ENCODE Data Coordina/on Center

Transcription

1 ENCODE Data Coordina/on Center Human Genome Mee/ng, Geneva 28 April 2014 J. Michael Cherry Department of Genetics Stanford University Stanford, California USA 1

2 Intro to the DCC Standards defini/on Using ontologies Accessing metadata

3 ENCODE Experiments 3

4 Types of assays in ENCODE project

5 ENCODE 3 Consor/um Structure Data Produc/on Groups RNA Histone Mods DNase DNAme TF Binding RBP Binding Data Coordina/on Center Technology Development Groups Data Analysis Center Analysis Working Group Computa/onal Analysis Groups Gene Models Chroma/n States Element ID 5

6 hwp://encodeproject.org 6

7 Role of the Data Coordina/on Center Genome Browser Produc/on labs Analysis groups Data files Metadata DCC DCC ENCODE Portal Integrative websites! Scientific! community! Role: Data genera-on Data organiza-on Data access Tasks: Perform assays Data processing & valida/on Web- based searches Perform analyses Data file storage Data downloads Validate data Metadata cura/on Submit data files Submit metadata

8 Challenge: How do you define standards for diverse assays in mul/ple species?

9 Intro to the DCC Standards defini/on Using ontologies Accessing metadata

10 What are metadata? Experimental Variables (/ssue, an/body target, assay) Experimental Design (Replicates and Controls) Non- experimental variables: (sequencing machine, protocols, product lots) Quality Assessment (IDR, unique reads, mapping ra/o) Credit (who, when, where) Validated Experiment Data processing choices (sodware, parameters, versions)

11 Define their rela/onship to each other An/bodies Experiment has Replicate has has Libraries + Biosample has has Donor has Files Biosample has

12 Intro to the DCC Metadata defini/on Using ontologies Accessing metadata

13 Single annota/on, accessed via mul/ple queries circulatory system mesoderm part_of develops_from develops_from part_of heart develops_from myoblast part_of develops_from Explicit rela/onships Inferred rela/onships hwp://uberon.org/ hwp://cellontology.org/ cardiac muscle cell

14 Instant interoperability & func/onality circulatory system mesoderm part_of develops_from develops_from part_of heart develops_from myoblast part_of develops_from Explicit rela/onships Inferred rela/onships hwp://uberon.org/ hwp://cellontology.org/ cardiac muscle cell

15 Why use standards? Consistency of language and iden/fiers facilitates iden/fica/on of data programma/cally. Alterna/ve spellings & phrases are synonyms. Independent of a par/cular data model. F = f = Female = female X X X Biological concepts are defined to provide scope Mitochondria: A semiautonomous, self replica8ng organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryo8c cells. It is notably the site of 8ssue respira8on. Rela/onships between terms can be computed to provide addi/onal annota/on details for grouping, searching, or analysis

16 Intro to the DCC Metadata defini/on Using ontologies Accessing metadata

17 the new ENCODE Portal hwp://

18 the new ENCODE Portal hwp://

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22 Conclusions We developed a single data model that reflects the experimental process to store the 30+ assays done by the ENCODE produc/on labs Using ontologies to annotate metadata provides instant interoperability with other datasets & search func/onality Intro to the DCC Metadata defini/on Using ontologies Accessing metadata Applica/on built on a REST API & JSON- LD supports programma/c querying across other scien/fic resources

23 Contact encode-

24 Sources of ENCODE data ENCODE Portal hwp://encodeproject.org/ UCSC Genome Browser hwp://genome.ucsc.edu/cgi- bin/hggateway ENSEMBL hwp:// NCBI Bioproject: hwp:// GEO: Integra-ve websites ENCODE and Roadmap Epigenomics: hwp:// roadmap.org/ HaploReg: hwp:// RegulomeDB: hwp://regulomedb.org/

25 ENCODE metadata resources NHGRI project page: hwp:// Protocols hwp://encodeproject.org/encode/protocols/cell/ Standards pages hwp://encodeproject.org/encode/datastandards.html hwp://encodeproject.org/encode/valida/on/ SoGware and tools hwp://encodeproject.org/encode/sodwaretools.html File formats pages hwp://encodeproject.org/encode/fileformats.html hwp://genome.ucsc.edu/faq/faqformat.html