BioAssay Ontology
type: Ontology
license: https://creativecommons.org/licenses/by-sa/4.0/
version info: 2.7.2
label: BAO
comment: Created by: Hande Küçük McGinty, Janice Kranz, Joseph Ostrow, Alex Clark, Yu Lin, Saminda Abeyruwan, Uma Vempati, Kunie Sakurai, Vance Lemmon, Ubbo Visser, John Turner, Stephan Schurer*
comment: Contact: Stephan Schurer stephan dot schurer at gmail dot com
date: 8 Jul 2021

screened entity
type: Class
subclass of: assay screened entity component

small molecule
type: Class
IAO_0000115: Small molecule is an organic compound with a low molecular weight (<800 Da) which is used to screen against a biological target, e.g. protein, nucleic acid, cell or organism to test its ability to bind it and bring about a change in activity. It is either isolated from a natural source or is synthesized.
subclass of: screened entity

small molecule probe
type: Class
IAO_0000115: A small molecule useful to interrogate a biological system of interest. It has to be active in the system studies, i.e. cell permeable or active in vivo and be sufficiently efficacious and selective. The term probe also refers to the MLI screening effort, which has the goal to generate chemical probes. In addition, the MLI requires a novel chemical probe to be superior to the state of the art in terms of efficacy and selectivity and in-vivo properties. A list of probes generated is available here: http://mli.nih.gov/mli/mlp-probes/
subclass of: small molecule

morpholino oligonucleotide
type: Class
IAO_0000115: Morpholinos are antisense oligos that bind to specific mRNAs to reduce gene expression. They are small (~25 base) and possess altered back structures compared to DNA or RNA making them resistant to cleavage by nucleases. They are used extensively as tools to investigate zebrafish, Xenopus and sea urchin embryonic development.
subclass of: screened entity

miRNA
type: Class
IAO_0000118: micro RNA
IAO_0000118: micro ribonucleic acid
IAO_0000115: miRNAs or microRNAs are short RNAs (~22 nucleotides long) that bind to complementary sequences in the three prime untranslated regions (3' UTRs) of target messenger RNA transcripts (mRNAs), usually resulting in gene silencing.
subclass of: screened entity

shRNA
type: Class
IAO_0000118: short hairpin ribonucleic acid
IAO_0000118: short hairpin RNA
IAO_0000115: Short hairpin RNA (shRNA) can be used to achieve stable knockdown of gene expression. shRNA molecules are cloned into lentiviral or other vectors and expressed by a pol III type promoter.
subclass of: screened entity

siRNA
type: Class
IAO_0000118: small interfering ribonucleic acid
IAO_0000115: In the RNAi pathway, the double stranded RNAs first get processed into 20-25 nucleotide small interfering RNAs (siRNAs) by an RNase III-like enzyme called Dicer. The siRNAs enter into endoribonuclease-containing complexes known as RNA-induced silencing complexes (RISCs), and bring about the cleavage of the target mRNAs to achieve gene silencing.
subclass of: screened entity

esiRNA
type: Class
IAO_0000118: Endoribonuclease-prepared siRNA
IAO_0000115: esiRNAs are endoribonuclease-prepared siRNA pools comprised of a heterogeneous mixture of siRNAs that all target the same mRNA sequence.
subclass of: screened entity

compound library
type: Class
IAO_0000115: The name of a small molecule collection from one source, which can be either commercial or academic, e.g., MLSMR, LOPAC, etc. This collection is generally diverse and contains compounds that modulate diverse biological targets.
subclass of: perturbagen library

perturbagen library
type: Class
IAO_0000115: It is a collection of perturbagens, e.g., compound, siRNA, miRNA, etc, which are sold by different vendors, or generated in academic institutions.
subclass of: assay screened entity component

siRNA library
type: Class
IAO_0000118: small interfering ribonucleic acid library
IAO_0000115: siRNA libraries consist of large number of siRNAs, which represent a single organism, a diseased state, etc. They bring about the cleavage of the target mRNAs to achieve gene silencing.
subclass of: perturbagen library

miRNA library
type: Class
IAO_0000118: micro ribonucleic acid library
IAO_0000118: micro RNA library
IAO_0000115: It is a collection of miRNAs or microRNAs, which represents a single organism, a diseased state, etc. miRNAs bind the complementary sequences in the 3' UTRs of target mRNA transcripts, usually resulting in gene silencing.
subclass of: perturbagen library

MLSMR library
type: Class
subclass of: compound library

LOPAC 1280
type: Class
subclass of: compound library

DIVERSet
type: Class
subclass of: compound library

NINDS library
type: Class
subclass of: compound library

shRNA library
type: Class
subclass of: perturbagen library

The NatProd Collection
type: Class
subclass of: compound library

assay screened entity component
type: Class

Tox21 Compound Library
type: Class
IAO_0000115: The Tox21 compound collection is a library of approximately 10,000 (10K) environmental chemicals and drugs (~10,500 chemicals (~8,300 unique)), also referred to as the 'Tox21 10K library'. Several publications, from NCATS and EPA. See also https://www.epa.gov/chemical-research/toxicology-testing-21st-century-tox21 or https://ncats.nih.gov/tox21/about/operations.
subclass of: compound library

bivalent small molecule-peptide
type: Class
IAO_0000119: PubChem AID: 451462
IAO_0000116: Date from BAE: 5/5/2016
IAO_0000115: A synthetic ligand consisting of a small molecule tethered (covalently or non-covalently) to a peptide.
subclass of: screened entity

FDA-approved compound library
type: Class
IAO_0000119: PubChem AID: 1117303
IAO_0000116: Date from BAE: 9/30/2016
IAO_0000115: Any compound library consisting solely of small molecules that have been approved by the FDA. Often used for 'drug re-purposing' assays. The specific compounds included in any given FDA-approved compound library may differ based on availability or timing.
subclass of: compound library