Meetings & Events

The CIViC team regularly holds curation jamborees and development hackathons. At curation jamborees, we work with attendees on actual CIViC curation tasks, both educating users and improving the knowledgebase with group curation. During development hackathons, we help developers to integrate their applications and knowledgebases with CIViC via the API, or help developers work on the CIViC codebase by implementing features or fixing bugs.

Upcoming Meetings & Events

No upcoming events currently scheduled.

Past Meetings & Events

2018 CIViC Hackathon and Curation Jamboree


Dates

October 15th and October 16th, 2018

Location

The Scripps Research Institute

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Eventbrite: Cancer Variant Interpretation Hackathon and Curation Jamboree

Description

A hackathon and curation jamboree were held as a pre-meeting of ASHG, led by the CIViC project team, in collaboration with the ClinGen Somatic working group, and hosted by the Scripps Research Institute. The focus of this meeting was to continue to develop community consensus on data standards for interpretation of variants in cancer, engage software developers for improved variant interpretation software, engage clinical experts for curation of content and enhance integration and interoperability of resources. Additional related topics were proposed by meeting participants.

Meeting Goals

  • Establish community standards and best practices for curation and representation of clinically actionable variants in cancer.

  • Further curation of clinically actionable variants in cancer.

  • Further development of the CIViC web interface for expert crowdsourcing the curation of clinically actionable variants.

  • Promote formation of a collaborative network for community-based development of precision medicine resources.

  • Enhance integration and interoperability of resources through standardization of entities, improvement of APIs, and use of ontologies.

  • Improve drug normalization in variant interpretation knowledgebases.

  • Further develop text-mining strategies for identifying evidence of clinically actionable variants (e.g., CIViCmine).

  • Improve/enhance integration of MyVariant.info into CIViC.

  • Integrate ClinGen Allele Registry’s variant normalization into MyVariant.info.

  • Develop standard operating procedures for curating somatic assertions.

  • Develop standard operating procedures for classifying somatic variant oncogenicity.

  • Develop prototype data models for representing compound/complex variants.

  • Examine ways to incentivize the curation community, e.g. Zenodo, bioCADDIE for citable records

2016 Clinical Interpretation Knowledgebase Hackathon and Curation Jamboree at the NGS in Molecular Pathology Symposium


Dates

Tuesday Nov 29 through Friday Dec 2, 2016

Location

Netherlands Cancer Institute (NKI), Amsterdam

More Info

NGS in Molecular Pathology Symposium

Description

Precision medicine refers to the use of prevention and treatment strategies that are tailored to the unique features of each individual and their disease. In the context of cancer this might involve the identification of specific mutations shown to predict response to a targeted therapy. The biomedical literature describing these associations is large and growing rapidly. Currently these interpretations exist largely in private or encumbered databases resulting in extensive repetition of effort. Realizing precision medicine requires this information to be centralized, debated and interpreted for application in the clinic. CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer. Our goal is to enable precision medicine by providing an educational forum for dissemination of knowledge and active discussion of the clinical significance of cancer genome alterations. This hackathon and jamboree was held to help establish community standards in this space, introduce and engage users with the existing CIViC resource, engage in variant curation activities, and improve the features, user-friendliness and utility of the CIViC curation interface.

Goals

  • Establish community standards and best practices for curation of clinically actionable variants in cancer.

  • Further curation of clinically actionable variants in cancer.

  • Further development of the CIViC web interface for expert crowdsourcing the curation of clinically actionable variants.

Meeting Format

The 2016 CIViC hackathon and jamboree took the form of an unconference with some presentations but an emphasis on hands-on activities learning to curate variants in the CIViC interface or develop the CIViC code base. Participants formed small expert groups to tackle domain-specific variant curation (jamboree) or new website feature development (hackathon) areas.

Who Attended

Hackathon

Software developers, engineers and computational biologists interested in learning and applying back-end and front-end web development skills. Prerequisites: Familiarity with either Ruby/Rails (back-end) or Javascript/Angular (front-end) would be beneficial.

Jamboree

Pathologists and oncologists (certified or in training), genome scientists, and other researchers interested in the problem of sequence variant interpretation for cancer precision medicine. Prerequisites: Basic understanding of the genetic basis of cancer.