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@@ -1 +1 @@
-ae2762a5
+e6b5948d

_tex/index.tex

@@ -203,7 +203,7 @@
   pdfcreator={LaTeX via pandoc}}
 
 \title{Towards an open-source model for data and metadata standards}
-\author{Ariel Rokem \and Vani Mandava}
+\author{Ariel Rokem \and Vani Mandava \and Nicoleta Cristea}
 \date{}
 
 \begin{document}
@@ -351,7 +351,34 @@ \subsection{High-energy physics (HEP)}\label{high-energy-physics-hep}
 
 \subsection{Earth sciences}\label{earth-sciences}
 
-XXX
+The need for geospatial data exchange between different systems began to
+be recognized in the 1970s and 1980s, but proprietary formats still
+dominated. Coordinated standardization efforts brought the Open
+Geospatial Consortium (OGC) establishment in the 1990s, a critical step
+towards open standards for geospatial data. The 1990s have also seen the
+development of key standards such as the Network Common Data Form
+(NetCDF) developed by the University Corporation for Atmospheric
+Research (UCAR) and the Hierarchical Data Format (HDF), a set of file
+formats (HDF4, HDF5) that are widely used, particularly in climate
+research. The GeoTIFF format, which originated at NASA in the late
+1990s, is extensively used to share image data. In the 1990s, open web
+mapping also began with MapServer (https://mapserver.org) and continued
+later with other projects such as OpenStreetMap (www.openstreetmap.org).
+The following two decades, the 2000s-2020s, brought an expansion of open
+standards and integration with web technologies developed by OGC, as
+well as other standards such as the Keyhole Markup Language (KML) for
+displaying geographic data in Earth browsers. Formats suitable for cloud
+computing also emerged, such as the Cloud Optimized GeoTIFF (COG),
+followed by Zarr and Apache Parquet for array and tabular data,
+respectively. In 2006, the Open Source Geospatial Foundation (OSGeo,
+https://www.osgeo.org) was established, demonstrating the community's
+commitment to the development of open-source geospatial technologies.
+While some standards have been developed in the industry (e.g., Keyhole
+Markup Language (KML) by Keyhole Inc., which Google later acquired),
+they later became international standards of the OGC, which now
+encompasses more than 450 commercial, governmental, nonprofit, and
+research organizations working together on the development and
+implementation of open standards (https://www.ogc.org).
 
