Information Management - LTER

Last updated: 09/20/2009

Table of Contents

1. Introduction
2. Information Management Team
3. Infrastructure
4. Jornada Information Management System
5. Geographic Information System
6. Jornada Basin LTER Website
7. Data Management
8. EcoTrends Support
9. Jornada Basin LTER Policies
10. Restricted Access Datasets
11. EML Metadata
12. Documentation and Periodic Review
13. LTER Network and Community Activities
14. Short-term and Long-term Goals

List of Figures and Tables

IM.1 Jornada Information Management System overview
IM.2 Data management process
IM.3 GIS and remote sensing data

1. Introduction (Top)
The Jornada Information Management System (JIMS) comprises four major components: the management of research data and formal data management protocols, the acquisition and management of spatial data, the provision of networking and computing services, and the people that support the system. JIMS is a multi-organization information management system that contains data and metadata holdings and ancillary information from the Jornada Basin LTER (JRN) and the USDA ARS Jornada Experimental Range (JER).

2. Information Management Team (Top)
The Jornada information management team is comprised of full and part-time personnel funded by both the JRN and JER who collaborate in providing information management support to both organizations. JRN and JER jointly fund Barbara Nolen's position (GIS administrator). JRN funds the following positions: Ken Ramsey (information manager), John Anderson (site manager). JER funds the following positions: Valerie LaPlante (data management, multimedia development, desktop support) and Jim Lenz (network, systems, and desktop support). In addition, JRN and JER employ part-time students to perform data entry for each organization.

3. Infrastructure (Top)
The JRN site offices and laboratories located at Wooton Hall on the campus of NMSU are connected to a local area network (LAN) through a firewall to the NMSU network (Gigabit Ethernet). Most computers and all servers are connected to the LAN using Gigabit Ethernet (1000 Mb). We anticipate increasing bandwidth from the field station to the NMSU campus from 1.54 MB to 50 MB, in the coming year to support data and video streaming, remote education (K-12), IP phones, video conferencing, and expanded wireless coverage of the research site (78,000+ hectares).

The Jornada servers are jointly funded by the JER and JRN. The system is comprised of than 11 servers running a variety of operating systems and applications. Operating systems include Netware, Windows, Linux, and Solaris. We are currently consolidating servers and plan on migrating to Windows 2008 Server operating systems running in a virtualized and clustered environment to provide high availability for all network services and to minimize maintenance efforts. Network services include files, printing, databases, email, FTP, web, Subversion (source code repository), Internet map, and web applications. To gain access to network services other than FTP, WWW, and email requires authentication and encryption using VPN client software, if not directly connected to the LAN.

The JER purchased the storage area network (SAN) in 2007 that provides 21+ TB of storage which is routinely backed up using a fiber channel, dual LTO4, drive tape library with a capacity to backup nearly 17 TB of compressed data without changing tapes. JER plans on purchasing an additional SAN switch and storage enclosure to allow mirroring the SAN for high availability and to offload impacts of centralized backups to the mirror to improve server performance during backups. The expansion of the SAN will allow imagery users to migrate large storage islands from individual computers to the SAN which will minimize LAN-based backups and increase LAN performance as well as increase throughput to the SAN by connecting computers directly to the SAN.

Figure IM.1

4. Jornada Information Management System (Top)
The Jornada GIS will be the core component to JIMS and will support applications and services to support discovery, access, geospatial analysis, and management of data and associated metadata stored in JIMS (Fig. 1). The Jornada Information Management System (JIMS) is being fully integrated with the Geographic Information System (GIS) and is comprised of a relational database management system and metadata repository.

The current metadata repository consists of JRN formatted metadata files and Ecological Metadata Language (EML) documents stored and available on the JRN data catalog. Available Jornada EML metadata can be searched at the LTER Network Office (LNO) MetaCat server at http://metacat.lternet.edu/knb or accessed directly from the data catalog at http://jornada.nmsu.edu/data-catalogs/data. With the shift from ASCII data to the GIS databases, we plan on generating EML level 5 (attributes) describing the data stored database tables. In the interim, we plan on generating EML level 4 for all JRN datasets once the metadata database is fully populated.

