COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource

public sequences ready for download!

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COVID-19 PubSeq - query metadata (part 1)

1 What does this mean?

This means that when someone uploads a SARS-CoV-2 sequence using one of our tools (CLI or web-based) they add some metadata which is expressed in a schema that looks like

- name: hostSchema
  type: record
  fields:
    host_species:
        doc: Host species as defined in NCBITaxon, e.g. http://purl.obolibrary.org/obo/NCBITaxon_9606 for Homo sapiens
        type: string
        jsonldPredicate:
          _id: http://www.ebi.ac.uk/efo/EFO_0000532
          _type: "@id"
          noLinkCheck: true
    host_sex:
        doc: Sex of the host as defined in PATO, expect male () or female ()
        type: string?
        jsonldPredicate:
          _id: http://purl.obolibrary.org/obo/PATO_0000047
          _type: "@id"
          noLinkCheck: true
    host_age:
        doc: Age of the host as number (e.g. 50)
        type: int?
        jsonldPredicate:
          _id: http://purl.obolibrary.org/obo/PATO_0000011

this metadata gets transformed into an RDF database which means information can easily be fetched related to uploaded sequences. We'll show an example below where we query a live database.

There is more: when a new sequence gets uploaded COVID-19 PubSeq kicks in with a number of workflows running in the cloud. These workflows generate a fresh variation graph (GFA) containing all sequences, an RDF file containing metadata, and an RDF file containing the variation graph in triples. Soon we will at multi sequence alignments (MSA) and more. Anyone can contribute data, tools and workflows to this initiative!

2 Fetch sequence data

The latest run of the pipeline can be viewed here. Each of these generated files can just be downloaded for your own use and sharing! Data is published under a Creative Commons 4.0 attribution license (CC-BY-4.0). This means that, unlike some other 'public' resources, you can use this data in any way you want, provided the submitter gets attributed.

If you download the GFA or FASTA sequences you'll find sequences are named something like keep:e17abc8a0269875ed4cfbff5d9897c6c+123/sequence.fasta which refers to an internal Arvados Keep representation of the FASTA sequence. Keep is content-addressable which means that the value e17abc8a0269875ed4cfbff5d9897c6c uniquely identifies the file by its contents. If the contents change, the identifier changes! We use these identifiers throughout.

3 Predicates

To explore an RDF dataset, the first query we can do is open and gets us a list. Lets look at all the predicates in the dataset by pasting the following in a SPARQL end point http://sparql.genenetwork.org/sparql/

select distinct ?p
{
   ?o ?p ?s
}

you can ignore the openlink and w3 ones. To reduce results to a named graph set the default graph. To get a list of graphs in the dataset, first do

select distinct ?g
{
    GRAPH ?g {?s ?p ?o}
}

Limiting search to metadata add http://covid-19.genenetwork.org/graph/metadata.ttl in the top input box. Now you can find a predicate for submitter that looks like http://biohackathon.org/bh20-seq-schema#MainSchema/submitter.

To list all submitters, try

Oh wait, it returns things like nodeID://b76150! That is not helpful, these are anonymous nodes in the graph. These point to another triple and by

select distinct ?s
{
   ?o <http://biohackathon.org/bh20-seq-schema#MainSchema/submitter> ?id .
   ?id ?p ?s
}

you get a list of all submitters including "University of Washington, Seattle, WA 98109, USA".

To lift the full URL out of the query you can use a header like

PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
select distinct ?dataset ?submitter
{
   ?dataset pubseq:submitter ?id .
   ?id ?p ?submitter
}

which reads a bit better. We can also see the submitted sequences. One of them submitted by University of Washington is http://collections.lugli.arvadosapi.com/c=030bcb8fda7f19743157359f5855f7a6+126/sequence.fasta (note the ID may have changed so pick one with above query). To see the submitted metadata replace sequence.fasta with metadata.yaml http://collections.lugli.arvadosapi.com/c=030bcb8fda7f19743157359f5855f7a6+126/metadata.yaml

Now we got this far, lets count the datasets submitted with

PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
select (COUNT(distinct ?dataset) as ?num)
{
   ?dataset pubseq:submitter ?id .
   ?id ?p ?submitter
}

Run this query.

4 Fetch submitter info and other metadata

To get datasets with submitters we can do the above

PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
select distinct ?dataset ?p ?submitter
{
   ?dataset pubseq:submitter ?id .
   ?id ?p ?submitter
}

Run this query.