 \subsection{Neuroscience}\label{neuroscience}
 

index.docx

@@ -65,6 +65,7 @@
 <meta name="citation_title" content="Towards an open-source model for data and metadata standards">
 <meta name="citation_author" content="Ariel Rokem">
 <meta name="citation_author" content="Vani Mandava">
+<meta name="citation_author" content="Nicoleta Cristea">
 <meta name="citation_language" content="en">
 <meta name="citation_reference" content="citation_title=Without appropriate metadata, data-sharing mandates are pointless;,citation_abstract=Funders and investigators must demand appropriate metadata standards to take data from foul to FAIR. Funders and investigators must demand appropriate metadata standards to take data from foul to FAIR.;,citation_author=Mark A Musen;,citation_publication_date=2022-09;,citation_cover_date=2022-09;,citation_year=2022;,citation_issue=7926;,citation_volume=609;,citation_journal_title=Nature;,citation_publisher=Springer Science; Business Media LLC;">
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@@ -112,6 +113,14 @@ <h1 class="title">Towards an open-source model for data and metadata standards</
                   </div>
                       <div class="quarto-title-meta-contents">
             <p class="author">Vani Mandava <a href="https://orcid.org/0000-0003-3592-9453" class="quarto-title-author-orcid"> <img src="data:image/png;base64,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"></a></p>
+          </div>
+                <div class="quarto-title-meta-contents">
+                    <p class="affiliation">
+                        University of Washington
+                      </p>
+                  </div>
+                      <div class="quarto-title-meta-contents">
+            <p class="author">Nicoleta Cristea <a href="https://orcid.org/0000-0002-9091-0280" class="quarto-title-author-orcid"> <img src="data:image/png;base64,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"></a></p>
           </div>
                 <div class="quarto-title-meta-contents">
                     <p class="affiliation">
@@ -226,7 +235,7 @@ <h2 data-number="3.2" class="anchored" data-anchor-id="high-energy-physics-hep">
 </section>
 <section id="earth-sciences" class="level2" data-number="3.3">
 <h2 data-number="3.3" class="anchored" data-anchor-id="earth-sciences"><span class="header-section-number">3.3</span> Earth sciences</h2>
-<p>XXX</p>
+<p>The need for geospatial data exchange between different systems began to be recognized in the 1970s and 1980s, but proprietary formats still dominated. Coordinated standardization efforts brought the Open Geospatial Consortium (OGC) establishment in the 1990s, a critical step towards open standards for geospatial data. The 1990s have also seen the development of key standards such as the Network Common Data Form (NetCDF) developed by the University Corporation for Atmospheric Research (UCAR) and the Hierarchical Data Format (HDF), a set of file formats (HDF4, HDF5) that are widely used, particularly in climate research. The GeoTIFF format, which originated at NASA in the late 1990s, is extensively used to share image data. In the 1990s, open web mapping also began with MapServer (https://mapserver.org) and continued later with other projects such as OpenStreetMap (www.openstreetmap.org). The following two decades, the 2000s-2020s, brought an expansion of open standards and integration with web technologies developed by OGC, as well as other standards such as the Keyhole Markup Language (KML) for displaying geographic data in Earth browsers. Formats suitable for cloud computing also emerged, such as the Cloud Optimized GeoTIFF (COG), followed by Zarr and Apache Parquet for array and tabular data, respectively. In 2006, the Open Source Geospatial Foundation (OSGeo, https://www.osgeo.org) was established, demonstrating the community’s commitment to the development of open-source geospatial technologies. While some standards have been developed in the industry (e.g., Keyhole Markup Language (KML) by Keyhole Inc., which Google later acquired), they later became international standards of the OGC, which now encompasses more than 450 commercial, governmental, nonprofit, and research organizations working together on the development and implementation of open standards (https://www.ogc.org).</p>
 </section>
 <section id="neuroscience" class="level2" data-number="3.4">
 <h2 data-number="3.4" class="anchored" data-anchor-id="neuroscience"><span class="header-section-number">3.4</span> Neuroscience</h2>

index.html

@@ -14,7 +14,7 @@
     "\n",
     "Data and metadata standards that use tools and practices of OSS (“open-source standards” henceforth) reap many of the benefits that the OSS model has provided in the development of other technologies. The present report explores how OSS processes and tools have affected the development of data and metadata standards. The report will triangulate common features of a variety of use cases; it will identify some of the challenges and pitfalls of this mode of standards development, with a particular focus on cross-sector interactions; and it will make recommendations for future developments and policies that can help this mode of standards development thrive and reach its full potential."
    ],
-   "id": "dcc262d7-9156-4db6-be64-b8ef45cddf54"
+   "id": "8d55f75f-fab6-44ca-b603-3269de038767"
   }
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  "nbformat": 4,

index.pdf

@@ -18,7 +18,7 @@
     "\n",
     "Wilkinson, Mark D, Michel Dumontier, I Jsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, et al. 2016. “The FAIR Guiding Principles for Scientific Data Management and Stewardship.” *Sci Data* 3 (March): 160018."
    ],
-   "id": "5f0f87de-bcf2-4c1c-bf0a-c54253dff641"
+   "id": "2b171357-281b-489b-bf0d-87cb2addb305"
   }
  ],
  "nbformat": 4,

