	2005 LTER Information Managers Meeting
		August 4-7, 2005 in Montréal, Canada
	"Enabling the LTER Decade of <Synthesis/>"

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LTER Site: Andrews LTER

Contributor: Suzanne Remillard and Don Henshaw (Aug 02, 2005)

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Information Management (IM) folks at the Andrews Experimental Forest have spent the past year preparing for the mid-term review. We are pleased to announce that we had a very successful and positive review in mid-July. Our Information Management System was emphasized as one of the exemplary pieces to the Andrews LTER. Descriptions of our system are online at http://www.fsl.orst.edu/lter/research/component/infomgt.cfm?topnav=63

The IM team is led by Don Henshaw who has been heavily involved with cross-site synthesis and network-level efforts, and has also guided site preparation for the mid-term review. Gody Spycher continues to populate our SQLServer metadata database with remaining core and other legacy databases, develop programs for QA and other maintenance functions, and work with scientists to cleanup and analyze data. Gody plans on retiring within the next year, and we will begin to strategize about IM at the Andrews without Gody. Suzanne Remillard is recently hired as the Andrews LTER Information Manager and will begin taking over duties from Gody. Suzanne continues as the database administrator for the combined ClimDB/HydroDB effort, and actively maintains our web pages and attends to many data processing and IM tasks. Theresa Valentine continues to work with spatial data and is incorporating the HJ Andrews LTER spatial data into our general data catalog Theresa has also received seed money from Forest Service R&D to continue development of WatershedDB, a collection of spatial data for HydroDB sites including research area and watershed boundaries, gaging station locations, stream networks, and DEMs. Theresa also published a new, updated Andrews Experimental Forest map (http://www.fsl.orst.edu/lter/about/site/map.cfm?topnav=157).

Andrews Databases Online / EML: We currently have 130 databases (metadata and data) online and available. This includes over 500 data tables. Of these databases, 18 are spatial databases, with 50 more in preparation (300 coverages / Shape files). Our maintenance tasks are heavy, with over 100 tables updated annually. In addition, we receive about 10 new databases per year. We have only 6 databases left to migrate to SQLServer and an additional 40 legacy databases not online (to be migrated too). Our metadata database dynamically generates EML, and also produces downloadable PDF files for each study database. We are now contributing EML to the LTER Metacat through dynamic harvest list and EML generation scripts. Our next major focus is to review our EML with respect to accepted syntax and best practices, and revise our EML generation accordingly.

Reservation program: Gody and Suzanne have developed a new reservation system for the Andrews field station. This system not only enables the tracking of users, but also allows for the management of billing. There is also an online reservation request form.

Andrews goes wireless and adds spread spectrum telemetry
Fred Bierlmaier, the on-site Andrews system administrator, maintains the site Local Area Network (LAN), local web server, wireless LAN, digital radio and spread spectrum telemetry networks, telephone communications, and local personal computers. Fred recently installed the wireless LAN which links the dormitories, cafeteria, shop, and director's residence to the wired LAN with a wireless bridge. Wireless access points are also installed in the conference hall and throughout most of the compound, and access points are planned for the classroom and library. A telemetry system based on 900 megahertz spread spectrum radios was installed in 2004 to access specific study data coming from data loggers on a nearby watershed.
LTER Graduate Student Collaborative Symposium: The first LTER Graduate Student Collaborative Research Symposium was held on April 13th through the 17th at H. J. Andrews LTER. This symposium was created in order to facilitate future graduate student interaction and participation in the broader community of LTER scientists, as well as to stimulate graduate student engagement in comparative and collaborative research efforts. There were a total of 66 graduate students representing 24 United States LTER sites and 11 students from international LTER sites (representing China, Mongolia, South Africa, Austria, Czech Republic, Brazil, Mexico and Switzerland). There were also 2 invited speakers (Dr. Whendee Silver and Dr. Scott Collins), 2 post-docs, 1 undergraduate, and multiple LTER information managers in attendance. Overall, there were 71 presentations (including LTER site review presentations and personal research presentations) and 13 training and collaborative workshops. The workshops in addition to being very informative also sparked at least five long-term cross-site collaborations. These collaborations are using long-term datasets that are available from LTER sites and will be used for cross-site comparison and eventually appearing in peer-reviewed publications. The most rewarding aspect of the event at its close was the feeling that we are not simply working at individual LTER sites but that we are all part of a large and warm community—an LTER network.

LTER Site: Arctic LTER

Contributor: Jim Laundre (Aug 03, 2005)

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The Arctic LTER now has all of it legacy metadata converted to EML. With the help of Duane Costa, Mark Servilla and Inigo San Gil we have successfully converted the structured text files to level ~ 2.5 eml and harvested the files to metacat. One more revision will be done to add a complete title to the files. Our original metadata files did not have titles and the current eml files use the file names as titles. Moving forward we are developing an Excel entry sheet for entering metadata information. The metadata sheet can be copied into to the researcher’s excel workbooks and included with their data. An Excel VBA macro will be used to output an eml file.

The current field season is going well. Spring was early with ice cover on Toolik completely gone by June11th. July has been cool with some occasional snow. This year there will be power and internet connection during the winter months at Toolik Station. With year-round power we have made the current weather data available online, which can be viewed at http://ecosystems.mbl.edu/arc/ .

LTER Site: Baltimore Ecosystem Study

Contributor: Jonathan M. Walsh (Aug 03, 2005)

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BES Site Byte 2005-08-03

Jonathan M. Walsh

- We are approaching 5 years of online stream chemistry, and 4 years of online bird survey data
- We have EML level one capability. We have not reached level one compliance just yet because we wish to devise a means to ensure revision level control for our metadata before we expose it to the internet.
- We have a geodatabase running. It utilizes arcsde and db2 running on Linux.
- Metadata stored on our rdbms system will automatically populate our static “Data for download” page.
- We have begun designing experiments relating to urban design and the ecosystem and have formed an Urban Design Working Group.
- The third Vital Signs publication has been released. Brought to you by the Baltimore Neighborhood Indicators Alliance, the publication takes the pulse of Baltimore utilizing 40 indicators. The indicators fall into seven main categories ranging from housing, sanitation, and safety to workforce, health, environment, and child well-being. The Vital Signs are also featured in the Baltimore Sun every Monday. (See www.bnia.org)
- Watershed 263 Survey: We are surveying all BES-Affiliated researchers to gain information that describes the breadth of our research connected to Watershed 263. (Watershed 263 is a watershed comprised wholly by man-made waterbodies and has no “natural” water body) An online survey was developed for this purpose.
- Data management survey: A survey to study data management activities among BES researchers was completed. Results are forthcoming.
- BES Publications online: The BES publications have been imported into a database and are now searchable online. See http://www.beslter.org . There is a button on the top to access the publications database.

