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.

Search (from the web form)

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

Search from the Web Form

Enter the words and/or numericals into the box, then click the “send” button or press the “Enter” key.

• “Wild Card” (“?” stands for any single character, and “*” for any number of characters) is available.

• Boolean Operators (AND, OR, NOT) can be entered as follows.

  AND	“space”　or “AND” or “&&”
  OR	“OR” or “		”
  NOT	“NOT”

• To use the “Example” is an easy way.

  • (1) Click the “Example” under the search box, some examples are displayed.
  • (2) Select the one and click it, then its text is entered into the search box.
  • (3) Modify the text to suit your purpose. (e.g. organism names, taxonomy_id)

• Default search fields are as follows.

  tax_id	anamorph	in_part
  scientific_name	teleomorph	includes
  common_name	authority	misnomer
  synonym	blast_name	misspelling
  acronym	equivalent_name	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.

Refine Search

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

• 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, specified field is searched. When the field is not specified, all these field is searched.
  lineagerank	To search these fields, you need to specify the field-name and its value.

• Exact matching, please specify the field name 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

Search Examples

Search Result

Search Result (Taxon Information screen)

This is the result screen of the search by the web form.

• 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 Screen

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

• (1) scientific name links to Taxon Information screen.
• (2) taxonomy id links to NCBI Taxonomy Browser.
• (3) Delta icon left side of scientific name developes taxonomic tree of lower rank.
• (4) The right hand arrow icon of top scientific name developes upper level tree.
  If you click it, more 1 ranks are displayed.
• You can change 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/or link to the Taxon Information page.

When including taxonomy_id in URL