[antlr-interest] oncology query language, an interesting language implemented in ANTLR

[Arthur Goldberg]

Folks

I've built an oncology query language (OQL), which enables cancer 
researchers to refine queries of cancer profile data (genetic status as 
a function of patient and gene). We call it an advanced gene filter 
<http://www.cbioportal.org/cgx/onco_spec_lang_desc.jsp>. In particular, 
researchers can use OQL to define genetic alterations, and thereby 
better investigate which genes are involved in which cancerous activities.

It supports multiple genomic datatypes (expression, copy number and 
mutation), discrete and continuous thresholds for alteration, nicknames, 
and arbitrary ordering of datatypes in the query. It also provides 
extensive error-checking.

In one genetically detailed example, given what is known about the RB 
pathway, the events that are most likely selected for in the tumors are 
CCNE1 amplification,
RB1 deletions or mutations, and loss of expression of CDKN2A. To 
investigate this hypothesis, we use this OQL:

CCNE1: AMP MUTATED
RB1: HOMDEL MUTATED
CDKN2A: HOMDEL EXP < -1

to display only these events 
<http://www.cbioportal.org/cgx/index.do?cancer_type_id=ova&action=Submit&genetic_profile_ids=ova_mutations_next_gen&genetic_profile_ids=ova_gistic&genetic_profile_ids=ova_mrna_median_Zscores&MRNA_PROFILES_SELECTED=on&case_set_id=ova_4way_complete&Z_SCORE_THRESHOLD=1.0&case_ids=&gene_list=%0D%0ACCNE1%3A+AMP+MUTATED%3B%0D%0ARB1%3A+HOMDEL+MUTATED%3B%0D%0ACDKN2A%3A+HOMDEL+EXP+%3C+-1%0D%0A&tab_index=tab_visualize&gene_set_choice=user-defined_list&>.

BR
A

PS. It would be handy if the goldberg at cbio.mskcc.org account on 
antlr-interest at antlr.org could be made to work.

-- 
Senior Research Scientist
Computational Biology
Memorial Sloan-Kettering Cancer Center
cBio Cancer Genomics Portal <http://www.cbioportal.org/>

-- 
Arthur Goldberg
www.cs.nyu.edu/artg

We moved on Dec. 11. Our new address is
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