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repositories for Taxonomic Data: Where We Are and What is Missing

SYSTEMATIC BIOLOGY 2020年第6期69卷 1231-1253页

作者： Miralles, Aurelien Bruy, Teddy Wolcott, Katherine Scherz, Mark D. Begerow, Dominik Beszteri, Bank Bonkowski, Michael Felden, Janine Gemeinholzer, Birgit Glaw, Frank Gloeckner, Frank Oliver Hawlitschek, Oliver Kostadinov, Ivaylo Nattkemper, Tim W. Printzen, Christian Renz, Jasmin Rybalka, Nataliya Stadler, Marc Weibulat, Tanja Wilke, Thomas Renner, Susanne S. Vences, Miguel Sorbonne Univ Inst Systemat Evolut Biodiversite ISYEB Dept Origins & Evolut EPHECNRSMuseum Natl Hist Nat 57 Rue CuvierCP50 F-75005 Paris France Univ Munich LMU Systemat Bot & Mycol Menzingerstr 67 D-80638 Munich Germany Smithsonian Inst Natl Museum Nat Hist Washington DC 20560 USA Zool Staatssammlung Munchen ZSM SNSB Dept Herpetol Munchhausenstr 21 D-81247 Munich Germany Univ Konstanz Dept Biol Univ Str 10 D-78464 Constance Germany Ruhr Univ Bochum Dept Geobot Univ Str 150 D-44780 Bochum Germany Univ Duisburg Essen Fac Biol Dept Phycol Univ Str 2 D-45141 Essen Germany Univ Cologne Ctr Excellence Plant Sci CEPLAS Inst Zool Terr EcolDept Terr Ecol D-50674 Cologne Germany Univ Bremen MARUM Ctr Marine Environm Sci Leobenerstr 8 D-28359 Bremen Germany Alfred Wegener Inst Helmholtz Ctr Polar & Marine Res Handelshafen 12 D-27570 Bremerhaven Germany Justus Liebig Univ Giessen Dept Systemat Bot Heinrich Buff Ring 38 D-35392 Giessen Germany Univ Hamburg Ctr Nat Kunde CeNak Dept Sci Infrastruct Martin Luther King Pl 3 D-20146 Hamburg Germany GFBio Gesell Biolog Daten eV Res 2 Campus Ring 1 D-28759 Bremen Germany Bielefeld Univ Ctr Biotechnol CeBiTec Biodata Min Grp POB 100131 D-33501 Bielefeld Germany Senckenberg Res Inst Dept Bot & Mol Evolut Senckenberganlage 25 D-60325 Frankfurt Germany Nat Hist Museum Frankfurt Senckenberganlage 25 D-60325 Frankfurt Germany DZMB Senckenberg Meer Zooplankton Res Grp Martin Luther King Pl 3 D-20146 Hamburg Germany Univ Gottingen Dept Expt Phycol & Culture Collect Algae Nikolausberger Weg 18 D-37073 Gottingen Germany Helmholtz Ctr Infect Res HZI Dept Microbial Drugs Inhoffenstr 7 D-38124 Braunschweig Germany German Ctr Infect Res DZIF Partner Site Hannover Braunschweig Inhoffenstr 7 D-38124 Braunschweig Germany Justus Liebig Univ Gieen Dept Anim Ecol & Systemat Heinrich Buff Ring 26 D-35392 Giessen Germany Tech Univ Carolo Wilhelmina Braunschweig Zool Inst Dept Evolutionary Biol Mendelssohnstr 4

Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000-20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in >80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alphataxonomy. Because long-term-ideally perpetual-data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasifacts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved reuse of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyber

关键词： Big data cyberspecimen new species omics repositories specimen identifier taxonomy taxonomic data

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MUDABlue: An automatic categorization system for Open Source repositories

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JOURNAL OF SYSTEMS AND SOFTWARE 2006年第7期79卷 939-953页

作者： Kawaguchi, Shinji Garg, Pankaj K. Matsushita, Makoto Inoue, Katsuro Osaka Univ Grad Sch Informat Sci & Technol Suita Osaka 565 Japan ZeeSource Sunnyvale CA 94807 USA

Open Source communities typically use a software repository to archive various software projects with their source code. mailing list discussions, documentation, bug reports, and so forth. For example, SourceForge currently hosts over seventy thousand Open Source software systems. Because of the size of the rich information content, such repositories offer numerous opportunities for sharing information among projects. For example, one would like to know a set of projects that are related or similar to each other. so that the project groups can collaborate and share their work. With thousands of projects in typical repositories. however, manually locating related projects can be difficult. Hence, we propose MUDABlue, a toot that automatically categorizes software systems. MUDABlue has three major aspects: (1) it relies on no other information than the source code, (2) it determines category sets automatically. and (3) it allows a software system to be a member of multiple categories. MUDABlue has a Web interface to visualize determined categories, which eases browsing a software repository. We show the effectiveness of MUDABlue's categorization capability by comparing its generated Categories with that of some other existing research tools. (c) 2005 Elsevier Inc. All rights reserved.

