Habitat-lite: A GSC case study based on free text terms for environmental metadata

OMICS A Journal of Integrative Biology

Volumn 12, Issue 2, 2008, Pages 129-136

  Hirschman, Lynette ^a   Clark, Cheryl ^a   Cohen, K Bretonnel ^a   Mardis, Scott ^a   Luciano, Joanne ^a   Kottmann, Renzo ^b   Cole, James ^c   Markowitz, Victor ^d   Kyrpides, Nikos ^e   Morrison, Norman ^f   Schriml, Lynn M ^g   Field, Dawn ^h  

^a MITRE CORPORATION   (United States)

^b JACOBS UNIVERSITY BREMEN   (Germany)

^c MICHIGAN STATE UNIVERSITY   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^e DOE JOINT GENOME INSTITUTE   (United States)

^f UNIVERSITY OF MANCHESTER   (United Kingdom)

^g UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^h CENTRE FOR ECOLOGY AND HYDROLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

AUTOMATION; BIOINFORMATICS; CONFERENCE PAPER; DATA BASE; GENBANK; GENE SEQUENCE; GENOMICS; INFORMATION PROCESSING; PRIORITY JOURNAL; SPECIES HABITAT;

DATABASES, GENETIC; GENOMICS; REFERENCE STANDARDS;

EID: 45749132147     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/omi.2008.0016     Document Type: Conference Paper

References (17)

1. Cole, J.R., Chai, B., Farris, R.J., Wang, Q., Kulam-Syed-Mohideen, S., McGarrell, A.M., et al. (2007). The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res 35, D169-D172.
2. Dawyndt, P., Vancanneyt, M., Demeyer, H., and Swings, J. (2005). Knowledge accumulation and resolution of data inconsistencies during the integration of microbial information sources. IEEE Trans Knowledge Data Eng 17, 1111-1126.
3. Desantis, T.Z., Hugenholtz, P., and Larsen, N. (2006). Greengenes, a Chimera-checked 16S rRNA gene database and work-bench compatible with ARB. Appl Environ Microbiol 72, 5069-5072.
4. Field, D., Garrity, G.M., Gray, T., Morrison, N., Selengut, J.D., Sterk, P., et al. (2008a). The Minimum Information about a Genome Sequence (MIGS) specification. Nat Biotechnol 26, 541-547.
5. Field, D., Garrity, G.M., Sansone, S.-A., Sterk, P., Gray, T., Glockner, F.O. (2008b). Meeting Report: The 5th Genomic Standards Consortium Workshop. OMICS (this issue).
6. Floyd, M.M., Tang, J., Kane, M., and Emerson, D. (2005). Captured diversity in a culture collection: case study of the geographic and habitat distributions of environmental isolates held at the American Type Culture Collection. Appl Environ Microbiol 71, 2813-2823.
7. Gill, S.R., Pop, M., Deboy, R.T., Eckburg, P.B., Tumbaugh, P.J., Samuel, B.S., et al. (2006). Metagenomic analysis of the human distal gut microbiome. Science 312, 1355-1359.
8. Hunter, L. (2002). Ontologies for programs, not people. Genome Biol 3.
9. Kottmann, R., Gray, T., Murphy, S., Kagan, L., Kravitz, S., Lombardot, T., et al. (2008). A standard MIGS/MIMS compliant XML Schema: towards the development of the Genomic Contextual Data Markup Language (GCDML). OMICS (this issue).
10. Liolios, K., Mavrommatis, K., Tavernarakis, N., and Kyrpides, N.C. (2008). The Genomes OnLine Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 36, D475-D479.
11. Markowitz, V.M., Szeto, E., Palaniappan, K., Grechkin, Y., Chu, K., Chen, I-M.A., et al. (2008a). The Integrated Microbial Genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res 36, D528-D533.
12. Markowitz, V.M., Ivanova, N.N., Szeto, E., Palaniappan, K., Chu, K., Dalevi, D., et al. (2008b). IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res 36, D534-D538.
13. Martiny, J.B., and Field, D. (2005). Ecological perspectives on the sequenced genome collection. Ecol Lett 8, 1334-1345.
14. Morrison, N., Wood, J.A., Hancock, D., Shah, S., Hakes, L., Gray, T., et al. (2006). Standard annotation of environmental OMICS data: application to the transcriptomics domain. OMICS 10, 172-178.
15. Nealson, K.H., and Venter, J.C. (2007). Metagenomics and the Global Ocean Survey: what's in it for us, and why should we care? ISME 1, 185-190.
16. Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., et al. (2004). Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66-74.
17. Von Mering, C., Hugenholtz, P., Raes, J., Tringe, S.G., Doerks, T., Jensen, L.J., et al. (2007). Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315, 1126.