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Research data archiving

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274:). Accession numbers must be included in the final version of the manuscript. For other forms of data (e.g., microsatellite genotypes, linkage maps, images), the Journal endorses the principles of the Joint Data Archiving Policy (JDAP) in encouraging all authors to archive primary datasets in an appropriate public archive, such as Dryad, TreeBASE, or the Knowledge Network for Biocomplexity. Authors are encouraged to make data publicly available at time of publication or, if the technology of the archive allows, opt to embargo access to the data for a period up to a year after publication. The American Genetic Association also recognizes the vast investment of individual researchers in generating and curating large datasets. Consequently, we recommend that this investment be respected in secondary analyses or meta-analyses in a gracious collaborative spirit. 492: 303:, your own institutional or funder repository, or as Supporting Information on the Molecular Ecology web site. Data are important products of the scientific enterprise, and they should be preserved and usable for decades in the future. Authors may elect to have the data publicly available at time of publication, or, if the technology of the archive allows, may opt to embargo access to the data for a period up to a year after publication. Exceptions may be granted at the discretion of the editor, especially for sensitive information such as human subject data or the location of endangered species. 179:. Authors may elect to make the data publicly available as soon as the article is published or, if the technology of the archive allows, embargo access to the data up to three years after article publication. A statement describing Data Availability will be included in the manuscript as described in the instructions to authors. Exceptions to the required archiving of data may be granted at the discretion of the Editor-in-Chief for studies that include sensitive information (e.g., the location of endangered species). Our Editorial explaining the motivation for this policy can be found 25: 469:) project, which will provide scientific data archiving for ecological and environmental data produced by scientists worldwide. DataONE's stated goal is to preserve and provide access to multi-scale, multi-discipline, and multi-national data. The community of users for DataONE includes scientists, ecosystem managers, policy makers, students, educators, and the public. 708:
and some developing countries had organized formal and well-functioning national data archives. In addition, college and university campuses often have `data libraries' that make data available to their faculty, staff, and students; most of these bear minimal archival responsibility, relying for that function on a national institution (Rockwell, 2001, p. 3227).
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data. In general, the tradition of science has been for publications to contain sufficient information to allow fellow researchers to replicate and therefore test the research. In recent years this approach has become increasingly strained as research in some areas depends on large datasets which cannot easily be replicated independently.
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In the social sciences, data libraries are referred to as data archives. Data archives are professional institutions for the acquisition, preparation, preservation, and dissemination of social and behavioral data. Data archives in the social sciences evolved in the 1950s and have been perceived as an
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strongly encourages authors who re-use data archives archived data sets to include as fully engaged collaborators the scientists who originally collected them. We feel this will greatly enhance the quality and impact of the resulting research by drawing on the data collector’s profound insights into
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for secondary use in research. A data library is normally part of a larger institution (academic, corporate, scientific, medical, governmental, etc.). established for research data archiving and to serve the data users of that organisation. The data library tends to house local data collections and
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By 1964 the International Social Science Council (ISSC) had sponsored a second conference on Social Science Data Archives and had a standing Committee on Social Science Data, both of which stimulated the data archives movement. By the beginning of the twenty-first century, most developed countries
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Preservation and Data Sharing Services - act on a strategy of preservation of datasets in the collection, such as media refreshment and file format migration; download and keep records on updated versions from a central repository. Also, assist users in preparing original data for secondary use by
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now requests that, in general, authors place the bulk of their description of materials and methods online as supporting material, providing only as much methods description in the print manuscript as is necessary to follow the logic of the text. (Obviously, this restriction will not apply if the
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requires the reviewer to determine if all of the supplementary data and methods have been archived. The policy advises reviewers to consider several questions, including: "Should the authors be asked to provide supplementary methods or data to accompany the paper online? (Such data might include
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have differing policies regarding how much of their data and methods researchers are required to store in a public archive, and what is actually archived varies widely between different disciplines. Similarly, the major grant-giving institutions have varying attitudes towards public archiving of
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supports the efforts of databases that aggregate published data for the use of the scientific community. Therefore, before publication, large data sets (including microarray data, protein or DNA sequences, and atomic coordinates or electron microscopy maps for macromolecular structures) must be
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repository for ecological and evolutionary biology data. All accession numbers for GenBank, TreeBASE, and Dryad must be included in accepted manuscripts before they go to Production. If the data is deposited somewhere else, please provide a link. If the data is culled from published literature,
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for download). A data library may also maintain subscriptions to licensed data resources for its users to access the information. Whether a data library is also considered a data archive may depend on the extent of unique holdings in the collection, whether long-term preservation services are
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others; either for deposit in a central or institutional repository, or for less formal ways of sharing data. This may also involve marking up the data into an appropriate XML standard, such as the Data Documentation Initiative, or adding other metadata to facilitate online discovery.
