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Dear Till,
I hope you are well and that I am not bothering you too much. I am working on DNA metabarcoding of the stomach contents of Atlantic bluefin tuna by amplifying partial fragments of the COI …
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This may be a duplicate but I haven't found it yet
```YAML
host_taxid:
has_raw_value: Brachypodium distachyon [NCBI:txid15368]
term:
id: NCBI:txid15368
name: Brachypodium…
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I submitted Bakta annotations to NCBI this week and over half had some fatal errors. They weren't hard to fix, but I wanted to let you know in case there's something that can be done with a future upd…
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As per link below, NCBI have changed the 'country' qualifier to 'geo_loc_name', which mean the `ncbi_byid()` function no longer parses the XML and produces a 'country' field.
[https://ncbiinsights.…
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Great tool ! I wonder if taxor can be used to index NCBI nt sequences ? Based on the documentation, taxor build uses the ftp link in the file (third column) to download the reference sequence from NCB…
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1. Use the taxid field of the UCSC JSON to create links like https://www.ncbi.nlm.nih.gov/datasets/taxonomy/5866
1. Make the species link to to the NCBI taxonomy page.
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- At the moment we just split ncbi's ncbiGeoLocation field into division = geoLocAdmin1 and country=geoLocCountry. The division could still be further split into geoLocAdmin1 and geoLocAdmin2, e.g.
…
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Hello, I am trying to build a database for taxor using ncbi refseq sequences from Prokaryotes, Archaea, Bacteria, Virus and Fungii (almost 50k orgamisms in total).
` taxor build --input-file ../../t…
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I worked a bit on the labelling matching with ENA / NCBI as I had a lot of mismatch issues with the development of the FAIR Data Station. I forked the repo and did an analysis on the terms in MIxS and…
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Please update the `download_summary.py` script so that if the `current_folder` and `previous_folder` columns are identical is produces an error message in the `error_flag` column.
For example, in …