We describe two improvements to the algorithm used by Delta-Intkey. The first improves transparency as the number of remaining taxa decreases, by normalizing the range of the coefficient to [0,1]. The second concerns numeric ranges, which require consistent treatment of sub-intervals and their end-points. A stand-alone Bestchar program for categorical data is provided, in the Python and R languages. The source code is freely available and dedicated to the Public Domain.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"56 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124365826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

CONTENT ASSESSMENT OF THE PRIMARY BIODIVERSITY DATA PUBLISHED THROUGH GBIF NETWORK: STATUS, CHALLENGES AND POTENTIALS gbif网络发表的初级生物多样性数据内容评价:现状、挑战和潜力

Biodiversity Informatics Pub Date : 2013-07-09 DOI: 10.17161/BI.V8I2.4124

G. Samy, V. Chavan, Arturo H. Ariño, J. Otegui, D. Hobern, R. Sood, Estrella Robles

{"title":"CONTENT ASSESSMENT OF THE PRIMARY BIODIVERSITY DATA PUBLISHED THROUGH GBIF NETWORK: STATUS, CHALLENGES AND POTENTIALS","authors":"G. Samy, V. Chavan, Arturo H. Ariño, J. Otegui, D. Hobern, R. Sood, Estrella Robles","doi":"10.17161/BI.V8I2.4124","DOIUrl":"https://doi.org/10.17161/BI.V8I2.4124","url":null,"abstract":"With the establishment of the Global Biodiversity Information Facility (GBIF) in 2001 as an inter-governmental co-ordinating body, concerted efforts were made during the past decade to establish a global research infrastructure to facilitate the sharing, discovery and access to primary biodiversity data. As on date the participants in GBIF have enabled the discovery and access to over 267+ million such data records. While this remarkable achievement in terms of volume of data must be acknowledged, concerns about the quality and ‘fitness-for-use’ of the data should also be carefully considered in future developments. This contribution is therefore a direct response to the calls for comprehensive content assessment of the GBIF mobilised data. It is the first comprehensive assessment of the coverage of the content mobilised so far through GBIF, as well as a mean to identify the existing gaps and reflect on fitness-for-use requirements. This paper describes the complementary methodologies adopted by the GBIF Secretariat and University of Navarra for the development of a comprehensive content assessment. Outcomes of these research initiatives are summarised in four categories, namely, (a) data quality assessment, (b) trends/patterns assessment, (c) fitness-for-use assessment, and (d) ecosystem specific data diversity assessment. In conclusion we make specific suggestions to the GBIF community on the adoption of common indicators to assess progress towards future targets as well as recommendations to populate such exercise at various levels within the GBIF Network from national level to thematic levels.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129975132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 61

Bridging the biodiversity data gaps: Recommendations to meet users’ data needs 弥合生物多样性数据差距:满足用户数据需求的建议

Biodiversity Informatics Pub Date : 2013-07-09 DOI: 10.17161/BI.V8I2.4126

D. Faith, B. Collen, Arturo H. Ariño, Jeremy Kerr, V. Chavan

{"title":"Bridging the biodiversity data gaps: Recommendations to meet users’ data needs","authors":"D. Faith, B. Collen, Arturo H. Ariño, Jeremy Kerr, V. Chavan","doi":"10.17161/BI.V8I2.4126","DOIUrl":"https://doi.org/10.17161/BI.V8I2.4126","url":null,"abstract":"A strong case has been made for freely available, high quality data on species occurrence, in order to track changes in biodiversity. However, one of the main issues surrounding the provision of such data is that sources vary in quality, scope, and accuracy. Therefore publishers of such data must face the challenge of maximizing quality, utility and breadth of data coverage, in order to make such data useful to users. Here, we report a number of recommendations that stem from a content need assessment survey conducted by the Global Biodiversity Information Facility (GBIF). Through this survey, we aimed to distil the main user needs regarding biodiversity data. We find a broad range of recommendations from the survey respondents, principally concerning issues such as data quality, bias, and coverage, and extending ease of access. We recommend a candidate set of actions for the GBIF that fall into three classes: 1) addressing data gaps, data volume, and data quality, 2) aggregating new kinds of data for new applications, and 3) promoting ease-of-use and providing incentives for wider use. Addressing the challenge of providing high quality primary biodiversity data can potentially serve the needs of many international biodiversity initiatives, including the new 2020 biodiversity targets of the Convention on Biological Diversity, the emerging global biodiversity observation network (GEO BON), and the new Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES).","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"127 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116318217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 31

On the dates of GBIF mobilised primary biodiversity records 在GBIF调动原始生物多样性记录的日期

Biodiversity Informatics Pub Date : 2013-07-09 DOI: 10.17161/BI.V8I2.4125

J. Otegui, Arturo H. Ariño, V. Chavan, S. Gaiji

引用次数: 14

Assessment of user needs of primary biodiversity data: Analysis, concerns, and challenges 初级生物多样性数据的用户需求评估:分析、关注和挑战

Biodiversity Informatics Pub Date : 2013-07-09 DOI: 10.17161/BI.V8I2.4094

Arturo H. Ariño, V. Chavan, D. Faith

引用次数: 13

Discovery and publishing of primary biodiversity data associated with multimedia resources: The Audubon Core strategies and approaches 与多媒体资源相关的原始生物多样性数据的发现和发布:奥杜邦核心战略和方法

Biodiversity Informatics Pub Date : 2013-07-09 DOI: 10.17161/BI.V8I2.4117

R. Morris, V. Barve, Mihail-Constantin Carausu, V. Chavan, J. Cuadra, Chris Freeland, G. Hagedorn, Patrick R. Leary, Dimitry Mozzherin, Annette Olson, G. Riccardi, Ivan Teage, G. Whitbread

{"title":"Discovery and publishing of primary biodiversity data associated with multimedia resources: The Audubon Core strategies and approaches","authors":"R. Morris, V. Barve, Mihail-Constantin Carausu, V. Chavan, J. Cuadra, Chris Freeland, G. Hagedorn, Patrick R. Leary, Dimitry Mozzherin, Annette Olson, G. Riccardi, Ivan Teage, G. Whitbread","doi":"10.17161/BI.V8I2.4117","DOIUrl":"https://doi.org/10.17161/BI.V8I2.4117","url":null,"abstract":"The Audubon Core Multimedia Resource Metadata Schema is a representation-free vocabulary for the description of biodiversity multimedia resources and collections, now in the final stages as a proposed Biodiversity Informatics Standards (TDWG) standard. By defining only six terms as mandatory, it seeks to lighten the burden for providing or using multimedia useful for biodiversity science. At the same time it offers rich optional metadata terms that can help curators of multimedia collections provide authoritative media that document species occurrence, ecosystems, identification tools, ontologies, and many other kinds of biodiversity documents or data. About half of the vocabulary is re-used from other relevant controlled vocabularies that are often already in use for multimedia metadata, thereby reducing the mapping burden on existing repositories. A central design goal is to allow consuming applications to have a high likelihood of discovering suitable resources, reducing the human examination effort that might be required to decide if the resource is fit for the purpose of the application.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125433958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 21

Niche Modeling: Model Evaluation 生态位建模:模型评价

Biodiversity Informatics Pub Date : 2012-08-29 DOI: 10.17161/BI.V8I1.4300

A. Townsend Peterson

引用次数: 29

DISENTANGLING INTERPOLATION AND EXTRAPOLATION UNCERTAINTIES IN SPECIES DISTRIBUTION MODELS: A NOVEL VISUALIZATION TECHNIQUE FOR THE SPATIAL VARIATION OF PREDICTOR VARIABLE COLINEARITY 物种分布模型中解缠插值和外推不确定性:预测变量共线性空间变化的一种新的可视化技术

Biodiversity Informatics Pub Date : 2012-08-13 DOI: 10.17161/BI.V8I1.4326

D. Rödder, J. Engler

{"title":"DISENTANGLING INTERPOLATION AND EXTRAPOLATION UNCERTAINTIES IN SPECIES DISTRIBUTION MODELS: A NOVEL VISUALIZATION TECHNIQUE FOR THE SPATIAL VARIATION OF PREDICTOR VARIABLE COLINEARITY","authors":"D. Rödder, J. Engler","doi":"10.17161/BI.V8I1.4326","DOIUrl":"https://doi.org/10.17161/BI.V8I1.4326","url":null,"abstract":"Abstract. - Species distribution models (SDMs) are increasingly used in many scientific fields, with most studies requiring the application of the SDM to predict the likelihood of occurrence and/or environmental suitability in locations and time periods outside the range of the data set used to fit the model. Uncertainty in the quality of SDM predictions caused by errors of interpolation and extrapolation has been acknowledged for a long time, but the explicit consideration of the magnitude of such errors is, as yet, uncommon. Among other issues, the spatial variation in the colinearity of the environmental predictor variables used in the development of SDMs may cause misleading predictions when applying SDMs to novel locations and time periods. In this paper, we provide a framework for the spatially explicit identification of areas prone to errors caused by changes in the inter-correlation structure (i.e. their colinearity) of environmental predictors used for SDM development. The proposed method is compatible with all SDM algorithms currently employed, and expands the available toolbox for assessing the uncertainties raising from SDM predictions. We provide an implementation of the analysis as a script for the R statistical platform in an online appendix.","PeriodicalId":269455,"journal":{"name":"Biodiversity Informatics","volume":"322 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122734872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

The Darwin Core extension for genebanks opens up new opportunities for sharing genebank datasets 达尔文核心扩展基因库为共享基因库数据集开辟了新的机会

Biodiversity Informatics Pub Date : 2012-07-16 DOI: 10.17161/BI.V8I1.4095

D. Endresen, H. Knüpffer

引用次数: 18

A new era for specimen databases and biodiversity information management in South Africa 南非标本数据库和生物多样性信息管理的新时代

Biodiversity Informatics Pub Date : 2012-06-21 DOI: 10.17161/BI.V8I1.4263

W. Coetzer

引用次数: 18