title: Ontology application and use at the ENCODE DCC.
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.
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Venkat S
authors.initials: VS
authors.lastname: Malladi
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Drew T
authors.initials: DT
authors.lastname: Erickson
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Nikhil R
authors.initials: NR
authors.lastname: Podduturi
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Laurence D
authors.initials: LD
authors.lastname: Rowe
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Esther T
authors.initials: ET
authors.lastname: Chan
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Jean M
authors.initials: JM
authors.lastname: Davidson
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Benjamin C
authors.initials: BC
authors.lastname: Hitz
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Marcus
authors.initials: M
authors.lastname: Ho
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Brian T
authors.initials: BT
authors.lastname: Lee
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Stuart
authors.initials: S
authors.lastname: Miyasato
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Gregory R
authors.initials: GR
authors.lastname: Roe
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Matt
authors.initials: M
authors.lastname: Simison
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Cricket A
authors.initials: CA
authors.lastname: Sloan
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: J Seth
authors.initials: JS
authors.lastname: Strattan
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: Forrest
authors.initials: F
authors.lastname: Tanaka
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: W James
authors.initials: WJ
authors.lastname: Kent
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
authors.forename: J Michael
authors.initials: JM
authors.lastname: Cherry
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA euriehong@stanford.edu.
authors.forename: Eurie L
authors.initials: EL
authors.lastname: Hong
mesh_terms: D000818:Animals; D066289:Data Curation / Q000379:methods*; D030541:Databases, Genetic; D063990:Gene Ontology; D053263:Gene Regulatory Networks / Q000502:physiology*; D006801:Humans; D051379:Mice; D058977:Molecular Sequence Annotation / Q000379:methods*; D014158:Transcription, Genetic / Q000502:physiology*