[cBioPortal update] New feature: Annotation of mutation effect and drug sensitivity via OncoKB

[JianJiong Gao]

We are very excited to announce that we have updated the cBioPortal for Cancer Genomics (http://cbioportal.org) with new features and improvements.

The major new feature we released today is annotation of mutation effect and drug sensitivity on the Mutations tab and the patient view pages view OncoKB (http://oncokb.org). Here is an example lung case.

Other improvements include:

• Improved OncoPrint visualization using WebGL: faster, more zooming flexibility, visualization of recurrent variants
• Improved Network tab with SBGN view for a single interaction
• Performance improvement of tables in the study view page
• Mutation type summary on the Mutations tab

Best regards,

The cBioPortal Team

http://cbioportal.org

cbiop...@cbio.mskcc.org

[lidia...@irbbarcelona.org]

Dear cBioPortal Team,

I really think that OncoKB annotations of somatic mutations are a really valuable addition to your data portal. I would like to know if there is a feasible way of accessing to this data table programatically. If I am not wrong, this information is not provided in the "Extended Mutation Data" that you serve through the API. The first thing I tried was downloading the "Mutations" table obtained doing a conventional query (e.g http://www.cbioportal.org/cross_cancer.do?cancer_study_list=&cancer_study_id=all&data_priority=1&case_ids=&patient_case_select=sample&gene_list=TP53&clinical_param_selection=null&tab_index=tab_visualize&Action=Submit&Action=Submit#crosscancer/overview/1/TP53/sarc_mskcc%2Csarc_tcga%2Cthyroid_mskcc_2016%2Cacc_tcga%2Cchol_jhu_2013%2Cchol_nccs_2013%2Cchol_nus_2012%2Cchol_tcga%2Cgbc_shanghai_2014%2Cblca_bgi%2Cblca_dfarber_mskcc_2014%2Cblca_mskcc_solit_2012%2Cblca_mskcc_solit_2014%2Cblca_plasmacytoid_mskcc_2016%2Cblca_tcga%2Cblca_tcga_pub%2Cmm_broad%2Ces_dfarber_broad_2014%2Ces_iocurie_2014%2Ccoadread_genentech%2Ccoadread_mskcc%2Ccoadread_tcga%2Ccoadread_tcga_pub%2Cbrca_bccrc%2Cbrca_bccrc_xenograft_2014%2Cbrca_broad%2Cbrca_metabric%2Cbrca_sanger%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pub2015%2Ccesc_tcga%2Cescc_icgc%2Cescc_ucla_2014%2Cegc_tmucih_2015%2Chnsc_broad%2Chnsc_jhu%2Chnsc_tcga%2Chnsc_tcga_pub%2Cnpc_nusingapore%2Clihc_amc_prv%2Clihc_riken%2Clihc_tcga%2Cpaac_jhu_2014%2Cpaad_icgc%2Cpaad_tcga%2Cpaad_utsw_2015%2Cpanet_jhu_2011%2Cmeso_tcga%2Cnepc_wcm%2Cprad_broad%2Cprad_broad_2013%2Cprad_fhcrc%2Cprad_mich%2Cprad_mskcc%2Cprad_mskcc_2014%2Cprad_mskcc_cheny1_organoids_2014%2Cprad_su2c_2015%2Cprad_tcga%2Cprad_tcga_pub%2Ccscc_dfarber_2015%2Crms_nih_2014%2Ctet_nci_2014%2Clgg_tcga%2Clgg_ucsf_2014%2Clgggbm_tcga_pub%2Cpcpg_tcga%2Ctgct_tcga%2Cucec_tcga%2Cucec_tcga_pub%2Call_stjude_2015%2Claml_tcga%2Claml_tcga_pub%2Cesca_broad%2Cesca_tcga%2Cstad_pfizer_uhongkong%2Cstad_tcga%2Cstad_tcga_pub%2Cstad_uhongkong%2Cstad_utokyo%2Cuvm_tcga%2Cacyc_mskcc%2Cccrcc_irc_2014%2Cccrcc_utokyo_2013%2Ckirc_bgi%2Ckirc_tcga%2Ckirc_tcga_pub%2Cnccrcc_genentech_2014%2Csclc_clcgp%2Csclc_jhu%2Csclc_ucologne_2015%2Cluad_broad%2Cluad_mskcc_2015%2Cluad_tcga%2Cluad_tcga_pub%2Cluad_tsp%2Clusc_tcga%2Clusc_tcga_pub%2Ccellline_ccle_broad%2Ccellline_nci60%2Cscco_mskcc%2Cmpnst_mskcc%2Cskcm_broad%2Cskcm_broad_dfarber%2Cskcm_tcga%2Cskcm_yale%2Cdesm_broad_2015%2Cthym_tcga%2Cthca_tcga%2Cthca_tcga_pub%2Cmbl_broad_2012%2Cmbl_icgc%2Cmbl_pcgp%2Cnbl_amc_2012%2Cucs_jhu_2014%2Cucs_tcga%2Ckirp_tcga%2Ckich_tcga%2Ckich_tcga_pub%2Cdlbc_tcga%2Cpcnsl_mayo_2015%2Cov_tcga%2Cov_tcga_pub%2Cgbm_tcga%2Cgbm_tcga_pub%2Cgbm_tcga_pub2013).
However, I noticed that the field Annotation is empty. I think I could manage to parse the html to obtain this information but this can be a tedious work...
Any suggestion?

