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#+TITLE: COVID-19 PubSeq Uploading Data (part 3)
#+AUTHOR: Pjotr Prins
# C-c C-e h h publish
# C-c ! insert date (use . for active agenda, C-u C-c ! for date, C-u C-c . for time)
# C-c C-t task rotate
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#+OPTIONS: ^:nil
* Table of Contents :TOC:noexport:
- [[#uploading-data][Uploading Data]]
- [[#step-1-upload-sequence][Step 1: Upload sequence]]
- [[#step-2-add-metadata][Step 2: Add metadata]]
- [[#obligatory-fields][Obligatory fields]]
- [[#optional-fields][Optional fields]]
- [[#step-3-submit-to-covid-19-pubseq][Step 3: Submit to COVID-19 PubSeq]]
- [[#trouble-shooting][Trouble shooting]]
- [[#step-4-check-output][Step 4: Check output]]
- [[#bulk-sequence-uploader][Bulk sequence uploader]]
- [[#run-the-uploader-cli][Run the uploader (CLI)]]
- [[#example-uploading-bulk-genbank-sequences][Example: uploading bulk GenBank sequences]]
* Uploading Data
The COVID-19 PubSeq allows you to upload your SARS-Cov-2 strains to a
public resource for global comparisons. A recompute of the pangenome
gets triggered on upload. Read the [[./about][ABOUT]] page for more information.
* Step 1: Upload sequence
To upload a sequence in the [[http://covid19.genenetwork.org/][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 [[https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/qc_fasta.py][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
[[./blog?id=using-covid-19-pubseq-part1][Query metadata with SPARQL]] or by simply downloading and checking one
of the files on the [[./download][download]] page. We find GenBank [[https://www.ncbi.nlm.nih.gov/nuccore/MT536190][MT536190.1]] has not
been included yet. A FASTA text file can be [[https://www.ncbi.nlm.nih.gov/nuccore/MT536190.1?report=fasta&log$=seqview&format=text][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.
* 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 [[./blog?id=using-covid-19-pubseq-part1][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
[[https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml][schema]]. From this schema we generate the input form. Note that
optional fields have a question mark in the ~type~. You can add
metadata yourself, btw, because this is a public resource! See also
[[./blog?id=using-covid-19-pubseq-part5][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.
** Obligatory fields
*** Sample ID (sample_id)
This is a string field that defines a unique sample identifier by the
submitter. In addition to sample_id we also have host_id,
provider_sample_id and submitter_sample_id where host is the host the
sample came from, provider sample is the institution sample id and
submitter is the submitting individual id. host_id is important when
multiple sequences come from the same host. Make sure not to have
spaces in the sample_id.
Here we add the GenBank ID MT536190.1.
*** Collection date
Estimated collection date. The GenBank page says April 6, 2020.
*** Collection location
A search on wikidata says Los Angeles is
https://www.wikidata.org/entity/Q65
*** Sequencing technology
GenBank entry says Illumina, so we can fill that in
*** 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.
** Optional fields
All other fields are optional. But let's see what we can add.
*** 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
[[https://www.medrxiv.org/content/10.1101/2020.04.24.20078691v1][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).
*** Collecting institution
We can fill that in.
*** Specimen source
We have that: nasopharyngeal swab
*** Source database accession
Genbank which is http://identifiers.org/insdc/MT536190.1#sequence.
Note we plug in our own identifier MT536190.1.
*** Strain name
SARS-CoV-2/human/USA/LA-BIE-070/2020
* 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!
** 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.
* 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][DOWNLOAD]] page. After completion
of above output this [[http://sparql.genenetwork.org/sparql/?default-graph-uri=&query=PREFIX+pubseq%3A+%3Chttp%3A%2F%2Fbiohackathon.org%2Fbh20-seq-schema%23MainSchema%2F%3E%0D%0APREFIX+sio%3A+%3Chttp%3A%2F%2Fsemanticscience.org%2Fresource%2F%3E%0D%0Aselect+distinct+%3Fsample+%3Fp+%3Fo%0D%0A%7B%0D%0A+++%3Fsample+sio%3ASIO_000115+%22MT536190.1%22+.%0D%0A+++%3Fsample+%3Fp+%3Fo+.%0D%0A%7D&format=text%2Fhtml&timeout=0&debug=on&run=+Run+Query+][SPARQL query]] shows some of the metadata we put
in.
