From 246c516e4a8c98394c695dcb446995319d557e01 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 22 Aug 2020 14:07:53 +0100 Subject: Generated --- doc/blog/using-covid-19-pubseq-part3.html | 149 +++++++++++++++--------------- 1 file changed, 74 insertions(+), 75 deletions(-) (limited to 'doc/blog/using-covid-19-pubseq-part3.html') diff --git a/doc/blog/using-covid-19-pubseq-part3.html b/doc/blog/using-covid-19-pubseq-part3.html index df4a286..80304c3 100644 --- a/doc/blog/using-covid-19-pubseq-part3.html +++ b/doc/blog/using-covid-19-pubseq-part3.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + COVID-19 PubSeq Uploading Data (part 3) @@ -248,40 +248,40 @@ for the JavaScript code in this tag.

Table of Contents

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1 Uploading Data

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1 Uploading Data

The COVID-19 PubSeq allows you to upload your SARS-Cov-2 strains to a @@ -301,8 +301,8 @@ gets triggered on upload. Read the ABOUT page for more inf

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2 Step 1: Upload sequence

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2 Step 1: Upload sequence

To upload a sequence in the web upload page hit the browse button and @@ -330,8 +330,8 @@ an improved pangenome.

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3 Step 2: Add metadata

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3 Step 2: Add metadata

The web upload page contains fields for adding metadata. Metadata is @@ -357,12 +357,12 @@ the web form. Here we add some extra information.

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3.1 Obligatory fields

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3.1 Obligatory fields

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3.1.1 Sample ID (sampleid)

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3.1.1 Sample ID (sampleid)

This is a string field that defines a unique sample identifier by the @@ -380,8 +380,8 @@ Here we add the GenBank ID MT536190.1.

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3.1.2 Collection date

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3.1.2 Collection date

Estimated collection date. The GenBank page says April 6, 2020. @@ -389,8 +389,8 @@ Estimated collection date. The GenBank page says April 6, 2020.

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3.1.3 Collection location

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3.1.3 Collection location

A search on wikidata says Los Angeles is @@ -399,8 +399,8 @@ A search on wikidata says Los Angeles is

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3.1.4 Sequencing technology

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3.1.4 Sequencing technology

GenBank entry says Illumina, so we can fill that in @@ -408,8 +408,8 @@ GenBank entry says Illumina, so we can fill that in

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3.1.5 Authors

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3.1.5 Authors

GenBank entry says 'Lamers,S., Nolan,D.J., Rose,R., Cross,S., Moraga @@ -420,16 +420,16 @@ Freehan,A. and Garcia-Diaz,J.', so we can fill that in.

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3.2 Optional fields

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3.2 Optional fields

All other fields are optional. But let's see what we can add.

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3.2.1 Host information

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3.2.1 Host information

Sadly, not much is known about the host from GenBank. A little @@ -443,8 +443,8 @@ did to the person and what the person was like (say age group).

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3.2.2 Collecting institution

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3.2.2 Collecting institution

We can fill that in. @@ -452,8 +452,8 @@ We can fill that in.

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3.2.3 Specimen source

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3.2.3 Specimen source

We have that: nasopharyngeal swab @@ -461,8 +461,8 @@ We have that: nasopharyngeal swab

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3.2.4 Source database accession

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3.2.4 Source database accession

Genbank which is http://identifiers.org/insdc/MT536190.1#sequence. @@ -471,8 +471,8 @@ Note we plug in our own identifier MT536190.1.

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3.2.5 Strain name

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3.2.5 Strain name

SARS-CoV-2/human/USA/LA-BIE-070/2020 @@ -482,8 +482,8 @@ SARS-CoV-2/human/USA/LA-BIE-070/2020

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4 Step 3: Submit to COVID-19 PubSeq

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4 Step 3: Submit to COVID-19 PubSeq

Once you have the sequence and the metadata together, hit @@ -493,8 +493,8 @@ submitted and the workflows should kick in!

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4.1 Trouble shooting

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4.1 Trouble shooting

We got an error saying: {"stem": "http://www.wikidata.org/entity/",… @@ -508,9 +508,8 @@ submit button.

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5 Step 4: Check output

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5 Step 4: Check output

The current pipeline takes 5.5 hours to complete! Once it completes @@ -521,8 +520,8 @@ in.

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6 Bulk sequence uploader

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6 Bulk sequence uploader

Above steps require a manual upload of one sequence with metadata. @@ -544,8 +543,8 @@ host: 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] + 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 @@ -553,11 +552,11 @@ 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] + 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] + source_database_accession: [http://identifiers.org/insdc/LC522350.1#sequence] additional_collection_information: Optional free text field for additional information virus: @@ -565,28 +564,28 @@ virus: 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] + 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] + 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] + 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] + 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

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6.1 Run the uploader (CLI)

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6.1 Run the uploader (CLI)

Installing with pip you should be @@ -621,8 +620,8 @@ The web interface using this exact same script so it should just work

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6.2 Example: uploading bulk GenBank sequences

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6.2 Example: uploading bulk GenBank sequences

We also use above script to bulk upload GenBank sequences with a FASTA @@ -634,7 +633,7 @@ took above for uploading a GenBank sequence are already automated.

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Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-05-30 Sat 18:12. +
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-08-22 Sat 07:43.
-- cgit v1.2.3