Applications have been developed to generate EML and support a new database-driven data catalog and data cart that will require users to register with JIMS and acknowledge our data policies prior to downloading data packages containing data and associated metadata. An audit mechanism has been developed to track user downloads. Once a person has registered with JIMS, they will have simply login to access data packages in the future. This system will also allow JRN to notify users that have downloaded data from JIMS of corrections or updates to data previously downloaded. The new data catalog will fully support the new data accessibility requirements adopted by the LTER Executive Board in 2009. See our website for a listing of short-term and long-term information management goals at http://jornada.nmsu.edu/lter/about/info-mgmt-goals.

5. Geographic Information System (Top)
The Jornada geodatabase is the repository for vector and raster data layers and associated metadata for mapping, site management, and geospatial analysis. The geodatabase allows GIS data and associated metadata to be discovered and accessed by researchers and information management personnel. Research locations are maintained in the geodatabase and are in the process of being linked to research data in the information management system to support spatial analysis. We are migrating raster data from the geodatabase to ArcGIS Image Server to provide more efficient access and management of the extensive remote sensing holdings. A major effort is migrating all research locations from shapefiles to the geodatabase.

The Jornada GIS Server provides web-based interactive maps to support research and education activities for the JER, JRN, the NMSU Chihuahuan Desert Rangeland Research Center, and the Chihuahuan Desert Nature Park. GIS data and metadata can be accessed by the public via the interactive map, http://jornada.nmsu.edu/data-catalogs/maps/interactive or the spatial/GIS data catalog at http://jornada.nmsu.edu/data-catalogs/maps/spatial. The GIS metadata are available in XML and in the future will be available EML. We are in the process of updating all GIS and remote sensing metadata in the geodatabase and are developing enhancements to the interactive map to enable access to research data and associated metadata. GIS and remote sensing data are currently available by request from Barbara Nolen (GIS administrator). The Jornada Basin Map Gallery allows online viewing of maps produced by the Jornada Basin Spatial Data Laboratory with downloadable PDF files of the maps. The map gallery is available at http://jornada.nmsu.edu/data-catalogs/maps/static.

Table IM.3 GIS and remote sensing data

6. Jornada Basin LTER Website (Top)
The JRN website follows design guidelines adopted by the LTER IM Committee. The website has been updated with new features and functionality including a new menu system and PHP template that provide a consistent user interface. The full menu is displayed for browsers that do not support JavaScript. The current JRN data catalog has been updated to implement as much of the new LTER Data Accessibility requirements and is located at http://jornada.nmsu.edu/data-catalogs/data. The new dynamic data catalog and data cart will fully implement the data accessibility requirements when it is deployed later this Fall. Contact information for JRN personnel is available at http://jornada.nmsu.edu/people. The searchable JRN bibliography can be accessed at http://jornada.nmsu.edu/biblio.
Web galleries make thematically grouped static maps (http://jornada.nmsu.edu/data-catalogs/maps/static) available for download. The Jornada Basin LTER Schoolyard web site, Schoolyard Desert Discovery Project, can be accessed at http://jornada.nmsu.edu/education/schoolyard. See http://jornada.nmsu.edu/lter/about/info-mgmt-goals for short- and long-term website development goals.



Figure IM.2

7. Data Management (Top)
The purpose of data management for the JRN is to provide protocols and services for data collection, verification, organization, archive, and distribution. Procedures are conducted in accordance with recommendations and guidelines developed by the LTER Information Managers Committee. Data access, acknowledgement, and data management policies are located at http://jornada.nmsu.edu/lter/data/data-policies. A full description of Data Management is described on this page.

One of the biggest hurdles moving forward archiving data in the GIS databases is migrating historic and current data into formats consistent with database rules to support geospatial analysis. Processing data files that have been collected or designed without database protocols is an enormous workload that could be minimized significantly by continued interaction with researchers and data managers (Fig. 2). We need to revisit the current data management processes to address this issue.

Currently, Site and Data Manager involvement begins during the Project Design phase with the completion of the Jornada Notification of Research form by the researcher prior to the start of work; this alerts both Site and Data Manager to the new study and potential LTER data sets. Upon initiation of a new study, the researcher completes Project Documentation that provides the second level of "metadata" documentation. Research related forms are at http://jornada.nmsu.edu/data-catalogs/documentation.

