Biomedical Engineering Reference
In-Depth Information
pathogens for non-human animals that acquire a mutation that confers trans-
missibility to humans or between humans; nomenclature changes, wherein an
old name is replaced with a new name. Although completeness is a worthy
goal, you can expect some omissions in this Appendix.
For each genus listed in the Appendix, the taxonomic hierarchy is pro-
vided. The value of the hierarchy is that readers can instantly see the succes-
sion of parent classes for the genus. If you know something about the parent
classes, you also know something about the lower genera; that is the basic
premise of this topic. Hierarchies were produced by a short computer pro-
gram, previously published by the author [1,146]. The program utilizes the
ancestral information contained in the publicly available taxonomy file used
by the European Bioinformatics Institute (EBI). The EBI taxonomy file con-
tains over 400 000 species, and each record in the file contains the name of
the species, an identifier for the species, and an identifier for the parent
(superclass) for the species.
Here is part of a sample record in the publicly available Taxonomy file:
ID: 50
PARENT ID: 49
RANK: genus
SCIENTIFIC NAME: Chondromyces
The sample record provides an ID number for the entry organism,
Chondromyces, and for its parent class. Since every organism and class has a par-
ent (i.e., every parent has a parent up to the root of the classification), a computer
program can reconstruct the full parental lineage for one organism, or a list of
1400 organisms. The EBI taxonomy file is available for public download through
anonymous ftp, from the EBI server:
ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/
.
The computer output is listed below. Each record contains the name of a
genus known to contain infectious species. This is followed by the list of
species, for the genus, that are infectious, and the ancestral lineage for the
genus. Students and clinicians can inspect the organisms in the Appendix
and quickly learn the higher taxa to which they apply. Applying knowledge
of higher taxa will allow readers to infer something about the biology of the
lower species, and will help direct
the student
to the most appropriate
resources in the printed literature or on the Web.
Abiotrophia
Species: Abiotrophia defectiva
Hierarchy: Abiotrophia: Aerococcaceae: Lactobacillales: Bacilli:
Firmicutes
Acanthamoeba
Species: Acanthamoeba rhysoides, Acanthamoeba polyphaga,
Acanthamoeba palestinensis, Acanthamoeba hatchetti, Acanthamoeba
culbertsoni, Acanthamoeba castellani, Acanthamoeba astronyxis
