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diff --git a/doc/blog/using-covid-19-pubseq-part3.html b/doc/blog/using-covid-19-pubseq-part3.html index 7903791..6838bc7 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"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <head> -<!-- 2020-05-29 Fri 10:00 --> +<!-- 2020-05-29 Fri 14:22 --> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <title>COVID-19 PubSeq Uploading Data (part 3)</title> @@ -248,16 +248,42 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#orgbfd8594">1. Uploading Data</a></li> -<li><a href="#org3243122">2. Introduction</a></li> -<li><a href="#orgc7011c9">3. Step 1: Sequence</a></li> -<li><a href="#org83d22ff">4. Step 2: Metadata</a></li> +<li><a href="#orgb5456df">1. Uploading Data</a></li> +<li><a href="#org5b96fa9">2. Introduction</a></li> +<li><a href="#orga21edf3">3. Step 1: Upload sequence</a></li> +<li><a href="#orga03c092">4. Step 2: Add metadata</a> +<ul> +<li><a href="#org2ab94ef">4.1. Obligatory fields</a> +<ul> +<li><a href="#org9972a05">4.1.1. Sample ID (sample<sub>id</sub>)</a></li> +<li><a href="#orgf4992bb">4.1.2. Collection date</a></li> +<li><a href="#org2f55ae7">4.1.3. Collection location</a></li> +<li><a href="#orgb10db8a">4.1.4. Sequencing technology</a></li> +<li><a href="#orgf846ffe">4.1.5. Authors</a></li> +</ul> +</li> +<li><a href="#org2056637">4.2. Optional fields</a> +<ul> +<li><a href="#orgb2348b1">4.2.1. Host information</a></li> +<li><a href="#orgd963089">4.2.2. Collecting institution</a></li> +<li><a href="#org3257813">4.2.3. Specimen source</a></li> +<li><a href="#org8a596c8">4.2.4. Source database accession</a></li> +<li><a href="#orgd1f5c90">4.2.5. Strain name</a></li> +</ul> +</li> +</ul> +</li> +<li><a href="#orgb9edfdf">5. Step 3: Submit to COVID-19 PubSeq</a> +<ul> +<li><a href="#orgc929675">5.1. Trouble shooting</a></li> +</ul> +</li> </ul> </div> </div> -<div id="outline-container-orgbfd8594" class="outline-2"> -<h2 id="orgbfd8594"><span class="section-number-2">1</span> Uploading Data</h2> +<div id="outline-container-orgb5456df" class="outline-2"> +<h2 id="orgb5456df"><span class="section-number-2">1</span> Uploading Data</h2> <div class="outline-text-2" id="text-1"> <p> <i>Work in progress!</i> @@ -265,8 +291,8 @@ for the JavaScript code in this tag. </div> </div> -<div id="outline-container-org3243122" class="outline-2"> -<h2 id="org3243122"><span class="section-number-2">2</span> Introduction</h2> +<div id="outline-container-org5b96fa9" class="outline-2"> +<h2 id="org5b96fa9"><span class="section-number-2">2</span> Introduction</h2> <div class="outline-text-2" id="text-2"> <p> The COVID-19 PubSeq allows you to upload your SARS-Cov-2 strains to a @@ -276,27 +302,214 @@ upload. Read the <a href="./about">ABOUT</a> page for more information. </div> </div> -<div id="outline-container-orgc7011c9" class="outline-2"> -<h2 id="orgc7011c9"><span class="section-number-2">3</span> Step 1: Sequence</h2> +<div id="outline-container-orga21edf3" class="outline-2"> +<h2 id="orga21edf3"><span class="section-number-2">3</span> Step 1: Upload sequence</h2> <div class="outline-text-2" id="text-3"> <p> +To upload a sequence in the <a href="http://covid19.genenetwork.org/">web upload page</a> hit the browse button and +select the FASTA file on your local hard disk. +</p> + +<p> We start with an assembled or mapped sequence in FASTA format. The PubSeq uploader contains a <a href="https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/qc_fasta.py">QC step</a> which checks whether it is a likely SARS-CoV-2 sequence. While PubSeq deduplicates sequences and never -overwrites metadata it probably pays to check whether your data +overwrites metadata, you may still want to check whether your data already is in the system by querying some metadata as described in -<a href="./blog?id=using-covid-19-pubseq-part1">Query metadata with SPARQL</a>. +<a href="./blog?id=using-covid-19-pubseq-part1">Query metadata with SPARQL</a> or by simply downloading and checking one +of the files on the <a href="./download">download</a> page. We find GenBank <a href="https://www.ncbi.nlm.nih.gov/nuccore/MT536190">MT536190.1</a> has not +been included yet. A FASTA text file can be <a href="https://www.ncbi.nlm.nih.gov/nuccore/MT536190.1?report=fasta&log$=seqview&format=text">downloaded</a> to your local +disk and uploaded through our <a href="./">web upload page</a>. Make sure the file does +not include any HTML! +</p> + +<p> +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. +</p> +</div> +</div> + +<div id="outline-container-orga03c092" class="outline-2"> +<h2 id="orga03c092"><span class="section-number-2">4</span> Step 2: Add metadata</h2> +<div class="outline-text-2" id="text-4"> +<p> +The <a href="./">web upload page</a> contains fields for adding metadata. Metadata is +not only important for attribution, is also important for +analysis. The metadata is available for queries, see <a href="./blog?id=using-covid-19-pubseq-part1">Query metadata +with SPARQL</a>, and can be used to annotate variations of the virus in +different ways. +</p> + +<p> +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 +<a href="https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml">schema</a>. From this schema we generate the input form. Note that +opitional fields have a question mark in the <code>type</code>. You can add +metadata yourself, btw, because this is a public resource! See also +<a href="./blog?id=using-covid-19-pubseq-part5">Modify metadata</a> for more information. +</p> + +<p> +To get more information about a field click on the question mark on +the web form. Here we add some extra information. +</p> +</div> + +<div id="outline-container-org2ab94ef" class="outline-3"> +<h3 id="org2ab94ef"><span class="section-number-3">4.1</span> Obligatory fields</h3> +<div class="outline-text-3" id="text-4-1"> +</div> +<div id="outline-container-org9972a05" class="outline-4"> +<h4 id="org9972a05"><span class="section-number-4">4.1.1</span> Sample ID (sample<sub>id</sub>)</h4> +<div class="outline-text-4" id="text-4-1-1"> +<p> +This is a string field that defines a unique sample identifier by the +submitter. In addition to sample<sub>id</sub> we also have host<sub>id</sub>, +provider<sub>sample</sub><sub>id</sub> and submitter<sub>sample</sub><sub>id</sub> where host is the host the +sample came from, provider sample is the institution sample id and +submitter is the submitting individual id. host<sub>id</sub> is important when +multiple sequences come from the same host. Make sure not to have +spaces in the sample<sub>id</sub>. +</p> + +<p> +Here we add the GenBank ID MT536190.1. +</p> +</div> +</div> + +<div id="outline-container-orgf4992bb" class="outline-4"> +<h4 id="orgf4992bb"><span class="section-number-4">4.1.2</span> Collection date</h4> +<div class="outline-text-4" id="text-4-1-2"> +<p> +Estimated collection date. The GenBank page says April 6, 2020. +</p> +</div> +</div> + +<div id="outline-container-org2f55ae7" class="outline-4"> +<h4 id="org2f55ae7"><span class="section-number-4">4.1.3</span> Collection location</h4> +<div class="outline-text-4" id="text-4-1-3"> +<p> +A search on wikidata says Los Angelos is +<a href="https://www.wikidata.org/entity/Q65">https://www.wikidata.org/entity/Q65</a> +</p> +</div> +</div> + +<div id="outline-container-orgb10db8a" class="outline-4"> +<h4 