In the Data Collection phase, the data manager helps researchers design field and laboratory data sheets that facilitate data entry and analysis. Prior to JIMS data entry, the investigator completes Data Set Documentation to provide the metadata that fully describe the data set. Both Project and Data set documentation are provided with the data set when it is requested or obtained from our website. JIMS data entry programs error-check and verify data as they are entered. Computer files are subjected to further verification by graphing and/or error-checking programs, and/or examination by field investigators. Final quality assurance of the data rests with the investigator who submits data for inclusion in the Data Management System. Direct communication with the Information Manager, Ken Ramsey, is used to encourage the timely submission of documentation and data by researchers.

Error-checked data files are stored with associated documentation files on the file server. Backup data files are maintained on portable hard drives, CD-R media, and DVD media to guard against loss of data access that can result from changing technology. Image data are archived on LTO and LTO4 tapes. Routine tape data backups of the file, database, mail, web, and ftp server are done daily, weekly, and monthly. One set of off-site copies are maintained elsewhere on the NMSU campus of routine backup tapes, CD disks, and DVD disks with a second set of MO, CD and DVD disks maintained off-campus in case of a catastrophe on campus.

Online availability of our LTER data is through our website, which includes a catalog of Jornada data sets. A listing of long-term datasets is available at http://jornada.nmsu.edu/data-catalogs/long-term. Policy statements regarding submission of data, data access, and data acknowledgment may be found on our web page, http://jornada.nmsu.edu/lter/data/data-policies. Data are routinely updated online, typically within one day of JIMS receiving updated data. Data are either Unrestricted and available online or Restricted with release authority by responsible investigator usually within 2 days of request. Restricted datasets are those in preparation for publication, student research that is protected to allow them the opportunity to publish, ongoing studies less than 2 years old, and long-term studies where a 2 year period provides an insufficient dataset for analyses.

Ongoing LTER Network participation includes the Data Table of Contents (MetaCat), All-Site Bibliography, and Climate databases as well as representation and participation at the annual Information Managers (IM) Meeting, IM Executive Committee, and workshops associated with expanding the capability of the site to acquire, maintain and exchange information in a timely fashion that can be shared readily with other LTER and non-LTER users.

A plant voucher collection is maintained, catalogued, and databased providing reference material and documentation of Jornada plant species at research sites. A more extensive voucher collection of Jornada Basin species is incorporated within the New Mexico State University Department of Biology Herbarium and New Mexico State University Range Science Herbarium. Both herbaria are actively databasing their collections with New Mexico Biodiversity Collections Consortium (NMBCC).

8. EcoTrends Support(Top)
Ken Ramsey has supported the EcoTrends Project since the initial workshops in Sevilleta as a member of the EcoTrends Technical Committee. Ken developed the EcoTrends database with the assistance of Christine Laney (EcoTrends Project Coordinator). The database is used by Christine to manage the massive volume of data files and associated metadata (both source and derived), the R scripts used to generate derived data files and graphs, and ancillary information about the project. Ken and Justin Jensen (student programmer) created web-based metadata management interfaces to the database and the EcoTrends Committee page used by the EcoTrends Editorial Committee to facilitate discussions and interactions regarding EcoTrends book content. The EcoTrends database is used by the LTER Network PASTA framework to create EML metadata describing the derived data products and links to source data and metadata files on the EcoTrends website developed by LNO Network Information System Developers.

9. Jornada Basin LTER Policies (Top)
Jornada Basin LTER information management policies can be accessed on our website (http://jornada.nmsu.edu/lter/data/data-policies) and are compliant with the LTER Data Access Policy (http://www.lternet.edu/data/netpolicy.html). The policies are periodically reviewed by the Jornada Basin LTER Information Manager, Site Manager, and Executive Committee. Any changes to the policies are approved by the Jornada Basin LTER Executive Committee (see http://jornada.nmsu.edu/people) for current members.

10. Restricted Access Datasets (Top)
Any exceptions to the JRN data access policy must be approved by the Executive Committee. A listing of restricted datasets and associated justifications and approvals from the JRN Executive Committee is available at http://jornada-www.nmsu.edu/restricteddatasets.php. This list is reviewed annually by the Executive Committee. As of 01/31/2006, 9% (13) of the 147 our research datasets are classified as restricted access.

