Sentence examples for parsing database from inspiring English sources
Perl (version 5.8.6) and Perl CGI (please see Availability and requirements for more information) scripts were written for data file parsing, database loading and to create web-interfaces connected to the database using the perl modules DBI and DBD::mysql (please see Availability and requirements for more information).
All user queries are processed by Perl CGI scripts that execute database queries, parse database outputs and deliver results as HTML pages.
It's really not necessary to know all the ins and outs of all kinds of programming languages, since all a bioinformatician does is text parsing and database management.
To distinguish these connections, we parsed our database of cross-covariance functions, and extracted functions that had peak delays between 1 and 4 ms, and halfwidths less than 10 ms (Fig. 11A,B: example cross-covariance functions).
Since ApiLoc does not provide web service interface, we download and parse the database without scripts.
Our parse tree database is managed by MySQL containing ∼17 million Medline abstracts.
The syntactic and semantic information of sentences are stored in our parse tree database and extraction is performed by means of database queries.
As the model is parsed, the database is accessed using the Data Access Library that contains the object-oriented wrapper classes and their functions.
The translated SQL queries are evaluated against the parse tree database so that the returned information is the intended interactions from abstracts.
> In the extraction phase, drug-protein interactions such as < protein, metabolizes, drug> and protein protein interactions such as < protein, regulates, protein> are extracted from the parse tree database.
But it's also a long way from what Watson was created for: to use that prodigious ability to parse massive databases of natural-language information to act as an aid to humans in highly technical areas, working alongside them rather than competing with them to be the best.
