Last updated:2015.8.31.

TXSearch HELP

About TXSearch

TXSearch is a NCBI Taxonomy retrieval system provided by DDBJ. When you submit nucleotide sequence data to International Nucleotide Sequence Database(INSD), you need to use the organism name description based on NCBI Taxonomy.

What you can do using TXSearch

How to Use TXSearch (from the web form)

Taxonomy Search

Top(Tree ):http://ddbj.nig.ac.jp/tx_search/

txhelp01_top-e

Search from the Web Form

Enter the words and/or numericals into the box, then click the "send" bottun or press the "Enter" key.

txhelp03-searchbox

  • A space between 2 words/numericals works as "AND".
  • To use the "Example" is an easy way.
  1. Click the "Example" under the search box, some examples are displayed. (1)
  2. Select the one and click it, then its text is entered into the search box.(2)
  3. Modify the text to suit your purpose. (e.g. organism names, taxonomy_id)(3)
    txhelp02-searchExample
  • Default search fields are as follows.
    tax_id
    scientific_name
    common_name
    synonym
    acronym
    anamorph
    teleomorph
    authority
    blast_name
    equivalent_name
    in_part
    includes
    misnomer
    misspelling
    type_material
     
  • If you search some particular fields、specify the field by refine search.
  • Because the maximum number of results displayed in the screen is fixed in 1000 (in ascending order of scientific_name), to view the all results, please execute the refine search to narrow the number down to 1000.
  • "Wild Card" ("?" stands for any single character, and "*" for any number of characters) is available.
  • Boolean Operaters(AND, OR, NOT) can be entered as follows.
  • AND "space" or "AND" or "&&"
    OR "OR" or "||"
    NOT "NOT"

Refine Search

You can narrow the scope of your search by specifying some paritular fields, and/or combining some field searchs.

  • When the result is more than 1000, please execute the refine search so that less than 1000 is included in the search result (In this system the maximum result display number is fixed as 1000 which is unmodifiable)

  • The description to search a specific field is, field name:value(e.g. tax_id:9606)
  • multiple fields
    Connect "field name:value" units, separating by space (e.g. scientific_name:(Homo Sapiens) rank:species)
  • Following fields can be specified
  • Searchable fields
    tax_id
    scientific_name
    common_name
    synonym
    acronym
    anamorph
    teleomorph
    authority
    blast_name
    equivalent_name
    in_part
    includes
    misnomer
    misspelling
    type_material
    When the field name is specified, soecufied field is searched
    When the field name is specified, specified field is searched. When the field is not specified, all these field is searched.
    lineage
    rank
    To search these fields, you need to specify the field-name and its value.
  • Exact matching
  • Please specify the field names as follows.

    scientific_name_ex
    common_name_ex
    synonym_ex
    acronym_ex
    anamorph_ex
    teleomorph_ex
    authority_ex
    blast_name_ex
    equivalent_name_ex
    in_part_ex
    includes_ex
    misnomer_ex
    misspelling_ex
    type_material_ex

Example

Text what you search
human AND lineage:Mammalia search the taxon which contains "human" in the defauld search fields, and linage is "Mammalia"
human AND rank:subspecies search the taxon which contains "human" in the defauld search fields, and rank is "subspecies"
human AND NOT(lineage:Eukaryota) search the taxon which contains "human" in the defauld search fields, and linage is NOT "Eukaryota"
tax_id:9606 tax_id is 9606
Homo Sapiens search the taxon which contains both "Homo" AND "Sapiens" in the default fields
scientific_name:"Homo sapiens" search the taxon whose scientific_name includes "Homo sapiens"
scientific_name_ex:"Homo sapiens" search the taxon whose scientific_name is "Homo sapiens" (Exact search).
Note: When the search words contains a space, the words should be encloseed in double quotation marks.
scientific_name:(Homo sapiens) search the taxon which contains both "Homo”and "sapiens" in the scientific_name field.
scientific_name:Homo sapiens search the taxon which contains both "Homo”in the scientific_name fiel, and contains "sapiens" in the default search fields.
50000 search the taxon which contains "50000" in the default search fields.
(In this case, both the taxon which contains "50000" in the name, such as "Crinipellis sp. GDGM 50000", and "Sarracenia alabamensis" whose tax_id is "50000" are retrieved. To search either one, you should specify the field name you want to retrieve.
tax_id:(741158 OR 63221)
or
tax_id:(741158 || 63221)
searchs tax_id field either 741158 OR 63221 
scientific_name:(Acetobacter c*) search the taxon which contains both "Acetobacter" and "the strings" containing any number of characters starting with "c" in the scientific_name field.
scientific_name:(Acetobacter sp*) search the taxon which contains both "Acetobacter" and "the strings" containing any number of characters starting with "sp" in the scientific_name field.
tax_id:960? search the tax_id field in 960? (? is one character)

Search Result

Search Result(Taxon Information screen)

This is the result screen of the search by the web form.
txhelp04-result02

  • Scientific name, taxonomy id, rank, division code, genetic code, mitochondrial genetic code, names other than scientific name, and lineage of specified taxonomy id's taxon are displayed.
  • taxonomy id links to NCBI Taxonomy Browser
  • genetic code id, mitochondrial genetic code id links to Genetic code table
  • Each name in the lineage line links to the tree

Tree

Click the name in the lineage, then the tree will be displayed on the screen.
tx_help05result_tree-e

  • scientific name links to Taxon Information screen.(1)
  • taxonomy id links to NCBI Taxonomy Browser.(2)
  • Delta icon left side of scientific name developes taxonomic tree of lower rank.(3)
  • The right hand arrow icon of top scientific name developes upper level tree. If you click it, more 1 ranks are displayed.(4)
  • You can chanage the number of ranks displayed on the browser by the modification of depth parameter value in the URL.

method including taxonomy_id into the URL

You can make the URL which include taxonomy_id. Using this, you can display the search result directly, and/ir link to the Taxon Information page.

Available Parameters

  • id(required item) :taxonomy_id
  • view:Tree or Taxon informatiion
  • depth:number of lanks


id(required item): specifies target taxonomy id.

Example


view: View of Tree of Taxon information. In case of not specified, automatically tree view is selected.

Example


depth:specifies number of hierarchy. Default is 2.

Example

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