11. EML Metadata (Top)
All JRN datasets are being documented in the Ecological Metadata Language (EML). EML documents are initially generated at EML compliance level 2. The creation of level 2 EML (discovery) and subsequent creation of level 5 EML (integration) are performed on a priority basis. Long-term datasets are the highest priority candidates for generating EML documentation, with climate being next in priority. After the long-term and climate datasets are completed, the rest of the research datasets will be documented in EML, starting with the oldest datasets. The final effort will be to document all JRN GIS and remote sensing data holdings in EML. All JRN EML documentation are available on the LTER Network Query interface (http://metacat.lternet.edu/knb) or on the JRN data catalog (http://jornada.nmsu.edu/data-catalogs/data). As of 01/31/2006, (1) 35% of 147 research datasets have associated EML documentation, (2) 50% of our long-term datasets have associated EML documentation, and 1 of the 51 EML documents available are at level 5 EML (integration); (4) with the remaining EML files at level 2 (discovery).

12. Documentation and Periodic Review (Top)
We are currently in the process of documenting the JIMS interfaces, architecture, and data management procedures and protocols to maintain continuity in the event of Jornada information management team member turn over. The JRN information management system is reviewed periodically to ensure it meets the need of site science, information managers, intersite science, policy makers, and the public. This review is done at a minimum of once a year. Both internal and external input and feedback, in the form of site reviews, renewal reports, and informatics partners (primarily JER), are used to enhance the information management system.

13. LTER Network and Community Activities (Top)
Ongoing LTER Network participation includes the databases for Data Table of Contents, All-Site Bibliography, SiteDB (site description), Metacat (EML metadata), and ClimDB (climate data). It also includes representation and participation at the annual Information Managers (IM) Meeting, IM Executive Committee, and LTER site review teams, as well as workshops associated with expanding the capability of the site to acquire, maintain and exchange information readily with other LTER and non-LTER users. Past workshop themes have included Ecological Metadata Language (EML), wireless technology, Canopy Project Databank, web services, ontologies, and Geographic Information Systems.

The Jornada Basin LTER has collaborated with several non-LTER organizations to explore the implementation of new technologies and approaches to enhance the usefulness and accessibility to JRN data, associated metadata, and ancillary information. A collaboration between the San Diego Super Computer Center (SDSC) and LTER Network Office supported a cross-site LTER workshop and SDSC GIS and a web services development workshop which resulted in a collaboration with SDSC to explore the use of web services to provide access to JRN climate data.

Ongoing collaborations with the Evergreen State College Canopy Project (http://canopy.evergreen.edu/) and several LTER sites are exploring the use of Databank (http://canopy.evergreen.edu/canopy), an XML template approach to database structure reuse and development with an intuitive interface and associated analytical tools. The XML templates are associated with 2D and 3D visualization and preliminary analytical tools. When a template is used to create a new research database, the associated visualization and analytical tools are available for the newly created database without further development requirements. This approach to data structure reuse and automated EML metadata documentation will be a useful tool for both scientists and information managers.

The Shortgrass Steppes LTER (http://sgs.cnr.colostate.edu/), Sevilleta LTER (http://sev.lternet.edu/), and Jornada Basin LTER sites have expanded the initial collaboration with the Canopy Project to explore using Databank to perform cross-site analysis of grassland NPP data. The Kruger National Park (South Africa) and the Konza Prairie LTER (http://www.konza.ksu.edu/) have recently joined this cross-site collaboration effort. The collaboration has also moved from a more information management research focus to one of broader scientific interest with a focus on NPP.

Jornada Scientists and information managers are collaborating with the NMSU Bioinformatics Center and the Sapelo Island Microbial Observatory (SIMO)/ Georgia Coastal Ecosystem LTER (http://gce-lter.marsci.uga.edu/lter/) to develop a database system to store and access genomic and biochemical information collected by JRN scientists. This system will include interfaces to access and utilize the data and associated metadata that will be stored with the system. The system will be based on the databases and interfaces for the SIMO.

The Jornada Basin LTER and the Chihuahuan Desert Nature Park (CDNP) are collaborating to develop and host web sites and tools to support K-12 student ecological research activities and teacher workshops for teachers in southern New Mexico and western Texas public schools. We are initially developing an ecological glossary, Meet the Scientist web site, and the capability for teachers to upload and access data collected by students to a central JRN server. Future activities include developing classroom web pages to highlight achievements and access to the classs data. The Jornada Basin LTER will develop the databases and web sites and services to support and host the schoolyard activities conducted by CDNP.

14. Short-term and Long-term Goals (Top)
A listing of completed, short-term, and long-term information management goals may be found at http://jornada.nmsu.edu/lter/about/info-mgmt-goals.