 |
|
|
|
        |
|
||
MagIC Help Library |
|
|
|
 |
|
|
|
|
|
|
|
|
|
||
MagIC Help Library |
|
|
|
|
|
|
|
1 Introduction
1.1 Preface
The Magnetics Information Consortium (MagIC) initiative has been established to address the need for a public digital archive for the international magnetics research community. As a multi-user facility MagIC provides a place for the community to archive new data as soon after their collection as reasonable, preferably at the time of publication in the peer-reviewed literature. These data are stored in and served from an Oracle 10x database that is part of the overarching online EarthRef.org database, while software tools are provided to help the scientist in preparing data for automated uploading. The MagIC Databases Team already has transferred the data and metadata of existing magnetic databases (GPMDB, PINT, etc.) created under the auspices of IAGA into the MagIC database.
The databases of the Magnetics Information Consortium (MagIC) thus contain user-contributed data associated with paleomagnetic and rock magnetic sources. Data may be part of data published in Earth sciences journals, theses or books. These data are contributed on a Publication-by-Publication basis and in the form of two corresponding MagIC Format ASCII Text (*.txt) and Microsoft Excel© SmartBook (*.xls) files created by the MagIC Console Software. These SmartBook files are uploaded into the MagIC database by using the MagIC Contribution Wizard.
1.1.1 Goals and Philosophy
The overarching goal of the Magnetics Information Consortium (MagIC) is to develop and maintain databases and associated information technology for the international paleomagnetic, geomagnetic and rock magnetic community. MagIC is hosted under the umbrella of EarthRef.org allowing coordination with other information technology initiatives in the Earth sciences, such as GERM, SBN and ERESE. This facilitates interdisciplinary research, by allowing ready access to relevant information in related disciplines. MagIC serves the larger scientific and educational community by making its databases freely accessible and by providing visualization tools designed for users with various levels of expertise.
The PMAG Portal and the RMAG Portal (still under development) form the access points to a new generation of community-based paleomagnetic and rock magnetic databases. These web portals share the same underlying MagIC Data Model, allowing for searches and access to information in both databases. Users can upload their own data (for free) using the standard MagIC Metadata and Data Model available online as long as these uploads are associated with a citable publication and the user have registered. Substantial effort has gone into making the data model flexible enough to accommodate the broad range of data collected in rock and paleomagnetic studies. Where feasible, contributors are encouraged to upload all their measurements and descriptions of lab procedures, in addition to their higher level (published) results. Digital information that does not fit readily into the MagIC always can be uploaded and archived in the ERDA online archive.
MagIC is managed with the help of in particular a Steering Committee and a Metadata and Method Codes Committee that both have a wide representation from the paleomagnetic and rock magnetic research community, nationally and internationally. MagIC also promotes a community dialog on how modern paleo, rock and geomagnetic databases should evolve, and what online tools are needed for data analysis. The dialog includes sponsoring discussions at workshops and promoting special sessions at scientific meetings. MagIC has evolved substantially since its inception at the PMAG Workshop held in March 2002 at Scripps Institution of Oceanography in La Jolla.
From the start MagIC has been incorporating PMAG data from the IAGA databases, namely GPMDB, PINT2003, TRANS, PSVRL and SECVR. However, the new data model allows contributors to archive more information than before, and provides ready access to the data online without the need to resort to commercial database software. RMAG is the first attempt to generate a database of rock magnetic data.
1.1.2 User and Data Policy
All data in the MagIC database are User-Contributed and uploaded on a Publication-by-Publication basis. The MagIC database primarily contains Activated Contributions from Peer-Reviewed Publications and Student Theses, including those In Press. These uploads are available to the entire MagIC userbase and are permanently archived under a strict version control. The various user actions, contribution types, levels of data ownership and data deletions are explained in detail below.
All database contributors and users are to adhere to the EarthRef.org Copyright Policy.
Data sets for publications In Preparation or In Review can be uploaded as Private Contributions Only and can be accessed by the data owners alone. These Private Contributions optionally can be set up by the data owner to have Group Access allowing select groups of users to access such hidden MagIC data sets with a group name and password.
Unpublished Data Sets that cannot be published (elsewhere) in the peer-reviewed literature can be uploaded into the MagIC database as an EarthRef.org Data Publication. These uploads should be accompanied with a list of authors, affiliations, a title, a short abstract and a technical note that describes the analytical methods applied. These publications will be assigned an EarthRef.org DOI and their citation will be permanently stored in the EarthRef.org Reference Database.