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Collection Development & Management - acquire, maintain, and manage a collection of data files used for secondary analysis by the local user community; purchase institutional data subscriptions; act as a site representative to data providers and national data archives for the
128:. This policy mandates that datasets cited in AGU papers must be archived by a recognised data center; it permits the creation of "data papers"; and it establishes AGU's role in maintaining data archives. But it makes no requirements on paper authors to archive their data. 325:
journal at submission, either uploaded via the journal's online submission service, or if the files are too large or in an unsuitable format for this purpose, on CD/DVD (five copies). Such material cannot solely be hosted on an author's personal or institutional web site.
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since at least 2013. Their policy states that 'all data relating to the article must be made available in Supplementary files or deposited in external repositories and linked to within the article. The policy recommends that data are deposited in a repository such as the
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User Instruction — providing hands-on training to groups of users in locating data resources on particular topics, how to download data and read it into spreadsheet, statistical, database, or GIS packages, how to interpret codebooks and other
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please deposit the collated data in Dryad for the convenience of your readers. Any impediments to data sharing should be brought to the attention of the editors at the time of submission so that appropriate arrangements can be worked out.
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Technical Assistance - including easing registration procedures, troubleshooting problems with the dataset, such as errors in the documentation, reformatting data into something a user can work with, and helping with statistical
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The primary data underlying the conclusions of an article are critical to the verifiability and transparency of the scientific enterprise, and should be preserved in usable form for decades in the future. For this reason,
437:. A 2018 study found a data availability rate of 53%, reflecting either weak enforcement of this policy or an incomplete understanding among editors, reviewers, and authors of how to interpret and implement this policy. 135:. This process was recognized as wasteful of time and energy and obtained mixed results. Information could become lost or corrupted over the years. In some cases, authors simply refuse to provide the information. 385:
Datasets and code should be deposited in an appropriate, recognised, publicly available repository. Where no data-specific repository exists, authors should deposit their datasets in a general repository such as
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Prior to organized data archiving, researchers wanting to evaluate or replicate a paper would have to request data and methods information from the author. The academic community expects authors to
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the natural history of the study system, reducing the risk of errors in novel analyses, and stimulating the cross-disciplinary and cross-cultural collaboration and training for which the
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requires, as a condition for publication, that the data supporting the results in the paper and metadata describing them must be archived in an appropriate public archive such as
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Data archiving is more important in some fields than others. In a few fields, all of the data necessary to replicate the work is already available in the journal article. In
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Reference Assistance — locating numeric or geospatial datasets containing measurable variables on a particular topic or group of topics, in response to a user query.
560:(ARL) published a report presenting results from a survey of ARL member institutions involved in collecting and providing services for numeric data resources. 262:
requires that newly reported nucleotide or amino acid sequences, and structural coordinates, be submitted to appropriate public databases (e.g., GenBank; the
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requires authors to deposit the data associated with accepted papers in a public archive. For gene sequence data and phylogenetic trees, deposition in
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requires that research data should be archived in the researcher's own institution or an appropriate nationwide infrastructure for at least 10 years.
