-Work in progress! -
-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. +public resource for global comparisons. A recompute of the pangenome +gets triggered on upload. Read the ABOUT page for more information.
To upload a sequence in the web upload page hit the browse button and select the FASTA file on your local hard disk. @@ -332,9 +330,9 @@ an improved pangenome.
The web upload page contains fields for adding metadata. Metadata is
not only important for attribution, is also important for
@@ -348,7 +346,7 @@ 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
+optional 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.
This is a string field that defines a unique sample identifier by the submitter. In addition to sampleid we also have hostid, @@ -382,37 +380,37 @@ Here we add the GenBank ID MT536190.1.
Estimated collection date. The GenBank page says April 6, 2020.
-A search on wikidata says Los Angelos is +A search on wikidata says Los Angeles is https://www.wikidata.org/entity/Q65
GenBank entry says Illumina, so we can fill that in
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., @@ -422,17 +420,17 @@ Freehan,A. and Garcia-Diaz,J.', so we can fill that in.
All other fields are optional. But let's see what we can add.
Sadly, not much is known about the host from GenBank. A little sleuthing renders an interesting paper by some of the authors titled @@ -445,27 +443,27 @@ did to the person and what the person was like (say age group).
We can fill that in.
We have that: nasopharyngeal swab
Genbank which is http://identifiers.org/insdc/MT536190.1#sequence. Note we plug in our own identifier MT536190.1. @@ -473,9 +471,9 @@ Note we plug in our own identifier MT536190.1.
SARS-CoV-2/human/USA/LA-BIE-070/2020
@@ -484,20 +482,36 @@ SARS-CoV-2/human/USA/LA-BIE-070/2020Once 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!
+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. +
+
The current pipeline takes 5.5 hours to complete! Once it completes
the updated data can be checked on the DOWNLOAD page. After completion
@@ -505,24 +519,122 @@ of above output this
+
+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 YAML format. The YAML matches
+the web form and gets validated from the same schema looks. The YAML
+that you need to create/generate for your samples looks like
+
-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.
+Installing with pip you should be
+able to run
+
+Alternatively the script can be installed from github. Run on the
+command line
+
+after installing dependencies (also described in INSTALL with the GNU
+Guix package manager).
+
+The web interface using this exact same script so it should just work
+(TM).
+
+We also use above script to bulk upload GenBank sequences with a FASTA
+and YAML extractor specific for GenBank. This means that the steps we
+took above for uploading a GenBank sequence are already automated.
6 Bulk sequence uploader
+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
+
+6.1 Trouble shooting
+6.1 Run the uploader (CLI)
+bh20sequploader sequence.fasta metadata.yaml
+
+
+
+
+
+python3 bh20sequploader/main.py example/sequence.fasta example/maximum_metadata_example.yaml
+
+
+
+6.2 Example: uploading bulk GenBank sequences
+