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

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

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

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

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

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

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

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

The LINCS Data Portal and FAIR LINCS Dataset Landing Pages

<p>The LINCS Data Portal (LDP) presents a unified interface to access LINCS datasets and metadata with mappings to several external resources. LDP provides various options to explore, query, and download LINCS dataset packages and reagents that have been described using the LINCS metadata standards.</p><p>We recently introduced LINCS Dataset Landing Pages to provide integrated access to important content for each LINCS dataset. The landing pages provide deep metadata for each LINCS dataset including description of the assays, authors, data analysis pipelines, and standardized reagents such as small molecules cell lines, antibodies, etc, with rich annotations. The landing pages are a key component to make LINCS data persistent and reusable, by integrating LINCS datasets, data processing pipelines, analytes, perturbations, model systems and related concepts as uniquely identifiable digital research objects.</p><p>LDP supports ontology-driven concept search, free text search, facet filtering, logical intersection of filters (AND, OR), and list, table, and matrix views. LDP enables download of LINCS dataset packages, which consist of released datasets and associated metadata. LDP also provides several specialized apps including small molecule compounds and cell lines. A landing page facilitates interactive exploration of all LINCS datasets via several classifications.</p>LDP is built on a robust API and is integrated with the MetaData Registry and interfaces with other components of the Integrated Knowledge Environment (IKE) developed in our Center. All LINCS datasets are also indexed in bioCADDIE DataMed

Additional file 1: Table S1. of Drug target ontology to classify and integrate drug discovery data

SPARQL query results to identify kinase domains in the KINOMEscan assay with gatekeeper annotations. Shown are TDL classification, DTO ID, kinase domain description, and protein name. (XLSX 28 kb