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software:gplates:grot:start [2020/09/17 20:16] – [Rotation Line Data] christiansoftware:gplates:grot:start [2021/07/28 16:51] (current) – [Rotation Line Data] christian
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 With the advent of GPlates 1.5 came the ability to read a new version of the rotation file format called ''*.grot''. In analogy to ''JSON'' and ''OGR_GMT'' formats it allows for much more verbose and structured addition of metadata to rotation sequences. With the advent of GPlates 1.5 came the ability to read a new version of the rotation file format called ''*.grot''. In analogy to ''JSON'' and ''OGR_GMT'' formats it allows for much more verbose and structured addition of metadata to rotation sequences.
- 
-''Revision: 1793 Date: 2012-05-11'' 
  
 ^ Revision      ^ GROT version ^ Date      ^ ^ Revision      ^ GROT version ^ Date      ^
 | 1 (svn: 1793) | 1.0         | 2012-05-11 | | 1 (svn: 1793) | 1.0         | 2012-05-11 |
  
 +For the document revisions, please see the [[https://wiki.paleoearthlabs.org/software/gplates/grot/start?do=revisions|History of this page]].
  
   - [[.:attributenames|GROT format attribute names]]   - [[.:attributenames|GROT format attribute names]]
   - [[.:examplefiles|Example files]]   - [[.:examplefiles|Example files]]
- 
- 
 ===== Introduction ===== ===== Introduction =====
  
