commonmeta-ruby 3.5.4 → 3.6

data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/ghost_post_with_related_identifiers_and_link_to_peer-reviewed_article.yml

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-      string: '{"id":"2bdebfc5-e02e-42c2-90c5-e873e2d0435d","doi":"https://doi.org/10.53731/r294649-6f79289-8cw18","url":"https://blog.front-matter.io/posts/nine-simple-ways-to-make-it-easier-to-re-use-your-data","title":"Nine
-        simple ways to make it easier to (re)use your data","summary":"This paper
-        in markdown format was written by Ethan White et al. The markdown file and
-        the associated bibliogaphy and figure files are available from the Github
+      string: '{"archive_url":null,"authors":[{"name":"Martin Fenner","url":"https://orcid.org/0000-0003-1419-2405"}],"blog":{"api":true,"archive_prefix":null,"authors":null,"backlog":0,"canonical_url":null,"category":"computerAndInformationSciences","created_at":"2023-01-02","current_feed_url":"https://blog.front-matter.io/atom/","description":"The
+        Front Matter Blog covers the intersection of science and technology since
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+        Matter","blog_slug":"front_matter","doi":"https://doi.org/10.53731/r294649-6f79289-8cw18","id":"2bdebfc5-e02e-42c2-90c5-e873e2d0435d","image":"http://blog.martinfenner.org/images/Data_formatting.jpg","indexed_at":1694126132,"language":"en","published_at":1372179840,"reference":[{"doi":"http://doi.org/10.1890/0012-9623-90.2.205","key":"ref1"},{"doi":"http://doi.org/10.1002/bult.134","key":"ref2"},{"doi":"http://doi.org/10.1890/120103","key":"ref3"},{"doi":"http://doi.org/10.1146/annurev.ecolsys.37.091305.110031","key":"ref4"},{"doi":"http://doi.org/10.1002/aris.2011.1440450113","key":"ref5"},{"doi":"http://doi.org/10.1890/1051-0761(1997)007[0330:nmftes]2.0.co","key":"ref6"},{"doi":"http://doi.org/10.1890/1051-0761(1997)007","key":"ref7"},{"key":"ref8","url":"http://esa.org/ecovisions/ppfiles/ecologicalvisionsreport.pdf"},{"doi":"http://doi.org/10.1016/j.tree.2005.04.023","key":"ref9"},{"doi":"http://doi.org/10.1371/journal.pone.0035087","key":"ref10"},{"doi":"http://doi.org/10.7287/peerj.preprints.1","key":"ref11"},{"doi":"http://doi.org/10.1371/journal.pone.0000308","key":"ref12"},{"key":"ref13","url":"https://github.com/tpoisot/datasharingpaper/blob/master/datasharing-ms.md"},{"doi":"http://doi.org/10.1126/science.1197962","key":"ref14"},{"doi":"http://doi.org/10.1038/461171a","key":"ref15"},{"doi":"http://doi.org/10.5060/D2251G48","key":"ref16"},{"doi":"http://doi.org/10.1016/j.tree.2010.11.006","key":"ref17"},{"doi":"http://doi.org/10.1086/650340","key":"ref18"},{"key":"ref19","url":"http://jstatsoft.org/v21/i12/paper"},{"doi":"http://doi.org/10.1371/journal.pone.0029715","key":"ref20"},{"doi":"http://doi.org/10.1007/s00799-007-0015-8","key":"ref21"}],"relationships":[{"type":"IsPreprintOf","url":"https://doi.org/10.4033/iee.2013.6b.6.f"}],"summary":"This
+        paper in markdown format was written by Ethan White et al. The markdown file
+        and the associated bibliogaphy and figure files are available from the Github
         repository of the paper. I used this version, an earlier version was published
         as PeerJ Preprint. Special thanks to Ethan White for allowing me to reuse
-        this paper.","content_html":" <p><img /></p><blockquote>This paper in markdown
-        format was written by Ethan White et al. The markdown file and the associated
-        bibliogaphy and figure files are available from the <a href=\"https://github.com/weecology/data-sharing-paper\">Github
-        repository of the paper</a>.</blockquote>\n<blockquote>I used <a href=\"https://github.com/weecology/data-sharing-paper/commit/b5a73eb0942a18bb29810025a528aea48a8465e7\">this</a>
-        version, an earlier version was published as <a href=\"https://doi.org/10.7287/peerj.preprints.7v1\">PeerJ
-        Preprint</a>. Special thanks to Ethan White for allowing me to reuse this
-        paper. The paper is used here as an example document to show how markdown
-        can handle scholarly documents, in particular tables, figures and citations.