Tells you one submitter is "Roychoudhury,P.;Greninger,A.;Jerome,K." with a URL predicate (http://purl.obolibrary.org/obo/NCIT_C42781) explaining "The individual who is responsible for the content of a document." Well formed URIs point to real information about the URI itself. Welcome to the power of the semantic web.

Let's focus on one sample with

PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
select distinct ?dataset ?submitter
{
   ?dataset pubseq:submitter ?id .
   ?id ?p ?submitter .
   FILTER(CONTAINS(?submitter,"Roychoudhury")) .
}

That is a lot of samples! We just want to pick one, so let's see if we can get a sample ID by listing sample predicates

PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
select distinct ?p
{
   ?dataset ?p ?o .
   ?dataset pubseq:submitter ?id .
}

which lists a predicate named http://biohackathon.org/bh20-seq-schema#MainSchema/sample. Let's zoom in on those of Roychoudhury with

PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
select distinct ?sid ?sample ?p1 ?dataset ?submitter
{
   ?dataset pubseq:submitter ?id .
   ?id ?p ?submitter .
   FILTER(CONTAINS(?submitter,"Roychoudhury")) .
   ?dataset pubseq:sample ?sid .
   ?sid ?p1 ?sample
}

Run query.

which shows pretty much everything known about their submissions in this database. Let's focus on one sample "MT326090.1" with predicate http://semanticscience.org/resource/SIO_000115.

PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
PREFIX sio: <http://semanticscience.org/resource/>
select distinct ?sample ?p ?o
{
   ?sample sio:SIO_000115 "MT326090.1" .
   ?sample ?p ?o .
}

Run this query.

This query tells us the sample was submitted "2020-03-21" and originates from http://www.wikidata.org/entity/Q30, i.e., the USA and is a biospecimen collected from the back of the throat by swabbing. We have also added country and label data to make it a bit easier to view/query the database and place the sequence on the map. We use wikidata entities for disambiguation. By using 'Q30' for the USA we don't have to figure out the different ways people spell the name. To get from the wikidata entity to a human readable form we provide a country name translation for convenience. For example when the predicate is http://purl.obolibrary.org/obo/GAZ_00000448 we can do

Which will show the geoname spelled out as 'United States'.

For this sample we can also track it back to the original GenBank submission using the listed http://identifiers.org/insdc/MT326090.1 link.

5 Fetch all sequences from Washington state

Now we know how to get at the origin we can do it the other way round and fetch all sequences referring to Washington state

Run query

Which shows the date and links to NCBI and raw sequence data in FASTA format, e.g.

"date"  "name"  "identifier"  "seq"
"2020-01-15"  "MT252760.1"  "http://identifiers.org/insdc/MT252760.1#sequence"  "http://collections.lugli.arvadosapi.com/c=0164784cba5e3e39b7ba8d83fdc92649+126/sequence.fasta"
"2020-01-15"  "MT252720.1"  "http://identifiers.org/insdc/MT252720.1#sequence"  "http://collections.lugli.arvadosapi.com/c=0387a3e47dd8a0c9ea0a4a21931f6308+126/sequence.fasta"
(...)

The query lists 300 sequences originating from Washington state! Which in April was almost half of the set coming out of GenBank.

Likewise to list all sequences from Turkey we can find the wikidata entity is Q43:

Run query.

6 Discussion

The public sequence uploader collects sequences, raw data and (machine) queriable metadata. Not only that: data gets analyzed in the pangenome and results are presented immediately. The data can be referenced in publications and origins are citeable.

7 Acknowledgements

The overall effort was due to magnificent freely donated input by a great number of people. I particularly want to thank Thomas Liener for the great effort he made with the ontology group in getting ontology's and schema sorted! Peter Amstutz and Arvados/Curii helped build the on-demand compute and back-ends. Thanks also to Michael Crusoe for supporting the Common Workflow Language initiative. And without Erik Garrison this initiative would not have existed!

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Other documents

We fetch sequence data and metadata. We query the metadata in multiple ways using SPARQL and onthologies
We submit a sequence to the database. In this BLOG we fetch a sequence from GenBank and add it to the database.
We modify a workflow to get new output
We modify metadata for all to use! In this BLOG we add a field for a creative commons license.
We explore the Arvados command line and API
Generate the files needed for uploading to EBI/ENA
Documentation for PubSeq REST API