LTER Site: Bonanza Creek LTER

Contributor: Brian Riordan (Aug 01, 2005)

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It has been a busy half a year at BNZ. I took over the reins as Data Manager on Dec.1st. Since then I have redesigned our database for a flat file mysql database to a relation database supporting views, triggers, and stored queries. In addition, we rebuild the servers to have up to date hardware and software. I have taken all of the old ascii dataset and generated mysql tables for each one. This will allow us to generate complex searching capabilities as well as ensure better data-backups. We have installed a robust back-up unit that now backs up our servers as well has the majority of the BNZ staff.

We are in the process of generating full PDF’s of our publications as well as deploy a more error free searching format for locating publications.

The next step is to redo our Coldfusion queries to generate results form the new database.
In addition, we are exploring the best way to generate our EML out of this new format. Currently we have little to no metadata in EML format. I have handed out the Excel worksheet that FCE created and the PI’s have responded well to it.

All in all it has been a year of learning for me. I have gained a lot of knowledge about the BNZ database/website as well has how to make it better. The next year will be focused on deploying the database and generating EML for each data file. If this EML will be generated dynamically or stored as hard files is still to be decided.

See everyone soon!

LTER Site: California Current Ecosystem

Contributor: Karen Baker (Aug 27, 2005)

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In its first year as an LTER site, the CCE information management effort focused on building technical, organizational, and social infrastructure. The use of mail, storage and server facilities are coordinated centrally within the Integrative Oceanography Department at SIO/UCSD. Participation in an Ocean Informatics Environment is providing a contemporary approach to training as one dimension of design team and working group activities.

Initial projects included design of a web site (http://ccelter.sio.ucsd.edu) and establishment of the LTER network virtual pointer (http://cce.lternet.edu). A new shipboard organization scheme has been deployed, centered around event numbers as a long-term integrative element. Work to establish dictionaries and controlled vocabularies is proceeding in parallel with design of metadata forms. From discussions, an emerging common language includes critical informatics terms such as data types, core data, metadata, and integrative indexes. A site software and data survey is being conducted as a part of the process of establishing a culture of LTER data practices. This represents an opportunity for learning about existing data handling within local environments.

Collaborative local activities included coordination with the Palmer LTER, the Southern California Coastal Ocean Observing System (SCCOOS), the Palmer LTER and the California Cooperative Oceanographic Fisheries Investigations (CalCOFI) program which provides an ongoing 50 year field time series for a grid encompassing the CCE sampling lines as well as with the Palmer LTER. As LTER Network participants, we contributed to several working groups at the 2005 annual IM meeting: Dictionary Process Unit Repository; SiteDB and Web Design; and Community Process. In collaboration with science studies participants, we are working to open up discursive data practices and technical perspectives by incorporating collaborative design as one element of focus for a comparative environmental research study. We are using this approach as a powerful tool to address immediate needs and choices within information management in general and standards’ development in particular.

LTER Site: Central Arizona - Phoenix

Contributor: Corinna Gries and Peter McCartney (Aug 08, 2005)

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This year at CAP the main web site saw some improvements and additions. Overall programming changes were implemented to increase the speed at which database searches retrieve and display results. CAP’s new ‘Integrated Project Areas’ are described and associated subprojects and people are displayed in the same way as LTER core areas. An image library with search interface was added and currently we are working on a CAP sites atlas. An application built on ArcIMS/html viewer that allows users to display a map with the locations of all sites at which research activities are taking place within the CAP area. This will enable the user to locate sites at which for instance all long term monitoring programs are currently active. With appropriate background layers other questions may be answered, e.g. in which watershed a site is located or which soil conditions are prevalent at a certain site, etc. This application was developed in collaboration with the ASU GIS lab.

However, the main thrust this year was finishing the programming for an intranet (http://iis.asu.edu/intranet). This web application allows CAP researchers in a secure environment to enter and edit their personal information, their publications, calendar events, information on datasets they are producing, and information for each subproject. For each subproject beginning and end, a short description, associated people, and an annual report can be entered. Although we are still working out bugs this application has been successfully employed to gather information for this year’s annual report to NSF. With this year’s experiences further improvements, especially in the area of editing and bulk uploading of publications will be implemented next year.

The Center for Environmental Studies, where CAP LTER is housed, became the International Institute for Sustainability with a large private endowment to help promote ASU's development of a strong research and educational mission in sustainability.

ASU was awarded a 5 year grant for the "Decision Center for a Desert City". This project compliments CAP LTER by providing a strong outreach to the decision-making community in central Arizona. Funded by the NSF Decision Making Under Uncertainty program, the project focuses on the social and ecological issues surrounding long -term water management in the Phoenix basin. Plans are under development this summer for a tri-university partnership in a distributed water information system which will expand the core data archive that was started by CAP LTER to a state-wide integrated system.

IIS completed its NSF ITR project "Integrating Urban Models Through Network Services". This project focused on developing solutions for integrating distributed models maintained by different research and management institutions within the valley. The project developed web service wrappers to Grass and R software packages, web interfaces for model execution requests, extensions to EML metadata for documenting model inputs and outputs, and a set of actors for Kepler designed to interface with our Xylopia web services. Development started under this project will continue as part of the DCDC project.

IIS Informatics lab collaborated with our Departments of Anthropology and Computing Science on a successful NSF Human and Social Dynamics proposal on developing a national cyberinfrastructure for Archaeology. This pilot project supported a workshop at NCEAS in December which had participation from SEEK and GEON personnel, plus a small pilot study using OWL ontologies to guide automated reclassification of archaeological datasets. A larger proposal is now being considered by the NSF CyberTools program which, if funded will allow IIS to expand and refine the work we have done with EML, Xanthoria, etc to a broader disciplinary base.

Robin Schroeder (whom many of you know as Robin Schoeninger) has taken a position as assistant curator for the ASU lichen herbarium and data manager for all ASU natural history collections. She will continue to collaborate with our lab helping to maintain and expand our internet biodiversity applications. An advertisement for a new programmer position at IIS will be forthcoming.

The ASU GIS lab has moved to a new home with the ASU Institute for Geography. Again, we are expecting the fruitful collaboration to continue.

LTER Site: Coweeta LTER

Contributor: Barrie Collins (Jun 20, 2005)

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Coweeta LTER IM will be part of our mid-term review June 28-29, 2005. The past year has been a continuance of our infrastructure development. Key accomplishments include bringing online 1100 publications (full pdf form), internet map services, GIS for the entire southern Appalachian study region, as well as full participation in EML and the Metacat Data Harvester.

Our focus in the coming year(s) will be to continue to link data, publications, research, researchers, and spatial data to increase the stream of information. Navigational structures have been brought into the 21st century as we endeavor to understand how to serve a very deep web site to a varied user base efficiently and effectively.

That's about all for now, I reckon.