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journals, it is a condition of publication that authors make available the data, code and research materials supporting the results in the article.
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for articles tracing the history of data libraries and its relationship to the archivist profession, going back to the 1960s and '70s up to 1996.
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articles from 1993 to the present, focusing on data libraries, data archives, data support, and information technology for the social sciences.
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Heim, Kathleen M. "Social Scientific Information Needs for Numeric Data: The Evolution of the International Data Archive Infrastructure."
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The need for data archiving and due diligence is greatly increased when the research deals with health issues or public policy formation.
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Such material must be hosted on an accredited independent site (URL and accession numbers to be provided by the author), or sent to the
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deposited in an approved database and an accession number provided for inclusion in the published paper. "Materials and methods" –
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offered, and whether it serves a broader community (as national data archives do). Most public data libraries are listed in the
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CESSDA Members are data archives and other organisations that archive social science data and provide data for secondary use:
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expects that data supporting the results in the paper should be archived in an appropriate public archive, such as GenBank,
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The data collected by tropical biologists are often long-term, complex, and expensive to collect. The Board of Editors of
843:"The Case for Due Diligence When Empirical Research is Used in Policy Formation" by Bruce McCullough and Ross McKitrick. 620: 1113: 857: 671: 1594: 666: 557: 491: 416: 73: 450:(NSF) has tightened requirements on data archiving. Researchers seeking funding from NSF are now required to file a 661: 744: 1021: 473: 240:, respectively, is required. There are many possible archives that may suit a particular data set, including the 1287: 752: 1584: 1247: 1136: 656: 1117:
The Case for Due Diligence When Empirical Research is Used in Policy Formation by McCullough and McKitrick
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Library service providing support at the institutional level for the use of numerical and other types of
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Rockwell, R. C. (2001). Data Archives: International. IN: Smelser, N. J. & Baltes, P. B. (eds.)
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allowing large amounts of data to be stored and accessed from central locations. For example, the
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source code for modelling studies, detailed experimental protocols or mathematical derivations.)
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is a global registry of research data repository indexing data archives from all disciplines:
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Clubb, J., Austin, E., and Geda, C. "'Sharing research data in the social sciences.'" In
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is one of only two journals that pays the fees for authors depositing data at Dryad.
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Promoting a culture of collaboration with researchers who collect and archive data:
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The Role of Data and Program Code Archives in the Future of Economic Research
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https://web.archive.org/web/20150318230743/http://www.sa.dk/dda/default.htm
532: 1443: 1403: 793: 723: 917: 832:”Policy on Referencing Data in and Archiving Data for AGU Publications” 168: 985: 741: 524: 271: 1032: 777:
https://socialsciences.cornell.edu/ciser-data-and-reproduction-archive
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external links, and converting useful links where appropriate into
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in research. Amongst the support activities typically available:
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The requirement of data archiving is a recent development in the
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International Encyclopedia of the Social and Behavioral Sciences
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White, Howard D. (1977). Machine-Readable Social Science Data.
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Inter-university Consortium for Political and Social Research:
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Oak Ridge National Laboratory Distributed Active Archive Center
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Pangaea - Data Publisher for Earth & Environmental Science
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Inter-university Consortium for Political and Social Research
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Inter-university Consortium for Political and Social Research
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To allow others to verify and build on the work published in
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paper is fundamentally a study of a new method or technique.)
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University of California Irvine Machine Learnimg Repository
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Thoughts on Refereed Journal Publication by Chuck Doswell
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Marwick, Ben; Birch, Suzanne E. Pilaar (5 April 2018).
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The following list refers to scientific data archives.
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Proceedings of the National Academy of Sciences (U.S.)