id="orgb10db8a"><span class="section-number-4">4.1.4</span> Sequencing technology</h4> +<div class="outline-text-4" id="text-4-1-4"> +<p> +GenBank entry says Illumina, so we can fill that in +</p> +</div> +</div> + +<div id="outline-container-orgf846ffe" class="outline-4"> +<h4 id="orgf846ffe"><span class="section-number-4">4.1.5</span> Authors</h4> +<div class="outline-text-4" id="text-4-1-5"> +<p> +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. +</p> +</div> +</div> +</div> + +<div id="outline-container-org2056637" class="outline-3"> +<h3 id="org2056637"><span class="section-number-3">4.2</span> Optional fields</h3> +<div class="outline-text-3" id="text-4-2"> +<p> +All other fields are optional. But let's see what we can add. +</p> +</div> + +<div id="outline-container-orgb2348b1" class="outline-4"> +<h4 id="orgb2348b1"><span class="section-number-4">4.2.1</span> Host information</h4> +<div class="outline-text-4" id="text-4-2-1"> +<p> +Sadly, not much is known about the host from GenBank. A little +sleuthing renders an interesting paper by some of the authors titled +<a href="https://www.medrxiv.org/content/10.1101/2020.04.24.20078691v1">SARS-CoV-2 is consistent across multiple samples and methodologies</a> +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). +</p> +</div> +</div> + +<div id="outline-container-orgd963089" class="outline-4"> +<h4 id="orgd963089"><span class="section-number-4">4.2.2</span> Collecting institution</h4> +<div class="outline-text-4" id="text-4-2-2"> +<p> +We can fill that in. +</p> +</div> +</div> + +<div id="outline-container-org3257813" class="outline-4"> +<h4 id="org3257813"><span class="section-number-4">4.2.3</span> Specimen source</h4> +<div class="outline-text-4" id="text-4-2-3"> +<p> +We have that: nasopharyngeal swab </p> </div> </div> +<div id="outline-container-org8a596c8" class="outline-4"> +<h4 id="org8a596c8"><span class="section-number-4">4.2.4</span> Source database accession</h4> +<div class="outline-text-4" id="text-4-2-4"> +<p> +Genbank which is <a href="http://identifiers.org/insdc/MT536190.1#sequence">http://identifiers.org/insdc/MT536190.1#sequence</a>. +Note we plug in our own identifier MT536190.1. +</p> +</div> +</div> -<div id="outline-container-org83d22ff" class="outline-2"> -<h2 id="org83d22ff"><span class="section-number-2">4</span> Step 2: Metadata</h2> +<div id="outline-container-orgd1f5c90" class="outline-4"> +<h4 id="orgd1f5c90"><span class="section-number-4">4.2.5</span> Strain name</h4> +<div class="outline-text-4" id="text-4-2-5"> +<p> +SARS-CoV-2/human/USA/LA-BIE-070/2020 +</p> +</div> +</div> +</div> +</div> + +<div id="outline-container-orgb9edfdf" class="outline-2"> +<h2 id="orgb9edfdf"><span class="section-number-2">5</span> Step 3: Submit to COVID-19 PubSeq</h2> +<div class="outline-text-2" id="text-5"> +<p> +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! +</p> +</div> + +<div id="outline-container-orgc929675" class="outline-3"> +<h3 id="orgc929675"><span class="section-number-3">5.1</span> Trouble shooting</h3> +<div class="outline-text-3" id="text-5-1"> +<p> +We got an error saying: {"stem": "<a href="http://www.wikidata.org/entity/">http://www.wikidata.org/entity/</a>",… +which means that our location field was not formed correctly! After +fixing it to look like <a href="http://www.wikidata.org/entity/Q65">http://www.wikidata.org/entity/Q65</a> (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. +</p> +</div> +</div> </div> </div> <div id="postamble" class="status"> -<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-05-29 Fri 10:00</small>. +<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-05-29 Fri 14:22</small>. </div> </body> </html> |