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

Terence Parr parrt at cs.usfca.edu
Wed Mar 16 13:20:31 PDT 2011


Heh, that is cool! added your email above.
Adding to showcase.

http://www.antlr.org/showcase/list

Ter
On Mar 16, 2011, at 10:10 AM, Arthur Goldberg wrote:

> 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
> 2741 Arlington Ave.
> Bronx NY 10463
> 
> 
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