-        The document was slightly modified from the orginal: added YAML frontmatter
-        (needed by jekyll, author names are also stored there), and changed the anchor
-        text for some links. This post is using the APA citation style. Please restrict
-        your comments to issues related to Scholarly Markdown, for the content of
-        the article contact Ethan directly.</blockquote>\n<h2>Abstract</h2>\n<p>Sharing
-        data is increasingly considered to be an important part of the scientific
-        process. Making your data publicly available allows original results to be
-        reproduced and new analyses to be conducted. While sharing your data is the
-        first step in allowing reuse, it is also important that the data be easy to
-        understand and use. We describe nine simple ways to make it easy to reuse
-        the data that you share and also make it easier to work with it yourself.
-        Our recommendations focus on making your data understandable, easy to analyze,
-        and readily available to the wider community of scientists.</p>\n<h2>Introduction</h2>\n<p>Sharing
-        data is increasingly recognized as an important component of the scientific
-        process (Whitlock, McPeek, Rausher, Rieseberg, &amp; Moore, 2010). The sharing
-        of scientific data is beneficial because it allows replication of research
-        results and reuse in meta-analyses and projects not originally intended by
-        the data collectors (Poisot, Mounce, &amp; Gravel, 2013). In ecology and evolutionary
-        biology, sharing occurs through a combination of formal data repositories
-        like <a href=\"http://www.ncbi.nlm.nih.gov/genbank/\">GenBank</a> and <a href=\"http://datadryad.org/\">Dryad</a>,
-        and through individual and institutional websites.</p>\n<p>While data sharing
-        is increasingly common and straightforward, much of the shared data in ecology
-        and evolutionary biology are not easily reused because they do not follow
-        best practices in terms of data structure, metadata, and licensing (M. B.
-        Jones, Schildhauer, Reichman, &amp; Bowers, 2006). This makes it more difficult
-        to work with existing data and therefore makes the data less useful than it
-        could be (M. B. Jones et al., 2006; O. J. Reichman, Jones, &amp; Schildhauer,
-        2011). Here we provide a list of 9 simple ways to make it easier to reuse
-        the data that you share.</p>\n<p>Our recommendations focus on making your
-        data understandable, easy to work with, and available to the wider community
-        of scientists. They are designed to be simple and straightforward to implement,
-        and as such represent an introduction to good data practices rather than a
-        comprehensive treatment. We contextualize our recommendations with examples
-        from ecology and evolutionary biology, though many of the recommendations
-        apply broadly across scientific disciplines. Following these recommendations
-        makes it easier for anyone to reuse your data including other members of your
-        lab and even yourself.</p>\n<h2>1. Share your data</h2>\n<p>The first and
-        most important step in sharing your data is to share your data. The recommendations
-        below will help make your data more useful, but sharing it in any form is
-        a big step forward. So, why should you share your data?</p>\n<p>Data sharing
-        provides substantial benefits to the scientific community (Fienberg &amp;
-        Martin, 1985). It allows</p>\n<ol><li>the results of existing analyses to
-        be reproduced and improved upon (Fienberg &amp; Martin, 1985; Poisot et al.,
-        2013),</li><li>data to be combined in meta-analyses to reach general conclusions
-        (Fienberg &amp; Martin, 1985),</li><li>new approaches to be applied to the
-        data and new questions asked using it (Fienberg &amp; Martin, 1985), and</li><li>approaches
-        to scientific inquiry that couldn’t even be considered without broad scale
-        data sharing (Hampton et al., 2013).</li></ol>\n<p>As a result, data sharing
-        is increasingly required by funding agencies (Poisot et al. (2013); e.g.,
-        <a href=\"http://www.nsf.gov/bfa/dias/policy/dmp.jsp\">NSF</a>, <a href=\"http://grants.nih.gov/grants/guide/notice-files/NOT-OD-03-032.html\">NIH</a>,
-        <a href=\"http://www.nserc-crsng.gc.ca/Professors-Professeurs/FinancialAdminGuide-GuideAdminFinancier/Responsibilities-Responsabilites_eng.asp\">NSERC</a>,
-        <a href=\"http://www.fwf.ac.at/en/public_relations/oai/index.html\">FWF</a>),
-        journals (Whitlock et al., 2010), and potentially by law (e.g. <a href=\"http://doyle.house.gov/sites/doyle.house.gov/files/documents/2013%2002%2014%20DOYLE%20FASTR%20FINAL.pdf\">FASTR</a>).</p>\n<p>Despite
-        these potential benefits to the community, many scientists are still reluctant
-        to share data. This reluctance is largely due to perceived fears of 1) competition
-        for publications based on the shared data, 2) technical barriers, and 3) a
-        lack of recognition for sharing data (Hampton et al., 2013; Palmer et al.,
-        2004). These concerns are often not as serious as they first appear, and the
-        minimal costs associated with data sharing are frequently offset by individual
-        benefits to the data sharer (Hampton et al., 2013; Parr &amp; Cummings, 2005).
