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 [email protected] account on > [email protected] 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 List: http://www.antlr.org/mailman/listinfo/antlr-interest Unsubscribe: http://www.antlr.org/mailman/options/antlr-interest/your-email-address -- You received this message because you are subscribed to the Google Groups "il-antlr-interest" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/il-antlr-interest?hl=en.
