Analysis of bio-ontologies to describe chemical biology HTS assays.

<p>Coverage of biomedical concepts/terms to describe HTS assays (shown as rows) by various existing biomedical ontologies (shown as columns) is depicted. The color codes are as follows: green: the concept is well described by the ontology, pink: the concept is partially described, red: no (or little) information is available in the ontology, yellow: the concept is imported from an external reference/ontology, blue: the ontology only includes a placeholder to an external reference of that concept.</p

Network visualization of PubChem assays (nodes) connected by BAO assay relationships (edges) to describe screening campaigns.

<p>Shown are 682 assays that are each part of a set of at least 7 connected assays comprising 85 campaigns. Assays are identified by their AID. BAO assay annotations are also shown, including, assay format (node shape), assay target main class (node color), and BAO assay relationships (edge color). Screening campaign-disease associations were obtained from the assay descriptions (shown as areas surrounded by dotted lines).</p

Summary of PubChem assay annotations.

<p>Statistics of 944 curated PubChem assay by the BAO main classes ‘assay stage’ (A) ‘assay format’ (B), ‘assay design’ (C) and ‘detection technology’ (D).</p

Summary of the standardized ‘endpoint’ in PubChem assay annotations.

<p>Summary of the standardized ‘endpoint’ in PubChem assay annotations.</p

Generation of a hierarchy-flattened BAO format.

<p>The hierarchy-flattened format of BAO contains only the most specific leaf nodes. Lead node IDs were maintained in this process. The labels/names in the flattened version of BAO reflect the class hierarchy in BAO.</p

Formal BAO annotation of a PubChem screening campaign.

<p>In the campaign to identify inhibitors of Kruppel-like factor 5, the investigators screened compounds, both to identify inhibitors of KLF5 and to eliminate cytotoxic compounds. The compounds tested at each stage are shown in red boxes. The endpoints (result type) from each of the assays are listed to the right. Abbreviations: Comp: compounds, opt: optimization, conc: concentration, inh: inhibition, 1×: compound tested in singlicate, 3×: compound tested in triplicate, and CID: compound ID.</p

List of ontologies used in BAO.

<p>List of ontologies used in BAO.</p

Illustration of the major bioassay components, corresponding specifications, and their relations.

<p>Approximation of the BAO logical model. The relationships depicted by blue arrows are as follows: 1) ‘has assay format’, 2) ‘has specification’, 3) ‘has perturbagen’, and 4) ‘has measure group’, and those by red arrows are as follows: 1) ‘is assay format of’, 2) ‘is specification of’, 3) ‘is perturbagen of’, and 4) ‘is measure group of’.</p