Skip to content

Latest commit

 

History

History
150 lines (111 loc) · 4.66 KB

services.md

File metadata and controls

150 lines (111 loc) · 4.66 KB
Raw

Online Service Providers

The biows manager

The biows manager allows you to retrieve information from biology-related webservices, including the Uniprot database:

biows.queryUniProtKB("P38398")

The embl nucleotide sequence database at the ebi:

biows.queryEMBL("M10051")

And also RefSeq:

biows.queryRefseq("NM_000059")

The chemspider manager

The chemspider manager makes functionality avaiable to interact with the ChemSpider database. For example, we can download a structure with a chemspider identifier number:

Script code/ChemSpiderDownload.groovy

chemspider.download(9606)

You can also use ChemSpider to resolve InChIKeys to entries in the database:

Script code/ChemSpiderResolve.groovy

chemspider.resolve("RCINICONZNJXQF-MZXODVADSA-N")

Some methods require a security token that can be set via the preferences (see http://www.chemspider.com/AboutServices.aspx). But when that is done, we can search specific compounds:

chemspider.exactSearch(
  opsin.parseIUPACName("methane")
)

Similarly, we can also do a similarity search:

chemspider.similaritySearch(
  opsin.parseIUPACName(
    "acetyl salicylic acid"
  ), 0.95
)

And by substructure:

chemspider.substructureSearch(
  opsin.parseIUPACName("benzene")
)

The opentox manager

OpenTox is a platform for toxicology, allowing for sharing of data as well as creating and running computational models [1]. The opentox manager integrates much of its functionality [2].

There are various methods to list what is available. Some information is available from a central registration server, e.g. http://apps.ideaconsult.net/ontology/:

registry = "https://apps.ideaconsult.net/ontology";
algorithms = opentox.listAlgorithms(registry);
descriptors = opentox.listDescriptors(registry);
models = opentox.listModels(registry);

Similarly, using a particular OpenTox service, e.g. an ambit instance at http://apps.ideaconsult.net/ambit2/, we can list data sets and features (properties) [3]:

service = "http://apps.ideaconsult.net/ambit2/";
dataSets = opentox.listDataSets(service);
features = opentox.listFeatures(service);

Instead of listing, we can also search for various types, such as the ToxTree models [4]:

models = opentox.searchModels(registry, "ToxTree");

We can select one of the available models, and then make a prediction for a compound:

toxTreeModel =
  "http://apps.ideaconsult.net:8080/ambit2/model/3";
opentox.predictWithModel(
  service, toxTreeModel,
  cdk.fromSMILES("CCC")
)

The pubchem manager

The pubchem manager makes functionality available to interact with the PubChem database. For example, we can download a structure with a PubChem compound identifier number:

pubchem.download(2244)

Or as a 3d structure:

pubchem.download3d(2244)

And we can search compounds based on a label:

Script code/PubChemSearch.groovy

pubchem.search("tamoxifen")

References

  1. Hardy B, Douglas N, Helma C, Rautenberg M, Jeliazkova N, Jeliazkov V, et al. Collaborative development of predictive toxicology applications. J Cheminform. 2010 Aug 31;2(1):7. doi:10.1186/1758-2946-2-7 (Scholia)
  2. Willighagen E, Jeliazkova N, Hardy B, Grafström R, Spjuth O. Computational toxicology using the OpenTox application programming interface and Bioclipse. BMC Research Notes. 2011;4(1):487. doi:10.1186/1756-0500-4-487 (Scholia)
  3. Jeliazkova N, Jeliazkov V. AMBIT RESTful web services: an implementation of the OpenTox application programming interface. J Cheminform. 2011 May 16;3(1):18. doi:10.1186/1758-2946-3-18 (Scholia)
  4. Patlewicz G, Jeliazkova N, Safford RJ, Worth A, Aleksiev B. An evaluation of the implementation of the Cramer classification scheme in the Toxtree software. SAR and QSAR in Environmental Research. 2008 Jan 1;19(5–6):495–524. doi:10.1080/10629360802083871 (Scholia)