- About PMN
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- Pathway Tools Biocyc Bundle
SAVI is a Semi-Automated Validation and Integration pipeline designed to select the final set of pathways contained in the database for each species
The SAVI pipeline uses the inital set of pathways predicted by the Pathologic program for a given plant species, the enzyme predictions from E2P2 for the species, and six sets of pre-sorted SAVI pathways to generate the final set of pathways in each species-specific database. These pathways describe the basic "primary" metabolism shared throughout the plant kingdom and also provides access to experimentally verified and computationally-predicted specialized (secondary) metabolic pathways.
Ubiquitous land Plant Pathway (UPP) 8.00
Non-PMN Pathway (NPP) 8.00
Common Viridiplantae Pathway (CVP) 5.00
Conditionally Accepted PMN Pathway (CAPP) 5.00
Accept-if-Predicted Pathway (AIPP) 5.00
Manually Check Pathway (MCP) 2.00
The SAVI pathway sets are used to help expedite the validation and new pathway integration process when generating new single-species databases. These lists are not comprehensive and grow over time as more pathways are reviewed and created.
These SAVI pathway lists are updated during the preparation of each new PMN release and current and archived versions are available at our ftp site.
The Ubiquitous land Plant Pathway (UPP) list contains pathways that are expected to be present in all "land"plants, also referred to as "higher" plants or Embryophyta.
The UPP list can be used to:
The Common Viridiplantae Pathway (CVP) list contains pathways that are expected to be present in all or most Viridiplantae species including algae. The CVP is a subset of the UPP.
The CVP list can be used to:
The Non-PMN Pathway (NPP) list contains pathways that are excluded from PMN databases for several reasons including:
The NPPs are automatically removed whenever they are predicted for new species using the Pathologic program
The Accept-if-Predicted Pathway (AIPP) list contains pathways that are automatically accepted if they are predicted for any plant species database, similar to the UPP or CVP.However AIPP pathways are not automatically imported into databases if they are not predicted by the Pathologic program.
AIPPs are chosen based on several criteria including:
The Conditionally Accepted PMN Pathway (CAPP) list contains pathways that are only accepted if they are predicted by the Pathologic program and meet additional criteria assigned to each pathway by PMN curators. Each CAPP can have criteria based on reactions and/or expected taxonomic range that are used to determine whether it should be accepted for a given species.
A CAPP taxonomic range criterion is usually added to avoid rejecting true positive pathways when key enzymes are missing due to genome or proteome annotation problems.
The Manually Check Pathway (MCP) list contains a very small number of pathways that are likely to be relevant to the users of the databases and are likely to be reported in published literature for many plant species. The current manual list contains four pathways: three pathways describe different C4 photosynthetic variants and one related to photosynthesis in seeds. Curators attempt to find references to determine whether any of the pathways on this list exist in a given species whenever they are predicted using the Pathologic program