Barrie

LTER Site: Florida Coastal Everglades

Contributor: Linda Powell (Aug 03, 2005)

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Over the past year, Linda Powell (information manager) and Mike Rugge (project manager), have concentrated their efforts on several important components of the Florida Coastal Everglades (FCE) LTER program’s information management system: 1) designing and implementing a new tool to capture EML, 2) expanding the Oracle9i Database and 3) upgrading the FCE web page.

One our site’s of the most significant accomplishments has been the creation of a new EML tool called ‘Excel2EML’. Since the inception of the FCE LTER, comprehensive metadata for each dataset has been entered into an Excel metadata template by our individual researchers. The challenge for the FCE was to find a way to capture EML compliant (tier 4 or 5) metadata using the Excel spreadsheet format our researchers were happy using and to convert it to a valid EML XML document. Mike Rugge spent several intensive months developing and tweaking the Excel2EML tool and in November of this past year, the tool was made available to the IM community through a LTER network office (LNO) CVS (http://cvs.lternet.edu/cgi bin/viewcvs.cgi/eml/tools/Excel2EML/). We were able to add a MAC OS X version of the tool to the CVS in February 2005. Links to the Excel2EML CVS can also be found in the Data section of the FCE website at http://fcelter.fiu.edu/data/tools/. Three quarters of the FCE legacy metadata have been re-entered into the new EML metadata templates and converted and will be ready to be harvested by the LNO metacat by the third week of August 2005.

In the upcoming weeks, we will be upgrading our information management system by adding three large servers to replace existing equipment: 1) a web server, 2) an Oracle9i database server and 3) a data server. Our plan is to integrate our project management information, data and corresponding metadata and project GIS coverages into our Oracle9i database. We still have a few web pages driven by our original MS Access database and Mike Rugge is nearly finished migrating this project information into the Oracle9i database. We have been busy collecting and entering LTER and LTER related project information into our Oracle9i database in order to enhance our web-based interactive mapping application called the ‘FCE LTER Interactive Everglades Map’ found on our web site at http://fcelter.fiu.edu/gis/everglades-map/.

As we are beginning to prepare for our 2006 funding renewal, several enhancements have been made to the FCE website. We’ve slowly been adding detailed information into our ‘researcher profile’ pages and have expanded personnel queries to include FCE site roles, research interests, FCE working group membership, affiliated organization, and keywords. Mike Rugge has improved the FCE publications web page, allowing the user to query our archive by author, journal name, publication type, and keyword. In the past year, we worked with Susan Dailey (FCE Education and Outreach Coordinator) to add a FCE Schoolyard program component (http://fcelter.fiu.edu/schoolyard/) to the website. We plan to work with the FCE Graduate Student Organization to update their section of the website.

LTER Site: Georgia Coastal Ecosystems

Contributor: Wade Sheldon (Jul 31, 2005)

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We are already busy preparing for our 2006 renewal proposal, so information management work at GCE has largely been focused on helping PIs with data synthesis projects, improving managment and access to GCE reprints and publications, and tightening integration between project databases through web application cross-references and content displays. The data synthesis efforts have been strongly aided by the development of the GCE Data Search Engine, a MATLAB application for metadata-based indexing, searching and integration of data sets stored as GCE data structures (http://gce-lter.marsci.uga.edu/lter/research/tools/toolbox_search.htm). This tool has been well recieved by PIs, and several use it to manage and analyze their own data in addition to GCE data sets. We also began using this indexing technology to generate detailed data summaries to enhance distribution of near-real-time and historic ancillary data on the GCE Data Portal web site (http://gce-lter.marsci.uga.edu/portal/). This is particularly useful beause we began providing full public access to the portal site this year to support our SLTER participants and UGA students as well as the broader LTER community. All portal data sets can be searched and retrieved alongside public data from the GCE Data Catalog using the GCE Data Search Engine client (i.e. via direct HTTP in MATLAB). All data access from the GCE Data Catalog and GCE Data Portal and all software downloads are now tracked in our data access database, requiring contact and affiliation information from downloaders, but we did add support for web browser cookies and stored logins in the Search Engine client to streamline the downloading process for regular data users.

We are holding off on implementing new data search applications on the GCE web site until the standardized LTER query interfaces in development are more mature, but we did significantly enhance the query capabilities of our existing data catalog interface this year (http://gce-lter.marsci.uga.edu/lter/asp/db/data_catalog.asp). Specifically, we added support for searching by LTER core area, searching by study dates, and also by text in individual or combined metadata sections. Metadata content searches are highly targeted and extremely fast compared to xml-based searches, and the searchable content can easily be tailored in the future by creating simple database views and adding them to the array of available metadata sections. These new query capabilities also allow search hyperlinks to be added anywhere on our web site to support improved cross-referencing between databases, such as searching for relevant data sets for individual species records in our taxonomic database (e.g. http://gce-lter.marsci.uga.edu/lter/asp/db/species_details.asp?id=Geukensia%20demissa)

This year we began acquiring and managing more full text reprints for GCE publications and we now have a searchable reprint archive linked to our bibliographic database on the private GCE web site for project participants. We also automatically generate downloadable reprint archives complete with HTML indices of all reprints (both with and without abstracts) to allow PIs and students to install up-to-date libraries of GCE publications on their local systems for research purposes. We also improved linkages between our bibliographic and personnel databases and began providing an automated reprint request service on the public web site for both GCE and UGA Marine Institute publications (http://gce-lter.marsci.uga.edu/lter/asp/db/biblio_query.asp). Reprint requests are emailed to first listed GCE-affiliated author and cc'd to the IM office, and if no authors are active GCE participants the request is directed to the IM or UGAMI librarian instead. Quite a few international researchers and students have been using this service to request reprints from journals that are not widely available overseas.

We continue to provide complete Level 5 EML metadata for all data sets added to the GCE Data Catalog, as well as customizable versions of species lists in EML format from the GCE taxonomic database (http://gce-lter.marsci.uga.edu/lter/asp/db/all_species_lists.asp). We improved our EML implementation to better match the current Best Practices recommendations this year (e.g. reorganized geographic coverage content to describe the overall bounding box under eml/dataset/coverage, with individual site descriptions moved to the eml/dataset/methods/sampling/studyExtent tree, as well as inclusion of standard "place" keywords). All dynamically-generated EML documents are harvested weekly for inclusion in the LNO and KNB metacats and also the NBII metadata clearinghouse.

On the IT front we experienced our first major hardware problem this year when a SCSI hard drive in our database server's RAID-5 array failed and an auxiliary drive developed some bad sectors. The RAID did its job and kept the system up until new drives could be obtained, but that process turned out to be very complicated (and expensive) due to the age of the drives, taking over six weeks. After this experience we decided it was time to acquire a new database server, so I was able to purchase a PowerEdge 2800 with dual Xeon cpus and a faster RAID-5 array and re-task the older server as a development box. We also tightened security for accessing all servers by generating SSL certificates and requiring HTTPS (or SSH/SFTP) for all authentication. Less secure transport protocols (e.g. FTP, WebDav) are now disabled on all our systems and all machines are protected by firewalls (in addition to the rule-based URL filter on the web server). This required some PI hand-holding, particularly installing and using SFTP software, but should help us minimize our "attack surface".

