Colony of thermophilic bacteria at Mickey Hot Springs, Oregon






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Bacteria Biotope at BioNLP-ST'13


MEM OntoBiotope - About


Context

To date, new sequencing methods allow accessing complex environments such as microbial ecosystems. Therefore, the sequence annotation process is facing radical changes concerning the volume of data and the nature of the annotation to be considered. Not only biochemical functions still need to be assigned to newly identified genes, but we have to take into account the conditions and the properties of the ecosystem in which microorganisms are living, and are identified, as well as the interactions and relationships developed with their environment and other living organisms. Metagenomic studies of ecosystems yield important information on the phylogenetic composition of the microbiota, either through the analysis of overwhelming amounts of random sequence data, or through focused studies designed to characterize phylogenetic composition by amplification and sequencing of 16S rRNA genes. In many cases, these approaches allow the identification of species that have been described in literature, or to classify "new species" as close to these earlier described species or belonging to the same genus.


Objectives

The co-development of the OntoBiotope ontology involved the Bibliome-INRA text-mining team, that provide Knowledge Acquisition (KA) tools, and several microbiologists that contribute with their expertise. The program of this project includes a workshop gathering all actors of the ontology development, and a training session on KA for microbiologists. We expect the ontology to leverage a wide range of large scale phenotypic, phylogenetic and metagenomic studies. The OntoBiotope includes a hierarchy of habitats, bacteria-habitat relationships and habitat properties. The habitat subpart is now available for download

INRA Participants

Microbiology (83)

  • Nutrition and Animal (41)

    • UR 0496 (AlimH) ; UR 1204 (AlimH) ; UR 1341 (AlimH) ; UMR 1319 (AlimH ; MICA CT1, CT2, CT3) ; UMR 1331 (AlimH ; SA)

    • UR 0117 (CEPIA) ; UR 0342 (CEPIA) ; UMR 1010 (CEPIA) ; UMR 1208 (CEPIA) ; UMR 408 (CEPIA ; MICA CT2) ; UR 638 (CEPIA ; MICA CT2) ; UMR 792 (CEPIA ; MICA CT1) ; UMR 0782 (CEPIA ; MICA CT3) ; UMR 1083 (CEPIA ; MICA CT1) ; UMR 1163 (CEPIA ; MICA CT1) ; UMR 1253 (CEPIA ; MICA CT2)

    • UR 0454 (MICA CT2, CT3) ; UR 0545 (MICA CT3) ; UR 1077 (MICA CT1) ; UMR 1014 (MICA CT2) ; UMR 1128 (MICA CT2, CT3) ; USC 1043 (MICA CT2) ; USC 2018 (MICA CT2) ; USC 2019 (MICA CT2) ; USC 2020 (MICA CT2) ; UMR 1282 (SA ; MICA CT2)

    • UR 143 (GA) UMR 1069 (PHASE) ; UMR 1213 (PHASE) ; UMR 1289 (PHASE) ; UMR 5242 (PHASE)

    • UR 0346 (SA) ; UR 892 (SA) ; UMR 0483 (SA) ; UMR 0754 (SA) ; UMR 0956 (SA) ; UMR 1161 (SA) ; UMR 1225 (SA) ; UMR 1233 (SA) ; UMR 1300 (SA) ; UMR 1309 (SA)

  • Plant, Agronomy et Ecology (38)

    • UMR 1332 (BV ; GAP ; SPE) ; UMR 1345 (SPE ; BV) ; UMR 0441 (SPE ; GAP) ; UMR 1095 (GAP ; SPE) ; UMR 1131 (GAP ; SPE) ; UMR 1349 (GAP ; SPE)

    • UR 407 (SPE) ; UR 1290 (SPE) ; UR 1321 (SPE) ; UMR 0203 (SPE) ; UMR 0217 (SPE CT1) ; UMR 0385 (SPE) ; UMR 1065 (SPE) ; UMR 1088 (SPE) ; UMR 1210 (SPE) ; UMR 1333 (SPE) ; USC 1330 (SPE) ; UR 0251 (EA CT3 ; SPE) ; UMR 1229 (EA CT3 ; SPE) ; UMR 1355 (EA ; SPE) ; USC 1342 (EA CT3 ; SPE) ; UMR 1062 (SPE ; EFPA) ; USC 1193 (EFPA ; SPE)

    • UR 0272 (EA CT3) ; UMR 1091 (EA CT4) ; UMR 1114 (EA) ; UMR 1347 (EA CT3) ; UR 1263

    • (EA CT4 ; EFPA) ; UMR 547 (EA CT2 ; EFPA) ; UMR 1220 (EA CT2, CT3 ; EFPA) ; UMR 1222 (EA CT3 ; EFPA)

    • UR 0588 (EFPA) ; UR 0874 (EFPA) ; UR 1138 (EFPA) ; UMR 42 (EFPA) ; UMR 745 (EFPA) ; UMR 1136 (EFPA) ; UMR 1202 (EFPA)

  • Both axes (4)

    • UMR 0614 (CEPIA ; EA CT3) ; USC 1366 (CEPIA ; EA CT3) ; UR 1264 (SPE ; MICA CT2) ; UR 50 (EA CT3 ; MICA CT3)

Schedule

  • Kick-off meeting in Paris, November 31, 2012

  • Training session of AlvisAE Annotation Editor in Paris, Spring, 2013.

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