Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Jan 17:7:75.
doi: 10.12688/f1000research.13197.2. eCollection 2018.

Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform

Ryan A Miller  1 , Peter Woollard  2 , Egon L Willighagen  1 , Daniela Digles  3 , Martina Kutmon  1   4 , Antonis Loizou  5 , Andra Waagmeester  1   6 , Stefan Senger  2 , Chris T Evelo  1   4   7
Affiliations

Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform

Ryan A Miller et al. F1000Res. .

Abstract

Open PHACTS is a pre-competitive project to answer scientific questions developed recently by the pharmaceutical industry. Having high quality biological interaction information in the Open PHACTS Discovery Platform is needed to answer multiple pathway related questions. To address this, updated WikiPathways data has been added to the platform. This data includes information about biological interactions, such as stimulation and inhibition. The platform's Application Programming Interface (API) was extended with appropriate calls to reference these interactions. These new methods of the Open PHACTS API are available now.

Keywords: API; Open PHACTS; WikiPathways; bioinformatics; drug discovery; pathway database; semantic.

PubMed Disclaimer

Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Parameters (bottom) and curl command (top) for the GET /pathways/interactions/byEntity call.
The GET portion tells the API to retrieve data with the associated call. It takes an entity URI, the Ensembl ID for AKT2, and returns a list interactions for AKT2. The obligatory parameters are shown in bold. Entity IDs that are acceptable for queries include Ensembl, Entrez Gene, and UniProt for genes, proteins, and RNAs. For metabolites the ID sources HMDB, ChEBI, and ChemSpider, for example, are acceptable entity IDs
Figure 2.
Figure 2.. Result in the JSON format of the AKT2 query from Figure 1.
The participants of the interaction are directed from source (hsa-let7b) to target (AKT2). It also shows the type of interaction (inhibition), and the biological types of the interaction participants.
Figure 3.
Figure 3.. Parameters (bottom) and curl command (top) for the GET /pathways/interactions/byEntity/count call.
It takes a URI for an entity, in this case the Ensembl ID for AKT2 and returns a count of the interactions to which this gene product is involved. Only the entity URI, app ID, and app key are required fields. Optional parameters are pathway organism, direction, or type of interaction.
Figure 4.
Figure 4.. Parameters (bottom) and curl command (top) for the /pathway/getInteractions call.
It is intended to take the pathway URI from WikiPathways and return a list of interaction involved in that particular pathway. Pathway URI, app ID, and app key are the only required values for this call.
See this image and copyright information in PMC

References

    1. Schreiber SL: Target-oriented and diversity-oriented organic synthesis in drug discovery. Science. 2000;287(5460):1964–1969. 10.1126/science.287.5460.1964 - DOI - PubMed
    1. Azzaoui K, Jacoby E, Senger S, et al. : Scientific competency questions as the basis for semantically enriched open pharmacological space development. Drug Discov Today. 2013;18(17–18):843–852. 10.1016/j.drudis.2013.05.008 - DOI - PubMed
    1. Williams AJ, Harland L, Groth P, et al. : Open PHACTS: semantic interoperability for drug discovery. Drug Discov Today. 2012;17(21–22):1188–1198. 10.1016/j.drudis.2012.05.016 - DOI - PubMed
    1. Digles D, Zdrazil B, Neefs JM, et al. : Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns. Medchemcomm. 2016;7(6):1237–1244. 10.1039/c6md00065g - DOI - PMC - PubMed
    1. Waagmeester A, Kutmon M, Riutta A, et al. : Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PLoS Comput Biol. 2016;12(6):e1004989. 10.1371/journal.pcbi.1004989 - DOI - PMC - PubMed

Publication types

Substances

LinkOut - more resources