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Insert Assay Annotations

The CDD Vault Electronic Lab Notebook now incorporates a key piece of CDD’s BioAssay Express technology.  The Assay Annotation tool helps your team easily annotate ELN entries.

 

What are Assay Annotations?

To help with the underlying data, we have created the Common Assay Template, which draws from a number of underlying vocabularies created by domain experts, including the BioAssay Ontology (BAO), Drug Target Ontology (DTO), Cell Line Ontology (CLO) and others. When text is available (e.g. for annotating legacy data), the interface makes use of machine learning and natural language processing to suggest terms, speeding up the process.

Here is a typical example of an annotated assay based on our Common Assay Template. You can see there are sections relating to the target and its biological and disease relevance, annotations describing specifics around the assay methodology, and finally some organizational details.

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Adding Annotations

To begin, click the Insert Assay Annotations icon in the toolbar:

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This will open a dialog to add, modify, or delete annotations:

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Please add as many annotations as are necessary to describe your experiment. The 3 tabs in the window - Target, Method, and Other - contain all terms in the Common Assay Template.  While these ontologies are very comprehensive, if you do not find what you are looking for, you can add a free text annotation:

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Advanced searching is enabled where a user can use type-ahead and partial matches to retrieve a list of available annotations.

In some cases, we know that certain annotations frequently occur together.  This means if one annotation is added, there is a high probability that the other annotation is correct too. These annotations are highlighted as Proposals:

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One source for proposals are relationships between annotations defined in the public ontologies as axioms. Another source are the curated assays in BioAssay Express where we use associative rules mining to extract expert knowledge.

 

Auto-generated text

Assay annotations are automatically converted into a consistent and concise high-level description of the experiment or assay. Here is the generated text for the above example:

 This is a primary assay to identify potential treatments for Plasmodium falciparum malaria, by investigating the biological process of regulation of peptidase activity, specifically targeting M18 aspartyl aminopeptidase [Plasmodium falciparum 3D7] from Plasmodium falciparum.

This is a functional/protease activity assay in a single protein format, using a direct enzyme activity measurement method, without an assay kit. It was conducted in 1536 well plates, with the detection method of fluorescence resonance energy transfer, using a ViewLux ultraHTS Microplate Imager. This assay tested the mode of action of inhibition by small molecule perturbagens.

You can copy (by clicking the "Copy to Clipboard" button)

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and paste the text to use as a starting point for a more detailed description.

 

Assay annotations are searchable

The benefit of Assay Annotations, of course, is that they are highly structured and searchable. This makes it easy to find and compare similar protocols within your CDD Vault ELN. And because standard terms are employed from biomedical ontologies, it affords the opportunity to securely compare your protocols with others – such as the 3500+ expertly annotated MLPCN (Molecular Libraries Probe Production Centers Network) PubChem Assay Protocols currently available to the public in BioAssay Express. Within your secure CDD Vault, assay annotations are immediately available for searching when looking across ELN entries. Supply a keyword and the matching annotations are displayed with their terms for effective filtering to find the most relevant entries quickly.

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Additional Documentation

Please visit the BioAssay Express public site a live demonstration of the technology.

The BioAssay Express documentation page contains a wide array of information on the tool.

The CDD Blog has a number of posts on BioAssay Express.

The Cheminformatics 2.0 site contains multiple posts on the topic of BioAssay Express.