There are several useful terms and phrases indexed in the [prop] field. Possible search strategies that specify the prop field are explained below.
(1) Using functional nametypes and classifications
unspecified [prop] not identified at the species level
uncultured [prop] environmental sample sequences
unclassified [prop] listed in an “unclassified” bin
incertae sedis [prop] listed in an “incertae sedis” bin
We do not explicitly flag names as “unspecified” in TAXON; rather, we rely on heuristics to index names as “unspecified” in the properties field. Many are missed. Taxa are indexed as “uncultured” if they are listed within an environmental samples bin or if their scientific names begin with the word “uncultured”.
(2) Using rank level of taxon
All of these search strategies below are valid. Taxonomy Entrez displays only taxa that are linked to public sequence entries, and because sequence entries are supposed to correspond to the Taxonomy database at or below the species level, the Entrez query: terminal [prop] NOT “at or below species level” [prop] should only retrieve problem cases.
above genus level [prop]
above species level [prop]
“at or below species level” [prop] (needs explicit quotes)
below species level [prop]
terminal [prop]
non terminal [prop]
(3) Inherited value assignment points
genetic code [prop]
mitochondrial genetic code [prop]
standard [prop] invertebrate mitochondrial [prop]
translation table 5 [prop]
The query “genetic code [prop]” retrieves all of the taxa at which one of the genomic genetic codes is explicitly set. The second query retrieves all of the taxa at which one of the mitochondrial genetic codes is explicitly set, and so on.
division [prop]
INV [prop]
invertebrates [prop]
The above terms index the assignments of the GenBank division codes, which are divided along crude taxonomic categories (see Chapter 1). We have placed the division flags in the database so as to preserve the original assignment of species to GenBank divisions.
From: Chapter 4, The Taxonomy Project
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