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-====== File body: The rotation sequences ======+ 
 +====== File header elements ====== 
 + 
 +New GPlates rotation files have a mandatory file header which must be present in all rotation files. The file header contains important information on how to processes different parts of the file and also carries important metadata, such as information on the Geological Time Scale used for rotations. The file header contains global metadata which are referenced in the file body. It adheres to specific format and contains mandatory attributes Apart from the mandatory metadata in the header, there are also optional blocks which allow the user to put revision information or any other data the user finds necessary. Future version of GPlates (> 1.3) will include the opportunity to edit this information through a GUI. 
 + 
 +The file header follows the core elements of the Dublin Core metadata initiative which specifies 15 standard tags to identify electronic documents (see [[http://dublincore.org/documents/dcmi-terms|DublinCore terms]]). 
 + 
 +Let’s start out with the mandatory information in the file header, here’s the overview: 
 + 
 +===== Rotation file version ===== 
 + 
 +The first line uses the ''@GPLATESROTATIONFILE:version"xx"'' attribute to specify that this file adheres to the new rotation file standard and gives the current rotation file version number. 
 + 
 +<code> 
 +  @GPLATESROTATIONFILE:version"1.0" 
 +</code> 
 + 
 +<note important>''@GPLATESROTATIONFILE:version'' -- File format versioning</note> 
 + 
 + 
 +===== Dublin Core document metadata ===== 
 + 
 +The subsequent attributes use the ''@DC'' parent attribute to denote a set of [[https://www.dublincore.org/|Dublin Core]] metadata describing the file content (see [[https://en.wikipedia.org/wiki/Dublin_Core|the Wikipedia article on Dublin Core]]. This also includes links to licenses, modification dates and proper citations for the file. See the [[software:gplates:grot:attributenames|GPlates GROT Format attribute list]] for a complete listing and explanation of the header attributes. 
 + 
 +<note important>''@DC'' — file metadata</note> 
 + 
 +<code> 
 +  @DC:namespace"http://purl.org/dc/elements/1.1/"  
 +  @DC:title"GPlates rotation file -  NEW ROTATION FORMAT SAMPLE FILE" 
 +  @DC:creator:name"Foo Bar"  
 +  @DC:creator:email"mailto:some.name@example.com" 
 +  @DC:creator:url"http://www.gplates.org"  
 +  @DC:creator:affiliation"EarthByte Research Group, School of Geosciences"  
 +  @DC:creator:affiliation"The University of Sydney, NSW 2006, Australia"  
 +  @DC:rights:license"Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)"  
 +  @DC:rights:url"http://creativecommons.org/licenses/by-nc-sa/3.0/" 
 +  @DC:date:created"2/06/11 4:08:05 PM"  
 +  @DC:date:modified"$Date: 2012-05-12 00:48:08 +1000 (Sat, 12 May 2012) $"  
 +  @DC:coverage:temporal"0-600 Ma" 
 +  @DC:bibliographicCitation"""Chin, Mueller, Cannon, Landgrebe, Heine,  
 +                              Watson, Turner (2012) The GPGIM vol:pp-pp,  
 +                              J. Digitial Earth. doi:xxxxxxxxx """ 
 +  @DC:description"""  
 +   A sample rotation file in the new GPlates rotation file format v1.1  
 +   
 +   Based on moving Indian/Atlantic hotspots (O'Neill et. al. 2005)  
 +   to 100 Ma and true polar wander corrected palaeomagnetic  
 +   reference frame (derived from Steinberger and Torsvik 2008)  
 +   from 100 - 200 Ma.  250 Ma is the extent of this rotation model.  
 +   Pacific absolute reference frame based on Wessell and Kroenke 2008  
 +   with a switch to Wessel et. al. 2006 at 118.4 Ma  
 +   Reference for rotation model: Seton et. al. (submitted to ESR)""" 
 +</code> 
 + 
 +==== Contributing authors ==== 
 + 
 +The next mandatory block is the contributor information related to individuals who have worked on various parts of the rotation sequences. In order to correctly attribute contributions which have not made it into publications, this section lists authors with their contact details and full name. The lines use the ''@DC:contributor'' form of the Dublin Core specifications and the value field contains multiple values. In most cases, especially in intra-institutional use, not all rotations are published in the form of a citable reference, enlisting contributing authors still provides a reference to the creator. 
 + 
 +<note important> ''@DC:contributor'' -- Contributing authors</note> 
 + 
 +Template 
 +<code> 
 +  @DC:contributor"id | Real Name | Email | URL | [Postal address, other contact details]  
 +</code> 
 + 
 +Example (single line) 
 +<code> 
 +  @DC:contributor"""FOBA | Foo Bar | foo.bar@example.com | 
 +   http://www.example.com | The FooBar Geodynamics Group, BarFoo University, Jupiter""" 
 +</code> 
 + 
 +Example (multi line) 
 +<code>    
 +  @DC:contributor"""FILA | 
 +                    Firstname Lastname |  
 +                    first.last@example.com | 
 +                    http://www.example.com |  
 +                    FooBar Research Group, BarFoo University""" 
 +</code> 
 + 
 +===== Bibliographic and reference section ===== 
 + 
 +The next mandatory block encompasses the bibliographic or reference data valid for the file globally. The field contain a reference to a bibliographic data base in BibTeX format as well as to the GPlates Information Model (GPGIM) website and a base URL for the [[https://doi.org|Digital Object Identifier (DOI)]]. All these attribute will be referenced from the individual MPRS or rotations. 
 + 
 +<note important>''@BIBINFO'' — Optional inclusion of bibliographic databases</note> 
 + 
 +The inclusion of mandatory bibliographic reference data allows a future use of GPlates in conjunction with hyperlinks (through the DOI) to a  PICT PICT publication as well as direct links to a bibliographic companion database file: 
 + 
 +<code> 
 +  @BIBINFO:bibfile"file://rotationfile.bib" 
 +  @BIBINFO:doibase"https://doi.org/"  
 +  @GPML:namespace"http://www.earthbyte.org/Resources/GPGIM/public/" 
 +</code>   
 +  
 +===== Geological time scales ===== 
 + 
 +One of the most important piece of metadata is information about the geological time scales (GTS) used to convert relative geological ages to absolute times.  
 + 
 +<note important>''@GEOTIMESCALE'' -- Mandatory inclusion of Geological Time Scales</note> 
 + 
 +These GTS constantly evolve and a Base Aptian on some timescale from the 1990’s has a few Million Years difference to a Base Aptian from the 2010’s. The GTS are listed in the header section and are referenced through a tag at individual rotation level. 
 + 
 +Template 
 +<code> 
 +  @GEOTIMESCALE" ID | DOI/URL/ISSN (specify) | CiteKey | Bibliographic record/Comment"  
 +</code> 
 + 
 +Multiline specification of GTS 
 +<code>   
 +  @GEOTIMESCALE""" GEEK07 |  
 +                doi:10.1016/B978-044452748-6.00097-3 | 
 +                Gee.ToC.07 |  
 +                Gee, J.S. and Kent, D.V. (2012) 5.12 - Source of Oceanic \  
 +   Magnetic Anomalies and the Geomagnetic Polarity Timescale, in: Treatise on\  
 +   Geophysics, Volume 5, Pages 455--507, Elsevier, Amsterdam""" 
 +  # 
 +  @GEOTIMESCALE""" CK95G94 |  
 +               doi:10.1029/94JB03098; doi:10.1029/94JB01889| 
 +               Cande.JGR.95; Gradstein.JGR.94 |  
 +               S. C. Cande and D. V. Kent. Revised Calbration of the\  
 +   geomagnetic polarity timescale for the Late Cretaceous and Cenozoic. \  
 +   J. Geophys. Res., 100(B4):6093--6095, 1995.;  
 +   F. M. Gradstein, F. P. Agterberg, J. G. Ogg, J. Hardenbol, P. van Veen,\  
 +   J. Thierry, and Z. Huang. A Mesozoic time scale. J. Geophys. Res.,\  
 +   99:24051--24074, 1994. doi:10.1029/94JB01889.""" 
 +  # 
 +  @GEOTIMESCALE""" Absolute  
 +               | 
 +               | 
 +               Absolute numerical time in Ma""" 
 + 
 +</code> 
 + 
 +===== OPTIONAL: Revision history ===== 
 + 
 +The optional revision history block is used for versioning. The actual list of applicable subattributes depends on the versioning system used.  
 + 
 +<note important>''@REVISIONHIST'' -- Optional inclusion of versioning information</note> 
 + 
 +Each Keyword shouldbe shortened and prefixed by ''@REVISIONHIST[keyword]"value"''. Example for a Subversion repository setup: 
 + 
 +<code> 
 +  @REVISIONHIST"$Id: CHHEI_RotFileStd.tex 1793 2012-05-11 14:48:08Z christian $" 
 +</code> 
 + 
 +<note warning>FIXME This needs to be adopted to GIT and other systems taking over from SVN.</note> 
 + 
 + 
 + 
 +====== File body elements: The rotation sequences ======
  