关键词： software acquisition reusable libraries software libraries storage repositories indexing methods clustering

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Quantitative Analysis of Learning Object repositories

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IEEE TRANSACTIONS ON LEARNING TECHNOLOGIES 2009年第3期2卷 226-238页

作者： Ochoa, Xavier Duval, Erik Ctr Tecnol Informac Escuela Super Politecn Litoral Guayaquil Ecuador Katholieke Univ Leuven Dept Comp Wetenschappen B-3001 Louvain Belgium

This paper conducts the first detailed quantitative study of the process of publication of learning objects in repositories. This process has been often discussed theoretically, but never empirically evaluated. Several question related to basic characteristics of the publication process are raised at the beginning of the paper and answered through quantitative analysis. To provide a wide view of the publication process, this paper analyzes four types of repositories: Learning Object repositories, Learning Object Referatories, Open Courseware Initiatives, and Learning Management Systems. For comparison, Institutional repositories are also analyzed. Three repository characteristics are measured: size, growth, and contributor base. The main findings are that the amount of learning objects is distributed among repositories according to a power law, the repositories mostly grow linearly, and the amount of learning objects published by each contributor follows heavy-tailed distributions. The paper finally discusses the implications that this findings could have in the design and operation of Learning Object repositories.

关键词： Learning objects publication repositories LOR OCW LMS

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Visual information retrieval from large distributed online repositories

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COMMUNICATIONS OF THE ACM 1997年第12期40卷 63-71页

作者： Chang, SF Smith, JR Beigi, M Benitez, A COLUMBIA UNIV NEW MEDIA TECHNOL CTRNEW YORKNY 10027

Provides information on WebSEEk, an Internet-based search system and MetaSEEk, an Internet meta-visual information retrieval system. Content-based visual query; Criteria for classifying visual information retrieval systems; WebSEEk's approaches in handling challenges of Internet visual information retrieval; Meta-search engines for images; Three main problems that should be solved by a scalable Internet retrieval solution.

关键词： .visual content visual query visual features Visual Information repositories images and videos Distributed Online meta-search information retrieval systems information For example

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Trustrace: Mining Software repositories to Improve the Accuracy of Requirement Traceability Links

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IEEE TRANSACTIONS ON SOFTWARE ENGINEERING 2013年第5期39卷 725-741页

作者： Ali, Nasir Gueheneuc, Yann-Gael Antoniol, Giuliano Ecole Polytech Dept Genie Informat & Genie Logiciel Montreal PQ H3C 3A7 Canada

Traceability is the only means to ensure that the source code of a system is consistent with its requirements and that all and only the specified requirements have been implemented by developers. During software maintenance and evolution, requirement traceability links become obsolete because developers do not/cannot devote effort to updating them. Yet, recovering these traceability links later is a daunting and costly task for developers. Consequently, the literature has proposed methods, techniques, and tools to recover these traceability links semi-automatically or automatically. Among the proposed techniques, the literature showed that information retrieval (IR) techniques can automatically recover traceability links between free-text requirements and source code. However, IR techniques lack accuracy (precision and recall). In this paper, we show that mining software repositories and combining mined results with IR techniques can improve the accuracy (precision and recall) of IR techniques and we propose Trustrace, a trust-based traceability recovery approach. We apply Trustrace on four medium-size open-source systems to compare the accuracy of its traceability links with those recovered using state-of-the-art IR techniques from the literature, based on the Vector Space Model and Jensen-Shannon model. The results of Trustrace are up to 22.7 percent more precise and have 7.66 percent better recall values than those of the other techniques, on average. We thus show that mining software repositories and combining the mined data with existing results from IR techniques improves the precision and recall of requirement traceability links.

关键词： Traceability requirements feature source code repositories experts trust-based model

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FLEXIBLE ORGANIZATION OF repositories FOR PROVISIONING CLOUD INFRASTRUCTURES

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COMPUTING AND INFORMATICS 2012年第4期31卷 743-757页

作者： Kosinska, Joanna Kosinski, Jacek Zielinski, Slawomir Zielinski, Krzysztof AGH Univ Sci & Technol Dept Comp Sci PL-30059 Krakow Poland

The paper proposes an architecture of a system automating the provisioning process of cloud computing infrastructures. Its structure and components are specified, based on an analysis of three types of requirements: infrastructure providers, service providers and end users. These considerations have led us to formulate a new infrastructural model, offered to end users as a collection of Virtual Machines (VM) connected by a. dedicated Virtual Private Network (VPN) with QoS guarantees. The role of repositories in cloud provisioning systems is specified along with the relevant data acquisition processes. The applicability of the proposed system is illustrated by practical usage scenarios.

