Skip to main content

Advertisement

Table 1 Existential Ruleforms

From: Ultra-Structure database design methodology for managing systems biology data and analyses

Ruleform Description Examples
BioEntity Things that participate in biological processes or are otherwise of biological interest amino acids, chromosomes, gene annotations
Resource A source of information in the system people, lab groups, software, books, output files of computational analyses
Event Instances of some process or occurrence experiments, software invocations, biological processes
Attribute Facets of entities that are of in terest mass, length, atomic number, statistical scores, GenBank accession number
Relationship Binary relationships (predicates) that can exist between entities of the system is-a, part-of, has-exon, overlaps
Location General idea of a location or address; where an entity can be found in a variety of spaces genomic locations, lab freezer locations, intracellular locations, geographic coordinates
Location Context A location space; the framework in which a Location can sensibly be interpreted 18th draft human genome coordinate, 17th draft human genome coordinate, Giddings Lab freezer, Earth latitude and longitude
Unit A unit of measurement dalton, kilogram, meter
  1. Several existential ruleforms (declaring the existence of various entities in the system) are described, with illustrative examples.