Ontology application and use at the ENCODE DCC

Venkat S. Malladi, Drew T. Erickson, Nikhil R. Podduturi, Laurence D. Rowe, Esther T. Chan, Jean M. Davidson, Benjamin C. Hitz, Marcus Ho, Brian T. Lee, Stuart Miyasato, Gregory R. Roe, Matt Simison, Cricket A. Sloan, J. Seth Strattan, Forrest Tanaka, W. James Kent, J. Michael Cherry, Eurie L. Hong

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

The Encyclopedia of DNA elements (ENCODE) project is an ongoing collaborative effort to create a catalog of genomic annotations. To date, the project has generated over 4000 experiments across more than 350 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory network and transcriptional landscape of the Homo sapiens and Mus musculus genomes. All ENCODE experimental data, metadata and associated computational analyses are submitted to the ENCODE Data Coordination Center (DCC) for validation, tracking, storage and distribution to community resources and the scientific community. As the volume of data increases, the organization of experimental details becomes increasingly complicated and demands careful curation to identify related experiments. Here, we describe the ENCODE DCC's use of ontologies to standardize experimental metadata. We discuss how ontologies, when used to annotate metadata, provide improved searching capabilities and facilitate the ability to find connections within a set of experiments. Additionally, we provide examples of how ontologies are used to annotate ENCODE metadata and how the annotations can be identified via ontology-driven searches at the ENCODE portal. As genomic datasets grow larger and more interconnected, standardization of metadata becomes increasingly vital to allow for exploration and comparison of data between different scientific projects.

Original languageEnglish (US)
Article numberbav010
JournalDatabase
Volume2015
DOIs
StatePublished - Jan 1 2015
Externally publishedYes

Fingerprint

Encyclopedias
Ontology
Metadata
DNA
genomics
Gene Regulatory Networks
Experiments
Mus musculus
standardization
Standardization
Chromatin
chromatin
Genes
Cells
cell lines
Organizations
Genome
Tissue
Cell Line
genome

ASJC Scopus subject areas

  • Information Systems
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Malladi, V. S., Erickson, D. T., Podduturi, N. R., Rowe, L. D., Chan, E. T., Davidson, J. M., ... Hong, E. L. (2015). Ontology application and use at the ENCODE DCC. Database, 2015, [bav010]. https://doi.org/10.1093/database/bav010

Ontology application and use at the ENCODE DCC. / Malladi, Venkat S.; Erickson, Drew T.; Podduturi, Nikhil R.; Rowe, Laurence D.; Chan, Esther T.; Davidson, Jean M.; Hitz, Benjamin C.; Ho, Marcus; Lee, Brian T.; Miyasato, Stuart; Roe, Gregory R.; Simison, Matt; Sloan, Cricket A.; Strattan, J. Seth; Tanaka, Forrest; Kent, W. James; Cherry, J. Michael; Hong, Eurie L.

In: Database, Vol. 2015, bav010, 01.01.2015.

Research output: Contribution to journalArticle

Malladi, VS, Erickson, DT, Podduturi, NR, Rowe, LD, Chan, ET, Davidson, JM, Hitz, BC, Ho, M, Lee, BT, Miyasato, S, Roe, GR, Simison, M, Sloan, CA, Strattan, JS, Tanaka, F, Kent, WJ, Cherry, JM & Hong, EL 2015, 'Ontology application and use at the ENCODE DCC', Database, vol. 2015, bav010. https://doi.org/10.1093/database/bav010
Malladi VS, Erickson DT, Podduturi NR, Rowe LD, Chan ET, Davidson JM et al. Ontology application and use at the ENCODE DCC. Database. 2015 Jan 1;2015. bav010. https://doi.org/10.1093/database/bav010
Malladi, Venkat S. ; Erickson, Drew T. ; Podduturi, Nikhil R. ; Rowe, Laurence D. ; Chan, Esther T. ; Davidson, Jean M. ; Hitz, Benjamin C. ; Ho, Marcus ; Lee, Brian T. ; Miyasato, Stuart ; Roe, Gregory R. ; Simison, Matt ; Sloan, Cricket A. ; Strattan, J. Seth ; Tanaka, Forrest ; Kent, W. James ; Cherry, J. Michael ; Hong, Eurie L. / Ontology application and use at the ENCODE DCC. In: Database. 2015 ; Vol. 2015.
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