918:"Guide to Publication Policies of the Nature Journals" 651: 855:"Data Sharing and Replication" a website by Gary King 728:
Consortium of European Social Science Data Archives:
406: 454:as a two-page supplement to the grant application. 1176:. Canadian Library Association, Ottawa, ON, 2005. 1112:Data sharing and replication – Gary King website 1011:”DFG Guidelines on the Handling of Research Data” 483:maintains an overview of funder's data policies. 38:may not follow Knowledge's policies or guidelines 1561: 687:NASA SeaBASS - Data archive for ocean color data 141: 531:provides access to them through various means ( 441: 763:The Roper Center for Public Opinion Research: 641:National Archive of Computerized Data on Aging 1281: 1063:(vol. 5, pp. 3225- 3230). Amsterdam: Elsevier 591: 966: 1262:(Canadian Association of Public Data Users) 945:”Preparing Your Supporting Online Material” 734:Finnish Social Science Data Archive (FSD): 1288: 1274: 645:National Archive of Criminal Justice Data 551: 461:initiative has resulted in funding of the 219: 1172:Geraci, D., Humphrey, C., and Jacobs, J. 1146:for Open Data in Science, at Citizendium 984: 495:Data Repository and an Archive Repository 74:Learn how and when to remove this message 1256:(Association of Public Data Users - USA) 1186:Martinez, Luis & Macdonald, Stuart, 775:The Cornell Center for Social Sciences: 490: 116:. It was made possible by advances in 1562: 1200:IASSIST Bibliography of Selected Works 1077:Registry of Research Data Repositories 934:"General Policies of Science Magazine" 724:https://www.cessda.eu/About/Consortium 546:Registry of Research Data Repositories 249: 1269: 1102:The US National Committee for CODATA 742:http://www.sa.dk/content/us/about_us 284: 18: 973:Advances in Archaeological Practice 636:Knowledge Network for Biocomplexity 621:ESO/ST-ECF Science Archive Facility 596: 301:Knowledge Network for Biocomplexity 13: 1159: 1086:Statistical checklist required by 1035:Numeric Data Products and Services 751:; specific page (only in Danish): 697: 672:National Oceanographic Data Center 463:Data Observation Network for Earth 16:Long-term storage of research data 14: 1611: 1223: 769:The Social Science Data Archive: 667:National Snow and Ice Data Center 626:International Tree-Ring Data Bank 558:Association of Research Libraries 431:the Digital Archaeological Record 417:Journal of Archaeological Science 408:Journal of Archaeological Science 264:EMBL Nucleotide Sequence Database 1590:Information retrieval techniques 771:http://dataarchives.ss.ucla.edu/ 765:https://ropercenter.cornell.edu/ 662:National Geophysical Data Center 372: 23: 1235: 1053: 1040: 1026: 1015: 1004: 993: 960: 949: 938: 486: 927: 910: 899: 888: 877: 866: 848: 837: 826: 1: 1137:NASA Astrophysics Data System 819: 657:National Climatic Data Center 650:NCAR Research Data Archive: 499:Research data is archived in 266:; DNA Database of Japan; the 146: 142:Selected policies by journals 873:Supporting Data and Material 442:Policies by funding agencies 7: 782: 759:http://www.icpsr.umich.edu/ 448:National Science Foundation 10: 1616: 740:The Danish Data Archives: 606:CISL Research Data Archive 592:Examples of data libraries 446:In the United States, the 343: 122:American Geophysical Union 1303: 1050:13 (January, 1977):1-110. 