Sample data fields in cell bank databases.

<p>The same information is attributed to different data fields in the cell banks we reviewed. This table shows how the two sample terms ‘medium’ and ‘organ’ are handled in the respective databases. The fields marked by * are free text fields. They are also used for other types of data.</p

Relationships imported from EFO.

<p>In CCONT, we use the relationships inherited from EFO <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048584#pone.0048584-Malone1" target="_blank">[21]</a>. In this table we show the labels of the relationships and their description if available.</p

Ontology evaluation techniques (Obrst et al. [16]).

<p>This table summarizes the evaluation techniques suggested by Obrst et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048584#pone.0048584-Obrst1" target="_blank">[16]</a> for use with ontologies in life sciences. The techniques one to three were applied when evaluating CCONT.</p

Number of chemical compounds for each role in CCONT.

<p>Chemical compounds play different roles for the growth of cell lines. In column two we show how many compounds are necessary for describing a specific role. Column three shows the respective number of roles already present in EFO.</p

List of cell banks compared.

<p>The databases of five widely used cell banks were included into the comparison of data fields. The table shows the name of the Internet addresses were they can be reached. The Internet addresses were last accessed on March 1, 2012.</p

On the Ontology Based Representation of Cell Lines

<div><p>Cell lines are frequently used as highly standardized and reproducible <em>in vitro</em> models for biomedical analyses and assays. Cell lines are distributed by cell banks that operate databases describing their products. However, the description of the cell lines' properties are not standardized across different cell banks. Existing cell line-related ontologies mostly focus on the description of the cell lines' names, but do not cover aspects like the origin or optimal growth conditions. The objective of this work is to develop an ontology that allows for a more comprehensive description of cell lines and their metadata, which should cover the data elements provided by cell banks. This will provide the basis for the standardized annotation of cell lines and corresponding assays in biomedical research. In addition, the ontology will be the foundation for automated evaluation of such assays and their respective protocols in the future. To accomplish this, a broad range of cell bank databases as well as existing ontologies were analyzed in a comprehensive manner. We identified existing ontologies capable of covering different aspects of the cell line domain. However, not all data fields derived from the cell banks' databases could be mapped to existing ontologies. As a result, we created a new ontology called <em>cell culture ontology (CCONT)</em> integrating existing ontologies where possible. CCONT provides classes from the areas of cell line identification, origin, cell line properties, propagation and tests performed.</p> </div

The ‘supplement’ subtree of CCONT.

<p>The class ‘supplement’ is defined in CCONT to identify substances that are necessary to support the growth of cell lines in culture. In other words, these substances are assigned specific roles in the process of cell culturing. As a consequence, we decided to place the ‘supplement’ class below EFO's ‘growth condition’ class in the ‘Role’ subtree.</p

The head of CCONT's OWL file.

<p>Technically, for the definition of CCONT we started with a fresh OWL file. Following the considerations described in this article, we reused the two ontologies EFO and IEV's event ontology. This is reflected by corresponding XML namespace definitions and OWL import statements.</p

Cell lines used in the liver cancer research network.

<p>To establish a common platform in the research network, these cell lines were chosen and procured centrally. These cell lines also serve as test items for CCONT.</p

Sample data fields in cell bank databases.

<p>The table lists data elements derived from cell banks. The last three columns show, which of the cell line related ontologies have classes that cover the data elements: full coverage, partial coverage, not covered.</p