COVID-19 PubSeq Uploading Data (part 3)
Table of Contents
1 Uploading Data
Work in progress!
2 Introduction
The COVID-19 PubSeq allows you to upload your SARS-Cov-2 strains to a public resource for global comparisons. Compute it triggered on upload. Read the ABOUT page for more information.
3 Step 1: Upload sequence
To upload a sequence in the web upload page hit the browse button and select the FASTA file on your local hard disk.
We start with an assembled or mapped sequence in FASTA format. The PubSeq uploader contains a QC step which checks whether it is a likely SARS-CoV-2 sequence. While PubSeq deduplicates sequences and never overwrites metadata, you may still want to check whether your data already is in the system by querying some metadata as described in Query metadata with SPARQL or by simply downloading and checking one of the files on the download page. We find GenBank MT536190.1 has not been included yet. A FASTA text file can be downloaded to your local disk and uploaded through our web upload page. Make sure the file does not include any HTML!
Note: we currently only allow FASTA uploads. In the near future we'll allow for uploading raw sequence files. This is important for creating an improved pangenome.
4 Step 2: Add metadata
The web upload page contains fields for adding metadata. Metadata is not only important for attribution, is also important for analysis. The metadata is available for queries, see Query metadata with SPARQL, and can be used to annotate variations of the virus in different ways.
A number of fields are obligatory: sample id, date, location,
technology and authors. The others are optional, but it is valuable to
enter them when information is available. Metadata is defined in this
schema. From this schema we generate the input form. Note that
opitional fields have a question mark in the type. You can add
metadata yourself, btw, because this is a public resource! See also
Modify metadata for more information.
To get more information about a field click on the question mark on the web form. Here we add some extra information.
4.1 Obligatory fields
4.1.1 Sample ID (sampleid)
This is a string field that defines a unique sample identifier by the submitter. In addition to sampleid we also have hostid, providersampleid and submittersampleid where host is the host the sample came from, provider sample is the institution sample id and submitter is the submitting individual id. hostid is important when multiple sequences come from the same host. Make sure not to have spaces in the sampleid.
Here we add the GenBank ID MT536190.1.
4.1.2 Collection date
Estimated collection date. The GenBank page says April 6, 2020.
4.1.3 Collection location
A search on wikidata says Los Angelos is https://www.wikidata.org/entity/Q65
4.1.4 Sequencing technology
GenBank entry says Illumina, so we can fill that in
4.1.5 Authors
GenBank entry says 'Lamers,S., Nolan,D.J., Rose,R., Cross,S., Moraga Amador,D., Yang,T., Caruso,L., Navia,W., Von Borstel,L., Hui Zhou,X., Freehan,A. and Garcia-Diaz,J.', so we can fill that in.
4.2 Optional fields
All other fields are optional. But let's see what we can add.
4.2.1 Host information
Sadly, not much is known about the host from GenBank. A little sleuthing renders an interesting paper by some of the authors titled SARS-CoV-2 is consistent across multiple samples and methodologies which dates after the sample, but has no reference other than that the raw data came from the SRA database, so it probably does not describe this particular sample. We don't know what this strain of SARS-Cov-2 did to the person and what the person was like (say age group).
4.2.2 Collecting institution
We can fill that in.
4.2.3 Specimen source
We have that: nasopharyngeal swab
4.2.4 Source database accession
Genbank which is http://identifiers.org/insdc/MT536190.1#sequence. Note we plug in our own identifier MT536190.1.
4.2.5 Strain name
SARS-CoV-2/human/USA/LA-BIE-070/2020
5 Step 3: Submit to COVID-19 PubSeq
Once you have the sequence and the metadata together, hit the 'Add to Pangenome' button. The data will be checked, submitted and the workflows should kick in!
6 Step 4: Check output
The current pipeline takes 5.5 hours to complete! Once it completes the updated data can be checked on the DOWNLOAD page. After completion of above output this SPARQL query shows some of the metadata we put in.
6.1 Trouble shooting
We got an error saying: {"stem": "http://www.wikidata.org/entity/",… which means that our location field was not formed correctly! After fixing it to look like http://www.wikidata.org/entity/Q65 (note http instead on https and entity instead of wiki) the submission went through. Reload the page (it won't empty the fields) to re-enable the submit button.