dfornika/LexMapr

LexMapr: A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology Terms

LexMapr

A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology Terms

Build status

The main script file for processing is bin/lexmapr

Dependencies

• nltk
• inflection
• wikipedia
• python-dateutil

Usage

usage: lexmapr [-h] [-o [OUTPUT]] [--format FORMAT] input_file [log_file]

positional arguments:
  input_file            Input csv file
  log_file              Log file

optional arguments:
  -h, --help            show this help message and exit
  -o [OUTPUT], --output [OUTPUT]
                        Output file
  --format FORMAT       Output format

Example input files (in lexmapr/tests/input)

Filename	Description
small_simple.csv	A small simple test dataset
enteroForFreq.csv	Dataset from EnteroBase
genomeTrackerMaster.csv	Dataset from GenomeTrakr
bccdcsample.csv	Dataset from BCCDC
zheminSamples.csv	Zhemin's samples from EnteroBase
GRDI-UniqueSamples.csv	Dataset from GRDI

Resources Files (in lexmapr/resources)

Filename	Description
CombinedResourceTerms.csv	All the ontology terms with their ids extracted and combined in a single file
SynLex.csv	Synonym Lexicon
AbbLex.csv	Abbreviation/Acronym Lexicon
NefLex.csv	Non English FoodNames Lexicon
ScorLex.csv	Spellings correction Lexicon
SemLex.csv	Semantic Tagging Lexicon
inflection-exceptions.csv	Exception list for avoiding false positives during inflection treatment
candidateProcesses.csv	Additional processes which are candidates for inclusion
wikipediaCollocations.csv	Additional compound terms (collocations) detected out of datasets which are candidates for inclusion
mining-stopwords.csv	Stop Words list for treatment refined for domian under consideration