We also revised our project management structure this year by forming an executive committee to direct the project, and it was unanimously decided that the information manager should serve as a full voting member on this committee. This formal acknowledgement of the central role the IM program plays at our site is very encouraging, and should improve the already strong integration of our science and IM programs in long term planning. In addition to forming an executive committee we also established formal bylaws for GCE, and we developed a secure web application for voting on project referenda in accordance with these bylaws. This application allows our broadly distributed PIs to vote on important issues that arise between annual meetings and will also help us establish a formal record of major project decisions for posterity.

LTER Site: Harvard Forest

Contributor: Emery Boose and Julie Pallant (Sep 15, 2005)

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The functionality of our web page was greatly increased this year through incorporation of online databases in MySQL. This addition has streamlined our application process for on-site research, fellowship positions, and undergraduate (REU) students. In addition, we are posting more dynamic web pages with information submitted to our databases. The 16th annual Harvard Forest LTER Symposium abstracts were submitted and posted entirely on-line.

There is growing interest at our site in extending wireless networking to our main research area (Prospect Hill Tract, 1000 acres). Some interesting technical challenges are presented by the local topography and dense forest (not to mention hurricanes, ice storms, etc). We are also designing and installing a series of long-term hydrological stations across Prospect Hill. One of the goals of the wireless network would be to permit near-real time collection, processing, and display of hydrological data, as we currently do for meteorological data (http://harvardforest.fas.harvard.edu/hfmet/).

Miscellaneous items - Major renovations to our main building (Shaler Hall) involved installation of new network and telephone wiring as well as a new audio-visual system. Great strides were made in the reorganization and classification of the Harvard Forest Library and inclusion of our holdings in the University’s on-line catalog, with generous help from professional librarians at Harvard. A major lightning storm in July caused extensive damage to our phone system, meteorological station, eddy flux towers, and soil warming experiment (whose instrument shack burned to the ground).

We are currently updating our information management system in preparation for our LTER renewal submission in Feb 06. Updates will include data and metadata from our Schoolyard LTER program last year. Plans for the beginning of LTER IV (assuming we’re funded) include migrating our scientific metadata from EML to MySQL, migrating core datasets from flat files to MySQL, and incorporating more spatial data into our information management system.

LTER Site: Hubbard Brook LTER

Contributor: John Campbell (Jul 29, 2005)

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We have made significant progress with our EML implementation. We now have 115 EML documents harvested into the metacat. All of our non-geospatial datasets were converted to EML last year, and this year we converted all of our spatial metatadata to EML. We used the Esri2Eml stylesheet that was developed at CAP and are grateful for help from Corinna Gries. A stylesheet was developed for displaying metadata for non-geospatial data and we will incorporate this into our web page shortly (see http://www.hubbardbrook.org/eml/generate_html_from_eml.php). We also plan to develop a separate stylesheet for displaying metadata for spatial datasets.

We are in the process of completely redesigning our web page and have made considerable progress on this front. A major part of this effort involves redesigning the way data are queried and downloaded. We have moved all our data into a MySQL database and will query it with php applications (see example at: http://www.hubbardbrook.org/search_portal_db.php). We also linked the EML based metadata to the new LTER network data policy and will register users to track data downloads see (http://www.hubbardbrook.org/data_policy.php?target=801d8c3700665679e56756c2b8ab84081b).

During the last year we imported our site bibliography into Endnote to remain consistent with the LTER network office. The bibliography contains nearly 2000 publications that have been published since the inception of the Hubbard Brook Ecosystem Study. We will continue to develop the bibliography and plan to modify the query interface on our web page.

In the last year, there has been considerable interest in implementing wireless technology and real-time data at Hubbard Brook. Past efforts have been hampered by a number of complications including mountainous terrain, remote location, dense forest cover, and a lack of electricity. We are currently exploring practical and cost efficient ways to overcome these challenges and are in the proposal writing phase.

The Hubbard Brook information management team consists of Ellen Denny, Netta Kies, Phyllis Likens and John Campbell. Ellen works at the USDA Forest Service in Durham and helps maintain the Hubbard Brook web site and has been working on the redesign. Netta Kies is a summer employee at the Forest Service and will return to Wesleyan University for her senior year in the fall. Netta has been developing the web database and associated php applications. Phyllis Likens is an employee of the Institute of Ecosystem Studies in Millbrook, NY. Phyllis compiles the Hubbard Brook publication list, maintains the document archives, and helps with the personnel database and curriculum vitas. John Campbell continues in his role as Information Manager for the Hubbard Brook LTER working on a variety of tasks

LTER Site: Jornada Basin

Contributor: Ken Ramsey (Aug 02, 2005)

Site Byte:

The information management team of the Jornada Basin LTER has been very busy in the last year responding to research needs, creating Geographic Information System (GIS) products, implementing Ecological Metadata Language (EML), application development and deployment, database population, effectively doubling server storage capacity, and participating in LTER Network planning activities. The information management team consists of Barbara Nolen (GIS/Remote Sensing), John Anderson (Site Manager), Ken Ramsey (Information Manager), and Justin Jensen (student programmer). The information management team receives network and desktop systems support from Jim Lenz of the USDA ARS Jornada Experimental Range (JER).

Barbara Nolen has had a productive year. Her products this year includes a broad scale map showing major JRN and JER research sites, a Schmidt’s delineation of the Chihuahuan Desert, digital elevation models of the Chihuahuan Desert and New Mexico, and LandSat images of the Chihuahuan Desert and New Mexico. Barbara is currently working on a tour book for the World Congress of Soil Science and mapping landforms of the Chihuahuan Desert and New Mexico.

The Jornada Basin LTER hired a student programmer, Justin Jensen, this year to develop PHP and Java applications for the Jornada Information Management System (JIMS) databases. With support from Central Arizona Phoenix LTER (CAP) and the LTER Network Office (LNO), Ken and Justin went to Tempe, AZ for assistance in implementing Xanthoria to generate EML from the JIMS database tables. Corinna Gries (CAP), Robin Schroeder (CAP), Ken, and Justin spent 3 days in Tempe developing the initial implementation of Xanthoria that generated most of the major elements of level 5 EML based on LTER Best Practices. Justin and Ken completed the XSL style sheets and Xanthoria configuration file following the trip to CAP.

Ken is currently completing the population of the JIMS databases with data, associated metadata, and personnel information needed to generate EML and develop and implement a new content management system for a new dynamically generated web site currently under development. This includes associating people with research projects and datasets within related database tables. JRN is set to deploy a searchable people directory, dynamic data catalog, and semi-automated LTER ClimDB harvest mechanism (68+ stations) following internal revue of the interfaces. As the JIMS databases are populated with a research project, EML instance documents will be generated, archived locally, harvested to the LNO Metacat node, and made available on the JRN web site.

