Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases

TitleDevelopment of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases
Publication TypeJournal Article
Year of Publication2007
AuthorsBarbosa-Silva, A, Pafilis E, Ortega JM, Schneider R
JournalGenetics and Molecular Research
Volume6
Issue4
Pages1142 - 1150
KeywordsData integration, Sequence Retrieval System, SOAP, Web services, XML
Abstract

Data integration has become an important task for biological database providers. The current model for data exchange among different sources simplifies the manner that distinct information is accessed by users. The evolution of data representation from HTML to XML enabled programs, instead of humans, to interact with biological databases. We present here SRS.php, a PHP library that can interact with the data integration Sequence Retrieval System (SRS). The library has been written using SOAP definitions, and permits the programmatic communication through webservices with the SRS. The interactions are possible by invoking the methods described in WSDL by exchanging XML messages. The current functions available in the library have been built to access specific data stored in any of the 90 different databases (such as UNIPROT, KEGG and GO) using the same query syntax format. The inclusion of the described functions in the source of scripts written in PHP enables them as webservice clients to the SRS server. The functions permit one to query the whole content of any SRS database, to list specific records in these databases, to get specific fields from the records, and to link any record among any pair of linked databases. The case study presented exemplifies the library usage to retrieve information regarding registries of a Plant Defense Mechanisms database. The Plant Defense Mechanisms database is currently being developed, and the proposal of SRS.php library usage is to enable the data acquisition for the further warehousing tasks related to its setup and maintenance.

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