{"info":{"_postman_id":"1c3f41d4-983e-4cb8-8266-b72fcea3fe53","name":"0.0.3beta4","description":"

PhenoGen REST API

\n

We are building a REST API to provide access to all public data. Eventually this will also
include running most functions available through the website. Keep checking back for new functions.

\n

Domains for Function Calls:

\n

Functions can be called at either:
https://rest.phenogen.org
or
https://rest-test.phenogen.org
Please note this is a development and testing version of the API. Please do not use this
for actual data analysis. Only for development.

\n

Help

\n

https://rest-doc.phenogen.org - temporarily unavailable (as of 6/17/22), but will be available within a
few days
All functions should include help as a response if you call the function with this appended to the
end ?help=Y. The response returns a JSON object with supported methods and then list of parameters
and description of each parameter as well as a list of options if there is a defined list of values.

\n

R Methods for the API

\n

We are developing methods to call the REST API from R and to retrieve the data directly from PhenoGen into
R. For now this is limited to the datasets at https://phenogen.org/web/sysbio/resources.jsp -> New RNA
Sequencing Datasets Experimental Details/Downloads
We will turn this into an R package and release it.
GitHub Repository -
https://github.com/TabakoffLab/PhenoGenRESTR

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Get data for a specific browser track from a specific region or for a gene.

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(Required) ID of the track

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Genome Version

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(Required) Chromosome Location

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(Required) Minimum coordinate

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(Required) Maximum coordinate

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Bin Size for binned data

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Data Version(optional) - allows you to select previous versions of data otherwise the most recent version is used.

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Genome Version - rn7,rn6,rn5,mm10

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Organism - Rn,Mm

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tissue

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Animal Panel - HRDP,LXS,BXH/HXB

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Seqeuncing Type - totalRNA,smallRNA

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(Required) Level used for quantitation. [Gene,Transcript]

\n","type":"text/plain"},"key":"analysisLevel","value":"gene"},{"description":{"content":"

(Required) Tissue for expression values [Brain,Liver,Heart,Kidney]

\n","type":"text/plain"},"key":"tissue","value":""},{"description":{"content":"

(Required) Return values for individual samples or strain means.

\n","type":"text/plain"},"key":"strainMeans","value":"0"},{"description":{"content":"

HRDP version if specific version is required. Otherwise latest version that meets other constraints.

\n","type":"text/plain"},"key":"version","value":"LATEST"},{"description":{"content":"

Specific genome version requested [rn5,rn6,rn7]

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(Required) Annotation used for quantitation. [Ensembl,Reconstruction]

\n","type":"text/plain"},"key":"annotation","value":""},{"description":{"content":"

(Required) Level used for quantitation. [Gene,Transcript]

\n","type":"text/plain"},"key":"analysisLevel","value":"gene"},{"description":{"content":"

(Required) Tissue for expression values [Brain,Liver,Heart,Kidney]

\n","type":"text/plain"},"key":"tissue","value":""},{"description":{"content":"

(Required) Return values for individual samples(default-0) or strain means(1).

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HRDP version if specific version is required. Otherwise latest version that meets other constraints.[5,6]

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Specific genome version requested [rn5,rn6,rn7]

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Optional filter by genome version - rn7,rn6,rn5,mm10

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Optional filter by organism - Rn,Mm

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(Required) Marker Set ID to retreive the file list. - Required

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(Required) Gene parameter This should correspond to a PhenoGen ID or an Affy Transcript Cluster ID of the gene.

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(Required) Type parameter - This parameter specifies the data source to use [seq, array]. Default: seq

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(Required) Cutoff parameter - This parameter specifies -log(Pvalue) cutoff to use the returned values must be >=cutoff. The default is 2.0.

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(Required) Tissues parameter - This parameter specifies tissues to retreive eQTLs for as a comma seperated list. Options depend on source type. For rat options are source:RNASeq: [Brain,Liver] source:Array:[Brain,Heart,Liver,BAT].

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(Required) GenomeVersion parameter - This parameter specifies genomeVersion to return results for. Currently supported versions [mm10,rn5,rn6]

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(Required) Version parameter - This parameter specifies the rna_dataset version to use for the results. This corresponds to the version of the HRDP dataset. The default is the most recent version

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(Required) This parameter is required to pull up a gene report. This should correspond to the ensembl ID or PhenoGen ID of the gene.

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(Required) This parameter specifies the type of report returned. Options: [generic,snp,transcript]

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(Required) Any supported Gene ID

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This parameter specifies the species to use to find the ID specified. [Rn,Mm,Hs] default: Rn

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The number of connections from the source to traverse to find matching IDs. Lower levels will be more directly connected and help eliminate retreiving loosly connected IDs. If IDs expected to be returned aren't returned increaseing the level by 1-2 may help.

\n","type":"text/plain"},"key":"level","value":"1"},{"description":{"content":"

This parameter specifies ID Types of interest and limits results to IDs of the specified type(s). Comma seperated list of target IDs.

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