Last Fall, Inigo San Gil (LNO) attended the 5th Genomics Standards Consortium (GSC) workshop in the United Kingdom to represent LTER and present the Ecological Metadata Language (EML) standard and its potential relationship with the "Minimum Information about a Genome/Metagenome Sequence" (MIGS/MIMS) and its implementation, the Genomic Contextual Data Markup Language (GCDML). Genome sequencing-the ability to decode the DNA base sequences in chromosomes-and its associated science, genomics, and many other "omics" technologies have evolved beyond the original one-dimensional scope of the data.
Nowadays it is common to conduct geo-distributed studies with many ecological variables. The new metadata needed adds to the laboratory pipelines, protocols, and methodology, that were the classical metadata scope captured in some of the omics data submissions (NCBI, Genbank, EMBL, Sanger, TIGR). The GSC stakeholders, including the National Genomic clearinghouses and international counterparts, are developing the new standards to gather the necessary metadata.
The adoption of EML as the LTER network standard has been key to building the network's architectures for synthesis that rely on high quality standardized metadata. Since the community's success in adopting a standard depends, among other critical factors, on the tools and trainings developed to use the standard, LTER's significant experience in adopting EML may help GSC to achieve similar success.
Another outcome of the workshop is the possibility of collaboration between LTER and GSC to provide training for GCDML and the associated catalog entry tool, GenCat. LTER is also investigating EML enhancements to better accommodate genomics data, possibly integrating the GCDML schema into EML. Inigo and a number of LTER and genomics community collaborators have published an informational article in the journal OMICS documenting the discussion and interactions. Further collaboration between the GSC and LTER is expected to leverage the efforts in designing a comprehensive metadata standard for genomic and metagenomic data that will benefit the ecological genomics community.
Reference
Inigo San Gil, Sheldon, W, Schmidt, T, Servilla, M, Aguilar, R, Gries, C, Gray, T, Field, D, Cole, J, Yun Pan, J, Palanisamy, G, Henshaw, D, O'Brien, M, Kinkel, L, McMahon, K, Kottman, R, Amaral-Zettler, L, Hobbie, J, Goldstein, P, Guralnick, R, Brunt, J, and Michener, W. 2008. Defining linkages between the GSC and NSF's LTER program: How does the Ecological Metadata Language relate to GCDML and other outcomes. OMICS A Journal Of Integrative Biology, 12, 2.
LTER hosting environmental informatics conference
The LTER Information Management Committee and LNO join the National Center for Ecological Analysis and Synthesis (NCEAS), NASA, Oak Ridge National Laboratories, PISCO, NBII, and Evergreen State College in hosting "Environmental Information Management Conference 2008" at the University of New Mexico (UNM) September 10-11, 2008. The conference provides a forum for information management practitioners, scientists, and informatics researchers to present and discuss advances in environmental information management, analysis, and modeling. The conference theme is "Managing Sensor Data in Near Real Time," but there will be broad coverage of EIM topics. UNM previously hosted two successful EIM conferences: "Environmental Information Management and Analysis" (May 1993), and "Data and Information Management in the Ecological Sciences" (August 1997). Online registration and lodging information is available at http://conference.ecoinformatics.org/index.php/eim/eim2008/.
Shared cyberinfrastructure for earth observing networks
In February, Tim Kratz (NTL), Corinna Gries (CAP), and James Brunt (LNO) attended an invitational workshop organized by the National Science Foundation (NSF) to promote collaboration in cyberinfrastructure (CI) design, implementation, and maintenance between NSF-funded environmental observation networks (EONs) The networks attending included LTER, the National Ecological Observatory Network (NEON), National Phenological Network (USA-NPN), Consortium of Universities for the Advancement of Hydrologic Science (CUAHSI), Water and Environmental Research Systems (WATERS) Network, Arctic Observing Network (AON), Ocean Observatories Inititiative (OOI) and EarthScope. The discussion between the EONs included overall goals and science questions, and the understanding that the CI needed to address those goals and questions. Each observatory gave a short presentation on their science objectives, CI architecture, and challenges. (These presentations are available at the workshop's wiki site, http://feon.wikidot.com/, hosted by the LTER Network Office.) The presentations were followed by group discussions focusing on technology, standards, and the organizational structures necessary to bring about a shared CI vision, technology, data exchange, and interoperability.
Conference participants identified a wide variety of CI needs which span the existing and developing EONs. Common technological challenges include data accessibility, scalability, and interoperability. For example, participants expressed a need to discover and access stored data quickly, securely, and through an easy-to-use interface. There was also a desire for the CI to scale easily to larger data storage requirements, multiple geographic locations, and more complex data. Recommendations include the development of standard software interfaces, based on data exchange and metadata standards, and identification of services that could be shared and contracted for on the open market.
Participants identified a need for coordination across the EONs driven by common scientific and infrastructure requirements. They also identified increasing communication between the EONs and with the computer science community as a major organizational challenge, and recommended the formation of a federation of EONs to include PIs, Management, and IT participants to coordinate and advance activities of emerging and established scientific EONs.
The proposed Federation of EONs (or FEONs) will define and develop a strategy to provide a common set of standards that allows for interoperability among these developing and legacy observation networks. EONs share many science interests that require common standards and interoperability to enable researchers to easily access data from all EONs.
A workshop report is being prepared to outline the topics discussed and any action items arising from the discussions. A follow up workshop scheduled for May 2008 was to be hosted by the National Center for Atmospheric Research to discuss how the NSF might most effectively craft programs to support the creation and use of new CI capabilities to support environmental research and education over the next decade.