The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability

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.

eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs

“…Using the same quantification workflow ensured that molecular phenotype identifiers (genes, transcripts, exons and events) were consistent between individual studies. Furthermore, we harmonised sample metadata between studies and mapped all biological samples (cell types and tissues) to a common set of 24 distinct ontology terms from UBERON [20], Cell Ontology [21] and Experimental Factor Ontology [22]. This will allow users to easily find if the same cell types or tissues has been profiled in multiple studies ( Table 1).…”

Extracting T Cell Function and Differentiation Characteristics from the Biomedical Literature

“…Transcription Factor names as well as associated aliases were integrated primarily from [8] with a large number of transcription factor aliases also provided by [9]. Cell types and associated aliases were gathered primarily from Cell Ontology [10], with all terms descending from either the T cell ( CL_0000084 ) or NK cell ( CL_0000623 ) terms. For all entities, a list of aliases not present in the corresponding ontologies was manually curated after identifying the need for them individually, and all aliases/names were used to identify entity spans based on exact, case-insensitive token sequence matches.…”

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities

“…In this regard, PRO terms have been supplied for precise entity annotation as requested by other ontology developers (e.g. the family level term ‘CD59-like glycoprotein’ [http://purl.obolibrary.org/obo/PR_000001809] requested by the Cell Ontology [CL] (17)), and to other members of the GO Consortium (for example, the hyperoxidized form of Tpxi1 [http://purl.obolibrary.org/obo/PR_000028935] requested by PomBase (18)). GO itself uses PRO terms to define certain terms.…”