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#+TITLE: COVID-19 PubSeq Uploading Data (part 3)
#+AUTHOR: Pjotr Prins
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* Introduction

In this document we explain how to upload data into COVID-19 PubSeq.
This can happen through a web page, or through a command line
script. We'll also show how to parametrize uploads by using templates.
The procedure is much easier than with other repositories and can be
fully automated. Once uploaded you can use our export API to prepare
for other repositories.


* Table of Contents                                                     :TOC:noexport:
 - [[#introduction][Introduction]]
 - [[#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]]
   - [[#example-preparing-metadata][Example: preparing metadata]]

* 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 and submitter_sample_id where host is the host the
sample came from, provider sample is the institution 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

A minimal example of metadata looks like

#+begin_src json
  id: placeholder

  license:
      license_type: http://creativecommons.org/licenses/by/4.0/

  host:
      host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606

  sample:
      sample_id: XX
      collection_date: "2020-01-01"
      collection_location: http://www.wikidata.org/entity/Q148

  virus:
      virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049

  technology:
      sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632]

  submitter:
      authors: [John Doe]
#+end_src

a more elaborate example (note most fields are optional) may look 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]
      alignment_protocol: Protocol used for assembly
      sequencing_coverage: [70.0, 100.0]
      assembly_method: "http://purl.obolibrary.org/obo/GENEPIO_0001628"
      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: 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

more metadata is yummy when stored in RDF. [[https://yummydata.org/][Yummydata]] is useful to a wider community. Note
that many of the terms in above example are URIs, such as
host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606.  We use
web ontologies for these to make the data less ambiguous and more
FAIR. Check out the option fields as defined in the schema. If it is not listed,
check the [[https://github.com/arvados/bh20-seq-resource/blob/master/semantic_enrichment/labels.ttl][labels.ttl]] file. Also,
a little bit of web searching may be required or [[./contact][contact]] us.

** 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 ~--help~ shows

#+begin_src sh
Entering sequence uploader
usage: main.py [-h] [--validate] [--skip-qc] [--trusted] metadata sequence_p1 [sequence_p2]

Upload SARS-CoV-19 sequences for analysis

positional arguments:
  metadata     sequence metadata json
  sequence_p1  sequence FASTA/FASTQ
  sequence_p2  sequence FASTQ pair

optional arguments:
  -h, --help   show this help message and exit
  --validate   Dry run, validate only
  --skip-qc    Skip local qc check
  --trusted    Trust local validation and add directly to validated project
#+end_src

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


** Example: preparing metadata

Usually, metadata are available in a tabular format, such as
spreadsheets. As an example, we provide a script [[https://github.com/arvados/bh20-seq-resource/tree/master/scripts/esr_samples][esr_samples.py]] to
show you how to parse your metadata in YAML files ready for the
upload. To execute the script, go in the
~bh20-seq-resource/scripts/esr_samples and execute

#+BEGIN_SRC sh
python3 esr_samples.py
#+END_SRC

You will find the YAML files in the `yaml` folder which will be
created in the same directory.

In the example we use Python pandas to read the spreadsheet into a
tabular structure. Next we use a [[https://github.com/arvados/bh20-seq-resource/blob/master/scripts/esr_samples/template.yaml][template.yaml]] file that gets filled
in by ~esr_samples.py~ so we get a metadata YAML file for each sample.

Next run the earlier CLI uploader for each YAML and FASTA combination.
It can't be much easier than this. For ESR we uploaded a batch of 600
sequences this way writing a few lines of Python [[https://github.com/arvados/bh20-seq-resource/blob/master/scripts/esr_samples/esr_samples.py][code]]. See [[http://covid19.genenetwork.org/resource/20VR0995][example]].