NCBI Taxonomy Browser

Question

[Kidult]

First. I using local blast get the annotation look like this:

---

Agrocybe pediades 18S rRNA gene (partial), ITS1, 5.8S rRNA gene, ITS2 and 28S rRNA gene (partial), isolate 3268 274 276 0.992754

---

Agrocybe pediades Taxonomy Browser look like this: Lineage (full): root; cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Agaricomycetes; Agaricomycetidae; Agaricales; Bolbitiaceae; Agrocybe "Mushroom" is Fungi...? ( At least, I though they are, and the Taxonomy Brower tell me Agrocybe pediades is Fungi) When I Brower "Fungi" and set display level ---- 30 ( it maid be display all the Taxonomy result ?). And Search "Agrocybe" as a keyword, I can't find it in the page...

Here is my question:

1. Why Agrocybe doesn't display in the Fungi Taxonomy Browser Page ?
2. I Brower and Grab the Fungi page, because I want to get a list look like this:

---

eukaryota,Apicomplexa(apicomplexans) eukaryota,Apicomplexa(apicomplexans),Aconoidasida eukaryota,Apicomplexa(apicomplexans),Aconoidasida,Haemosporida(haemosporidians) eukaryota,Apicomplexa(apicomplexans),Aconoidasida,Haemosporida(haemosporidians),Haemoproteidae eukaryota,Apicomplexa(apicomplexans),Aconoidasida,Haemosporida(haemosporidians),Haemoproteidae,Haemocystidium eukaryota,Apicomplexa(apicomplexans),Aconoidasida,Haemosporida(haemosporidians),Haemoproteidae,Haemocystidium,Haemocystidium sp. JPM-2015 eukaryota,Apicomplexa(apicomplexans),Aconoidasida,Haemosporida(haemosporidians),Haemoproteidae,Haemoproteus eukaryota,Apicomplexa(apicomplexans),Aconoidasida,Haemosporida(haemosporidians),Haemoproteidae,Haemoproteus,Haemoproteus anatolicum eukaryota,Apicomplexa(apicomplexans),Aconoidasida,Haemosporida(haemosporidians),Haemoproteidae,Haemoproteus,Haemoproteus balmorali eukaryota,Apicomplexa(apicomplexans),Aconoidasida,Haemosporida(haemosporidians),Haemoproteidae,Haemoproteus,Haemoproteus belopolskyi

---

maybe you can tell me, where i can find this table ? (I call it id_to_taxonomy table)

[Kidult]

Now I can find the Agrocybe pediades in the Fungi Page... it maybe the network problem. But I still want to ask the Question 2. ---- id_to_taxonomy Table

[Michael]

You can download the Taxonomy files from here: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/ But there is no file in exactly that format. You can use Bio packages to parse the taxonomy into the desired formats like BioPerl's Bio::DB::Taxonomy

Answer 1

[Michael]

I don't understand fully what you have been trying, but it is there: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5399

• Go to https://www.ncbi.nlm.nih.gov
• Select Taxonomy
• Enter Agrocybe, Search

[Kidult]

Agrocybe is Fungi，but I Browser Fungi，they don't have Agrocybe in Fungi Taxonomy page（set display levels = 30）.

---

• Go to Taxonomy Browser
• Enter Fungi
• Set display levels == 30
• Go

[Michael]

That must be a local network or firewall problem, I see exactly the same result doing the above:

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=84607&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&lin=f&keep=1&srchmode=1&unlock

I get the same result irrespective of the display levels.

[piet]

that is because Agrocybe is a GENUS and the Fungus page only resolves to the taxonomic level of ORDERS.

[Kidult]

no... I already set the display level, then that Fungi page show me all the level including “sub-”level，I think it just a local network or firewall problem，i use vpn to open that page，Agrocybe were being there.