From d12a580db8146f8ebc511119698e63e3a5de0147 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 28 May 2020 08:42:05 -0500 Subject: Added Who uses the public sequence resource? to the FAQ --- doc/web/about.html | 135 ++++++++++++++++++++++++++++++----------------------- doc/web/about.org | 10 ++++ 2 files changed, 86 insertions(+), 59 deletions(-) (limited to 'doc') diff --git a/doc/web/about.html b/doc/web/about.html index cf718e7..bad4bb1 100644 --- a/doc/web/about.html +++ b/doc/web/about.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + About/FAQ @@ -247,28 +247,29 @@ for the JavaScript code in this tag.

Table of Contents

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1 What is the 'public sequence resource' about?

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1 What is the 'public sequence resource' about?

The public sequence resource aims to provide a generic and useful @@ -279,8 +280,8 @@ sequence comparison and protein prediction.

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2 Who created the public sequence resource?

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2 Who created the public sequence resource?

The public sequence resource is an initiative by bioinformatics and @@ -300,8 +301,8 @@ wrangling experts. Thank you everyone!

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3 How does the public sequence resource compare to other data resources?

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3 How does the public sequence resource compare to other data resources?

The short version is that we use state-of-the-art practices in @@ -320,8 +321,8 @@ public resources, including GISAID.

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4 Why should I upload my data here?

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4 Why should I upload my data here?

  1. We champion truly shareable data without licensing restrictions - with proper @@ -338,6 +339,7 @@ for bulk uploads
  2. Your data gets automatically integrated with the Swiss Institure of Bioinformatics COVID-19 knowledge base https://covid-19-sparql.expasy.org/ (Elixir Switzerland)
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  3. Your data will be used to develop drug targets

@@ -349,8 +351,8 @@ multiple resources.

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5 Why should I not upload by data here?

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5 Why should I not upload by data here?

Funny question. There are only good reasons to upload your data here @@ -372,8 +374,8 @@ for bulk uploads!

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6 How does the public sequence resource work?

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6 How does the public sequence resource work?

On uploading a sequence with metadata it will automatically be @@ -384,10 +386,25 @@ using workflows from the High Performance Open Biology Lab defined

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7 Is this about open data?

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7 Who uses the public sequence resource?

+The Swiss Institute of Bioinformatics has included this data in +https://covid-19-sparql.expasy.org/ and made it part of Uniprot. +

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+UTHSC and ORNL use COVID-19 PubSeq data for protein prediction and +drug development. +

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8 Is this about open data?

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All data is published under a Creative Commons 4.0 attribution license (CC-BY-4.0). You can download the raw and published (GFA/RDF/FASTA) data and store it for further processing. @@ -395,9 +412,9 @@ data and store it for further processing.

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8 Is this about free software?

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9 Is this about free software?

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Absolutely. Free software allows for fully reproducible pipelines. You can take our workflows and data and run it elsewhere! @@ -405,9 +422,9 @@ can take our workflows and data and run it elsewhere!

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9 How do I upload raw data?

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10 How do I upload raw data?

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We are preparing raw sequence data pipelines (fastq and BAM). The reason is that we want the best data possible for downstream analysis @@ -421,27 +438,27 @@ assembly variations into consideration. This is all work in progress.

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10 How do I change metadata?

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11 How do I change metadata?

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See the http://covid19.genenetwork.org/blog!

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11 How do I change the work flows?

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12 How do I change the work flows?

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See the http://covid19.genenetwork.org/blog!

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12 How do I change the source code?

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13 How do I change the source code?

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Go to our source code repositories, fork/clone the repository, change something and submit a pull request (PR). That easy! Check out how @@ -450,9 +467,9 @@ many PRs we already merged.

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13 Should I choose CC-BY or CC0?

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14 Should I choose CC-BY or CC0?

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Restrictive data licenses are hampering data sharing and reproducible research. CC0 is the preferred license because it gives researchers @@ -467,9 +484,9 @@ In all honesty: we prefer both data and software to be free.

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14 How do I deal with private data and privacy?

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15 How do I deal with private data and privacy?

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A public sequence resource is about public data. Metadata can refer to private data. You can use your own (anonymous) identifiers. We also @@ -479,18 +496,18 @@ plan to combine identifiers with clinical data stored securely at

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15 How do I communicate with you?

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16 How do I communicate with you?

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We use a gitter channel you can join.

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16 Who are the sponsors?

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17 Who are the sponsors?

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The main sponsors are listed in the footer. In addition to the time generously donated by many contributors we also acknowledge Amazon AWS @@ -500,7 +517,7 @@ for donating COVID-19 related compute time.

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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 2020-05-27 Wed 07:08. +
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-05-28 Thu 08:40.
diff --git a/doc/web/about.org b/doc/web/about.org index bb49c2a..8e535dc 100644 --- a/doc/web/about.org +++ b/doc/web/about.org @@ -8,6 +8,7 @@ - [[#why-should-i-upload-my-data-here][Why should I upload my data here?]] - [[#why-should-i-not-upload-by-data-here][Why should I not upload by data here?]] - [[#how-does-the-public-sequence-resource-work][How does the public sequence resource work?]] + - [[#who-uses-the-public-sequence-resource][Who uses the public sequence resource?]] - [[#is-this-about-open-data][Is this about open data?]] - [[#is-this-about-free-software][Is this about free software?]] - [[#how-do-i-upload-raw-data][How do I upload raw data?]] @@ -69,6 +70,7 @@ public resources, including GISAID. 4. Your data gets automatically integrated with the Swiss Institure of Bioinformatics COVID-19 knowledge base https://covid-19-sparql.expasy.org/ (Elixir Switzerland) +4. Your data will be used to develop drug targets Finally, if you upload your data here we have workflows that output formatted data suitable for uploading to EBI resources (and soon @@ -96,6 +98,14 @@ processed and incorporated into the public pangenome with metadata using workflows from the High Performance Open Biology Lab defined [[https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate][here]]. +* Who uses the public sequence resource? + +The Swiss Institute of Bioinformatics has included this data in +https://covid-19-sparql.expasy.org/ and made it part of [[https://www.uniprot.org/][Uniprot]]. + +[[https://uthsc.edu][UTHSC]] and [[https://www.ornl.gov/news/ornl-fight-against-covid-19][ORNL]] use COVID-19 PubSeq data for protein prediction and +drug development. + * Is this about open data? All data is published under a [[https://creativecommons.org/licenses/by/4.0/][Creative Commons 4.0 attribution license]] -- cgit v1.2.3