[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
>
>
> List: http://www.antlr.org/mailman/listinfo/antlr-interest
> Unsubscribe: http://www.antlr.org/mailman/options/antlr-interest/your-email-address
More information about the antlr-interest
mailing list