BioAssay Ontology


Announcement BAO version 2.0
The BAO team is pleased to announce the release of BAO version 2.0 build 2899.  Our primary vision in BAO 2.0 is to formally describe biological screening assays and their results.This release introduces significant changes both structural and functional.

To learn more about the release click here.

Contact us to be part of the BAO community.

How to cite BAO?

S. Abeyruwan, U. Vempati, H. Küçük, U. Visser, A. Koleti, A. Mir, K. Sakurai, C. Chung, J. Bittker, P. Clemons, S. Brudz, A. Siripala, A. Morales, M. Romacker, D. Twomey, S. Bureeva, V. Lemmon, and Schürer SC, “Evolving BioAssay Ontology (BAO): Modularization, Integration and Applications,” Journal of Biomedical Semantics, vol. 5, no. 1:S5, 2014.

Vempati UD, Przydzial MJ, Chung C, Abeyruwan S, Mir A, Sakurai K, Visser U, Lemmon VP, Schürer SC.  Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO).  PLoS One. 2012;7(11):e49198.  doi:  10:1371/journal.pone.0049198.  Epub 2012 Nov 14.

BAO 2.0 is release under the Creative Commons Attribution License Version 3

The BioAssay Ontology (BAO) describes biological screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 700 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation.

It is available online in OWL format: http://www.bioassayontology.org/bao/

Core Files:
bao_complete_bfo_dev.owl
bao_complete_examples.owl
bao_complete.owl
bao_core.owl
bao_external.owl
bao_metadata.owl
bao_module_biology.owl
bao_module_properties.owl
bao_module_vocabularies.owl
bao_ro_combinator.owl
bao_vocabulary_assay.owl
bao_vocabulary_assaykit.owl
bao_vocabulary_biology.owl
bao_vocabulary_computational.owl
bao_vocabulary_detection.owl
bao_vocabulary_format.owl
bao_vocabulary_function.owl
bao_vocabulary_instrument.owl
bao_vocabulary_materialentity.owl
bao_vocabulary_method.owl
bao_vocabulary_organization.owl
bao_vocabulary_people.owl
bao_vocabulary_phenotype.owl
bao_vocabulary_properties.owl
bao_vocabulary_quality.owl
bao_vocabulary_result.owl
bao_vocabulary_ro.owl
bao_vocabulary_role.owl
bao_vocabulary_screenedentity.owl
bao_vocabulary_software.owl
bao_vocabulary_unit.owl
External Files