InterfaceController Class Reference

Controller specifying the web api for InSilico DB. More...

Public Member Functions

 getDatasetList ($platform=NULL, $norm=NULL, $query=NULL, $curated=NULL)
 Retrieve a list of datasets.
 getDatasetPlatformList ($platform=NULL, $norm=NULL, $query=NULL, $curated=NULL)
 Retrieve a list of (dataset, platform) tuples.
 getDatasetInfo ($dataset, $platform, $format=NULL, $features=NULL, $norm=NULL, $curation=NULL, $type=NULL)
 Get information about a dataset.
 getDataset ($dataset, $platform, $format, $features, $norm, $curation, $type, $timeout)
 Get dataset.
 getDefaultCuration ($dataset)
 Get the default curation for a given dataset.
 getCurations ($dataset)
 Get different curations for a given dataset.
 getPlatforms ($dataset)
 Get all platforms that are used in a given dataset.
 getAnnotations ($dataset, $curation=NULL, $platform=NULL, $type=NULL)
 Get sample annotations of a given dataset,.
 login ($login, $password)
 Login into the InSilico DB.
 logoutAction ()
 Logout.
 userAction ()
 Get your user details when logged in.

Detailed Description

Controller specifying the web api for InSilico DB.

Public web interface of the InSilico DB.

  • All URIs in web examples are relative to https://insilicodb.com/app/interface/
    All values returned by the web interface (except binary data) will be wrapped in a JSON object.
    This JSON object will also contain a "success" and "msg" value.
  • All R code examples are run with inSilicoDb 2.0 using R 2.15 and R/Bioconductor x.xx

Looking for extra functionality? Don't hesitate to contact us at support@insilicodb.com

Information about frequently used parameters:

Parameters:
datasetDataset identifier: the GEO or InSilico DB accession code.
Possible values: GSE4635, ISDB7470, GSE2109,...
platformThe platform of the chip (microarray, HTS,...) on which a measurement was done.
A platform is identified by its GEO accession code.
Possible values: GPL96, GPL97, GPL570, GPL571,...
normType of normalization to use when pre-processing a dataset.
More information at https://insilicodb.com/blog .
Possible values: ORIGINAL, FRMA, FRMACDF, BARCODE.
featuresType of features in which data is represented.
Two possible values: GENE or PROBE.
If not defined, genes are selected by default.
typeType of measurement.
Possible values: RNA, RNASeq,...
formatFile format in which the dataset should be returned.
Possible values:
  • CURESET : Curated R/Bioconductor ESET dataset.
  • GCT : Curated GenePattern dataset.
  • ORANGE : Curated Orange dataset. (EXPERIMENTAL)
  • ESET : R/Bioconductor ESET dataset without curation.
    Defaults to CURESET.
curationSpecific curation used to annotate a dataset.
A curation is identified by a InSilico DB Curation identifier.
You can annotate datasets yourself at https://insilicodb.com/app/browse
If not defined, the default curation of specified dataset will be used.
Author:
David Steenhoff support@insilicodb.com

Member Function Documentation

InterfaceController::getAnnotations ( dataset,
curation = NULL,
platform = NULL,
type = NULL 
)

Get sample annotations of a given dataset,.

Parameters:
dataset
platform
curation
type
Returns:
annotations Array of annotations (key, value pairs) per measurement of given dataset.
getannotations?dataset=GSE4635

Get different curations for a given dataset.

Parameters:
dataset
Returns:
curations Array with information about different curations of a given dataset.
The ID, curator, date and used keywords are given for every curation.
getcurations?dataset=GSE4635
InterfaceController::getDataset ( dataset,
platform,
format,
features,
norm,
curation,
type,
timeout 
)

Get dataset.

Retrieve a dataset by name and platform, in a specific format.
All parameters (except timeout) are required.
You can get most values by calling getDatasetInfo() first.

Parameters:
dataset
platform
features
norm
format
curation
type
timeoutTime in seconds to wait for the dataset, if it has to be generated.
Defaults to 120.
Returns:
file Binary file in specified format.
getdataset?dataset=GSE4635&platform=GPL96&format=CURESET&features=GENE&norm=FRMA&curation=14926&type=RNA
InterfaceController::getDatasetInfo ( dataset,
platform,
format = NULL,
features = NULL,
norm = NULL,
curation = NULL,
type = NULL 
)

Get information about a dataset.

Get information about the availability and the default parameters of a dataset.
Normally you call getDatasetInfo() before getDataset().

Parameters:
dataset
platform
features
norm
format
curation
Returns:
dataset Array of requested properties, augmented with default values and dataset state information.
getdatasetinfo?dataset=GSE4635&platform=GPL96
InterfaceController::getDatasetList ( platform = NULL,
norm = NULL,
query = NULL,
curated = NULL 
)

Retrieve a list of datasets.

Parameters:
platformIf defined, only datasets with measurements on given platform will be returned.
normIf defined, only datasets for which the specified normalization is available will be returned.
queryIf defined, only datasets found with this query will be returned.
Possible values: Thyroid, breast cancer, ...
curatedIf true, only manually curated datasets will be returned.
Returns:
datasets List of dataset identifiers.
getdatasetlist?platform=GPL570&norm=FRMA&query=Thyroid
R: getDatasetList(platform="GPL570", norm="FRMA", query="Thyroid")
InterfaceController::getDatasetPlatformList ( platform = NULL,
norm = NULL,
query = NULL,
curated = NULL 
)

Retrieve a list of (dataset, platform) tuples.

Parameters:
platformIf defined, only datasets with measurements on given platform will be returned.
normIf defined, only datasets for which the specified normalization is available will be returned.
queryIf defined, only datasets found with this query will be returned.
Possible values: Thyroid, breast cancer, ...
curatedIf true, only manually curated datasets will be returned.
Returns:
datasets List of dataset identifiers.
getdatasetplatformlist?platform=GPL570&norm=FRMA&query=Thyroid
R: getDatasetPlatformList(platform="GPL570", norm="FRMA", query="Thyroid")

Get the default curation for a given dataset.

Parameters:
dataset
Returns:
curation Array with curation information: ID, date and curator.
getdefaultcuration?dataset=GSE2109

Get all platforms that are used in a given dataset.

Parameters:
dataset
Returns:
platforms Array of used platforms.
getplatforms?dataset=GSE27708
InterfaceController::login ( login,
password 
)

Login into the InSilico DB.

A cookie will be set to keep your client logged in.

Parameters:
loginUsername or email address
passwordMD5 hash of your password.
Returns:
userid Your user ID.
login?login=support@insilicodb.com&password=9e597c7b9b32962fad6c1f598b99948c

Get your user details when logged in.

Returns:
user List of user details with ID, name, email.