http://uri.neuinfo.org/nif/nifstd/birnlex_591

2007-06-03

For some of the more specific instances of isogenic status used to classify inbred strains, there is an implied subsumptive graph - e.g., a Recombinant_congenic_strain is a type_of Congenic_strain where the congenic cross includes at least one recombination-derived mutation. This means there is a form of inference the owl:DistinctMembers declaration may invalidate. Since this enumerated class is considered temporary and not the appropriate manner in the long-term to present this information to a reasoner, these instances will be treated as a flat, non-hierarchical list for now.

http://uri.neuinfo.org/nif/nifstd/readable/pending_final_vetting

A taxon (plural taxa), or taxonomic unit, is a name designating an organism or group of organisms. A taxon is assigned a rank and can be placed at a particular level in a systematic hierarchy reflecting evolutionary relationships. A distinction is to be made between taxa/taxonomy and classification/systematics or the evolutionarily organized classification, cladistics. The former refers to biological names and the rules of naming, and as such, can be somewhat arbitrarily applied in regards to an organism's location in a phylogenetic classification scheme. The latter refers to rank ordering of taxa according to presumptive evolutionary (phylogenetic) relationships inferred based on organism characteristics such as adult or developmental morphology, DNA sequence, enzymatic pathways, ecosystem relations to other organisms, etc.. A prefix is used to indicate a ranking of lesser importance. The prefix super- indicates a rank above, the prefix sub- indicates a rank below. In zoology the prefix infra- indicates a rank below sub-. Note that rank is relative, and restricted to a particular systematic schema. For example, liverworts have been grouped, in various systems of classification, as a family, order, or a class. The use of a narrow set of ranks is challenged by users of cladistics; for example, the mere 10 ranks traditionally used between animal families (governed by the ICZN) and animal phyla (usually the highest relevant rank in taxonomic work) often cannot adequately represent the evolutionary history as more about a lineage's phylogeny becomes known. In addition, the class rank is quite often not an evolutionary but a phenetical and paraphyletic group and as opposed to those ranks governed by the ICZN, can usually not be made monophyletic by exchanging the taxa contained therein. This has given rise to phylogenetic taxonomy and the ongoing development of the PhyloCode, which is to govern the application of taxa to clades.

http://uri.neuinfo.org/nif/nifstd/readable/Bill_Bug

http://uri.neuinfo.org/nif/nifstd/readable/pending_final_vetting

http://uri.neuinfo.org/nif/nifstd/readable/Wikipedia_defSource

This is not a role in the BFO since. Moving these to the Enumeration class type - and all the taxon types will be defined as instances - just as with the other EnumerationClasses being used in AnnotationProperties (BB: 2007-06-07).

TaxonRank

2007-06-03

For some of the more specific instances of isogenic status used to classify inbred strains, there is an implied subsumptive graph - e.g., a Recombinant_congenic_strain is a type_of Congenic_strain where the congenic cross includes at least one recombination-derived mutation. This means there is a form of inference the owl:DistinctMembers declaration may invalidate. Since this enumerated class is considered temporary and not the appropriate manner in the long-term to present this information to a reasoner, these instances will be treated as a flat, non-hierarchical list for now.

This is not a role in the BFO since. Moving these to the Enumeration class type - and all the taxon types will be defined as instances - just as with the other EnumerationClasses being used in AnnotationProperties (BB: 2007-06-07).

http://uri.neuinfo.org/nif/nifstd/readable/pending_final_vetting

TaxonRank

As stated in the definition of this class (derived from Wikipedia), assignment of taxon type has been somewhat unlinked to putative phylogenetic relations, since some taxon assignments go back to the 19th century, when naming conventions were largely guided by relational morphological analysis, though even that was not necessarily applied systematically when choosing a taxon specifier. In BIRNLex, the Taxon assigned to an organism will be that commonly used by biologists in general, as given in the NCBI Taxonomic classification. As stated at the NCBI Taxonomy site, this representation does not provide a well-founded ontology of organism taxonomy, but is rather empiracally oriented, based on the needs of most biologists.

http://uri.neuinfo.org/nif/nifstd/readable/EnumerationClass