The Ocular Tissue Database

API Documentation

Basic Call

Let’s say you’d like expression data for all genes starting with the letters “MAK”

https://genome.uiowa.edu/otdb/api?term=MAK

Here’s the output:

<?xml version="1.0" encoding="UTF-8"?>
<results>
  <transcript.2941632>
    <tissues>
      <choroid>
        <rma>4.70169</rma>
        <plier>48.8023</plier>
        <rma_glaucoma>4.4146</rma_glaucoma>
        <plier_glaucoma>27.2876</plier_glaucoma>
      </choroid>
      <ciliary_body>
        <rma>3.58617</rma>
        <plier>22.9118</plier>
        <rma_glaucoma>3.98751</rma_glaucoma>
        <plier_glaucoma>23.5325</plier_glaucoma>
      </ciliary_body>
      .
      .
      .
With no other parameters specified, the output

Tweaking the Call

List of API parameters
Tweak Description Append to call Possible values Default Value
(i.e. if unspecified)
Search Type
  • symbol searches genes that begin with your search term
  • fuzzy will search gene symbols, descriptions and accessions that contain your term
  • affy and transcript will show all Affymetrix annotations for a given transcript ID
  • probeset shows Affymetrix annotations for a single probeset ID
  • expression retrieves gene expression per tissue. It requires a tissue= parameter (see “Tissues” below.) Data is sorted by PLIER values. Since there are a lot of results, you’ll see the first 100 of thousands. Use the offset parameter to see the next n values.
&type=
  • symbol
  • fuzzy
  • transcript
  • affy
  • probeset
  • expression
symbol
Search Term All API calls except expression require this parameter. The expected format depends upon the type of search. For gene symbol and fuzzy searches, this must be at least three characters long. Transcript and probeset IDs must be integers (obviously). &term= (None) (None)
Output Format Format results as JSON, XML, comma-separated (CSV) or tab-delimited values. CSV outputs are not available for affy and probeset search types. &format=
  • xml
  • json
  • csv
xml
Output Method If set to download, headers appropriate for the chosen output format are sent to the client. If unspecified or set explicitly to plain, the output sent as plain text (the text/plain MIME-type.) &method=
  • plain
  • download
plain
Tissues If unset, all ten tissues in the OTDB are retrieved. You can selectively query for a subset by supplying a comma-separated list of tissues to this parameter. &tissues=
  • choroid
  • ciliary_body
  • cornea
  • iris
  • lens
  • optic_nerve
  • optic_nerve_head
  • retina
  • sclera
  • trabecular_meshwork
All of them!
Dataset Search either the core or extended datasets. &set=
  • core
  • extended
core
Annotations Add Affy annotations to search results &annotate (None) (None)

Some Examples