sections/01-introduction.embed.ipynb

@@ -192,7 +192,7 @@ <h2 class="anchored" data-anchor-id="high-energy-physics-hep">High-energy physic
 </section>
 <section id="earth-sciences" class="level2">
 <h2 class="anchored" data-anchor-id="earth-sciences">Earth sciences</h2>
-<p>XXX</p>
+<p>The need for geospatial data exchange between different systems began to be recognized in the 1970s and 1980s, but proprietary formats still dominated. Coordinated standardization efforts brought the Open Geospatial Consortium (OGC) establishment in the 1990s, a critical step towards open standards for geospatial data. The 1990s have also seen the development of key standards such as the Network Common Data Form (NetCDF) developed by the University Corporation for Atmospheric Research (UCAR) and the Hierarchical Data Format (HDF), a set of file formats (HDF4, HDF5) that are widely used, particularly in climate research. The GeoTIFF format, which originated at NASA in the late 1990s, is extensively used to share image data. In the 1990s, open web mapping also began with MapServer (https://mapserver.org) and continued later with other projects such as OpenStreetMap (www.openstreetmap.org). The following two decades, the 2000s-2020s, brought an expansion of open standards and integration with web technologies developed by OGC, as well as other standards such as the Keyhole Markup Language (KML) for displaying geographic data in Earth browsers. Formats suitable for cloud computing also emerged, such as the Cloud Optimized GeoTIFF (COG), followed by Zarr and Apache Parquet for array and tabular data, respectively. In 2006, the Open Source Geospatial Foundation (OSGeo, https://www.osgeo.org) was established, demonstrating the community’s commitment to the development of open-source geospatial technologies. While some standards have been developed in the industry (e.g., Keyhole Markup Language (KML) by Keyhole Inc., which Google later acquired), they later became international standards of the OGC, which now encompasses more than 450 commercial, governmental, nonprofit, and research organizations working together on the development and implementation of open standards (https://www.ogc.org).</p>
 </section>
 <section id="neuroscience" class="level2">
 <h2 class="anchored" data-anchor-id="neuroscience">Neuroscience</h2>

sections/01-introduction.out.ipynb

@@ -20,7 +20,7 @@
     "\n",
     "## Earth sciences\n",
     "\n",
-    "XXX\n",
+    "The need for geospatial data exchange between different systems began to be recognized in the 1970s and 1980s, but proprietary formats still dominated. Coordinated standardization efforts brought the Open Geospatial Consortium (OGC) establishment in the 1990s, a critical step towards open standards for geospatial data. The 1990s have also seen the development of key standards such as the Network Common Data Form (NetCDF) developed by the University Corporation for Atmospheric Research (UCAR) and the Hierarchical Data Format (HDF), a set of file formats (HDF4, HDF5) that are widely used, particularly in climate research. The GeoTIFF format, which originated at NASA in the late 1990s, is extensively used to share image data. In the 1990s, open web mapping also began with MapServer (https://mapserver.org) and continued later with other projects such as OpenStreetMap (www.openstreetmap.org). The following two decades, the 2000s-2020s, brought an expansion of open standards and integration with web technologies developed by OGC, as well as other standards such as the Keyhole Markup Language (KML) for displaying geographic data in Earth browsers. Formats suitable for cloud computing also emerged, such as the Cloud Optimized GeoTIFF (COG), followed by Zarr and Apache Parquet for array and tabular data, respectively. In 2006, the Open Source Geospatial Foundation (OSGeo, https://www.osgeo.org) was established, demonstrating the community’s commitment to the development of open-source geospatial technologies. While some standards have been developed in the industry (e.g., Keyhole Markup Language (KML) by Keyhole Inc., which Google later acquired), they later became international standards of the OGC, which now encompasses more than 450 commercial, governmental, nonprofit, and research organizations working together on the development and implementation of open standards (https://www.ogc.org).\n",
     "\n",
     "## Neuroscience\n",
     "\n",
@@ -30,7 +30,7 @@
     "\n",
     "Another interesting use case for open-source standards is community/citizen science. This approach, which has grown in the last 20 years, has many benefits for both the research field that harnesses the energy of non-scientist members of the community to engage with scientific data, as well as to the community members themselves who can draw both knowledge and pride in their participation in the scientific endeavor. It is also recognized that unique broader benefits are accrued from this mode of scientific research, through the inclusion of perspectives and data that would not otherwise be included. To make data accessible to community scientists, and to make the data collected by community scientists accessible to professional scientists, it needs to be provided in a manner that can be created and accessed without specialized instruments or specialized knowledge. Here, standards are needed to facilitate interactions between an in-group of expert researchers who generate and curate data and a broader set of out-group enthusiasts who would like to make meaningful contributions to the science. This creates a particularly stringent constraint on transparency and simplicity of standards. Creating these standards in a manner that addresses these unique constraints can benefit from OSS tools, with the caveat that some of these tools require additional expertise. For example, if the standard is developed using git/GitHub for versioning, this would require learning the complex and obscure technical aspects of these system that are far from easy to adopt, even for many professional scientists."
    ],
-   "id": "1e9a8160-9b6c-4f0d-818f-35fa3159b74c"
+   "id": "44191b8a-4483-4fe8-bdb2-bdb58c0f2311"
   }
  ],
  "nbformat": 4,