Abstract
BackgroundThe Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, the CL has undergone multiple rounds of revision and expansion, most notably in its representation of hematopoietic cells. For in vivo cells, the CL focuses on vertebrates but provides general classes that can be used for other metazoans, which can be subtyped in species-specific ontologies.Construction and contentRecent work on the CL has focused on extending the representation of various cell types, and developing new modules in the CL itself, and in related ontologies in coordination with the CL. For example, the Kidney and Urinary Pathway Ontology was used as a template to populate the CL with additional cell types. In addition, subtypes of the class ‘cell in vitro’ have received improved definitions and labels to provide for modularity with the representation of cells in the Cell Line Ontology and Reagent Ontology. Recent changes in the ontology development methodology for CL include a switch from OBO to OWL for the primary encoding of the ontology, and an increasing reliance on logical definitions for improved reasoning.Utility and discussionThe CL is now mandated as a metadata standard for large functional genomics and transcriptomics projects, and is used extensively for annotation, querying, and analyses of cell type specific data in sequencing consortia such as FANTOM5 and ENCODE, as well as for the NIAID ImmPort database and the Cell Image Library. The CL is also a vital component used in the modular construction of other biomedical ontologies—for example, the Gene Ontology and the cross-species anatomy ontology, Uberon, use CL to support the consistent representation of cell types across different levels of anatomical granularity, such as tissues and organs.ConclusionsThe ongoing improvements to the CL make it a valuable resource to both the OBO Foundry community and the wider scientific community, and we continue to experience increased interest in the CL both among developers and within the user community.
Highlights
The Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types
The CL is a vital component used in the modular construction of other biomedical ontologies—for example, the Gene Ontology and the cross-species anatomy ontology, Uberon, use CL to support the consistent representation of cell types across different levels of anatomical granularity, such as tissues and organs
Cells are a fundamental unit of biology, and most other entities in biology have direct relationships to identifiable cell types, for example particular proteins being produced by unique cell types, tissues and organs containing specific combinations of cell types, or biological processes being dependent on particular cell types
Summary
The Cell Ontology (CL) was initially developed in 2004 with the goal of representing knowledge about in vivo and in vitro cell types [1]. We make use of the Jenkins Continuous Integration system, as developed and implemented by the Gene Ontology Consortium, for quality control and validation [8, 48] This system alerts the editorial team if changes are made that inadvertently introduce logical, terminological, or structural errors into the ontology (for example, a cell that is located in two disconnected locations, or two cell classes that share the same name). We are in the process of switching to Travis-CI as this provides more direct integration with the GitHub system, where we manage the ontology This system is used to generate releases, creating a package of ontology files in OWL2 and OBO formats that are pre-reasoned and in some cases simplified for legacy use for systems that do not support logical definitions (See Table 1 for listing of available CL files). N/A cl.owl yes yes http://purl.obolibrary.org/obo/ cl.owl cl.obo yes yes http://purl.obolibrary.org/obo/ cl.obo cl-basic.owl yes no http://purl.obolibrary.org/obo/ cl-basic.owl cl-basic.obo yes no http://purl.obolibrary.org/obo/ cl-basic.obo
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