Activated Contributions will undergo Data Reviews by editors and referees representing the international paleo- and rock magnetic research community. These Data Reviews are meant to help improve the quality of the data uploads and are not meant to critique the science and conclusions presented in the publications.
Data owners can manage a contribution to the MagIC database in three different ways:
Once a contribution has been uploaded into the MagIC database, the data owner can restrict its access or provide open access to the world, again in three different ways:
There can only be one data owner per contribution. However, data ownership can change based on the following hierarchy:
Activated Contributions cannot be deleted by the data owners. Private Contributions remain in the database until the data owner replaces it with an activated update or activates an existing private upload. If a private contribution has been Inactive for more than 2 years it will be removed from the data holdings by the MagIC Database Team.
The MagIC Database Team reserves the right to delete any Incorrect or Fraudulent Contributions without any further notice.
Each Activated Contribution will be assigned a Data Editor, who will select at least one Referee to review the data contribution for its correctness, completeness and clarity only. These reviews are meant to help improve the quality of the uploaded data in the MagIC Database. However, these reviews explicitly are not concerned with the science and conclusions presented in the publication.
Once the data review(s) are complete, the data owner should prepare an update of the data contribution and upload this as soon as possible into the MagIC Database. All activated versions of these data contributions will be retained in the database, will receive a time stamp and version number, and can be retroactively included in database searches.
1.1.3 MagIC Database Team and Committee Structure
The MagIC Database Team is responsible for the development and maintenance of the MagIC Database and Website. This team exists of the principal investigators, associated researchers, software engineers and undergraduate students.
The Steering Committee is intended to determine the direction to be followed in the development of paleomagnetic and rock magnetic databases, and includes broad international representation from the overall magnetics community as well as people involved in database development in related fields of Earth sciences.
Metadata and Method Codes Committee
The charge for the Metadata and Method Codes Committee is to engage in continuing broad consultation with the magnetics community on the kinds of information that need to be preserved in magnetic databases, and develop an appropriate metadata template for use in paleomagnetic and rock magnetic databases. In particular, it will be necessary to develop metadata structures that can be effectively exploited for existing lines of research while preserving the flexibility for accessing information required to develop new research ideas. The results of such consultation should then be incorporated into a metadata structure, which will be reviewed by the Steering Committee and presented to researchers in the international community for comment prior to finalizing the database structure. This committee will also be in charge of adding and editing the required method codes and controlled vocabularies.
Editorial and Review Committee
The charge for the MagIC Editors is to oversee the review process of all data submissions into the MagIC Database. They will assign each data contribution to any of the potential reviewers that also may include members outside of this committee.
Geological Timescale Committee
The charge for the Geological Timescale Committee is to work towards a nominal timescale to be used in the MagIC Database and will enhance its search capabilities and helps in the interpretation and compilation of disparate data sets.
The charge for the Paleolocations Committee is to work towards a nominal plate motion model through geological time to be used in the MagIC Database and will enhance its search capabilities and helps in the interpretation and compilation of disparate data sets.
1.1.4 History and Timeline
MagIC evolved from the PMAG Workshop held at Scripps Institution of Oceanography in La Jolla, from 24-26 March 2002. The Abstract Volume for this workshop is available online. At this workshop it was agreed that there is a critical need to update and integrate existing magnetic database efforts sponsored by IAGA to take advantage of the technological advances provided by modern web-based data handling capabilities. In September 2002 a small workshop was held at the Institute for Rock Magnetism at the University of Minnesota to discuss the new design of a new rock magnetic database and its integration with the efforts discussed at PMAG2002. A short report is published in EOS and is available online.
Three development stages mark MagIC's short history. In Phase I we focused on an internal review of the MagIC Data Model, the design of the Oracle 10x Database, the design of the SmartBooks, the coding of the MagIC Console Software and extensive testing. Also the PmagPy data analysis software was developed allowing scientists to translate paleomagnetic measurement data into the MagIC format. In Phase II we started to focus on the design and implementation of the Online Drilldown Interface, to populate, maintain and optimize the MagIC Database, and to implement Advanced Visualizations in the MagIC web portals. Currently we are in Phase III whereby we are planning to implement an Editorial and Reviewing System, we will start to use predominantly Flash, Web 2.0, AJAX and XML in our web and database interfaces, and we will start to work toward full Interoperability with other online databases using Webservices.
