Databases and Systems

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In SRS, databank structures are represented by Backus-Naur Form (as described
by Wirth [6]) abstract syntax trees or grammars. BNF grammatical rules consist of
terminal and non-terminal definitions. A non-terminal represents a rule and can in
turn be subdivided into terminals and non-terminals. Terminals and non-terminals
group together to form a production. We call a piece of input stream corresponding
to a single terminal a token and a set of tokens a token-list. Biological databank
structures generally use the following scheme: a databank consists of a sequence of
entries, an entry is made of data-fields, a data-field consists of tokens. Tokens are the
part of the input that are parsed by terminals or non-terminals. For instance, a parser
for a databank in an EMBL-like format might look like:
databank = {entry}
entry = id_line
(ra_line de_line oc_line)
end_line
id_line = 'ID' id
de_line = {'DE' word_list)
...
end_line = '//'
word_list = {word}
word = /[a-z]+/
This might operate on a text entry of the (EMBL-like) form:
ID HS40428 1 standard; DNA; HUM; 186 BP.
DE Human tumor suppressor (p53) gene, exon 3
OC Eukaryota; Metazoa; Chordata; Vertebrata
OC Mammalia; Eutheria; Primates
RA Herrmann M., El-Maghrabi R. E., Abumrad N.N.
//
This grammar defines the databank as being a list of entries. The first line of each
entry should be the ID-line followed by zero or more data lines, and the last line is
the string ‘//’. The non-terminals id_line, de_line and oc_line can be recursively
parsed and finally indexed.
Icarus parsers not only recognize entries, but can also perform some semantic
actions during the parsing process. To produce output, any terminal or non-terminal
can be associated with one or more different action commands, such as create a
token, extend (add text to) existing tokens, set some global states of the parsing
process, input/output directives, print commands, variable assignments and function
calls.
Parsers generally parse all they can, i.e. they decompose the input starting with
the root production and go on recursively until having only terminals. In SRS, this
scheme is referred to as forced parsing. This is in opposition to lazy parsing, in