From 5f36706b7c9dc1786e47848f0ce8aabd4e7ab851 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 30 May 2020 10:46:28 -0500 Subject: BLOG: checkout output --- doc/blog/using-covid-19-pubseq-part3.html | 127 ++++++++++++++++-------------- doc/blog/using-covid-19-pubseq-part3.org | 8 ++ 2 files changed, 78 insertions(+), 57 deletions(-) (limited to 'doc/blog') diff --git a/doc/blog/using-covid-19-pubseq-part3.html b/doc/blog/using-covid-19-pubseq-part3.html index 6838bc7..4132784 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) @@ -248,42 +248,43 @@ for the JavaScript code in this tag.

Table of Contents

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1 Uploading Data

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1 Uploading Data

Work in progress! @@ -291,8 +292,8 @@ for the JavaScript code in this tag.

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2 Introduction

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2 Introduction

The COVID-19 PubSeq allows you to upload your SARS-Cov-2 strains to a @@ -302,8 +303,8 @@ upload. Read the ABOUT page for more information.

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3 Step 1: Upload sequence

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3 Step 1: Upload sequence

To upload a sequence in the web upload page hit the browse button and @@ -331,8 +332,8 @@ an improved pangenome.

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4 Step 2: Add metadata

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4 Step 2: Add metadata

The web upload page contains fields for adding metadata. Metadata is @@ -358,12 +359,12 @@ the web form. Here we add some extra information.

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4.1 Obligatory fields

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4.1 Obligatory fields

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4.1.1 Sample ID (sampleid)

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4.1.1 Sample ID (sampleid)

This is a string field that defines a unique sample identifier by the @@ -381,8 +382,8 @@ Here we add the GenBank ID MT536190.1.

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4.1.2 Collection date

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4.1.2 Collection date

Estimated collection date. The GenBank page says April 6, 2020. @@ -390,8 +391,8 @@ Estimated collection date. The GenBank page says April 6, 2020.

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4.1.3 Collection location

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4.1.3 Collection location

A search on wikidata says Los Angelos is @@ -400,8 +401,8 @@ A search on wikidata says Los Angelos is

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4.1.4 Sequencing technology

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4.1.4 Sequencing technology

GenBank entry says Illumina, so we can fill that in @@ -409,8 +410,8 @@ GenBank entry says Illumina, so we can fill that in

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4.1.5 Authors

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4.1.5 Authors

GenBank entry says 'Lamers,S., Nolan,D.J., Rose,R., Cross,S., Moraga @@ -421,16 +422,16 @@ Freehan,A. and Garcia-Diaz,J.', so we can fill that in.

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4.2 Optional fields

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4.2 Optional fields

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

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4.2.1 Host information

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4.2.1 Host information

Sadly, not much is known about the host from GenBank. A little @@ -444,8 +445,8 @@ did to the person and what the person was like (say age group).

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4.2.2 Collecting institution

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4.2.2 Collecting institution

We can fill that in. @@ -453,8 +454,8 @@ We can fill that in.

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4.2.3 Specimen source

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4.2.3 Specimen source

We have that: nasopharyngeal swab @@ -462,8 +463,8 @@ We have that: nasopharyngeal swab

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4.2.4 Source database accession

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4.2.4 Source database accession

Genbank which is http://identifiers.org/insdc/MT536190.1#sequence. @@ -472,8 +473,8 @@ Note we plug in our own identifier MT536190.1.

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4.2.5 Strain name

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4.2.5 Strain name

SARS-CoV-2/human/USA/LA-BIE-070/2020 @@ -483,8 +484,8 @@ SARS-CoV-2/human/USA/LA-BIE-070/2020

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5 Step 3: Submit to COVID-19 PubSeq

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5 Step 3: Submit to COVID-19 PubSeq

Once you have the sequence and the metadata together, hit @@ -492,10 +493,22 @@ the 'Add to Pangenome' button. The data will be checked, submitted and the workflows should kick in!

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6 Step 4: Check output

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+The current pipeline takes 5.5 hours to complete! Once it completes +the updated data can be checked on the DOWNLOAD page. After completion +of above output this SPARQL query shows some of the metadata we put +in. +

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5.1 Trouble shooting

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6.1 Trouble shooting

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We got an error saying: {"stem": "http://www.wikidata.org/entity/",… which means that our location field was not formed correctly! After @@ -509,7 +522,7 @@ submit button.

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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 2020-05-29 Fri 14:22. +
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 10:44.
diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org index ade902d..4dd3078 100644 --- a/doc/blog/using-covid-19-pubseq-part3.org +++ b/doc/blog/using-covid-19-pubseq-part3.org @@ -18,6 +18,7 @@ - [[#obligatory-fields][Obligatory fields]] - [[#optional-fields][Optional fields]] - [[#step-3-submit-to-covid-19-pubseq][Step 3: Submit to COVID-19 PubSeq]] + - [[#step-4-check-output][Step 4: Check output]] - [[#trouble-shooting][Trouble shooting]] * Introduction @@ -135,6 +136,13 @@ 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! +* 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. + ** Trouble shooting We got an error saying: {"stem": "http://www.wikidata.org/entity/",... -- cgit v1.2.3