PubSeq REST API

We built a REST API for COVID-19 PubSeq. The API source code can be found in api.py. To see if the service is up try

curl http://covid19.genenetwork.org/api/version

{
  "service": "PubSeq",
  "version": 0.1
}

The Python3 version is

import requests
response = requests.get("http://covid19.genenetwork.org/api/version")
response_body = response.json()
assert response_body["service"] == "PubSeq", "PubSeq API not found"
response_body

PubSeq provides an API that is used to export formats that are suitable for uploading data to EBI/ENA from our EXPORT menu. This is documented here.

requests.get("http://covid19.genenetwork.org/api/ebi/sample-MT32690.1.xml").text

<?xml version="1.0" encoding="UTF-8"?>
<SAMPLE_SET>
  <SAMPLE alias="MT32690.1" center_name="COVID-19 PubSeq">
    <TITLE>COVID-19 PubSeq Sample</TITLE>
    <SAMPLE_NAME>
      <TAXON_ID>2697049</TAXON_ID>
      <SCIENTIFIC_NAME>Severe acute respiratory syndrome coronavirus 2</SCIENTIFIC_NAME>
      <COMMON_NAME>SARS-CoV-2</COMMON_NAME>
    </SAMPLE_NAME>
    <SAMPLE_ATTRIBUTES>
      <SAMPLE_ATTRIBUTE>
        <TAG>investigation type</TAG>
        <VALUE></VALUE>
      </SAMPLE_ATTRIBUTE>
      <SAMPLE_ATTRIBUTE>
        <TAG>sequencing method</TAG>
        <VALUE></VALUE>
      </SAMPLE_ATTRIBUTE>
      <SAMPLE_ATTRIBUTE>
        <TAG>collection date</TAG>
        <VALUE></VALUE>
      </SAMPLE_ATTRIBUTE>
      <SAMPLE_ATTRIBUTE>
        <TAG>geographic location (latitude)</TAG>
        <VALUE></VALUE>
     <UNITS>DD</UNITS>
      </SAMPLE_ATTRIBUTE>
      <SAMPLE_ATTRIBUTE>
        <TAG>geographic location (longitude)</TAG>
        <VALUE></VALUE>
     <UNITS>DD</UNITS>
      </SAMPLE_ATTRIBUTE>
      <SAMPLE_ATTRIBUTE>
     <TAG>geographic location (country and/or sea)</TAG>
     <VALUE></VALUE>
      </SAMPLE_ATTRIBUTE>
      <SAMPLE_ATTRIBUTE>
        <TAG>geographic location (region and locality)</TAG>
        <VALUE></VALUE>
      </SAMPLE_ATTRIBUTE>
      <SAMPLE_ATTRIBUTE>
        <TAG>environment (material)</TAG>
        <VALUE></VALUE>
      </SAMPLE_ATTRIBUTE>
      <SAMPLE_ATTRIBUTE>
        <TAG>ENA-CHECKLIST</TAG>
        <VALUE>ERC000011</VALUE>
      </SAMPLE_ATTRIBUTE>
    </SAMPLE_ATTRIBUTES>
  </SAMPLE>
</SAMPLE_SET>