JRN has developed a set of rules for generating EML based on the JRN IMS database schema and LTER EML Best Practices. John’s attendance of an EML workshop at LNO prior to this planning process was very helpful in allowing us to quickly determine JRN rules for EML content. The LTER Best Practices Document was crucial in guiding JRN during the process of developing and implementing EML.

Jim and Ken have made several improvements to the IMS servers and services in the last year. The total storage capacity for IMS servers was doubled by adding a 2 TB RAID enclosure and reallocating storage capacity among the file, database, and web servers. This brings the combined server capacity to just over 4 TB. The web server was moved to a newer server with SUSE Linux as the operating system and Apache web server. The operating system for the file server was upgraded to Netware 6.5 during the storage capacity reallocation. The Internet map server has been upgraded and is now performing at a significantly increased level of performance.

John has recently added 5 mini-flume hydrological research sites to the Jornada wireless system. John has installed the new LTER weather station and is currently finalizing its configuration and calibrations. The new weather station has also been added to the Jornada wireless system.

LTER Site: Kellogg Biological Station

Contributor: Sven Bohm (Aug 03, 2005)

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With the EML delivery well under way, we concentrated this last year on cleaning up and refactoring the data delivery code, and work towards removing the jsp pages in favor of testable java modules. We also started to develop some tools to help users do quality control, and some data processing for the longer term data. This will hopefully allow us to capture data earlier, when memories of the metadata are still fresh.

The goals for this year are to bring our air-photos online and integrate the spatial data points (field corners, sampling stations and the like) with the traditional data. Our new project server is finally online, with the old server used as a “live backup”. We have started linking the publication database to the datasets.

Thats about it.

LTER Site: Konza Prairie LTER

Contributor: Jincheng Gao (Aug 03, 2005)

Site Byte:

There have been lots of changes at the Konza site in the past year. We rebuilt our Local Area Network (LAN), updated our SQL Server and web site. In spring 2005, I took over the position of KNZ Information Manager and continued to work on data quality control, database population, and interactive maps of spatial data to prepare for the mid-term site review in early June. I am glad to let you know that we had a successful and positive review, and also received some good and constructive suggestions for the continuing development of our IM system.

A wireless network was installed at the Konza Prairie Biological Station last year that facilitates transferring data directly from the station to a data server on campus. A local network system was rebuilt and the network operating system was transferred from Novell to Window 2003. Symantec antivirus server was installed for retrieving and distributing virus signature and program updates. A new database server, SQL Server 2000, was established last year. All KNZ LTER metadata and data are stored and managed on the server. Right now, most metadata are stored in three formats- text, PDF, and EML. Most datasets are stored in both text files and in the SQL Server database. Metadata PDF files and EML are dynamically generated from metadata database. Our new web pages are dynamically generated, so that they can be more easily maintained and updated. The new web site is available on line (beta version), and will soon replace our old web site. Moreore information will be added to our new site over the next year.

In the coming year, we will continue to work on refining our new web site, database, and EML. More information and web search engine will be added to our web site. Metadata and dataset query interfaces and search applications will be our focus in order to improve data management. We will build query interfaces that will enable data searches based on watersheds or treatments, years, and key words in metadata. We will continue to work on our EML to ensure compliance with the Best Practices, and contribute to LTER Metacat. In a word, I am excited for this opportunity to join the IM community and share our information with you.

See you all in Montreal!

LTER Site: Luquillo LTER

Contributor: Eda C. Melendez-Colom (Aug 01, 2005)

Site Byte:

This last year, LUQ IM has been devoted to make progress in two areas: EML translation of all its metadata and local automation of the data manipulation to contribute to the NIS modules, namely, CLIMDB and All-Site Bibliography.

Conversion to EML was divided into two phases. First all the general information about the database’s related project, the abstract, methods, and personnel (author, contact, other investigators), among other EML elements were to be converted into EML and harvested into Metacat. A second phase, which will turn LUQ’s EML level to a 5th level, will include identities along with their attributes. With the help of Iñigo from the LNO, we completed Phase 1. This puts LUQ’s EML into a Level 3 to 4.

LUQ’s local metadata database went through a considerable transformation such that when updating or adding EML packages in the future, the transformation will be done automatically. Iñigo developed perl scripts that transformed xml files into EML packages.

The completion of Phase 2 is projected for next year, probably for this time of the year. This phase not only requires the transformation of the metadata, but of the data files themselves. As it turned out many of our data files were not exactly in a database-ready format. Transforming all these data files into a suitable databased format, has delayed this process. We believe that, at the end, LUQ’s metadata and data files will be even more suitable for synthesis as well as for EML transformations.

Special attention was given to the conversion of meteorological data into ClimDB. Tables that allows the user to convert regular mm/dd/yyyy-formated dates into the ClimDB dates format (strings with the format “yyymmdd”) were developed and the queries within Paradox that transform the dates using these tables were designed also. The rest of the transformation varies for each of the three stations whose data LUQ contributes for ClimDB each requiring different scripts or permanent queries for their transformation. All three have been updated or are in the process of being complete.

SiteDB was updated as well as the All-sites Bibliography (with 617 references as of July 31). Since all LUQ LTER Bibliography is entered in End Notes, the export process of the references is done by End Notes’ built in export format, which is accepted by the All-site Bibliographic module. This made LUQ collaboration to the NIS modules complete.

LTER Site: McMurdo Dry Valleys

Contributor: Chris Gardner (Aug 03, 2005)

Site Byte:

This year has been one of transition for MCM in terms of information management. The data management operations were moved from the University of Colorado at Boulder, where a student acted part time as the data manager, to Ohio State, where I will operate full time for the next couple years. We purchased a brand new SunFire V480 server with Solaris 10, and I've been working to get our Oracle database and GIS capabilities operating on the new machine. In addition, I have redesigned the look and feel of the website and hope to go live with it this fall at a new domain: www.mcmlter.org.

We have formed a "data management subgroup," which is comprised of one representative from each of the PIs' research groups. We recently met at the MCM LTER meeting in Portland, OR where we discussed ways to improve the data submission process and streamline our operation. I have also been sifting through our core and legacy data to ensure that we have no gaps in our database, and verifying my findings with this group. Our hope is that the subgroup will make the data management aspect of science more interactive for the MCM researchers, and therefore everyone will take a more active role.

Overall we're making a lot of progress at MCM, and after we have our database up-to-date and new website up, we can start to work on the metadata conversion to EML. Sorry I can't make it to the meeting this year!

LTER Site: Moorea Coral Reef

Contributor: Margaret O'Brien (Aug 23, 2005)

Site Byte:

The Moorea Coral Reef information management system will be housed at the Marine Science Institute of the University of California, Santa Barbara. Currently, the Science Coordinator (Andy Brooks) is filling the role of Information Manager, with consultation from Margaret O'Brien, the IM at our sister site, Santa Barbara Coastal, and Chris Jones of the PISCO project. MCR, SBC and PISCO share several investigators, post docs and staff, and so logically, these project will also share information management software and strategies. MCR will actively start its search for an Information Manager in the fall of 2005 whose skills will complement those of our collaborators..