-        Many data sharing initiatives allow for data embargoes or limitations on direct
-        competition that can last for several years while the authors develop their
-        publications and thus avoid competition for deriving publications from the
-        data. Also, logistical barriers to data sharing are diminishing as data archives
-        become increasingly common and easy to use (Hampton et al., 2013; Parr &amp;
-        Cummings, 2005). Datasets are now considered citable entities and data providers
-        receive recognition in the form of increased citation metrics and credit on
-        CVs and grant applications (Heather A Piwowar &amp; Vision, 2013; Heather
-        A. Piwowar, Day, &amp; Fridsma, 2007; Poisot et al., 2013). In addition to
-        increased citation rates, shared datasets that are documented and standardized
-        are also more easily reused in the future by the original investigator. As
-        a result, it is increasingly beneficial to the individual researcher to share
-        data in the most useful manner possible.</p>\n<h2>2. Provide metadata</h2>\n<p>The
-        first key to using data is understanding it. Metadata is information about
-        the data including how it was collected, what the units of measurement are,
-        and descriptions of how to best use the data. Clear metadata makes it easier
-        to figure out if a dataset is appropriate for a project. It also makes data
-        easier to use by both the original investigators and by other scientists by
-        making it easy to figure out how to work with the data. Without clear metadata,
-        datasets can be overlooked or not used due to the difficulty of understanding
-        the data (Fraser &amp; Gluck, 1999; A. S. Zimmerman, 2003), and the data becomes
-        less useful over time (Michener, Brunt, Helly, Kirchner, &amp; Stafford, 1997).</p>\n<p>Metadata
-        can take several forms, including descriptive file and column names, a written
-        description of the data, images (<em>i.e.,</em> maps, photographs), and specially
-        structured information that can be read by computers. Good metadata should
-        provide 1) the what, when, where, and how of data collection, 2) how to find
-        and access the data, 3) suggestions on the suitability of the data for answering
-        specific questions, 4) warnings about known problems or inconsistencies in
-        the data, and 5) information to check that the data are properly imported,
-        such as the number of rows and columns in the dataset and the total sum of
-        numerical columns (Michener et al., 1997; Strasser, Cook, Michener, &amp;
-        Budden, 2012; A. S. Zimmerman, 2003).</p>\n<p>Just like any other scientific
-        publication, metadata should be logically organized, complete, and clear enough
-        to enable interpretation and use of the data (A. Zimmerman, 2007). Specific
-        metadata standards exist (<em>e.g.,</em> Ecological Metadata Language <a href=\"http://knb.ecoinformatics.org/software/eml/\">EML</a>,
-        Directory Interchange Format <a href=\"http://gcmd.gsfc.nasa.gov/add/difguide/index.html\">DIF</a>,
-        Darwin Core <a href=\"http://rs.tdwg.org/dwc/\">DWC</a> (Wieczorek et al.,
-        2012), Dublin Core Metadata Initiative <a href=\"http://dublincore.org/metadata-basics/\">DCMI</a>,
-        Federal Geographic Data Committee <a href=\"http://www.fgdc.gov/metadata/geospatial-metadata-standards\">FGDC</a>
-        (O. J. Reichman et al., 2011; Whitlock, 2011). These standards are designed
-        to provide consistency in metadata across different datasets and also to allow
-        computers to interpret the metadata automatically. This allows broader and
-        more efficient use of shared data (Brunt, McCartney, Baker, &amp; Stafford,
-        2002; M. B. Jones et al., 2006). While following these standards is valuable,
-        the most important thing is to have metadata at all.</p>\n<p>You don’t need
-        to spend a lot of extra time to write good metadata. The easiest way to develop
-        metadata is to start describing your data during the planning and data collection
-        stages. This will help you stay organized, make it easier to work with your
-        data after it has been collected, and make eventual publication of the data
-        easier. If you decide to take the extra step and follow metadata standards,
-        there are tools designed to make this easier including: <a href=\"http://knb.ecoinformatics.org/morpho%20portal.jsp\">KNB
-        Morpho</a>, <a href=\"http://geology.usgs.gov/tools/metadata/tools/doc/xtme.html\">USGS
-        xtme</a>, and <a href=\"http://www.fgdc.gov/metadata/documents/workbook_0501_bmk.pdf\">FGDC
-        workbook</a>.</p>\n<h2>3. Provide an unprocessed form of the data</h2>\n<p>Often,
-        the data used in scientific analyses are modified in some way from the original
-        form in which they were collected. This is done to address the questions of
-        interest in the best manner possible and to address common limitations associated
-        with the raw data. However, the best way to process data depends on the question
-        being asked and corrections for common data limitations often change as better
-        approaches are developed. It can also be very difficult to combine data from
-        multiple sources that have each been processed in different ways. Therefore,
-        to make your data as useful as possible it is best to share the data in as
-        raw a form as possible.</p>\n<p>This is not to say that your data are best
-        suited for analysis in the raw form, but providing it in the raw form gives
-        data users the most flexibility. Of course, your work to develop and process
-        the data is also very important and can be quite valuable for other scientists
-        using your data. This is particularly true when correcting data for common
-        limitations. Providing both the raw and processed forms of the data, and clearly
-        explaining the differences between them in the metadata, is an easy way to
-        include the benefits of both data forms. An alternate approach is to share
-        the unprocessed data along with the code that process the data to the form
-        you used for analysis. This allows other scientists to assess and potentially
-        modify the process by which you arrived at the values used in your analysis.</p>\n<h2>4.