关键词： Virtualization resource management repositories cloud infrastructure

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repositories You Shouldn't Be Living Without 18

Repositories You Shouldn't Be Living Without

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49th ACM SIGCSE Technical Symposium on Computer Science Education (SIGCSE)

作者： Decker, Adrienne McGill, Monica M. DeLyser, Leigh Ann Quinn, Beth Berry, Miles Haynie, Kathy McKlin, Tom Rochester Inst Technol Rochester NY 14623 USA Knox Coll Galesburg IL USA CSforAll Consortium New York NY USA Univ Colorado Boulder CO 80309 USA Univ Roehampton London England Haynie Res & Evaluat Skillman NJ USA Findings Grp Decatur GA USA

ISBN: (纸本)9781450351034

Over the last few years, a number of repositories of information relevant to the computing education community have come online, each with different content and purpose. In this special session, we present an overview of these repositories and the content that each provides. Demonstrations of the functionality of the repositories will be shown and attendees are encouraged to come with their questions and suggestions for improvement if they are currently users of the repositories.

关键词： repositories K-12 computing broadening participation

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An Assistant to Populate repositories: Gathering Educational Digital Objects and Metadata Extraction

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IEEE REVISTA IBEROAMERICANA DE TECNOLOGIAS DEL APRENDIZAJE-IEEE RITA 2016年第2期11卷 87-94页

作者： Casali, Ana Deco, Claudia Beltramone, Santiago UNR Dept Comp Sci Fac Ciencias Exactas Ingn & Agrimensura S2000BTP Rosario Santa Fe Argentina UNR Ctr Int Franco Argentino Ciencias Informac & Sist RA-2000 Rosario Santa Fe Argentina Univ Nacl Rosario Fac Ciencias Exactas Ingn & Agrimensura S2000BTP Rosario Santa Fe Argentina Univ Catolica Argentina Sede Rosario S2002QEO Rosario Santa Fe Argentina

This paper presents an assistant to populate institutional repositories. This tool can detect all educational digital objects in a text format that are already published on institutional Websites and can be uploaded to a repository. This recopilation is a tedious task and is usually performed manually. In this paper, we propose a system architecture for automating this task of collecting text documents within a restricted domain in order to detect plausible documents that can be loaded into a repository. In addition, its metadata, such as language, category, title, authors, and their contact data, is automatically extracted. A prototype of this system was developed, and case studies in two different domains are analyzed.

关键词： Information gathering educational digital objetcs repositories metadata extraction

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Indicators for a webometric ranking of open access repositories

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SCIENTOMETRICS 2010年第3期82卷 477-486页

作者： Aguillo, Isidro F. Ortega, Jose L. Fernandez, Mario Utrilla, Ana M. CSIC CCHS Cybermetr Lab Madrid 28037 Spain CSIC VICYT Sci Programming Div Madrid 28006 Spain

The Ranking Web of World repositories ( http://***) is introduced. The objective is to promote Open access initiatives (OAI) supporting the use of repositories for scientific evaluation purposes. A set of metrics based on web presence, impact and usage is discussed. The Ranking is built on indicators obtained from web search engines following a model close to the Impact Factor one. The activity accounts for a 50% of the index, including number of pages, pdf files and items in Google Scholar database, while the visibility takes into account the external inlinks received by the repository (the other 50%). The Ranking provides the Top 300 repositories from a total of 592 worldwide, with a strong presence of US, German and British institutional repositories and the leadership of the large subject repositories. Results suggest the need to take into consideration other file formats and the usage information, an option is not feasible today.

关键词： repositories Open access Webometrics Indicators Visibility Usage Ranking

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Exploiting repositories in Mobile Software Ecosystems from a Governance Perspective

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INFORMATION SYSTEMS FRONTIERS 2019年第1期21卷 143-161页

作者： Fontao, Awdren de Lima dos Santos, Rodrigo Pereira Dias-Neto, Arilo Claudio Univ Fed Amazonas Inst Comp Manaus Amazonas Brazil Fed Univ State Rio de Janeiro Dept Appl Informat Rio De Janeiro RJ Brazil

Software organizations that maintain mobile platforms (e.g. Apple, Google, and Microsoft) open their infrastructure to attract and engage external developers to meet the demands of users. This scenario has been investigated as Mobile Software Ecosystem (MSECO). In MSECO, an organization provides content reuse repositories where users can search, download and evaluate apps, or where developers can get support materials. Such repositories are commonly inspired by reuse mechanisms and help an organization to control and evolve the whole ecosystem to keep it vibrant. In this scenario, it is important to understand how to govern MSECO as well as how reuse mechanisms can support this goal. As such, we investigated governance strategies that emerge from content reuse repositories based on four steps: (1) designing a governance process;(2) performing an initial evaluation of this process with managers who are experts in the main existing MSECO (Apple, Google, Nokia, Microsoft, and Samsung);(3) interviewing 18 MSECO managers to collect opinion about the process;and (4) conducting an exploratory analysis of the MSECO reuse repositories' structure based on the proposed governance process. Three types of content reuse repositories (Apps' Store, Developer's Central, and Apps' Management) were analyzed. As a result, this research allowed us to define a governance process from a repository perspective containing 11 activities.

关键词： Software ecosystems Mobile application Process Model Governance Reuse repositories

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