Fieldwork is conducted at the UC Berkeley Richard B. Gump South Pacific Research Station on Moorea near Lat: -17.5, Lon -149.83. Our researchers are from 4 campuses of the University of California (Santa Barbara, Davis, Santa Cruz, Davis) plus California State University, Northridge and the University of Hawaii. 2005 was the first active field season for the Moorea Coral Reef site. This season, we installed 3 permanent moorings and several seasonal moorings around the island and in lagoons to investigate coastal oceanographic processes. We also established permanent transects on all 3 sides and initated studies of coral structure and function, fish population dynamics, and of nutrient delivery at the reefs. Data has been delivered to the fileserver in Santa Barbara, and we anticipate insertion of data into the LTER-PISCO Metacat data catalog soon after analysis.

LTER Site: Niwot Ridge LTER

Contributor: Todd M. Ackerman (Aug 02, 2005)

Site Byte:

This past year we have continued to hammer out the conversion of our metadata into the EML format. A few different tactics were attempted and we decided to use 'home cooked' perl scripts. Perl DBI scripts have been developed to allow the text metadata headers of the Niwot datafiles to be updated following the existing protocols at Niwot, then these changes are then loaded into a MSSQL Server database. A cgi script then allows the EML to be harvested from the database (much thanks to Inigo for the harvesting help). Currently the content is somewhere between level 2 and level 3, and some minor additions to the database should allow level 3 content shortly. Our spatial data metadata is the next project to tackle, as well as determining the easiest method of getting the initial metadata into the database.

We have added a few more sites to ClimDB/HydroDB this year, those sites are C1 (sub-alpine, 3022m), D1 (alpine tundra, 3739m), and the hydrological site at Albion (3259m). Success with our wireless program (much thanks to our Climatologist Mark Losleben) has allowed us to now have eight field sites downloading near-real-time data, which has permitted us to add a few more real-time graphs to our website. This has proved very useful in error detection, allowing us to fix problems which previously would have gone unnoticed and lead to months of useless data.

The website received a MUCH needed facelift, bringing our web representation out of the early 90's and into the 2000's (http://culter.colorado.edu/NWT/). The focus was on increased usability and content, and of course appearance.

We have continued development on our Data Entry Form System (DEFS) which has been designed in VB .NET to greatly improve data entry of our field data sheets. This is a great improvement over our previous DOS-based key/re-key entry system, where data entry forms are designed to mimic the data collection forms.

LTER Site: North Temperate Lakes

Contributor: Barbara Benson (Aug 02, 2005)

Site Byte:

from Barbara Benson, Dave Balsiger, Jonathan Chipman, and Paul Hanson

Considerable work has been done in implementing the Ecological Metadata Language (EML) standard at NTL. The EML elements included in the NTL EML documents were expanded; particularly notable is the addition of taxonomic coverage. In April 2005 NTL LTER IM staff harvested EML documents for most of the NTL core data sets into the central metadata catalog, Metacat, for the LTER Network. These harvested EML documents are valid EML and describe identification, discovery, evaluation, access, and integration information. We are in the process of developing the metadata content further to be in full compliance with the EML Best Practices document developed by the LTER Information Managers.

The NTL LTER website underwent a major redesign during the past year. With the help of a professional graphics/web designer the website organization, appearance, navigation and usefulness were significantly enhanced. Website content was brought up to date.

Our development in the area of sensor networks has continued with the addition of another instrumented buoy at NTL and our leadership in the Global Lake Ecological Observatory Network (GLEON), a grassroots network of limnologists, information technology experts, and engineers who are coordinating the construction of a scalable, persistent network of lake ecology observatories. In March 2005 an international workshop of researchers studying lakes and coral reefs was held in San Diego to explore building capacity using sensor networks and linking infrastructure to share data. This year personnel from NTL visited the instrumented buoy on Yuan Yang Lake in Taiwan to help upgrade the instrumentation and interact with Taiwanese scientists. Within the next year monitoring buoys on lakes in New Zealand, Israel and Finland should be added to the global network. Lakes in mainland China, South Korea, Japan and Australia may be added to GLEON in the future. NTL is collaborating through an NSF grant with computer scientists at UCSD, SUNY-Binghamton, and Indiana University to solve problems that limit the extensibility and scalability of data-generating sensor networks: (1) automating instrument management and the updating of data flows from sensors to publicly-accessible biological databases and (2) developing a suite of new algorithms and software for detection (real-time) of events based on data from sensors and databases, with applications to classification of signals as deriving from biological or physical events or to sensor failure, allowing rapid response.

Programmers at the Center for Limnology are developing software that provides sample and data management for the Center for Limnology Chemistry Lab (the program is called ChemLab). This project was initiated because the overload on the existing chemistry lab data management was leading to unacceptable sample processing backlogs. Tracking status of bottles and tests using pen and paper is inefficient and time consuming, and there was duplication of effort with the field crew in labeling and tracking bottle metadata. The ChemLab software stores bottle metadata, bottle/test status and analytical results in a database accessible to both the field crew and the chem lab technicians.

The spatial data catalog was improved and upgraded in several significant ways. The existing “static” version of the Spatial Data Catalog was redesigned as part of the overall website redesign. All the spatial data sets were converted to a common file format and map coordinate system, and uniform metadata were created. Several new data sets were added, most notably demographic spatial data. Finally, we developed a new, alternate method for managing the spatial data, which permits direct, dynamic access to the data via an Oracle database with an ArcSDE (Spatial Data Engine) interface. This represents an improvement over the “static” spatial data catalog by (a) facilitating access to data and metadata; (b) ensuring that users are working with the current version of all data; (c) enabling development of cross-site or network-level spatial data applications; and (d) facilitating development of web-based mapping applications. Ongoing spatial data management activities include work on such web-based mapping systems, the addition of new data sets to the catalog, and testing methods for converting the XML-format spatial metadata to valid EML.

LTER Site: Palmer Station

Contributor: Karen Baker (Aug 27, 2005)

Site Byte:

PAL Information Management efforts focused on implementing a second-generation system designed over the last few years following research into and experience with site practices, federated network criteria, and metadata standards' requirements. Study of the infrastructuring concept along with last year's hardware implementations created a contemporary infrastructure within our local UCSD/SIO Integrative Oceanography Department so that the PAL data project could be migrated to a new storage system. Update and reorganization of the decade old file structure and its content is ongoing. The informatics team with designated information manager Karen Baker broadened to include Shaun Haber and Mason Kortz as web and database designers, Lynn Yarmey as dictionary and metadata analyst, and Jerry Wanetick as computational center director and systems administrator.

