Semantic resources project/Cell Types

= CT: Cell Type Ontology =

In the project we build on the Cell Type Ontology (CL) that is part of the Open Biomedical and Biological Ontologies (OBO) foundry. The cell type resource catalogs various cell types that covers prokaryotic, fungal, animal and plant worlds. Each cell type is described with a unique identifier, definition, synonyms and relationships with other cell types. Comments of the curation staff are also captured. Such a structured resource allows us to query and integrate the phenotypic data on these cell types in a uniform manner.

As a part of this project, our project focused on the hematopoietic cell types. We identified gaps in CL and worked with the developers of CL to provide additional coverage. Hematopoietic cells are frequently characterized by cell surface markers. We used identifiers from the Protein Ontology to characterize these markers. The Harvard Stem Cell Institute (HSCI) Blood genomics repository will use this enhanced resource. Such as use of fixed identifiers will make this resource interoperate with other phenotypic repositories of cell types.

= Data Sources =


 * CT Ontology
 * SourceForge files
 * dMAP file?

= Neurocommons Bundle =

Code link

= Cell Type Widget =

The "HSCI Blood Program" website , an SCF-based system, incorporates static cell-type derivation diagrams as part of the input form for metadata about experiments stored within the site's microarray database. These diagrams display cell types in a dendrogram (a tree-shaped hierarchy), showing the developmental relationships between different types and giving users an intuitive interface for finding and selecting the particular cell types that were used or measured in a given experiment.

We designed a web interface and programmatic API to the CL ontology, to allow cell type derivation diagrams in the same style to be produced from the CL ontology and embedded in other SCF interfaces or static web pages. This system includes three steps: (1) inference over the CL ontology for representing derived_from relationships, (2) design of an HTTP API for retrieving these relationships, and (3) implementation of a graphical display for dendrograms using Javascript UI tools.

= Notes & External Content =

Examining CL, the 'Cell Type Ontology'
CL on OBO Foundry

Bard, Rhee, and Ashburner. "An Ontology For Cell Types" Genome Biology 2005, 6:R21doi:10.1186/gb-2005-6-2-r21

Notable Terms
CL:0000578 "experimentally modified cell" CL:0000010 "cell line cell"

Term Submissions to CL
... placeholder for notes about which cell lines or types to submit to CL? ...