2015
DOI: 10.1093/database/bav010
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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 … Show more

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Cited by 44 publications
(29 citation statements)
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“…We support a convention for naming and numbering be extended more broadly in the field such that publications from all groups report regulatory elements in a standard way for all samples, not only those included in a specific consortium. Furthermore, an ontology, similar to that employed by ENCODE, would simplify making functional connections between samples, regions, cell types, and species 28 .…”
Section: To the Editormentioning
confidence: 99%
“…We support a convention for naming and numbering be extended more broadly in the field such that publications from all groups report regulatory elements in a standard way for all samples, not only those included in a specific consortium. Furthermore, an ontology, similar to that employed by ENCODE, would simplify making functional connections between samples, regions, cell types, and species 28 .…”
Section: To the Editormentioning
confidence: 99%
“…This inconsistency will likely increase as more groups generate new datasets and more cellular types and states are characterized. The Cell Ontology, which used expert curation to organize more than 2000 cell types into a hierarchical structure, offers a controlled vocabulary for cell types and has been proposed as a basis for consistently annotating large-scale single-cell atlases [12][13][14][15][16] .…”
Section: Introductionmentioning
confidence: 99%
“…The Data Coordination Center (DCC)[810] is charged with validating, tracking, storing, processing, visualizing and distributing these data files and their metadata to the scientific community. During 6 years of the pilot and initial scale-up phase, the project surveyed the landscape of the H .…”
Section: Introductionmentioning
confidence: 99%