-        Use standard data formats</h2>\n<p>Everyone has their own favorite tools for
-        storing and analyzing data. To make it easy to use your data it is best to
-        store it in a standard format that can be used by many different kinds of
-        software. Good standard formats include the type of file, the overall structure
-        of the data, and the specific contents of the file.</p>\n<h3>Use standard
-        file formats</h3>\n<p>You should use file formats that are readable by most
-        software and, when possible, are non-proprietary (Borer, Seabloom, Jones,
-        &amp; Schildhauer, 2009; Strasser, Cook, Michener, Budden, &amp; Koskela,
-        2011; Strasser et al., 2012). Certain kinds of data in ecology and evolution
-        have well established standard formats such as <a href=\"http://zhanglab.ccmb.med.umich.edu/FASTA/\">FASTA</a>
-        files for nucleotide or peptide sequences and the <a href=\"http://evolution.genetics.washington.edu/phylip/newicktree.html\">Newick
-        files</a> for phylogenetic trees. Use these well defined formats when they
-        exist, because that is what other scientists and most existing software will
-        be able to work with most easily.</p>\n<p>Data that does not have a well defined
-        standard format is often stored in tables. Tabular data should be stored in
-        a format that can be opened by any type of software to increase reuseability
-        of the data, i.e. text files. These text files use delimiters to indicate
-        different columns. Commas are the most commonly used delimiter (i.e., comma-delimited
-        text files with the .csv extension). Tabs can also be used as a delimiter,
-        although problems can occur in displaying the data correctly when importing
-        data from one program to another. In contrast to plain text files, proprietary
-        formats such as those used by Microsoft Excel (e.g, .xls, .xlsx) can be difficult
-        to load into other programs. In addition, these types of files can become
-        obsolete, eventually making it difficult to open the data files at all if
-        the newer versions of the software no longer support the original format (Borer
-        et al., 2009; Strasser et al., 2011, 2012).</p>\n<p>When naming files you
-        should use descriptive names so that it is easy to keep track of what data
-        they contain (Borer et al., 2009; Strasser et al., 2011, 2012). If there are
-        multiple files in a dataset, name them in a consistent manner to make it easier
-        to automate working with them. You should also avoid spaces in file names,
-        which can cause problems for some software (Borer et al., 2009). Spaces in
-        file names can be avoided by using camel case (e.g, RainAvg) or by separating
-        the words with underscores (e.g., rain_avg).</p>\n<h3>Use standard table formats</h3>\n<p>Data
-        tables are ubiquitous in ecology and evolution. Tabular data provides a great
-        deal of flexibility in how to structure the data, which makes it easy to structure
-        the data in a way that is difficult to (re)use. We provide three simple recommendations
-        to help ensure that tabular data are properly structured to allow the data
-        to be easily imported and analyzed by most data management systems and common
-        analysis software, such as R and Python.</p>\n<ul><li>Each row should represent
-        a single observation (i.e., a record) and each column should represent a single
-        variable or type of measurement (i.e., a field) (Borer et al., 2009; Strasser
-        et al., 2011, 2012). This is the standard format for tables in the most commonly
-        used database management systems and analysis packages and makes the data
-        easy to work with in the most general way.</li><li>Every cell should contain
-        only a single value (Strasser et al., 2012). For example, do not include units
-        in the cell with the values (Figure 1) or include multiple measurements in
-        a single cell, and break taxonomic information up into single components with
-        one column each for family, genus, species, subspecies, etc. Violating this
-        rule makes it difficult to process or analyze your data using standard tools,
-        because there is no easy way for the software to treat the items within a
-        cell as separate pieces of information.</li><li>There should only be one column
-        for each type of information (Borer et al., 2009; Strasser et al., 2011, 2012).