1.1.5 Acknowledgements
This Help Library is a public domain document to support the Magnetics Information Consortium (MagIC) in its efforts to promote and facilitate an Information Technology (IT) Infrastructure for the international paleomagnetic, rock magnetic and geomagnetic community. This document came together as a result of discussions between the members of the MagIC Steering Committee and MagIC Metadata Committee formed during the first PMAG Workshop held in La Jolla (USA) in March 2002. It is being updated continuously to make certain that all tools and software can be easily used without too much guidance. To view who is involved in the MagIC consortium, please visit the http://earthref.org/MAGIC/whoswho.htm website.
MagIC is supported by NSF Grants EAR03-18672, EAR07-44107 and EAR07-44108.
1.2 Getting Started
1.2.2 Become a Registered EarthRef.org User
To register click on the Register link in the Topmenu of the EarthRef.org website. If you have forgotten your password or username, please go to the http://earthref.org/databases/ERML/ webpage or click on the Forgot Password link in the Topmenu. Twice a year you will be sent a Reminder Email with all registration info and a simple link to edit your user profile.
Registration is required if you want to upload your data into the MagIC database. In return, you will be informed of new features on the website, software updates and other information related to the MagIC initiative through Bi-monthly Newsletters and other email alerts. Searching and downloading data from the database does not require an user name and password.
1.2.3 Reviewer and Editor Responsibilities
A reviewer of a MagIC database contribution is responsible for comparing the uploaded data to the data in the corresponding paper and commenting on any errors or omissions. An online review system is available to help reviewers with this task.
First the reviewer checks the reference to make sure it is correct and complete. Next the reviewer checks the various tables that have been filled out in the smartbook by the contributor. Tables with location data present the reviewer with a map so they can quickly check if the location is correct. Then the reviewer checks the method codes used by the contributor and verifies that they are correct and not missing significant descriptions of the data. Finally the reviewer writes any additional comments to the contributor and marks the review complete.
An editor for the MagIC database is responsible for overseeing the reviewing of new contributions to the MagIC database. The editor will be able to delegate the review process of new contributions to reviewers or review the contributions themselves. Reviews should be done in a timely manner. About a month to review a contribution is an appropriate timeline.
1.2.4 Online Search Features and Data Uploading
Two separate web portals have been developed within MagIC for Paleomagnetism (PMAG) and Rock Magnetism (RMAG). Both interrogate the same underlying MagIC and EarthRef.org databases. This ensures that the search forms for typical paleomagnetic and rock magnetic searches can be kept simple and transparent. However, it does not prevent paleomagnetists from performing rock magnetic queries when searching within the PMAG Web Portal, and vice versa, when starting out from within the RMAG Web Portal. By design each portal is merely a different entry point into the same database.
To search from within the PMAG Web Portal follow the http://earthref.org/MAGIC/search/ link. Here we provide you with search options of location, data type, geological age and reference. You can also do map searches using the Map filter. Each of these searches give you a simple first page from which you can drill down all the way to the measurement level. An advanced search lets you perform more complex searches, including custom Boolean expressions.
Once the RMAG Web Portal is active, to start the RMAG Web Portal follow the http://earthref.org/databases/RMAG/ link. From this web page you can perform simple searches based on experiment type or condition, sample type and reference. Again, in each search you will be allowed to drill down to the measurement level, and an advanced search option lets you perform more demanding search tasks.
The Online Upload Wizard has been developed to help you upload your own data. Uploading can be started by following the http://earthref.org/MAGIC/upload.htm link. The only requirement here is that you are a Registered EarthRef.org User. Uploading data can typically be completed in less than 5 minutes, depending on the number of data records involved. The Online Upload Wizard will ask you to log-in under your EarthRef.org Username and to upload two files (a Microsoft Excel© file and an plain text version of the same file) that were automatically generated by processing your data with the MagIC Console Software. These two files will be archived in the EarthRef.org database while the data and metadata they contain will be parsed into the MagIC database.
This data uploading naturally complements the scientific process of preparing your data for submittal to any Earth science journal. Because you can upload your data into the MagIC database while keeping it Private (as described in the User and Data Policy) you can use all visualization tools on the MagIC website to study and analyze your data, either on their own right or in combination with data already available in the database. You can also make your data Group Accessible by assigning a group name and password that you personally can give out to your colleagues, co-authors and reviewers. All in all, this approach gives you a multitude of flexibility in working with your paleo and rock magnetic data. When you're ready you can Activate your private contributions and make them Publicly Available to other MagIC and EarthRef.org users.
