bdionne / ops-owl-applications

ops-owl-applications

A set of applications used for the processing and QA of NCI Thesaurus (NCIt) OWL export.

CTCAE_to_OWL - takes a spreadsheet provided by CTCAE and converts it into OWL format

Extract Branches - separates the NCI Thesaurus into each of its disjoint branches

GO_BP_Map_to_NCIt - a program to automate mapping between GO and NCIt

GenerateCDISC - extracts the CDISC subsets and reports from NCIt

GenerateOWLAPIInferred - classifies the asserted NCIt and generates a new OWL file with inferences

HGNCtoOWL - takes the csv export from the HUGO HGNC website and converts it to OWL

OWLCompare - Allows users to take a list of codes and pull the concepts from NCIt as a report

OWLDiff - Outputs the delta of two OWL files

OWLDisjoint - Reapplies disjoint assertions that might have been removed by OWLAPI

OWLKb - extension of OWLAPI that applies NCIt specific business rules. This extension is used by most of the other NCIt processing programs

OWLScrubber - removes internal use only properties and editor identities from NCIt

OWLSummary - generates metrics for NCIt

ProtegeKbQA - examines the raw export from Protege for any anomalies or errors and outputs a report

Protege_History_Validation - compares the current and previous NCI versions to the history file to detect any gaps in history

UpdateCUI - takes the nci_code_cui.txt generated by the Metathesaurus production and creates a batch file to apply the changes to the NCIt

ValueSetProduction - examines the NCIt for "Concept_in_Subset" flags and generates a configuration file listing all value sets for use in the NCIt browser application

ctcae_publish - used for CTCAE4 to generate a printable PDF from the CTCAE data