-        The most common violation of this rule is <a href=\"http://en.wikipedia.org/wiki/Cross_tabulation\">cross-tab
-        structured data</a>, where different columns contain measurements of the same
-        variable (e.g., in different sites, treatments, etc.; Figure 1).</li></ul>\n<figure><img
-        src=\"http://blog.martinfenner.org/images/Data_formatting.jpg\" alt=\"Figure
-        1. Examples of how to restructure two common issues with tabular data. (a)
-        Each cell should only contain a single value. If more than one value is present
-        then the data should be split into multiple columns. (b) There should be only
-        one column for each type of information. If there are multiple columns then
-        the column header should be stored in one column and the values from each
-        column should be stored in a single column.\" loading=\"lazy\" /><figcaption><b><strong>Figure
-        1. Examples of how to restructure two common issues with tabular data</strong></b><span>.
-        (a) Each cell should only contain a single value. If more than one value is
-        present then the data should be split into multiple columns. (b) There should
-        be only one column for each type of information. If there are multiple columns
-        then the column header should be stored in one column and the values from
-        each column should be stored in a single column.</span></figcaption></figure>\n<p>While
-        cross-tab data can be useful for its readability, and may be appropriate for
-        data collection, this format makes it difficult to link the records with additional
-        data (e.g., the location and environmental conditions at a site) and it cannot
-        be properly used by most common database management and analysis tools (e.g.,
-        relational databases, dataframes in R and Python, etc.). If tabular data are
-        currently in a cross-tab structure, there are tools to help restructure the
-        data including functions in Excel, R (e.g., melt() function in the R package
-        reshape; Wickham (2007)), and Python (e.g., melt() function in the <a href=\"http://pandas.pydata.org/\">Pandas</a>
-        Python module.</p>\n<p>In addition to following these basic rules you should
-        also make sure to use descriptive column names (Borer et al., 2009). Descriptive
-        column names make the data easier to understand and therefore make data interpretation
-        errors less likely. As with file names, spaces can cause problems for some
-        software and should be avoided.</p>\n<h3>Use standard formats within cells</h3>\n<p>In
-        addition to using standard table structures it is also important to ensure
-        that the contents of each cell don’t cause problems for data management and
-        analysis software. Specifically, we recommend:</p>\n<ul><li>Be consistent.
-        For example, be consistent in your capitalization of words, choice of delimiters,
-        and naming conventions for variables.</li><li>Avoid special characters. Most
-        software for storing and analyzing data works best on plain text, and accents
-        and other special characters can make it difficult to import your data (Borer
-        et al., 2009; Strasser et al., 2012).</li><li>Avoid using your delimiter in
-        the data itself (e.g., commas in the notes filed of a comma-delimited file).
-        This can make it difficult to import your data properly. This means that if
-        you are using commas as the decimal separator (as is often done in continental
-        Europe) then you should use a non-comma delimiter (e.g., a tab).</li><li>When
-        working with dates use the YYYY-MM-DD format (i.e., follow the <a href=\"http://www.iso.org/iso/support/faqs/faqs_widely_used_standards/widely_used_standards_other/iso8601\">ISO
-        8601</a> data standard).</li></ul>\n<h2>5. Use good null values</h2>\n<p>Most
-        ecological and evolutionary datasets contain missing or empty data values.
-        Working with this kind of “null” data can be difficult, especially when the
-        null values are indicated in problematic ways. Unfortunately, there are many
-        different ways to indicate a missing/empty value, and very little agreement
-        on which approach to use.</p>\n<p>We recommend choosing a null value that
-        is both compatible with most software and unlikely to cause errors in analyses
-        (Table 1). The null value that is most compatible with the software commonly
-        used by biologists is the blank (i.e., nothing; Table 1). Blanks are automatically
-        treated as null values by R, Python, SQL, and Excel. They are also easily
-        spotted in a visual examination of the data. Note that a blank involves entering
-        nothing, it is not a space, so if you use this option make sure there aren’t
-        any hidden spaces. There are two potential issues with blanks that should
-        be considered:</p>\n<ol><li>It can be difficult to know if a value is missing
-        or was overlooked during data entry.</li><li>They can be confusing when spaces
-        or tabs are used as delimiters in text files.</li></ol>\n<p>NA and NULL are
-        reasonable null values, but they are only handled automatically by a subset
-        of commonly used software (Table 1). NA can also be problematic if it is also
-        used as an abbreviation (e.g., North America, Namibia, <em>Neotoma albigula</em>,
-        sodium, etc.). We recommend against using numerical values to indicate nulls
-        (e.g., 999, -999, etc.) because they typically require an extra step to remove
-        from analyses and can be accidentally included in calculations. We also recommend
-        against using non-standard text indications (e.g., No data, ND, missing, —)
-        because they can cause issues with software that requires consistent data
-        types within columns). Whichever null value that you use, only use one, use
-        it consistently throughout the data set, and indicate it clearly in the metadata.</p>\n<table><caption><strong>Tabel
-        1. Commonly used null values, limitations, compatibility with common software
-        and a recommendation regarding whether or not it is a good option</strong>.
