Integration and use of bioinformatic Web Services publicly available

Several bioinformatic Web Services are publicly available to query genomic and proteomic heterogeneous biomedical data, such as BLAST to search for nucleotide and amino acid sequences in gene and protein databanks, ArrayExpress to query gene expression data, UniProt to search in the UniProt databank for proteins related with search keyword(s), PubMed to search for scientific publications, etc. These services allow answer to simple user query, providing results that often include an appropriateness ranking score of the performed query.

Aim of this project is analyze some of such services and develop a software framework that, using the APIs available for using these services, integrates the results these services provide; the purpose is supporting complex and multi domain queries, with added value for the user, which are not directly executable on the single services.
Given a selected group of services (such as those above cited), it will be required to:

• Analyze the selected services, identifying their different way of querying
• Identify and "map" on the single services some examples of possible complex queries of interest
• Identify possible refinements or expansions of the initial query that can be executed by the user starting from the results of the initial query, with the aim of navigate and use at best the data exposed by the selected services
• Create a simple web application that supports the execution of such complex queries.

The project activity has an explorative nature, thus a frequent interaction with the project referent is suggested. Suitable software tools will be provided in order to ease the development of the integrated web application.
The software will be implemented in Java, Javascript and HTML programming languages.

References:

• BLAST:
  • http://www.ebi.ac.uk/Tools/webservices/services/wublast
  • http://blast.ncbi.nlm.nih.gov/blast_overview.shtml#access
  • http://www.ncbi.nlm.nih.gov/sutils/static/blinkhelp.html
• ArrayExpress:
  • http://www.ebi.ac.uk/microarray/doc/help/programmatic_access.html
  • http://www.ebi.ac.uk/microarray/doc/atlas/api.html
  • http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686529/
• UniProt:
  • http://www.uniprot.org/
• PubMed:
  • http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/eutils_help.html
  • http://www.ncbi.nlm.nih.gov/entrez/query/static/esoap_help.htm