 The file body contains all data outside the file header. These are Moving Plate Rotation Sequences (MPRS) which are in turn composed of individual lines listing rotation parameters. The file body contains all data outside the file header. These are Moving Plate Rotation Sequences (MPRS) which are in turn composed of individual lines listing rotation parameters.
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 ^ Parameter name ^ Description ^ ^ Parameter name ^ Description ^
-|PID1 | Plate ID 1 (moving plate) |+|''PID1'' | Plate ID 1 (moving plate) |
 |''FromAge''| Excuse the french. Start age. | |''FromAge''| Excuse the french. Start age. |
-|POLELAT | Rotation pole latitude | +|''POLELAT'' | Rotation pole latitude | 
-|POLELON | Rotation pole longitude | +|''POLELON'' | Rotation pole longitude | 
-|ANGLE | Rotation pole angle | +|''ANGLE'' | Rotation pole angle | 
-|PID2 | Fixed Plate, plate ID 2 |+|''PID2''| Fixed Plate, plate ID 2 |
  
 New optional meta data attributes from the dictionary can be added to the individual lines. Rotation metadata attributes The optional attributes follow the structure layed out in Sec. FIXME  and can consist of the following elements: New optional meta data attributes from the dictionary can be added to the individual lines. Rotation metadata attributes The optional attributes follow the structure layed out in Sec. FIXME  and can consist of the following elements:
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 </code> </code>
  
-==== Uncertainty data for rotations ====+===== Uncertainty data for rotations =====
  
 The Hellinger method allows to compute statistical uncertainties for rotations, representing them as a series of parameters and a 3D-covariance matrix. Hellinger Statistics attributes for individual rotations The Hellinger method allows to compute statistical uncertainties for rotations, representing them as a series of parameters and a 3D-covariance matrix. Hellinger Statistics attributes for individual rotations
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 </code> </code>
  
-==== Bibliography information ====+===== Bibliography information ===== 
 + 
 +Each rotation file should come with a companion bibliographic reference database which maps ''@REF''-Keys to DOIs or citations. 
  
-Each rotation file should come with a companion bibliographic reference database in the ascii-based [[http://www.bibtex.org/Format/|BibTeX format]], see [[software:gplates:grot:start|GROT: A new rotation file format for GPlates]]. The choice for BibTeX is driven by the fact that the format is text-based, accepted as one of the bibliographic data standards and many software tools allow to either directly use this format (BibDesk, JabREF) or import/export it (e.g. Endnote). At a future data the bibliographic information can possibly be incorporated consistently into the rotation file format without the need for two separate files.+Through the ''@BIBINFO:bibfile'' mapping a bibliographic data base, e.g. in [[http://www.bibtex.org/Format/|BibTeX format]]. The choice for BibTeX is driven by the fact that the format is text-based, accepted as one of the bibliographic data standards and many software tools allow to either directly use this format (BibDesk, JabREF) or import/export it (e.g. Endnote). At a future data the bibliographic information can possibly be incorporated consistently into the rotation file format without the need for two separate files.
  
 Online resources: Online resources: