assayswhere

Assayswhere is a proposed framework for cataloging and locating biological assays across research databases. It aims to define a standardized metadata schema to describe assay type, biological target, readout modality, organism, experimental conditions, reagents, and provenance, enabling researchers to search for relevant assays and compare protocols.

The term assayswhere blends the words assay and where, reflecting its goal of helping users find assays across multiple repositories. The concept has been discussed in scientific data interoperability circles as a way to improve discoverability, reproducibility, and integration of assay data, though it is not a currently implemented standard in the major databases.

Structure and standards for assayswhere emphasize interoperability with existing biomedical ontologies and data models. Proponents suggest aligning with established resources such as the Ontology for Biomedical Investigations (OBI) and related controlled vocabularies, and exposing metadata in machine-readable formats like JSON-LD. The approach prioritizes persistent identifiers, such as DOIs for records and ORCID for researchers, to support traceability and interoperability across platforms.

Features of a functioning assayswhere system would include centralized indexing of assay records from participating databases, advanced search capabilities by parameters such as assay type, target, readout, organism, or conditions, and links to full protocols, datasets, and published results. The goal is to streamline discovery, enable meta-analyses, and promote reproducibility by providing standardized descriptors and provenance.

Adoption challenges include ensuring data quality and completeness, resolving licensing and access issues, and achieving consensus on metadata standards. Critics may raise concerns about governance, sustainability, and the risk of fragmenting reporting if adapters and mappings are incomplete.

See also: Ontology for Biomedical Investigations (OBI), assay ontology, data interoperability in biology.