COVID-19 PubSeq (part 6)
+Table of Contents
+ +1 Generating output for EBI
++Would it not be great an uploader to PubSeq also can export samples +to, say, EBI? That is what we discuss in this section. The submission +process is somewhat laborious and when you have submitted to PubSeq +why not export the same to EBI too with the least amount of effort? +
+ ++COVID-19 PubSeq is a data source - both sequence data and metadata - +that can be used to push data to other sources, such as EBI. You can +register samples programmatically with a specific XML interface. Note +that (at this point) if you want to submit a sequence (FASTA) it can +only be done through the Webin-CLI. Raw data (FASTQ) can go through +the XML interface. +
+ ++EBI sequence resources are presented through ENA. For example +Sequence: MT394864.1. +
+ ++EBI has XML Formats for +
+ +-
+
- SUBMISSION +
- STUDY +
- SAMPLE +
- EXPERIMENT +
- RUN +
- ANALYSIS +
- DAC +
- POLICY +
- DATASET +
- PROJECT +
+with the schemas listed here. Since we are submitting sequences we +should follow submitting full genome assembly guidelines and +ENA guidelines. The first step is to define the study, next the sample +and finally the sequence (assembly). +
+2 Defining the EBI study
++A study is defined here and looks like +
+ +<PROJECT_SET> + <PROJECT alias="COVID-19 Washington DC"> + <TITLE>Sequencing SARS-CoV-2 in the Washington DC area</TITLE> + <DESCRIPTION>This study collects samples from COVID-19 patients in the Washington DC area</DESCRIPTION> + <SUBMISSION_PROJECT> + <SEQUENCING_PROJECT/> + </SUBMISSION_PROJECT> + </PROJECT> +</PROJECT_SET> ++
+also a submission 'command' is required looking like +
+ +<SUBMISSION> + <ACTIONS> + <ACTION> + <ADD/> + </ACTION> + <ACTION> + <HOLD HoldUntilDate="TODO: release date"/> + </ACTION> + </ACTIONS> +</SUBMISSION> + ++
+The webin system accepts such sources using a command like +
+ ++curl -u username:password -F "SUBMISSION=@submission.xml" \ + -F "PROJECT=@project.xml" "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/" ++ + +
+as described here. Note that this is the test server. For the final +version use www.ebi.ac.uk instead of wwwdev.ebi.ac.uk. You may also +need the –insecure switch to circumvent certificate checking. +
+ ++work in progress (WIP) +
+3 Define the EBI sample
++work in progress (WIP) +
+4 Define the EBI sequence
++work in progress (WIP) +
+