Genome Property Definition Page

Namegenome properties
DescriptionProperties of organisms whose genomes have been sequenced. These properties include those whose state can be supported by inference from the genomic data itself as well as those supported by experimental observations. Properties are organized in a type of heirarchy called a Directed Acyclyic Graph (a DAG) in which child terms may have multiple parent terms. Thus, for instance, a property for the biosynthesis of a particular cofactor may be found as a child of both "biosynthesis" and "protein cofactors". Properties come in several types: PATHWAY properties describe metabolic pathways in which a series of enzymes convert substrates into products to produce desirable substances and/or degrade undesirable ones. A set of these steps have been determined to be both 1) unambiguously indicative of the property and 2) as universally detectable as is practical among the species believed to have this pathway active. The presence or absence of these steps in a genome are used to judge the status of the property. Those genomes with all of the set present are given the "YES" state, those with none are given the "NONE FOUND" state. Each pathway may be be given a threshold number of detected steps below which the state "NOT SUPPORTED" is assigned. Otherwise, the state "INCOMPLETE" is assigned. Under certain circumstances of additional evidence (such as the presence of a complete alternative pathway) a "NONE FOUND state may be strengthened to "NO". SYSTEM properties work in essentially the identical way, except they may not represent a metabolic pathway. In both of these cases the "value" field will hold a number representing the fraction of steps used to assign the state of the property which were found in the genome. MARKER properties are similar except that only a single type of protein is detected and serves as an indicator for the presence of a property. Here the value field holds the number of times the marker was detected in the genome. In all three of these types, other proteins outside of the set chosen for determineing the state of the property may also be detected. These may include proteins which are presently detectable only in some species, auxilliary or variable components, regulatory components, etc. Accessions of all of the detected proteins are stored for user retrieval. LITERATURE properties are set based on experimental evidence, not on the content of the sequenced genome. These properties may detect associated proteins which are stored as above. These may also store a number in the value field where apropriate. QUANTITATIVE properties are calculated from the sequenced genome and store a numeric quantity in the "value" field. TAXONOMY properties store information about the taxonomic classification of the organism. These are based on NCBIs taxonomy database and are used for organizing the output of properties queries to look for trends based on phylogeny. SUMMARY properties are parent properties of one or more related properties whose states are summarized in the state of the parent property. CATEGORY properties do not have states, but organize the properties through parent-child relationships.
Literature References
[ 1 ]Haft DH, Selengut JD, Brinkac LM, Zafar N, White O  Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics.  Bioinformatics 2005 Feb 1;21(3):293-306. Epub 2004 Sep 3.  PMID 15347579

Child Properties
GenProp0064biological niche
GenProp0066selfish genetic elements
GenProp0067quantitative content
GenProp0069cell surface component
GenProp0073cell motility
GenProp0076DNA handling
GenProp0167cellular growth, organization and division
GenProp0475Unknown biological process
GenProp0551regulatory systems
GenProp0864response to external environment
GenProp1048quorum-sensing, biofilm formation, and developmental systems
GenProp1067Defense systems