# Availabilty of mapping NCBI TaxID to Species name **URL:** \ **Category:** HUMAnN\ **Created:** [January 6, 2023, 11:12am UTC](https://forum.biobakery.org/t/availabilty-of-mapping-ncbi-taxid-to-species-name/4610 "2023-01-06T11:12:09Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![Younous](https://avatars.discourse-cdn.com/v4/letter/y/ee7513/32.png) [@Younous](https://forum.biobakery.org/u/Younous)\ **Post date:** [January 6, 2023, 11:12am UTC](https://forum.biobakery.org/t/availabilty-of-mapping-ncbi-taxid-to-species-name/4610/1 "2023-01-06T11:12:09Z")
Hello, I’m using HUMAnN version 3.6 with all the latest databases for MetaPhlAn, ChocoPhlAn and UniRef90. In the output files we have access, when available, to the species to which genefamilies are associated. This information can be very usefull but the species name often doesn’t match the NCBI name, making the comparison of species names from other sources very difficult. So I was wondering if a mapping file between “NCBI TaxID” and “Species name” was available. I found in this [topic](https://github.com/waldronlab/curatedMetagenomicData/issues/245) links to two files containing the information I need ([mpa\_v30\_taxonomy.txt](https://github.com/waldronlab/curatedMetagenomicData/files/6649324/mpa_v30_taxonomy.txt) and [mpa\_v30\_CHOCOPhlAn\_201901\_taxonomy.txt.gz](https://github.com/seandavi/MungeCuratedMGS/blob/master/inst/extdata/mpa_v30_CHOCOPhlAn_201901_taxonomy.txt.gz)), but they seem out of date. Indeed, many species available in ChocoPhlAn are missing from these mapping files. I’m using ChocoPhlAn v201901\_v31. Is there somewhere an up-to-date version available? Thank you very much in advance, Younous ---
**Author:** ![nickp60](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nickp60/32/1031_2.png) [@nickp60](https://forum.biobakery.org/u/nickp60)\ **Post date:** [January 6, 2023, 3:45pm UTC](https://forum.biobakery.org/t/availabilty-of-mapping-ncbi-taxid-to-species-name/4610/2 "2023-01-06T15:45:52Z")
Not sure about for ChocoPhlAn v201901\_v31, but if you switch to the current version I think you might be looking for [this](https://github.com/biobakery/humann/blob/master/humann/data/misc/mpa_vJan21_CHOCOPhlAnSGB_202103.tsv)? ---
**Author:** ![Younous](https://avatars.discourse-cdn.com/v4/letter/y/ee7513/32.png) [@Younous](https://forum.biobakery.org/u/Younous)\ **Post date:** [January 9, 2023, 12:45pm UTC](https://forum.biobakery.org/t/availabilty-of-mapping-ncbi-taxid-to-species-name/4610/3 "2023-01-09T12:45:28Z")
Thanks a lot for your answer! This is exactly the file I needed. However, it raises two questions to me: 1. I still have missing species in this file. For exemple, in the ChocoPhlAn folder where genomes were downloaded, I have _Acetobacter\_ascendens_ species. But it is absent from the file you shared. On the 12772 species I have in ChocoPhlAn, 9685 are available in the file and 3087 are not. 2. When executing `humann_databases --download chocophlan full ./chocophlan`, it downloads the file [http://huttenhower.sph.harvard.edu/humann\_data/chocophlan/full\_chocophlan.v201901\_v31.tar.gz](http://huttenhower.sph.harvard.edu/humann_data/chocophlan/full_chocophlan.v201901_v31.tar.gz). Is there a vJan21\_CHOCOPhlAnSGB\_202103 version? Maybe that will correspond with the content of the file you shared. ---
**Author:** ![nickp60](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nickp60/32/1031_2.png) [@nickp60](https://forum.biobakery.org/u/nickp60)\ **Post date:** [January 9, 2023, 5:45pm UTC](https://forum.biobakery.org/t/availabilty-of-mapping-ncbi-taxid-to-species-name/4610/4 "2023-01-09T17:45:45Z")
Hmm, I’m not sure then, sorry! I’m also interested in the answer so I’ll be following along to see what the dev team says. ---
**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\ **Post date:** [January 24, 2023, 7:01pm UTC](https://forum.biobakery.org/t/availabilty-of-mapping-ncbi-taxid-to-species-name/4610/5 "2023-01-24T19:01:27Z")
It sounds like you might be using MetaPhlAn 4 with HUMAnN 3.6? If so, please see this discussion: > [@Metaphlan4 species not included in Humann3.5 output?](https://forum.biobakery.org/t/metaphlan4-species-not-included-in-humann3-5-output/4542): > > Hi! I noticed that in the Humann3.5 pathway abundance output, only a subset of the Metaphlan4 species are present as contributors to pathway abundance (i.e. SGB species and some others are missing in the pathway file). Is this supposed to be the case? If so, is the Humann3.5 output not representative of all the species present based on the Metaphlan4 genomes? Thank you, Brandi