June 2004 Newsletter (Number 04/04)

GIS interface: Doug F. and Pat have been working on CHRONOS?s GIS interface with help from graduate student Hsin-I Yu. Special thanks go to Daryl Herzmann (ISU - Iowa Mesonet project) for his assistance. This is a work in progress and you can view the current version as it interfaces to Neptune at http://test.chronos.org/gis/ - select master.map. Pat has worked out some searches that are currently being implemented and Doug is working on the connection between this interface and the taxonomic information in Brian Huber's dictionary that will soon allow users to search for taxa and view the information in the dictionary from the same interface.

"First three": Doug G. has completed the connection between Neptune, PaleoStrat, and PaleoBiology. A PostgreSQL driver that runs version 3.00 of the ODBC protocol was built and installed with DB2. This allows fully functional operation of the Neptune database with Information Integrator. After some difficulty due to firewall issues, a connection between SDSC and the Paleostrat database has been established. Progress has been made on building an Information Integrator compatible, MS SQL-Server driver for this database, however some work remains before it is fully operational with II. Additional updates can be found at the wiki.

Ontology: A CHRONOS ontology generation system was designed, written and debugged by Doug G. This provides a mechanism to specify the connections and relationships between several independently developed databases. Related data items from different source schemas can be integrated by describing the typed relationships between the data objects. In developing the ontology, W3C standards were used, in particular the Resource Description Framework (RDF) and the Ontology Web Language (OWL). A Java program translates metadata about the databases, along with a simple XML file containing relationship information, into a correctly formatted RDF/OWL file.

The RDF Schema specification contains constructs that can be used as a standard mechanism for binding database columns to references or English language definitions. These constructs thus act as a bridge between the machine-readable data contained in a database and the human readable knowledge contained in the scientific literature.

If the database metadata are precisely specified by the ontology references, then the necessary conversions and other operations are defined implicitly. Thus a program that can read and parse the ontology can automatically perform operation on otherwise incompatible data representations. Updates and additional information can be found on the Wiki page: Ontology

Interface Control Document (ICD): The critical issue of Interoperability among the various geoinformatics project was discussed at the 'Linking Information Systems in Marine and Terrestrial Geosciences; Sediment Geochemistry' workshop by John Helly (SDSC). You can view the draft of CHRONOS ICD document at the wiki Doug F. is working on an animated diagram that visually shows links and ICD for the Earth science cyberinfrastucture. It will be made publicly accessible in July.

Mesozoic planktonic foraminifera online taxonomic dictionary: Brian Huber and his colleagues of the Mesozoic Planktonic Foraminifera Working Group are working to enter new data (taxonomic information and images) and edit the current content of the online dictionary. The database and interface to the dictionary, put on line by Liying Lin and updated after the workshop by Doug F., can be viewed and searched here

Time scale conversion tools: In addition to the Cande and Kent (1995), aka Berggren et al., 1995 time scale, we have developed a conversion tool for the Global Time Scale of Harland et al., 1989, and the Australian Geological Survey (AGSO) 1995 time scales. They can be accessed at Chiron
Stephanie Schueller has digitized boundary information on several other time scales with data provided by Jim Ogg (from the 2004 GTS book - from Holmes 1937 to DNAG 1983). They will be online soon.

CHRONOS PIs are required to submit an annual report by mid June using NSF's FastLane reporting system.

Personnel: We have received 28 applications for the position of XML-Java programmer for CHRONOS Central Hub. We will be interviewing the short-listed candidates during the week of June 21. We are also in the process of hiring a part-time administrative assistant to help with the accounting duties related to CHRONOS activities. The selected person is going to start mid July.

The steering committee members elected Cinzia C. to be CHRONOS Executive Director.

The next newsletter (July/August 2004) will appear before the end of July.

The 'Mesozoic Planktonic Foraminifera Working Group meeting', (Smithsonian, Washington DC.) organized by Brian Huber and sponsored by CHRONOS took place on May 20-22. It was attended by 14 foraminifer paleontologists from nine different countries for the purpose of revising and completing an Image Atlas of Mesozoic Planktonic Foraminifera for online public access by Summer 2005 on the CHRONOS services web site. Conceived and developed at the Smithsonian, the Mesozoic Atlas is a relational database with over 300 senior synonym species records that include original and emended species descriptions, morphologic descriptor fields, biostratigraphic range information, images of the species holotypes (many with new SEM images obtained at the NMNH SEM lab), and SEM images that illustrate the morphologic variability of the species concept.

The 'Geochemical Cycles workshop' is going to take place in San Antonio, TX (June 25-26, 2004 - organizers: Ethan Grossman, John McArthur and Cinzia C.) For information, consult the workshop's web site

A CHRONOS workshop on 'Mesozoic and Cenozoic paleoceanography' is being organized by Ben Flower in St. Petersburg, FL. (October 27-28, 2004). A workshop web site will appear on the CHRONOS web site during the summer.

The Second CHRONOS retreat is going to take place in Ames on August 2-3. It will be followed by NSF site review on August 4. Steering committee members will be present at the site review. Information on the logistical details of the retreat is available here.

32nd International Geological Congress, Florence, Italy, Aug. 20-29, 2004. Jim Ogg, Bruce Wardlaw and Cinzia C. will give talks and demo CHRONOS at ICS's booth.

8th International Conference on Paleoceanography in Biarritz, France from 5-10 September. Brian Huber is presenting a poster for CHRONOS.

Geological Society of America Annual Meeting, Denver, Colorado (Nov 7-10, 2004). CHRONOS steering committee and advisory board meetings tentatively scheduled for Nov 5 and Nov 7. CHRONOS has a booth (#900) and sponsors topical session #112 (oral and poster): "Geologic Time and CHRONOS: Databases, Tools, Outreach, Education, and the Geoinformatics Revolution" (Convenors: Cinzia Cervato and Walter S. Snyder). The abstract submission deadline is July 13. Keynote speakers are: Mike Benton (Bristol Univ.), Kenneth J. Hsu, Margaret Leinen (NSF), and W.B.F. Ryan (Columbia Univ.).

North American Paleontology Convention, Halifax, NS, Canada (June 19-26, 2005) Web site. Symposium on: The first step towards the development of taxonomic dictionaries for all Phanerozoic organisms (Convenors: Cinzia Cervato, ISU, and Richard Lane, NSF).

The kickoff meeting of CHRONOS Australia at Macquarie University (Sydney) was very successful. It was attended by scientists from Geoscience Australia, New South Wales Geological Survey, CSIRO, and Macquarie University. Cinzia C. made presentations to the group and the department of Earth sciences.

CHRONOS Europe: A meeting with scientists and representatives from European funding agencies, organized by H. Richard Lane, will take place in Florence on August 20. Cinzia C. will represent CHRONOS at the meeting.