-        Null values are indicated as being a null value for specific software if they
-        work consistently and correctly with that software. For example, the null
-        value “NULL” works correctly for certain applications in R, but does not work
-        in others, so it is not presented as part of the table.</caption><colgroup><col></col><col></col><col></col><col></col></colgroup><thead><tr><th>Null
-        values</th><th>Problems</th><th>Compatibility</th><th>Recommendation</th></tr></thead><tbody><tr><td><p>0</p></td><td><p>Indistinguishable
-        from a true zero</p></td><td></td><td><p>Never use</p></td></tr><tr><td><p>blank</p></td><td><p>Hard
-        to distinguish values that are missing from those overlooked on entry. Hard
-        to distinguish blanks from spaces, which behave differently.</p></td><td><p>R,
-        Python, SQL</p></td><td><p>Best option</p></td></tr><tr><td><p>999, -999</p></td><td><p>Not
-        recognized as null by many programs without user input. Can be inadvertently
-        entered into calculations.</p></td><td></td><td><p>Avoid</p></td></tr><tr><td><p>NA,
-        na</p></td><td><p>Can also be an abbreviation (e.g., North America), can cause
-        problems with data type (turn a numerical column into a text column). NA is
-        more commonly recognized than na.</p></td><td><p>R</p></td><td><p>Good option</p></td></tr><tr><td><p>N/A</p></td><td><p>An
-        alternate form of NA, but often not compatible with software</p></td><td></td><td><p>Avoid</p></td></tr><tr><td><p>NULL</p></td><td><p>Can
-        cause problems with data type</p></td><td><p>SQL</p></td><td><p>Good option</p></td></tr><tr><td><p>None</p></td><td><p>Can
-        cause problems with data type</p></td><td><p>Python</p></td><td><p>Avoid</p></td></tr><tr><td><p>No
-        data</p></td><td><p>Can cause problems with data type, contains a space</p></td><td></td><td><p>Avoid</p></td></tr><tr><td><p>Missing</p></td><td><p>Can
-        cause problems with data type</p></td><td></td><td><p>Avoid</p></td></tr><tr><td><p>-,+,.</p></td><td><p>Can
-        cause problems with data type</p></td><td></td><td><p>Avoid</p></td></tr></tbody></table>\n<h2>6.
-        Make it easy to combine your data with other datasets</h2>\n<p>Ecological
-        and evolutionary data are often most valuable when combined with other kinds
-        of data (e.g., taxonomic, environmental). You can make it easier to combine
-        your data with other data sources by including the data that is common across
-        many data sources (e.g., Latin binomials, latitudes and longitudes) It is
-        common for data to include codes or abbreviations. For example, in ecology
-        and evolution codes often appear in place of site locations or taxonomy. This
-        is useful because it reduces data entry (e.g., DS instead of <em>Dipodomys
-        spectabilis</em>) and redundancy (a single column for a species ID rather
-        than separate columns for family, genus, and species). However, without clear
-        definitions these codes can be difficult to understand and make it more difficult
-        to connect your data with external sources. The easiest way to link your data
-        to other datasets is to include additional tables that contain a column for
-        the code and additional columns that describe the item in the standard way.
-        For example, you might include a table with the species codes followed by
-        their most current family, genus, and specific epithet. For site location,
-        you could include a table with the site code followed by latitude and longitude.
-        Linked tables can also be used to include additional information about your
-        data, such as spatial extent, temporal duration, and other appropriate details.</p>\n<h2>7.
-        Perform basic quality control</h2>\n<p>Data, just like any other scientific
-        product, should undergo some level of quality control (O. J. Reichman et al.,
-        2011). This is true regardless of whether you plan to share the data because
-        quality control will make it easier to analyze your own data and decrease
-        the chance of making mistakes. However, it is particularly important for data
-        that will be shared because scientists using the data won’t be familiar with
-        quirks in the data and how to work around them.</p>\n<p>At its most basic,
-        quality control can consist of a few quick sanity checks of the data. More
-        advanced quality control can include automated checks on data as it is entered
-        and double-entry of data (Lampe &amp; Weiler, 1998; Paulsen, Overgaard, &amp;
-        Lauritsen, 2012). This additional effort can be time consuming, but is valuable
-        because it increases data accuracy by catching typographical errors, reader/recorder
-        error, out-of-range values, and questionable data in general (Lampe &amp;
-        Weiler, 1998; Paulsen et al., 2012).</p>\n<p>Before sharing your data we recommend
-        performing a quick “data review”. Start by performing some basic sanity checks
-        on your data. For example:</p>\n<ul><li>If a column should contain numeric
-        values, check that there are no non-numeric values in the data.</li><li>Check
-        that empty cells actually represent missing data, and not mistakes in data
-        entry, and indicate that they are empty using the appropriate null values
-        (see recommendation 6).</li><li>Check for consistency in unit of measurement,
-        data type (e.g., numeric, character), naming scheme (e.g., taxonomy, location),
-        etc.</li></ul>\n<p>These checks can be performed by carefully looking at the
-        data or can be automated using common programming and analysis tools like
-        R or Python.</p>\n<p>Then ask someone else to look over your metadata and
-        data and provide you with feedback about anything they didn’t understand.
