Post-processing of Large Bioactivity Data.

@article{Harris2019PostprocessingOL,
  title={Post-processing of Large Bioactivity Data.},
  author={Jason B. Harris},
  journal={Methods in molecular biology},
  year={2019},
  volume={1939},
  pages={
          37-47
        }
}
  • J. Harris
  • Published 2019
  • Biology, Computer Science
  • Methods in molecular biology
Bioactivity data is a valuable scientific data type that needs to be findable, accessible, interoperable, and reusable (FAIR) (Wilkinson et al. Sci Data 3:160018, 2016). However, results from bioassay experiments often exist in formats that are difficult to interoperate across and reuse in follow-up research, especially when attempting to combine experimental records from many different sources. This chapter details common issues associated with the processing of large bioactivity data and… 
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References

SHOWING 1-10 OF 11 REFERENCES
The ChEMBL bioactivity database: an update
TLDR
More comprehensive tracking of compounds from research stages through clinical development to market is provided through the inclusion of data from United States Adopted Name applications and a new richer data model for representing drug targets has been developed.
PubChem BioAssay: 2014 update
TLDR
An update for the PubChem BioAssay resource is provided, such as information content growth, new developments supporting data integration and search, and the recently deployed PubChem Upload to streamline chemical structure and bioassay submissions.
BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results
TLDR
The first ontology to describe HTS experiments and screening results using expressive description logic is developed and BAO opens new functionality for annotating, querying, and analyzing HTS datasets and the potential for discovering new knowledge by means of inference.
Minimum information about a bioactive entity (MIABE)
TLDR
The definition of reporting guidelines for bioactive entities — the Minimum Information About a Bioactive Entity (MIABE) — which has been developed by representatives of pharmaceutical companies, data resource providers and academic groups are proposed.
The Comparative Toxicogenomics Database: update 2017
TLDR
This update describes the new exposure module (that harmonizes exposure science information with core toxicogenomic data) and introduces a novel dataset of GO-disease inferences (that identify common molecular underpinnings for seemingly unrelated pathologies).
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology
TLDR
The first update of BindingDB since 2007 is provided, focusing on new and unique features and highlighting directions of importance to the field as a whole.
The ToxCast program for prioritizing toxicity testing of environmental chemicals.
TLDR
The ToxCast program will evaluate chemical properties and bioactivity profiles across a broad spectrum of data domains: physical-chemical, predicted biological activities based on existing structure-activity models, biochemical properties based on HTS Assays, cell-based phenotypic assays, and genomic and metabolomic analyses of cells.
Pharos: Collating protein information to shed light on the druggable genome
TLDR
Two resources developed by the IDG Knowledge Management Center are described: the Target Central Resource Database (TCRD) which collates many heterogeneous gene/protein datasets and Pharos (https://pharos.nih.gov), a multimodal web interface that presents the data from TCRD.
DrugBank: a comprehensive resource for in silico drug discovery and exploration
TLDR
DrugBank is a unique bioinformatics/cheminformatics resource that combines detailed drug data with comprehensive drug target information and is fully searchable supporting extensive text, sequence, chemical structure and relational query searches.
The FAIR Guiding Principles for scientific data management and stewardship
TLDR
This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.
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