PMI Knowledgebase has an established data acquisition and management framework that enables project field-studies and the derived data to be efficiently collected, curated and mined in a streamlined workflow. Currently the system supports various types of data from raw soil readings to tree specification to post-processed data like 454 sequences, isolates, experimental image data, ASCII-based text files, binary blobs etc.
Various PMI sub-teams have identified and standardized their experimental protocol and data acquisition processes. These processes capture data provenance, source hierarchy and protocol. These processes are termed as "PMI Workflows". Following are some of the PMI Workflows that are currently tracked and cataloged by PMI internal knowledgebase.
PMI Metabolomics workflow is a scientific study of chemical processes involving metabolites. Specifically, we perform a systematic study to identify unique chemical fingerprints that specific cellular processes leave behind. The metabolic profiling can give an instantaneous snapshot of the physiology of that cell. Details
These workflows are intended to preserve and share records and data from DNA sequence based microbial community analyses for the PMI project. Primarily these will include rRNA gene ampli5=1con sequencing generated by pyrosequence based analysis, but may also include important protein coding genes (e.g. AmoA - ammonia monooxygenase) or Sanger sequence based information. Details
The primary workflow is to extract the proteins from the biological sample, digest those proteins into smaller peptides using trypsin or another proteolytic enzyme, and then analyze those peptides using nanoscale high-performance liquid chromatography interfaced with tandem mass spectrometry (LC-MS-MS). Computer analysis of the resulting data provides identification of the peptides and proteins in the biological sample, and semi-quantitative estimates of their abundances. Details
Transcriptomics in the PMI involves precise measurements of RNA content in eukaryotic (plant or yeast) or prokaryotic (bacterial) cells. Details
The bacterial strain typing workflow is intended to provide 16S rDNA sequencing and analysis of bacterial taxonomy for strains isolated from Populus root and rhizosphere samples within the PMI project. Details
Whole Genome Sequencing is DNA based. DNA is extracted from prepared and extracted from samples. Details