Amid a year of multiple transitions, the site highest priority data management task was development of a long-term, extensible metadata strategy, bridging from decade old text forms to a relational database approach. From this effort emerged the recognition of a need to develop unit and attribute dictionaries. In considering the site information system holistically, the design and implementation of a personnel directory represents the initial module an important element to an integrated approach. Along with these activities, a Palmer web site redesign includes a three tier template, stylesheets and update of dynamic elements such as the photo gallery, glossary, and sampling grid program under the new architecture.

Collaborative local activities included coordination with the colocated LTER California Current Ecosystem (CCE) site and California Cooperative Oceanographic
Fisheries Investigations (CalCOFI) programs along with the Southern California Coastal Ocean Observing System (SCCOOS) program. The design and development of an Ocean Informatics Environment is ongoing, providing a comprehensive conceptual framework for all informatics activities. Making use of a design studio approach along with strategic design teams and working groups contributed to community efforts such as a joint data acquisition schema and promoted a shared understanding across multiple data types. Interaction with the Comparative Interoperability Project is providing opportunities to consider and articulate how IM work is carried out within different communities (Ribes et al, 2005; Baker et al, 2005; Millerand et al, 2005) and prompted development of two local reading groups. In additional, PAL and CCE contributed the notion of 'social informatics' to the first meeting of LTER social scientists in August of this year.

LTER Network activities included participation with the Dictionary Process Unit Repository design team that created a prototype web application in time for the annual Information Management meeting. Further, a Community Process Working Group provided a mechanism for exploring lessons learned in the design, development, implementation, and enactment of community standards.

LTER Site: Plum Island Ecosystem

Contributor: Hap Garritt (Aug 03, 2005)

Site Byte:

The Plum Island Ecosystems (PIE) LTER has recently, through the help of the LTER Network Office (Inigo San Gil and Duane Costa) and Jim Laundre ARC successfully converted 119 non-spatial legacy metadata files to ~ Level 2.5 EML including harvest into the LNO Metacat. We are continuing to make progress in standardizing a metadata document for the three different spatial data softwares (ESRI ARC, Clark University IDRISI and University of New Hampshire GHAAS-RGIS in use at PIE which will be followed up by conversion to EML.

In June 2005, PIE LTER hosted a workshop for developing plans for upgrading the Marshview Farm field facility into the Plum Island Coastal Research Facility. Attendees included PIE research personnel and also outside researchers who have had experience in managing field research facilities. Working groups met to discuss facility and infrastructure needs in the program areas of Research, Education and Outreach with the intent of developing new facilities that would complement existing available facilities in the area. The recommendations from the workshop will be incorporated into a facilities upgrade proposal in the near future

LTER Site: Santa Barbara Coastal

Contributor: Margaret O'Brien (Sep 12, 2005)

Site Byte:

This year as in previous, Santa Barbara Costal LTER's Information Management system collaborated with other local coastal and oceanographic programs with whom we also share collection and analysis methods and personel. Our data catalog is shared with PISCO (administered by Chris Jones and Jordan Morris) and we will be soon joined by the Moorea Coral Reef LTER site (whose Information Manager is yet to be hired). SBC's data needs are managed by Margaret O'Brien with reprentatives from its major research groups who provide data and metadata and receive introductory instruction to data storage methods (e.g., EML) as needed. Also during 2005, the LTER-PISCO IM office moved into a new building on the UCSB campus, putting us on the same floor as the NCEAS Ecoinformatics programmers. We are enjoying fruitful interactions with this group, also.

Data Catalog: During the past year, the contents of our Metacat data catalog was updated from version EML2.0beta6 to EML2.0.1. About 70% of core data is currently included and is at approximately level 4. For browsing, we have created canned queries using a thesaurus of research categories, and keyword and/or site queries are planned. The remaining core data will be added to the catalog by the end of the calendar year. In general, SBC has chosen the strategy of bringing "fewer datasets to a higher level". This is efficient because most of SBC's data goes (or will go) directly into metacat from collection/analysis, with multiple datasets making use of a common eml template with full attribute discriptions. Some of our current data packages will serve as templates for new packages. Currently, some data packages contain several data tables if these shared spatial, time or protocol coverage, however some of these will be separated to allow finer-grained searches. During the summer 2005, our metacat began replicating to the KNB network. Chris Jones has led an effort to redesign XSL stylesheets for displaying EML content in a modular form in HTML pages, using Cascading Style Sheets to control look and feel. This project is well underway, but still requires considerable work. Two implementations can be viewed at the data links below.

In addition to the data catalog, we have also been investigating the uses of EML for handling other information. We have recently inplemented a variant of EML in Metacat for our site's bibliography. We have found EML to be quite well suited to our needs, providing mechanisms for a separate listing of in-press pubs, fairly quick displays and filtering, document distribution, and possibly, a link to an associated dataset. This project is ongoing, and may result in some products that will be useful to the network as a whole.

Quite soon, we are anticipating upgrades in both our server hardware and Metacat software. In late August, we plan to migrate our data server and catalog to an IBM x336 with a 2.4tb raid array. SBC is already preparing for its 2006 renewal, and so a good deal of IM time has gone into assisting researchers with their synthesis projects. For the next several months, most of the IM projects will have data access, integration and synthesis as their promary goal.

Further information:
data catalogs with xsl/css style:
http://data.piscoweb.org
http://sbc.lternet.edu/data

bibliographic db (under construction):
http://sbc.lternet.edu/catalog/style/skins/sbclter/sbcPubsDisplay.jsp

LTER Site: Sevilleta LTER

Contributor: Kristin Vanderbilt (Jul 29, 2005)

Site Byte:

The Sevilleta LTER Information Management group continues its conversion of our text-file based information management system into MySQL. More data entry and QA/QC tools were developed during the past year that capitalize on the relational database. A particular coup for the Sevilleta IM, Kristin Vanderbilt, was getting the SEV publications database moved into MySQL and a web interface created that allows PIs to enter their own publication data.

The Sevilleta IM team has embraced wikis as a mechanism for posting FAQs about systems administration, data entry instructions, protocols, and data processing instructions. The wikis have been integrated into our PostNuke-based web page.

We continue to translate our legacy semi-structured text metadata into EML. It’s a time-consuming process, because for some of the data we have used Morpho for the conversion. Inigo San Gil from LNO has been working with us recently to develop a script that will do the conversion for much of our data. The output of the script will include attribute metadata, so we will be well on our way to Level 3 compliance as described by the EML Best Practices document. By the end of the year, with the help of Inigo, we expect to have most of our metadata available as EML. We successfully harvested some EML documents into metacat on July 28, 2005.