956:"Data sharing and mining" 313: 1595:Knowledge representation 1295: 1070: 1048:Drexel Library Quarterly 895:Policy on data archiving 703:international movement: 427:Archaeology Data Service 552:Importance and services 481:Digital Curation Centre 299:, TreeBASE, Dryad, the 297:Gene Expression Omnibus 229:The American Naturalist 221:The American Naturalist 133:share supplemental data 87:Research data archiving 1194:, issue 44, July 2005. 1183:9 (Spring 1987): 1-53. 736:http://www.fsd.uta.fi/ 730:http://www.cessda.org/ 718:http://www.re3data.org 710: 496: 439: 422:data disclosure policy 404: 370: 341: 311: 282: 247: 208: 206:are widely recognized. 118:information technology 93:of scholarly research 1181:Collection Management 1167:Sharing Research Data 884:Data archiving policy 705: 494: 412: 376: 349: 319: 290: 255: 225: 152: 1585:Digital preservation 1469:Protection (privacy) 809:Digital preservation 556:In August 2001, the 452:data management plan 44:improve this article 652:http://rda.ucar.edu 260:Journal of Heredity 251:Journal of Heredity 56:footnote references 1600:Structured storage 1206:2016-03-03 at the 986:10.1017/aap.2018.3 860:2007-03-28 at the 747:2014-12-29 at the 523:of numeric and/or 497: 388:Dryad (repository) 279:oxfordjournals.org 114:history of science 1570:Computer archives 1557: 1556: 1549:Wrangling/munging 1399:Format management 1216:IASSIST Quarterly 1144:Panton Principles 923:. March 14, 2007. 692:World Data Center 539:-ROMs or central 293:Molecular Ecology 286:Molecular Ecology 268:Protein Data Bank 99:academic journals 91:long-term storage 84: 83: 76: 1607: 1290: 1283: 1276: 1267: 1266: 1064: 1057: 1051: 1044: 1038: 1030: 1024: 1019: 1013: 1008: 1002: 997: 991: 990: 988: 964: 958: 953: 947: 942: 936: 931: 925: 924: 922: 914: 908: 903: 897: 892: 886: 881: 875: 870: 864: 852: 846: 841: 835: 830: 804:Digital curation 597:Natural sciences 402: 368: 339: 309: 280: 107:drug development 79: 72: 68: 65: 59: 27: 26: 19: 1615: 1614: 1610: 1609: 1608: 1606: 1605: 1604: 1580:Data publishing 1575:Data management 1560: 1559: 1558: 1553: 1529:Synchronization 1299: 1294: 1238: 1226: 1208:Wayback Machine 1162: 1160:Further reading 1131:, March, 2002. 1073: 1068: 1067: 1058: 1054: 1045: 1041: 1031: 1027: 1020: 1016: 1009: 1005: 998: 994: 965: 961: 954: 950: 943: 939: 932: 928: 920: 916: 915: 911: 904: 900: 893: 889: 882: 878: 871: 867: 862:Wayback Machine 853: 849: 842: 838: 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curation 797: 795: 792: 790: 787: 786: 778: 774: 772: 768: 766: 762: 760: 756: 754: 750: 746: 743: 739: 737: 733: 731: 727: 725: 721: 719: 715: 712: 711: 709: 704: 693: 690: 688: 685: 683: 680: 678: 675: 673: 670: 668: 665: 663: 660: 658: 655: 653: 649: 647: 644: 642: 639: 637: 634: 632: 629: 627: 624: 622: 619: 617: 614: 612: 609: 607: 604: 603: 602: 585: 581: 577: 573: 570: 569: 568: 566: 561: 559: 549: 547: 542: 538: 534: 529: 526: 522: 518: 514: 510: 506: 505:data archives 502: 493: 484: 482: 477: 475: 470: 468: 464: 460: 455: 453: 449: 438: 436: 432: 428: 423: 419: 418: 409: 401: 400:Royal Society 395: 393: 389: 383: 381: 380:Royal Society 373:Royal Society 367: 361: 358: 353: 346: 338: 332: 329: 324: 316: 304: 302: 298: 294: 287: 