The CDD Vault Electronic Lab Notebook now incorporates a key piece of CDD’s BioHarmony: Annotator technology. The Assay Annotation tool helps your teams maintain experimental reproducibility by easily annotating ELN entries using semantic web terms.
What are Assay Annotations?
To help curate the methodologies behind an assay, we have created the Common Assay Template which is designed to capture most of the high value data from bioassay protocols. This Common Assay Template 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 that 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.
Adding Annotations to your ELN entries
To begin, click the Insert Assay Annotation icon in the ELN toolbar:
This will open a form to add, modify, or delete annotations:
Using the Assay Annotation form, 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:
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:
One source for proposals are relationships between annotations defined in the public ontologies as axioms. Another source are the curated assays in BioHarmony: Annotator where we use associative rules mining to extract expert knowledge.
Auto-generated assay description
Assay annotations from the form 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, in Plasmodium falciparum, specifically targeting M18 aspartyl aminopeptidase [Plasmodium falciparum 3D7].
This is a functional, protease activity assay in a single protein format, using a direct enzyme activity measurement method. 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) and paste the text as a starting point for a more detailed experimental methods section.
This copied text can also facilitate experimental documentation and reproducibility between collaborators and even CRO's working in your ELN.
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 BioHarmony: Annotator. Within your secure CDD Vault, assay annotations are immediately available for searching when looking across ELN entries. Supply keywords and the matching annotations are displayed with their terms for effective filtering to find the most relevant entries quickly.
The CDD Blog has a number of posts on BioHarmony: Annotator.
The Cheminformatics 2.0 site contains multiple posts on the topic of BioAssay Express.