1.2.5 The MagIC Console Software
Getting your data organized, complete and ready to submit for either a paper publication or ingesting into a database is a time-consuming job. We have developed the MagIC Console Software to aid you in your collation of paleo and rock magnetic data and to make the data ready for upload in the MagIC database. Visit http://earthref.org/MAGIC/software.htm to download the Latest Software Version.
1.2.6 Hardware and Software Requirements
Browsers and Screen Resolution
This site will work with all modern browsers, such Microsoft Internet Explorer, Firefox, Safari and Chrome. To use many of the functions on this site, your browser should have JavaScript and Cookies enabled. A minimum screen resolution of at least 1024 x 768 is also recommended.
In order to view PDF (Portable Document Format) files accessible from the EarthRef.org and MagIC websites, you will need Adobe Acrobat Reader© that is available free for download at http://adobe.com. Some downloadable files from the EarthRef.org databases are available as compressed ZIP archives. These archives require the use of WinZip© for Microsoft Windows© users or Aladdin StuffIt Expander© for Macintosh© users to unzip them.
The MagIC Console Software program is coded in Visual Basic for Applications© in Microsoft Excel© and has been tested under Microsoft Windows© 2000/XP/Vista and Macintosh© OS 9.0/X. It is recommended that you run this software on 500 Mhz computers with at least 512 MB of RAM and 1024x768 native screen resolutions. Empty MagIC SmartBooks start at ~200 KB in file size, but increase to several MB's depending on the number of data records included.
1.2.7 Software Updates
Regular Software Updates will be published on the MagIC website. Each update will receive its own Version Number that will be stored in the MagIC SmartBooks as well. If your SmartBooks have an older version number, these files will be automatically updated the next time you open one with the MagIC Console Software. The newest software distributions are always available from http://earthref.org/MAGIC/software.htm. If you use the MagIC Console Software on a computer that is also connected to the Internet and it is outdated, you might be shown a message at start up that a newer version of this software is available for downloading from the MagIC website.
1.2.8 Important MagIC Website Links
1.3 Getting Help
In this Help Libary you will find detailed explanations on what Database Searches can be performed, how to Upload Your Own Data and how to use the MagIC Console Software to prepare your data for uploading. However, you will also find information on the MagIC User and Data Policy, the current Committee Structure, lists with Terminology and Definitions used in MagIC, and so on. Use this library when you run into problems or when you have questions. If you cannot find a good answer, please don't hesitate to Contact Us!
1.3.1 How to Use This Help Library
When using the MagIC Website you can always get help by clicking on the Help Tabs that appear in all the online search forms.
In a similar fashion you can get help by clicking on the Help Buttons (with the big question mark in it) in the MagIC Console Software. All Dialogboxes and Error Messages in this software package will provide you with one of these buttons.
These Help Tabs and Help Buttons will give you context sensitive help for each step in the online search forms or the software you are using. By clicking on these tabs or buttons a new browser window will open in which a particular page from the online MagIC Help Library is loaded. The shown help page explains in some detail what the current page is about, what your options are and what to do in order to proceed. Help subjects also include Error Messages that you may receive when searching on the web or when using the software. Each help item also contains a See also list of related files at the bottom of the page.
If you find that the help pages do not answer your question or help resolve your problem, please click the Feedback link to let us know how we can improve the help files system to serve you better. You can always Contact Us directly via email!
1.3.2 Contacting the MagIC Database Team
Chair of the MagIC Steering Committee
Institute of Geophysics and Planetary Physics
Scripps Institution of Oceanography
University of California, San Diego
La Jolla, CA 92093-0225, USA
1-858-534-3183 (office phone)
1-858-534-5332 (fax)
cconstable@ucsd.edu
EarthRef.org Database Manager and Webmaster
Developer MagIC Software Console
Chair of the MagIC Metadata Committee
College of Oceanic & Atmospheric Sciences
Oregon State University
104 COAS Admin Bldg
Corvallis, OR 97331-5503
1-541-737-5425 (office phone)
1-541-737-2064 (fax)
akoppers@coas.oregonstate.edu
Developer MagIC Python Software
Geological Research Division
Scripps Institution of Oceanography
University of California, San Diego
La Jolla, CA 92093-0220, USA
1-858-534-6084 (office phone)
1-858-534-0784 (fax)
ltauxe@ucsd.edu
See also ...
Contents MagIC Chapter 2 MagIC Website Chapter 3 MagIC Console Software Chapter 4 Importing Data With PmagPy and MagIC.py Chapter 5 MagIC Glossary
|
|
|