Kristin continues to be involved in outreach projects. She teaches portions of ecoinformatics training classes for personnel from OBFS and for junior faculty and postdocs who participate in a training course sponsored by the Science Environment for Ecological Knowledge project (http://seek.ecoinformatics.org). She is also involved in a research project with Judy Cushing from Evergreen State College, wherein templates for ecological databases are being designed for a pilot project focused on integrating grassland LTER NPP data. She also participated in a panel at the SSDBM meeting in June 2005 entitled “NSF Long Term Ecological Research Sites: Praxis et Theoria—LTER Information Management and CS Research.” Kristin also presented a poster entitled “Ecoinformatics Training: Toward Data Sharing and Collaborative Research” at the Workshop for Enhancing Collaborative Research on the Environment in Sub-Saharan Africa in Arlington, VA in January 2005.

LTER Site: Shortgrass Steppe

Contributor: Nicole Kaplan (Jul 21, 2005)

Site Byte:

The Shortgrass Steppe LTER Information Management (IM) team is working on projects to improve support for local and network science, and access to more integrated, metadata, data and other information. The team currently consists of Nicole Kaplan, who works closely with Bob Flynn, GIS and IT manager. A position on the team has been created to support database and web development, which is currrently being advertised for a comupter science student. It is important to balance our commitment to site support, Network initiatives and outside ecoinformatics projects. The SGS Principal Investigators are discussing the interpretation and application of newly adopted LTER Network data access and use policies. Nicole is involved with the Network IM and broader ecoinformatics communities as a member of LTER IMexec and Website Design Working Group Leader.
The SGS Information Management team has plans to improve on-line searching capabilities for data and metadata by developing new web site tools. They have recognized the need for better integration of related data sets, spatial and non-spatial data, publications and other research information. Recommendations from the LTER Network Wesite Design Working Group will be considered when implementating the second generation SGS web site (Kaplan 2005). Our field staff are in the process of collecting Global Positioning System coordinates to complete our spatial coverage of most legacy and all current long-term and short-term data stes. We are making progress toward integrating our non-spatial and spatial data sets, to enhance management of study impacts on field sites and support data discovery with level 2 Ecological Metadata Lanaguage from the SGS database.
Metadata in the SGS Information Management System vary in richness, since fifteen percent of our data sets are legacy data sets from the USFS and IBP. Because of this, information required to meet the new LTER standard metadata content of EML may not be available. Metadata for more recent and current SGS data sets can be submitted directly to the RDBMS by students and PIs via web-based forms. We recognize the importance of maintaining robust metadata to ensure the usability of data in the future and are making efforts to conform our metadata tables in the RDBMS to EML according to the EML Best Practices document. We have a strategy to bring metadata in the RDBMS to Level 2 EML by exporting metadata content in XML (Extensible Mark-up Language) and converting the XML to EML with XSLT (Extensible Stylesheet Language Transformation) conversion scripts. Experts at the LTER Network Office have contributed to our efforts by providing licenses for software tools, example code, and tools for harvesting SGS metadata to a Metacat, a remote ecological metadata catalog. The SGS has also contributed to a community model metadata management system in RDBMS that is being developed and implemented at various LTER sites by the LTER Network office. Lastly, a GIS EML tool developed at the CAP (Central Arizona Phoenix) LTER site was tested on SGS GIS metadata to generate EML.
The IM Team is developing a suite of programs to improve QAQC practices at SGS, called the Matrix. The Matrix currently checks and formats meteorological data for submission to CLIMdb (http://www.fsl.orst.edu/climdb/) and is being expanded to support data tables produced by floral dynamics research, which contains over sixty percent of our studies. The IM team will continue to work with researchers to develop tools to more efficiently process, quality check and publish their data with high integrity.
Nicole continues to participate in ecoinformatics community projects, such as the Canopy Databank Project (http://canopy.evergreen.edu/bcd/home.asp) at The Evergreen State College. LTER IMs are contributing to the development of templates for data entry, analysis and synthesis of aboveground net primary production data collected at distinct grassland sites. Synthesis of nutrient enrichment data is being demonstrated by the Science Environment for Ecological Knowledge (http://seek.ecoinformatics.org/) project and includes SGS data and input for constructing ontologies of aboveground grassland vegetation measurements.

References

Kaplan, N.E., C. Gries, and E.C. Meléndez-Colom (2005) Evaluating First Generation LTER Site Web Sites: Assessing our audience, meeting their needs, and making recommendations for the future. In DataBits: An electronic newsletter for Information Managers, Spring 2005 Issue.

LTER Site: Virginia Coast Reserve

Contributor: John Porter (Jul 12, 2005)

Site Byte:

It has been another busy year at the VCR/LTER, with a substantial revamping of the site web page (http://www.vcrlter.virginia.edu) and development of a program that automatically generates EML metadata from our existing metadatabase. We have also been involved with several outreach and service functions, including web support for the Statistical Ecology (http://www.esa.org/stat-ecol) and Long-Term Studies (http://www.esa.org/longterm) Sections of the Ecological Society of America and the Mid-Atlantic Region Ecological Observatory (http://mareo.org) and work on databases with the Taiwan Ecological Research Network (TERN). Additionally, we have been expanding our wireless networking capabilities to reach new field instrumentation.

We have been making extensive use of the PostNuke Content Mangement System (CMS) for developing special-purpose web pages with generally good results. As an open-source product aimed at "community" web sites, PostNuke provides many useful functions, but is not without limitations, the most notable of which is the inability to make menu bars page-specific. However, on balance it has worked surprisingly well.

Ecological Metadata Language (EML) production is now automated with a PERL program "make_eml.pl" that queries metadata from a relational database system using the perl DBI functions (allowing movement to another brand of database at a later time). Although we are able to generate more-or-less full EML metadata, there are areas where we need to alter our underlying system to accomodate EML needs. These include adding types to keywords (currently everything is listed as "thematic"), making measurement units more consistent, and improving information on taxonomic coverage. Aside from its length (due to the number of EML elements), the program was relatively easy to write - consisting of repeated "query -> create tag" sections. The biggest problem has been dealing with free text, where users make inconsistent use of paragraph markers in the text, thus potentially unbalancing XML tags and causing validation problems.

During the spring of 2005 we hosted Meei-ru Jeng of the Taiwan Forestry Reseach Institute for three months. During that time she worked on learning PERL, PHP, Mapserver, PostNuke and how to make these programs interact with MySQL databases. To hone her PERL skills and to help us reconcile our literature and personnel databases, she developed a program that creates an EndNote Import file wherein names and intiials of VCR researchers have full names substituted. These interactions continued this summer with visits by John Porter to Taiwan and China. Currently plans are being made for additional extended visits by Taiwanese information managers to US LTER sites.

Following up on successful wireless networking workshops at the LTER All-Sci meeting in 2003 and at the Ecological Society of America meeting in 2004, we wrote a paper for BioScience that was the cover story in the July 2005 issue. This is acompanied by yet-another-postnuke-web-site: http://wireless.vcrlter.virginia.edu. We hope that LTER information managers will be active contributors to that "community" web site as we gain additional experience with wireless networking.

12-Jul-2005

Web design by Wade Sheldon, Georgia Coastal Ecosystems LTER

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