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Diffstat (limited to 'doc/blog')
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part3.html | 127 | ||||
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part3.org | 8 |
2 files changed, 78 insertions, 57 deletions
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"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <head> -<!-- 2020-05-29 Fri 14:22 --> +<!-- 2020-05-30 Sat 10:45 --> <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> @@ -248,42 +248,43 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<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> +<li><a href="#org7fda7c8">1. Uploading Data</a></li> +<li><a href="#orgb062ac0">2. Introduction</a></li> +<li><a href="#org4061598">3. Step 1: Upload sequence</a></li> +<li><a href="#org51d80f8">4. Step 2: Add metadata</a> <ul> -<li><a href="#org2ab94ef">4.1. Obligatory fields</a> +<li><a href="#orgbb8f0bb">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> +<li><a href="#org0e615dc">4.1.1. Sample ID (sample<sub>id</sub>)</a></li> +<li><a href="#org4d5308a">4.1.2. Collection date</a></li> +<li><a href="#org429f153">4.1.3. Collection location</a></li> +<li><a href="#orgbd7fa51">4.1.4. Sequencing technology</a></li> +<li><a href="#orgc3b424f">4.1.5. Authors</a></li> </ul> </li> -<li><a href="#org2056637">4.2. Optional fields</a> +<li><a href="#org5c01347">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> +<li><a href="#org7fc5461">4.2.1. Host information</a></li> +<li><a href="#org140c8b5">4.2.2. Collecting institution</a></li> +<li><a href="#orgf231cf9">4.2.3. Specimen source</a></li> +<li><a href="#org74de839">4.2.4. Source database accession</a></li> +<li><a href="#org8927a67">4.2.5. Strain name</a></li> </ul> </li> </ul> </li> -<li><a href="#orgb9edfdf">5. Step 3: Submit to COVID-19 PubSeq</a> +<li><a href="#org38d48d8">5. Step 3: Submit to COVID-19 PubSeq</a></li> +<li><a href="#org5ec1337">6. Step 4: Check output</a> <ul> -<li><a href="#orgc929675">5.1. Trouble shooting</a></li> +<li><a href="#org070e13e">6.1. Trouble shooting</a></li> </ul> </li> </ul> </div> </div> -<div id="outline-container-orgb5456df" class="outline-2"> -<h2 id="orgb5456df"><span class="section-number-2">1</span> Uploading Data</h2> +<div id="outline-container-org7fda7c8" class="outline-2"> +<h2 id="org7fda7c8"><span class="section-number-2">1</span> Uploading Data</h2> <div class="outline-text-2" id="text-1"> <p> <i>Work in progress!</i> @@ -291,8 +292,8 @@ for the JavaScript code in this tag. </div> </div> -<div id="outline-container-org5b96fa9" class="outline-2"> -<h2 id="org5b96fa9"><span class="section-number-2">2</span> Introduction</h2> +<div id="outline-container-orgb062ac0" class="outline-2"> +<h2 id="orgb062ac0"><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 @@ -302,8 +303,8 @@ upload. Read the <a href="./about">ABOUT</a> page for more information. </div> </div> -<div id="outline-container-orga21edf3" class="outline-2"> -<h2 id="orga21edf3"><span class="section-number-2">3</span> Step 1: Upload sequence</h2> +<div id="outline-container-org4061598" class="outline-2"> +<h2 id="org4061598"><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 @@ -331,8 +332,8 @@ an improved pangenome. </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 id="outline-container-org51d80f8" class="outline-2"> +<h2 id="org51d80f8"><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 @@ -358,12 +359,12 @@ 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 id="outline-container-orgbb8f0bb" class="outline-3"> +<h3 id="orgbb8f0bb"><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 id="outline-container-org0e615dc" class="outline-4"> +<h4 id="org0e615dc"><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 @@ -381,8 +382,8 @@ Here we add the GenBank ID MT536190.1. </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 id="outline-container-org4d5308a" class="outline-4"> +<h4 id="org4d5308a"><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. @@ -390,8 +391,8 @@ Estimated collection date. The GenBank page says April 6, 2020. </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 id="outline-container-org429f153" class="outline-4"> +<h4 id="org429f153"><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 @@ -400,8 +401,8 @@ A search on wikidata says Los Angelos is </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 id="outline-container-orgbd7fa51" class="outline-4"> +<h4 id="orgbd7fa51"><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 @@ -409,8 +410,8 @@ GenBank entry says Illumina, so we can fill that in </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 id="outline-container-orgc3b424f" class="outline-4"> +<h4 id="orgc3b424f"><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 @@ -421,16 +422,16 @@ Freehan,A. and Garcia-Diaz,J.', so we can fill that in. </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 id="outline-container-org5c01347" class="outline-3"> +<h3 id="org5c01347"><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 id="outline-container-org7fc5461" class="outline-4"> +<h4 id="org7fc5461"><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 @@ -444,8 +445,8 @@ did to the person and what the person was like (say age group). </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 id="outline-container-org140c8b5" class="outline-4"> +<h4 id="org140c8b5"><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. @@ -453,8 +454,8 @@ We can fill that in. </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 id="outline-container-orgf231cf9" class="outline-4"> +<h4 id="orgf231cf9"><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 @@ -462,8 +463,8 @@ We have that: nasopharyngeal swab </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 id="outline-container-org74de839" class="outline-4"> +<h4 id="org74de839"><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>. @@ -472,8 +473,8 @@ Note we plug in our own identifier MT536190.1. </div> </div> -<div id="outline-container-orgd1f5c90" class="outline-4"> -<h4 id="orgd1f5c90"><span class="section-number-4">4.2.5</span> Strain name</h4> +<div id="outline-container-org8927a67" class="outline-4"> +<h4 id="org8927a67"><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 @@ -483,8 +484,8 @@ SARS-CoV-2/human/USA/LA-BIE-070/2020 </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 id="outline-container-org38d48d8" class="outline-2"> +<h2 id="org38d48d8"><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 @@ -492,10 +493,22 @@ the 'Add to Pangenome' button. The data will be checked, submitted and the workflows should kick in! </p> </div> +</div> + +<div id="outline-container-org5ec1337" class="outline-2"> +<h2 id="org5ec1337"><span class="section-number-2">6</span> Step 4: Check output</h2> +<div class="outline-text-2" id="text-6"> +<p> +The current pipeline takes 5.5 hours to complete! Once it completes +the updated data can be checked on the <a href="./download">DOWNLOAD</a> page. After completion +of above output this <a href="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</a> shows some of the metadata we put +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"> +<div id="outline-container-org070e13e" class="outline-3"> +<h3 id="org070e13e"><span class="section-number-3">6.1</span> Trouble shooting</h3> +<div class="outline-text-3" id="text-6-1"> <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 @@ -509,7 +522,7 @@ submit button. </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 14:22</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 2020-05-30 Sat 10:44</small>. </div> </body> </html> 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/",... |