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The version of NCBI used in BioNames is old, and in addition to the addition of taxa some have been deleted. For example, BioNames has:
http://bionames.org/taxa/ncbi/158801 Octopus kagoshimensis
http…
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PyCogent provided this [support](https://github.com/pycogent/pycogent/blob/master/cogent/parse/ncbi_taxonomy.py), and is useful for getting NCBI Taxon ID and rank information. The files consumed are p…
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I did some poking around with respect to HCV, GlyGen, and the NCBI Taxonomy:
* HCV-H glycans are from dataset GLY_000335, which provides the uniprot
tax id as taxid 63746. This is NOT a species, s…
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**Current term details**
Currently the term host_taxid is specifically for the NCBI taxonomy, should we expand this to allow use of other species taxonomies?
```
Term name - host taxid
Term ID -…
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Now that `INDEX:DOWNLOAD_BLAST_DB` reads from AWS, the biggest bottleneck in the index workflow is `INDEX:MAKE_HUMAN_VIRUS_DB:GET_HV_DESCENDENTS`. This relies on the NCBI script `gimme_taxa.py`, which…
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I used this command to download taxonomy:
kraken2-build --download-taxonomy --db $DBNAME --threads 24
and the error message showed like this:
Downloading nucleotide gb accession to taxon map...rs…
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### Task Description
Currently, the Taxonomy Importer does two things
1. It queries NCBI to pull properties for organisms in Chado
2. It constructs a taxonomic tree using the information from N…
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- [ ] Create a function that takes a vector of genera and returns another vector of the same length and order, providing NCBI taxid wherever possible and wherever unknown.
- [ ] save taxids in the …
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At the top level, 'Archaea' is labeled as 'Archeobacterium':
NCBI taxonomy lists it as 'Archaea' or 'Arc…
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http://www.ncbi.nlm.nih.gov/pubmed/25209669
'Our phylogenetic analyses recognize Euharamiyida as the sister group of Multituberculata, and place Allotheria within the Mammalia.'
currently NCBI taxon…