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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:

ChemSpiderDownload

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

ChemSpiderResolve

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 [Q27162585]. The opentox manager integrates much of its functionality [Q27134787].

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) [Q27921856]:

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 [Q52227990]:

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:

PubChemSearch

References