Click “TogoWS”
TogoWS is a web service that enables users to access and utilize major biological databases (such as those maintained by NCBI, EBI, DDBJ, KEGG, PDBj and CBRC) without any additional software to create interoperable workflows.
Since TogoWS caches data retrieved previously, repeated access does not influence the performance of the original database (resource). Rather, TogoWS aims to be server friendly by decreasing the load on the resource.
Although TogoWS provides SOAP and REST services, this tutorial will focus on how to use the REST service.
Click “REST service”
The TogoWS REST service enables users to retrieve information from a database by specifying the database name and ID or entry, as parameters in a URL.
URL requests of the major biological databases are listed here as examples.
Let’s see what we can do with a REST request.
In this example, we will retrieve information from PubMed.
The database name parameter is specified as “PubMed”
These numbers specify PMIDs.
Click the first URL (http://togows.dbcls.jp/entry/pubmed/16381885).
It will display a list of information including author names and abstract of the article assigned as PMID 16381885.
To retrieve the same information in XML format, add “.xml” after the PMID in the URL, as in the second example.
The same information is now displayed in XML format.
This method is useful to retrieve information of known PMID(s).
Now referring to the example URL, let’s retrieve the information on PMID 18430990.
Click the first example URL again.
Delete the numbers following “pubmed/” and type “18430990” in the URL.
Hit the return key.
Now the list displays information on PMID 18430990.
Specific fields of the list can also be retrieved.
For example, adding “/ti” after the PMID in the URL,
will retrieve the title of the article.
Instead of “/ti”, adding “/abstract” after the PMID in the URL,
will retrieve the abstract (without line breaks) of the article.
Adding “/au” after the PMID in the URL,
will retrieve the author name(s) of the article.
Adding “/so” after the PMID in the URL,
will retrieve the journal name of the article.
Similarly, MeSH terms assigned to the article can also be retrieved.
Add “/mesh” after the PMID in the URL.
The MeSH terms indexed to PMID 18430990 are retrieved.
By changing the database name parameter, information can be retrieved from other biological major databases provided by NCBI, EBI, DDBJ, KEGG, PDBj and CBRC.
統合TVは、ライフサイエンス統合データベースセンター(DBCLS)が発信する生命科学分野の有用なデータベース(DB)やウェブツールの活用法を動画で紹介するウェブサイトです。くわしくは はじめての方へ をご覧ください。ご意見、ご要望は、お問い合わせ からお願いします。TogoTV beta ('togo' means 'integration' in Japanese) is an archive of tutorial videos expounding how to use biological databases and tools. Although most of contents are currently depicted in Japanese, you can find English contents here. Please post any comments, suggestions, and requests at each content page, e-mail to the address described at the bottom of each page or contact form. This site is provided by Database Center for Life Science (DBCLS) and funded by MEXT Integrated Database Project in Japan.