* Bulk sequence uploader
Above steps require a manual upload of one sequence with metadata.
What if you have a number of sequences you want to upload in bulk?
For this we have a command line version of the uploader that can
directly submit to COVID-19 PubSeq. It accepts a FASTA sequence
file an associated metadata in [[https://github.com/arvados/bh20-seq-resource/blob/master/example/maximum_metadata_example.yaml][YAML]] format. The YAML matches
the web form and gets validated from the same [[https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml][schema]] looks. The YAML
that you need to create/generate for your samples looks like
#+begin_src json
id: placeholder
host:
host_id: XX1
host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606
host_sex: http://purl.obolibrary.org/obo/PATO_0000384
host_age: 20
host_age_unit: http://purl.obolibrary.org/obo/UO_0000036
host_health_status: http://purl.obolibrary.org/obo/NCIT_C25269
host_treatment: Process in which the act is intended to modify or alter host status (Compounds)
host_vaccination: [vaccines1,vaccine2]
ethnicity: http://purl.obolibrary.org/obo/HANCESTRO_0010
additional_host_information: Optional free text field for additional information
sample:
sample_id: Id of the sample as defined by the submitter
collector_name: Name of the person that took the sample
collecting_institution: Institute that was responsible of sampling
specimen_source: [http://purl.obolibrary.org/obo/NCIT_C155831,http://purl.obolibrary.org/obo/NCIT_C155835]
collection_date: "2020-01-01"
collection_location: http://www.wikidata.org/entity/Q148
sample_storage_conditions: frozen specimen
source_database_accession: [http://identifiers.org/insdc/LC522350.1#sequence]
additional_collection_information: Optional free text field for additional information
virus:
virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049
virus_strain: SARS-CoV-2/human/CHN/HS_8/2020
technology:
sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0009173,http://www.ebi.ac.uk/efo/EFO_0009173]
sequence_assembly_method: Protocol used for assembly
sequencing_coverage: [70.0, 100.0]
additional_technology_information: Optional free text field for additional information
submitter:
authors: [John Doe, Joe Boe, Jonny Oe]
submitter_name: [John Doe]
submitter_address: John Doe's address
originating_lab: John Doe kitchen
lab_address: John Doe's address
provider_sample_id: XXX1
submitter_sample_id: XXX2
publication: PMID00001113
submitter_orcid: [https://orcid.org/0000-0000-0000-0000,https://orcid.org/0000-0000-0000-0001]
additional_submitter_information: Optional free text field for additional information
#+end_src
** Run the uploader (CLI)
Installing with pip you should be
able to run
: bh20sequploader sequence.fasta metadata.yaml
Alternatively the script can be installed from [[https://github.com/arvados/bh20-seq-resource#installation][github]]. Run on the
command line
: python3 bh20sequploader/main.py example/sequence.fasta example/maximum_metadata_example.yaml
after installing dependencies (also described in [[https://github.com/arvados/bh20-seq-resource/blob/master/doc/INSTALL.md][INSTALL]] with the GNU
Guix package manager).
The web interface using this exact same script so it should just work
(TM).
** Example: uploading bulk GenBank sequences
We also use above script to bulk upload GenBank sequences with a [[https://github.com/arvados/bh20-seq-resource/blob/master/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py][FASTA
and YAML]] extractor specific for GenBank. This means that the steps we
took above for uploading a GenBank sequence are already automated.
The steps are: from the
~bh20-seq-resource/scripts/download_genbank_data/~ directory using the
[[https://github.com/arvados/bh20-seq-resource/tree/master/scripts/download_genbank_data][from_genbank_to_fasta_and_yaml.py]] script:
#+BEGIN_SRC sh
python3 from_genbank_to_fasta_and_yaml.py
dir_fasta_and_yaml=~/bh20-seq-resource/scripts/download_genbank_data/fasta_and_yaml
ls $dir_fasta_and_yaml/*.yaml | while read path_code_yaml; do
path_code_fasta=${path_code_yaml%.*}.fasta
bh20-seq-uploader --skip-qc $path_code_yaml $path_code_fasta
done
#+END_SRC
|