275: 273: 269: 265: 261: 252: 246: 243: 239: 235: 231: 230: 222: 217: 215: 212: 207: 205: 201: 196: 192: 191: 186: 182: 178: 174: 170: 166: 162: 158: 157: 149: 139: 136: 134: 129: 127: 123: 119: 115: 110: 108: 103: 100: 96: 92: 88: 78: 75: 67: 57: 53: 52:inappropriate 49: 45: 39: 37: 30: 21: 20: 1459:Preservation 1449:Philanthropy 1313:Augmentation 1236:Associations 1215: 1199: 1191: 1180: 1173: 1166: 1128: 1095: 1094:Policies of 1087: 1079: 1060: 1055: 1047: 1042: 1034: 1028: 1017: 1006: 995: 976: 972: 962: 951: 940: 929: 912: 901: 890: 879: 868: 850: 839: 828: 706: 701: 600: 583:institution. 579:methodology. 562: 555: 516: 513:data archive 512: 509:data library 508: 504: 500: 498: 487:Data library 479:The British 478: 471: 462: 456: 445: 415: 413: 407: 384: 377: 356: 351: 350: 344: 327: 322: 320: 314: 291: 285: 259: 256: 250: 227: 226: 220: 213: 210: 209: 203: 194: 189: 188: 154: 153: 147: 137: 130: 111: 104: 86: 85: 70: 61: 46:by removing 33: 1519:Stewardship 1409:Integration 1358:Degradation 1343:Compression 1323:Archaeology 1308:Acquisition 1174:Data Basics 1080:re3data.org 794:Data center 714:re3data.org 472:The German 1564:Categories 1539:Validation 1474:Publishing 1464:Processing 1434:Management 1348:Corruption 1338:Collection 820:References 525:geospatial 521:collection 420:has had a 272:Swiss-Prot 214:Biotropica 204:Biotropica 195:Biotropica 156:Biotropica 148:Biotropica 64:March 2024 1544:Warehouse 1509:Scrubbing 1489:Retention 1484:Reduction 1439:Migration 1414:Integrity 1382:Transform 1333:Cleansing 814:Open Data 789:Data bank 528:data sets 48:excessive 1514:Security 1504:Scraping 1479:Recovery 1353:Curation 1318:Analysis 1204:Archived 1197:See the 858:Archived 783:See also 745:Archived 565:datasets 457:The NSF 397:—  392:Figshare 363:—  334:—  306:—  277:—  238:TreeBASE 173:TreeBASE 165:Figshare 1524:Storage 1499:Science 1494:Quality 1424:Lineage 1419:Library 1394:Farming 1377:Extract 1363:Editing 1248:DISC-UK 1242:IASSIST 1192:Ariadne 611:DataONE 467:DataONE 459:Datanet 435:PANGAEA 366:Science 357:Science 352:Science 345:Science 234:GenBank 169:GenBank 89:is the 42:Please 34:use of 1444:Mining 1404:Fusion 1129:Nature 1088:Nature 541:server 337:Nature 328:Nature 323:Nature 315:Nature 270:; and 1260:CAPDU 1071:Notes 921:(PDF) 616:Dryad 519:is a 515:, or 433:, or 308:Wiley 242:Dryad 175:, or 161:Dryad 1534:Type 1429:Loss 1387:Load 1297:Data 1254:APDU 1213:See 507:. A 414:The 202:and 200:ATBC 185:here 181:here 177:NCBI 95:data 1372:ELT 1368:ETL 1328:Big 981:doi 537:DVD 503:or 474:DFG 390:or 236:or 211:NB: 126:WWW 50:or 1566:: 1190:. 975:. 971:. 548:. 535:-/ 533:CD 511:, 429:, 394:. 187:. 171:, 167:, 163:, 1370:/ 1289:e 1282:t 1275:v 989:. 983:: 977:6 465:( 77:) 71:( 66:) 62:( 58:. 40:.

Index

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inappropriate
footnote references
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long-term storage
data
academic journals
drug development
history of science
information technology
American Geophysical Union
WWW
share supplemental data
Biotropica
Dryad
Figshare
GenBank
TreeBASE
NCBI
here
here
ATBC
The American Naturalist
GenBank
TreeBASE
Dryad
EMBL Nucleotide Sequence Database
Protein Data Bank

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