A scenario parser uses this graph to generate a scenario specific reasoner.
This is why, in Fig. 10, we detail the decomposition of parsing time over each Atomic parser used internally by a specific generated translator.
For the purpose of reducing the proliferation of unwanted parse trees, and collecting information necessary for generating the semantic representations, the parser uses rules based on phrasal and lexical subcategories.
The proposed model can be applied to any type of application but the parser used to extract the information was developed specifically for environmental science applications, that is it takes into account the specific environmental input and output data, as well as the algorithms used in this field.
The NLR parser uses a variety of biologically defined input motif compositions to search the MAST xml-format output and report on confirmed NLRs only.
First, a set of syndromes in an existing JHU-APL CC parser used in civilian versions of ESSENCE were selected for evaluation.
As this parser uses Briscoe & Carroll-style grammatical relations, in addition to the expected head and dependent tokens, some grammatical relations include a type token (http://www.sussex.ac.uk/Users/johnca/grde scription/index.html).html
The Blast parser used for accessing the Blast outputs as well as the PAML wrapper and parser necessary for obtaining Ks values according to Yang and Nielsen [ 46] was done with the help of several BioPerl packages ([ 47], version 1.5.2. from December 2006).
It comes equipped with data integration modules that load data from common biological formats (e.g. GFF3, FASTA, OBO, BioPAX, GAF, PSI and chado see Supplementary Material for a full list), while custom sources can be added by writing data parsers using the Java application programming interface (API) or by creating XML files in the appropriate format, for which a Perl API exists.
A comparison of processing times of SENNA and other SRL systems or syntactical parsers used in the biomedical domain revealed that SENNA is the fastest Proposition Bank (PropBank) conforming SRL program currently available.
