Agenda. Machado) v biocaddie Supplement Proposals (Ohno- v Project Team Report (Hagstrom) v Technical Team Report (Xu, Farcas, Grethe)

Transcription

1 Agenda biocaddie Supplement Proposals (Ohno- Machado) Project Team Report (Hagstrom) Technical Team Report (Xu, Farcas, Grethe) Working Groups Report Project Plan Review 1

2 SUPPLEMENT PROPOSALS (Ohno-Machado) # Submitted Proposals 4/3/15 w Proposal 1- Discovering Duplicative Data (D3) w Proposal 2 FORCE11 w Proposal 3 - Count Everything: Integrating Clinical, Genomics, and mhealth APIs Across the BD2K Program w Proposal 4 - OmicsDI Additional Proposals w CEDAR-bioCADDIE 2

3 Discovering Duplicative Data (D3) David Page: Center for Predictive Computational Phenotyping Aim: To find and link human subjects datasets by constructing predictive models of phenotype from genotype, and phenotype from other phenotypic data. 3

4 FORCE11 Maryann Martone: FORCE11 Aim 1: Support pilot project to test data citation implementation based on machineprocessable system for identifying research resources using biomedical data Aim 2: Launch and support a Software Citation Group to define software citation principles and implementation 4

5 Count Everything: Integrating Clinical, Genomics, and mhealth APIs Across the BD2K Program David Haussler: Center for Big Data in Translational Genomics Isaac Kohane: Patient-Centered Information Commons Ida Sim: Mobile Data to Knowledge Aim 1: Establish a covering set of interoperable APIs sufficient to answer simple quantitative questions integrating over clinical, omic and mobile-sensor data Aim 2: The creation of a software toolkit that implements these APIs in one easily deployable package Aim 3: Deployment of the toolkit, across a number of medical institutions, creating a network of data providers serving a common view of a large swath of biomedical data 5

6 OmicsDI Peipei Ping: A Community Effort to Translate Protein Data to Knowledge: An Integrated Platform Eric Deutsch: Institute for Systems Biology Henning Hermjakob: ProteomeXchange Aim: To provide dataset discovery across a heterogeneous, distributed group of genomics, proteomics and metabolomics data resources spanning eight repositories in 2 continents and 6 organizations, including both open and controlled access data resources. 6

7 NIH BD2K Commons Pilot Supplement Goal: The Commons is intended to facilitate access and catalyze the sharing, use, reuse, interoperability and discoverability of shared digital research objects. NIH is making available a limited number of administrative supplements to support pilot efforts for development, testing, adapting, and re-using components in a way that will initiate progress towards achieving these two goals. interoperability between separate activities building components that will form the Commons foundation Deadline: May 8, 2015 NIH Review: August 2015 Awards: FY2016 Funding Department ADDS Availability: To BD2K Centers only 7

8 GUIDELINES Collaboration between two or more BD2K centers is expected and requests may also include appropriate external groups. One or more BD2K centers may also collaborate directly with biocaddie Data requiring secured handling must describe plan to manage Pilots planning on developing APIs should provide clear justification for the need to develop new APIs as opposed to reuse or modification of previously existing ones. Pilots investigating new search and unique identifier schemes should work closely with biocaddie. A unified and coordinated BD2K Github repository for source code and appropriate documentation should be developed to support work from this supplement. Centers planning on using cloud computing should develop metrics to determine how the cost of cloud computing services impacts their computing and IT personnel budget BD2K centers may submit more than one request as long as each is for a unique project. Applicants are strongly encouraged to discuss their proposed supplement requests with the NIH staff listed below (Vivien) prior to submission of a supplement application. 8

9 User Profile Dashboard Mailing List Groups Project Team Report (Hagstrom) DEMO biocaddie website tools Team Work Tool

10 Project Team Report (Hagstrom) User Profile Login: address DEMO biocaddie website tools Pass: Team to log in and reset passwords Dashboard Located top of screen black bar Shortcuts Group Links/mailing list members/edit

11 Mailing Lists List on dashboard Only members may send and receive Archive of all mail Only members may view discussions To include all select reply to all To reply to individual only select reply Groups Admin Support Team assigns people to groups Only group members are on mailing lists Only group members may view discussions Admin Support may add people to mailing list and not group list Admin Support may add people to view group pages but not participate in the mailing list

12 Team Work Tool Admin Support Team Log in: /password set by Admin Tool for Admin Support Team Task lists, Gantt Charts, Google Drive Participate in the mailing list Encourage Executive to send items for us to include in this system.

13 Technical Team Report (Xu, Farcas, Grethe) w List of Repositories - URL w Identification of key components of the prototype: Data harvesting Metadata management Search engine/web portal w Task assignment to different groups w Administrative issues discussed Development site setup Communicate with WGs 13

14 Working Group Reports WG1 BD2K Centers of Excellence Collaboration (Ohno-Machado) WG2 Data Identifiers Recommendations (Grethe) WG3 Core Metadata Specifications v1 (Sansone, Alter, Xu) 14

15 PROJECT PLAN - Y1/Q3 TIME CORE TEAM WORKING GROUP (WG)/ PILOT PROJECTS (PP) Y1/Q3 Disseminate white paper and solicit feedback Set up the web portal (datamed.biocaddie.org) Start design of data ingestion process with BD2K center data and Admin Supplement Projects [1] (consider recommendations of data sets resulting from WG1) BD2K Centers of Excellence Collaboration (WG1) Data identifiers recommendation (WG2) Core Metadata Specifications (WG3.0), v1 [1] Phase 1. Year 1(Quarters 3 and 4). We will start by formalizing collaborations with the centers The same happens for the administrative supplements already given to eight investigators. These are however more urgent, as they expire in 6 months. As indicated in the table, the web portal and initial design of the prototype, informed by centers, and admin supplements will be done in Phase 1. Administrative Supplements High priority: we will seek PIs of the eight projects to ensure the indexing of the data they produce. There is a vast array of projects included, some of which are repositories (e.g., toxicology repository), and some of which, like many of the centers, are producing tools to compute with the data (e.g., temporal reasoning in clinical data sets). 15