-        In the same way that friendly reviews of papers can help catch mistakes and
-        identify confusing sections of papers, a friendly review of data can help
-        identify problems and things that are unclear in the data and metadata.</p>\n<h2>8.
-        Use an established repository</h2>\n<p>For data sharing to be effective, data
-        should be easy to find, accessible, and stored where it will be preserved
-        for a long time (Kowalczyk &amp; Shankar, 2011). To make your data (and associated
-        code) visible and easily accessible, and to ensure a permanent link to a well
-        maintained website, we suggest depositing your data in one of the major well-established
-        repositories. This guarantees that the data will be available in the same
-        location for a long time, in contrast to personal and institutional websites
-        that do not guarantee the long-term persistence of the data. There are repositories
-        available for sharing almost any type of biological or environmental data.
-        Repositories that host specific data types, such as molecular sequences (e.g.,
-        DDBJ, GenBank, MG-RAST), are often highly standardized in data type, format,
-        and quality control approaches. Other repositories host a wide array of data
-        types and are less standardized (e.g., Dryad, KNB, PANGAEA). In addition to
-        the repositories focused on the natural sciences there are also all purpose
-        repositories where data of any kind can be shared (e.g., figshare).</p>\n<p>When
-        choosing a repository you should consider where other researchers in your
-        discipline are sharing their data. This helps you quickly identify the community’s
-        standard approach to sharing and increases the likelihood that other scientists
-        will discover your data. In particular, if there is a centralized repository
-        for a specific kind of data (e.g., GenBank for sequence data) then you should
-        use that repository.</p>\n<p>In cases where there is no <em>de facto</em>
-        standard it is worth considering differences among repositories in terms of
-        use, data rights, and licensing (Table 2) and whether your funding agency
-        or journal has explicit requirements or restrictions related to repositories.
-        We also recommend that you use a repository that allows your dataset to be
-        easily cited. Most repositories will describe how this works, but an easy
-        way to guarantee that your data are citable is to confirm that the repository
-        associates it with a persistent identifier, the most popular of which is the
-        digital object identifier (DOI). DOIs are permanent unique identifiers that
-        are independent of physical location and site ownership. There are also online
-        tools for finding good repositories for your data including <a href=\"http://databib.org/\">Databib</a>
-        and <a href=\"http://re3data.org/\">re3data</a>.</p>\n<table><caption><strong>Table
-        2. Popular repositories for scientific datasets</strong>. This table does
-        not include well-known molecular repositories (e.g. GenBank, EMBL, MG-RAST)
-        that have become<span> </span><em>de facto</em><span> </span>standards in
-        molecular and evolutionary biology. Consequently, several of these primarily
-        serve the ecological community. These repositories are not exclusively used
-        by members of specific institutions or museums, but accept data from the general
-        scientific community.</caption><colgroup><col></col><col></col><col></col><col></col><col></col><col></col></colgroup><thead><tr><th>Repository</th><th>License</th><th>DOI</th><th>Metadata</th><th>Access</th><th>Notes</th></tr></thead><tbody><tr><td><p>Dryad</p></td><td><p>CC0</p></td><td><p>Yes</p></td><td><p>Suggested</p></td><td><p>Open</p></td><td><p>Ecology
-        &amp; evolution data associated with publications</p></td></tr><tr><td><p>Ecological
-        Archives</p></td><td><p>No</p></td><td><p>Yes</p></td><td><p>Required</p></td><td><p>Open</p></td><td><p>Publishes
-        supplemental data for ESA journals and stand alone data papers</p></td></tr><tr><td><p>Knowledge
-        Network for Biocomplexity</p></td><td><p>No</p></td><td><p>Yes</p></td><td><p>Required</p></td><td><p>Variable</p></td><td><p>Partners
-        with ESA, NCEAS, DataONE</p></td></tr><tr><td><p>Paleobiology Database</p></td><td><p>Various
-        CC</p></td><td><p>No</p></td><td><p>Optional</p></td><td><p>Variable</p></td><td><p>Paleontology
-        specific</p></td></tr><tr><td><p>Data Basin</p></td><td><p>Various CC</p></td><td><p>No</p></td><td><p>Optional</p></td><td><p>Open</p></td><td><p>GIS
-        data in ESRI files, limited free space</p></td></tr><tr><td><p>Pangaea</p></td><td><p>Various
-        CC</p></td><td><p>Yes</p></td><td><p>Required</p></td><td><p>Variable</p></td><td><p>Editors
-        participate in QA/QC</p></td></tr><tr><td><p>figshare</p></td><td><p>CC0</p></td><td><p>Yes</p></td><td><p>Optional</p></td><td><p>Open</p></td><td><p>Also
-        allows deposition of other research outputs and private datasets</p></td></tr></tbody></table>\n<h2>9.
