Biodados Web services

Biodados Web services


LCAWS | GetAllChildren | TaxSimple

Welcome to our Web services page!

NCBI taxonomy database is a very comprehensive source of information which contain invaluable information on clade relationships. However, they are provided in flat TXT files with data organized in a hierarchical structure. Such data disposition hampers its use in local Bioinformatics applications since a considerable programming effort is required to build loading and searching routines. Here we provide three services to assist in the usage of this invaluabe resource in Bioinformatics applications.


LCAWS
DESCRIPTION: LCAWS service is intended to be a extremely fast way to find the lowest common ancestor of two or more taxa. This service was build in order to assist our study on gene origins.
INPUT:A requisition in SOAP format containing a set of taxonomic IDs.
OUTPUT:Taxonomic information related to the LCA (Lowest Common Ancestor) of the given set of IDs.
WSDL:http://merengue.icb.ufmg.br:8080/BioToolsService/services/lca?wsdl
REST:This service is also available as a REST Web service. Sample REST request: http://merengue.icb.ufmg.br:8080/BioToolsService/lca/9606+10096
OBS: The first response may return a ”no rank” node, but it also adds the next ranked node in the lineage, so users can add up counts to family, order, class, etc.


GetAllChildren
DESCRIPTION: This Web service returns all descendants which have a genome id associated for a given clade of a named organism, e.g. print all genome taxonomic IDs belonging to the order of Apis mellifera.
INPUT:A string represeting the tax ID of a given NCBI Taxonomy node.
OUTPUT:Taxonomy information of all genome taxonomic IDs which are descendants of the given taxon.
WSDL: http://merengue.icb.ufmg.br:8080/BioToolsService/services/taxonomy?wsdl
REST:This service is also available as a REST Web service. Sample REST request: http://merengue.icb.ufmg.br:8080/BioToolsService/taxonomy/getAllChildrenGenomeTaxIds?taxId=314146


TaxSimple
DESCRIPTION: TaxSimple is a database table which allows fast and easy taxonomy related queries built upon even distant tree nodes. The TaxSimple building script downloads the NCBI's flat TXT files containing taxonomic information and transforms it into a table of fourteen columns. In order to accomplish this task, it discards non popular and 'no rank' clades, then building a simpler taxonomic hierachy, based only on the most popular nodes. It includes the thirteen columns (each for a rank) plus a latest column named “genome” which holds the taxonomic ID of the sequenced organism (species, subspecies, strain, etc.).
VERSION:20120929
DOWNLOAD:taxsimple_20120929.tar.gz
OBS: TaxSimple is not distributed as Web service but as a SQL script containing the create table command. As new versions of NCBI taxonomy database are released, TaxSimple will be updated and made available on this page.


Attention
In order to use the services presented above, you will need to know how to make a SOAP client in your preferred language. If you don't know how to do it, please refer to one of the documents below:


Contact:
Phone: +55 31 3499-2654
miguel@icb.ufmg.br