COVID-19 PubSeq (part 1)
Table of Contents
-
-
- 1. What does this mean? -
- 2. Fetch sequence data -
- 3. Predicates -
- 4. Fetch submitter info and other metadata -
- 5. Fetch all sequences from Washington state -
- 6. Discussion -
- 7. Acknowledgements +
- 1. What does this mean? +
- 2. Fetch sequence data +
- 3. Predicates +
- 4. Fetch submitter info and other metadata +
- 5. Fetch all sequences from Washington state +
- 6. Discussion +
- 7. Acknowledgements
-As part of the COVID-19 Biohackathon 2020 we formed a working group -to create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for -Corona virus sequences. The general idea is to create a repository -that has a low barrier to entry for uploading sequence data using best -practices. I.e., data published with a creative commons 4.0 (CC-4.0) -license with metadata using state-of-the art standards and, perhaps -most importantly, providing standardised workflows that get triggered -on upload, so that results are immediately available in standardised -data formats. -
-1 What does this mean?
+ +1 What does this mean?
This means that when someone uploads a SARS-CoV-2 sequence using one @@ -328,8 +314,8 @@ initiative!
2 Fetch sequence data
+2 Fetch sequence data
The latest run of the pipeline can be viewed here. Each of these @@ -353,8 +339,8 @@ these identifiers throughout.
3 Predicates
+3 Predicates
To explore an RDF dataset, the first query we can do is open and gets
@@ -464,8 +450,8 @@ Now we got this far, lets
-
To get dataests with submitters we can do the above
@@ -575,8 +561,8 @@ to view/query the database.
Now we know how to get at the origin we can do it the other way round
@@ -603,8 +589,8 @@ half of the set coming out of GenBank.
The public sequence uploader collects sequences, raw data and
@@ -615,8 +601,8 @@ referenced in publications and origins are citeable.
The overall effort was due to magnificent freely donated input by a
@@ -631,7 +617,7 @@ Garrison this initiative would not have existed!
4 Fetch submitter info and other metadata
+4 Fetch submitter info and other metadata
5 Fetch all sequences from Washington state
+5 Fetch all sequences from Washington state
6 Discussion
+6 Discussion
7 Acknowledgements
+7 Acknowledgements
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 10:12.
+
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 12:06.