-        Use an established and liberal license</h2>\n<p>Including an explicit license
-        with your data is the best way to let others know exactly what they can and
-        cannot do with the data you shared. Following the <a href=\"http://pantonprinciples.org/\">Panton
-        Principles</a> we recommend:</p>\n<ol><li>Using well established licenses
-        in order to clearly communicate the rights and responsibilities of both the
-        people providing the data and the people using it.</li><li>Using the most
-        open license possible, because even minor restrictions on data use can have
-        unintended consequences for the reuse of the data (Poisot et al., 2013; Schofield
-        et al., 2009).</li></ol>\n<p>The Creative Commons Zero license (CC0) places
-        no restrictions on data use and is considered by many to be one of the best
-        license for sharing data (e.g., (Poisot et al., 2013; Schofield et al., 2009),
-        <a href=\"http://blog.datadryad.org/2011/10/05/why-does-dryad-use-cc0/\">Why
-        does Dryad use CC0</a>). Having a clear and open license will increase the
-        chance that other scientists will be comfortable using your data.</p>\n<h2>Concluding
-        remarks</h2>\n<p>Data sharing has the potential to transform the way we conduct
-        ecological and evolutionary research (Fienberg &amp; Martin, 1985; Poisot
-        et al., 2013; Whitlock et al., 2010). As a result, there are an increasing
-        number of initiatives at the federal, funding agency, and journal levels to
-        encourage or require the sharing of the data associated with scientific research
-        (Heather A Piwowar &amp; Chapman, 2008; Poisot et al., 2013; Whitlock et al.,
-        2010). However, making the data available is only the first step. To make
-        data sharing as useful as possible it is necessary to make the data usable
-        with as little effort as possible (M. B. Jones et al., 2006; O. J. Reichman
-        et al., 2011). This allows scientists to spend their time doing science rather
-        than cleaning up data.</p>\n<p>We have provided a list of 9 practices that
-        require only a small additional time investment but substantially improve
-        the usability of data. These practices can be broken down into three major
-        groups.</p>\n<ol><li>Well documented data are easier to understand.</li><li>Properly
-        formatted data are easier to use in a variety of software.</li><li>Data that
-        is shared in established repositories with open licenses is easier for others
-        to find and use.</li></ol>\n<p>Most of these recommendations are simply good
-        practice for working with data regardless of whether that data are shared
-        or not. This means that following these recommendations (2-7) make the data
-        easier to work with for anyone, including you. This is particularly true when
-        returning to your own data for further analysis months or years after you
-        originally collected or analyzed it. In addition, data sharing often occurs
-        within a lab or research group. Good data sharing practices make these in-house
-        collaborations faster, easier, and less dependent on lab members who may have
-        graduated or moved on to other things.</p>\n<p>By following these practices
-        we can assure that the data collected in ecology and evolution can be used
-        to its full potential to improve our understanding of biological systems.</p>\n<h2>Acknowledgments</h2>\n<p>Thanks
-        to Karthik Ram for organizing this special section and inviting us to contribute.
-        Carly Strasser and Kara Woo recommended important references and David Harris
-        and Carly Strasser provided valuable feedback on null values, all via Twitter.
-        Carl Boettiger, Matt Davis, Daniel Hocking, Heinz Pampel, Karthik Ram, Thiago
-        Silva, Carly Strasser, Tom Webb, and beroe (Twitter handle) provided value
-        comments on the manuscript. Many of these comments were part of the informal
-        review process facilitated by posting this manuscript as a preprint. The writing
-        of this paper was supported by a CAREER grant from the U.S. National Science
-        Foundation (DEB 0953694) to EPW. A <a href=\"https://doi.org/10.4033/iee.2013.6b.6.f\">peer-reviewed
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-        A. S. (2003). <em>Data sharing and secondary use of scientific data: Experiences
-        of ecologists</em> (PhD thesis). The University of Michigan.</p> ","published_at":1372179840,"updated_at":1694123190,"indexed_at":1694123633,"authors":[{"url":"https://orcid.org/0000-0003-1419-2405","name":"Martin
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