Thank you very much in advance,

Lídia

[hds...@gmail.com]

I downloaded and installed your new cbioportal, but I received

The version of the portal is out of sync withe the database! Please contact the site administrator to update the database.

Current DB version: 1.1.0

DB version expected by Portal : 1.2.1

How to upgrade DB to 1.2.2?

Howard

[Ethan Cerami]

Howard,

Sorry about that.  We have updated documentation that explains the new install process. 

https://github.com/cBioPortal/cbioportal/pull/1473

We are merging this soon.

Ethan

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[hds...@gmail.com]

Ethan,

You mean new package no longer works on old seed database?

Thank you.

Howard

On Monday, June 6, 2016 at 9:59:31 AM UTC-5, Jianjiong Gao wrote:

[JianJiong Gao]

Hi Lídia,

We are finalizing the OncoKB API but it is not public yet. We will announce it on oncokb.org once it's finalized. Please stay tuned.

-JJ

[JianJiong Gao]

Hi Howard,

Would you please try to update your database?

https://github.com/cBioPortal/cbioportal/blob/master/docs/Updating-your-cBioPortal-installation.md

-JJ

On Wed, Jul 20, 2016 at 12:10 PM, <hds...@gmail.com> wrote:
>
>
> Ethan,
> You mean new package no longer works on old seed database?
> Thank you.
>
>
> Howard
>
> On Monday, June 6, 2016 at 9:59:31 AM UTC-5, Jianjiong Gao wrote:
>>
>> We are very excited to announce that we have updated the cBioPortal for Cancer Genomics (http://cbioportal.org) with new features and improvements.
>>
>> The major new feature we released today is annotation of mutation effect and drug sensitivity on the Mutations tab and the patient view pages view OncoKB (http://oncokb.org). Here is an example lung case.
>>
>>
>>

>> Other improvements include:
>>
>> Improved OncoPrint visualization using WebGL: faster, more zooming flexibility, visualization of recurrent variants
>> Improved Network tab with SBGN view for a single interaction
>> Performance improvement of tables in the study view page
>> Mutation type summary on the Mutations tab
>>
>>
>> Best regards,
>> The cBioPortal Team
>> http://cbioportal.org
>> cbiop...@cbio.mskcc.org
>>

[Ethan Cerami]

Howard,

I am not sure if I follow the question, but we now have a new seed and new wiki documentation explaining the install process.

The very latest is in the HotFix branch:

https://github.com/cBioPortal/cbioportal/tree/hotfix/

with docs here:

https://github.com/cBioPortal/cbioportal/tree/hotfix/docs

If you clone from the hotfix branch and follow the docs within the hotfix branch, I believe everything will work.

Ethan

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Ethan Cerami
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