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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 df4a286..718b10f 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> -<!-- 2020-05-30 Sat 18:12 --> +<!-- 2020-08-24 Mon 04:31 --> <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> @@ -248,40 +248,40 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#org193669a">1. Uploading Data</a></li> -<li><a href="#orgc6b3a47">2. Step 1: Upload sequence</a></li> -<li><a href="#org9c08714">3. Step 2: Add metadata</a> +<li><a href="#orgdaec996">1. Uploading Data</a></li> +<li><a href="#org8472a05">2. Step 1: Upload sequence</a></li> +<li><a href="#org668a46d">3. Step 2: Add metadata</a> <ul> -<li><a href="#org4c2e907">3.1. Obligatory fields</a> +<li><a href="#orga044bef">3.1. Obligatory fields</a> <ul> -<li><a href="#orgdddcb2e">3.1.1. Sample ID (sample<sub>id</sub>)</a></li> -<li><a href="#orge9c2e76">3.1.2. Collection date</a></li> -<li><a href="#org62c55ce">3.1.3. Collection location</a></li> -<li><a href="#org460b377">3.1.4. Sequencing technology</a></li> -<li><a href="#org77b1e14">3.1.5. Authors</a></li> +<li><a href="#org8e17492">3.1.1. Sample ID (sample<sub>id</sub>)</a></li> +<li><a href="#orgd9805db">3.1.2. Collection date</a></li> +<li><a href="#org3bd4901">3.1.3. Collection location</a></li> +<li><a href="#org921de27">3.1.4. Sequencing technology</a></li> +<li><a href="#org39fa678">3.1.5. Authors</a></li> </ul> </li> -<li><a href="#org3cb346f">3.2. Optional fields</a> +<li><a href="#org5315804">3.2. Optional fields</a> <ul> -<li><a href="#orgb0cffbb">3.2.1. Host information</a></li> -<li><a href="#orgd2a43a6">3.2.2. Collecting institution</a></li> -<li><a href="#org8d5bcf7">3.2.3. Specimen source</a></li> -<li><a href="#org86b21b2">3.2.4. Source database accession</a></li> -<li><a href="#org771ea66">3.2.5. Strain name</a></li> +<li><a href="#orgf2b82d9">3.2.1. Host information</a></li> +<li><a href="#org8986ca7">3.2.2. Collecting institution</a></li> +<li><a href="#orge03eb0c">3.2.3. Specimen source</a></li> +<li><a href="#org6815a6e">3.2.4. Source database accession</a></li> +<li><a href="#org51b37e8">3.2.5. Strain name</a></li> </ul> </li> </ul> </li> -<li><a href="#org7d281f5">4. Step 3: Submit to COVID-19 PubSeq</a> +<li><a href="#org5778da6">4. Step 3: Submit to COVID-19 PubSeq</a> <ul> -<li><a href="#orgdf0f02d">4.1. Trouble shooting</a></li> +<li><a href="#orge803d65">4.1. Trouble shooting</a></li> </ul> </li> -<li><a href="#org29f8a92">5. Step 4: Check output</a></li> -<li><a href="#orgf493854">6. Bulk sequence uploader</a> +<li><a href="#org540cfdf">5. Step 4: Check output</a></li> +<li><a href="#org6c43ab3">6. Bulk sequence uploader</a> <ul> -<li><a href="#org37fadbc">6.1. Run the uploader (CLI)</a></li> -<li><a href="#org39adf09">6.2. Example: uploading bulk GenBank sequences</a></li> +<li><a href="#org99bb8b7">6.1. Run the uploader (CLI)</a></li> +<li><a href="#orga88593f">6.2. Example: uploading bulk GenBank sequences</a></li> </ul> </li> </ul> @@ -290,8 +290,8 @@ for the JavaScript code in this tag. -<div id="outline-container-org193669a" class="outline-2"> -<h2 id="org193669a"><span class="section-number-2">1</span> Uploading Data</h2> +<div id="outline-container-orgdaec996" class="outline-2"> +<h2 id="orgdaec996"><span class="section-number-2">1</span> Uploading Data</h2> <div class="outline-text-2" id="text-1"> <p> The COVID-19 PubSeq allows you to upload your SARS-Cov-2 strains to a @@ -301,8 +301,8 @@ gets triggered on upload. Read the <a href="./about">ABOUT</a> page for more inf </div> </div> -<div id="outline-container-orgc6b3a47" class="outline-2"> -<h2 id="orgc6b3a47"><span class="section-number-2">2</span> Step 1: Upload sequence</h2> +<div id="outline-container-org8472a05" class="outline-2"> +<h2 id="org8472a05"><span class="section-number-2">2</span> Step 1: Upload sequence</h2> <div class="outline-text-2" id="text-2"> <p> To upload a sequence in the <a href="http://covid19.genenetwork.org/">web upload page</a> hit the browse button and @@ -330,8 +330,8 @@ an improved pangenome. </div> </div> -<div id="outline-container-org9c08714" class="outline-2"> -<h2 id="org9c08714"><span class="section-number-2">3</span> Step 2: Add metadata</h2> +<div id="outline-container-org668a46d" class="outline-2"> +<h2 id="org668a46d"><span class="section-number-2">3</span> Step 2: Add metadata</h2> <div class="outline-text-2" id="text-3"> <p> The <a href="./">web upload page</a> contains fields for adding metadata. Metadata is @@ -357,12 +357,12 @@ the web form. Here we add some extra information. </p> </div> -<div id="outline-container-org4c2e907" class="outline-3"> -<h3 id="org4c2e907"><span class="section-number-3">3.1</span> Obligatory fields</h3> +<div id="outline-container-orga044bef" class="outline-3"> +<h3 id="orga044bef"><span class="section-number-3">3.1</span> Obligatory fields</h3> <div class="outline-text-3" id="text-3-1"> </div> -<div id="outline-container-orgdddcb2e" class="outline-4"> -<h4 id="orgdddcb2e"><span class="section-number-4">3.1.1</span> Sample ID (sample<sub>id</sub>)</h4> +<div id="outline-container-org8e17492" class="outline-4"> +<h4 id="org8e17492"><span class="section-number-4">3.1.1</span> Sample ID (sample<sub>id</sub>)</h4> <div class="outline-text-4" id="text-3-1-1"> <p> This is a string field that defines a unique sample identifier by the @@ -380,8 +380,8 @@ Here we add the GenBank ID MT536190.1. </div> </div> -<div id="outline-container-orge9c2e76" class="outline-4"> -<h4 id="orge9c2e76"><span class="section-number-4">3.1.2</span> Collection date</h4> +<div id="outline-container-orgd9805db" class="outline-4"> +<h4 id="orgd9805db"><span class="section-number-4">3.1.2</span> Collection date</h4> <div class="outline-text-4" id="text-3-1-2"> <p> Estimated collection date. The GenBank page says April 6, 2020. @@ -389,8 +389,8 @@ Estimated collection date. The GenBank page says April 6, 2020. </div> </div> -<div id="outline-container-org62c55ce" class="outline-4"> -<h4 id="org62c55ce"><span class="section-number-4">3.1.3</span> Collection location</h4> +<div id="outline-container-org3bd4901" class="outline-4"> +<h4 id="org3bd4901"><span class="section-number-4">3.1.3</span> Collection location</h4> <div class="outline-text-4" id="text-3-1-3"> <p> A search on wikidata says Los Angeles is @@ -399,8 +399,8 @@ A search on wikidata says Los Angeles is </div> </div> -<div id="outline-container-org460b377" class="outline-4"> -<h4 id="org460b377"><span class="section-number-4">3.1.4</span> Sequencing technology</h4> +<div id="outline-container-org921de27" class="outline-4"> +<h4 id="org921de27"><span class="section-number-4">3.1.4</span> Sequencing technology</h4> <div class="outline-text-4" id="text-3-1-4"> <p> GenBank entry says Illumina, so we can fill that in @@ -408,8 +408,8 @@ GenBank entry says Illumina, so we can fill that in </div> </div> -<div id="outline-container-org77b1e14" class="outline-4"> -<h4 id="org77b1e14"><span class="section-number-4">3.1.5</span> Authors</h4> +<div id="outline-container-org39fa678" class="outline-4"> +<h4 id="org39fa678"><span class="section-number-4">3.1.5</span> Authors</h4> <div class="outline-text-4" id="text-3-1-5"> <p> GenBank entry says 'Lamers,S., Nolan,D.J., Rose,R., Cross,S., Moraga @@ -420,16 +420,16 @@ Freehan,A. and Garcia-Diaz,J.', so we can fill that in. </div> </div> -<div id="outline-container-org3cb346f" class="outline-3"> -<h3 id="org3cb346f"><span class="section-number-3">3.2</span> Optional fields</h3> +<div id="outline-container-org5315804" class="outline-3"> +<h3 id="org5315804"><span class="section-number-3">3.2</span> Optional fields</h3> <div class="outline-text-3" id="text-3-2"> <p> All other fields are optional. But let's see what we can add. </p> </div> -<div id="outline-container-orgb0cffbb" class="outline-4"> -<h4 id="orgb0cffbb"><span class="section-number-4">3.2.1</span> Host information</h4> +<div id="outline-container-orgf2b82d9" class="outline-4"> +<h4 id="orgf2b82d9"><span class="section-number-4">3.2.1</span> Host information</h4> <div class="outline-text-4" id="text-3-2-1"> <p> Sadly, not much is known about the host from GenBank. A little @@ -443,8 +443,8 @@ did to the person and what the person was like (say age group). </div> </div> -<div id="outline-container-orgd2a43a6" class="outline-4"> -<h4 id="orgd2a43a6"><span class="section-number-4">3.2.2</span> Collecting institution</h4> +<div id="outline-container-org8986ca7" class="outline-4"> +<h4 id="org8986ca7"><span class="section-number-4">3.2.2</span> Collecting institution</h4> <div class="outline-text-4" id="text-3-2-2"> <p> We can fill that in. @@ -452,8 +452,8 @@ We can fill that in. </div> </div> -<div id="outline-container-org8d5bcf7" class="outline-4"> -<h4 id="org8d5bcf7"><span class="section-number-4">3.2.3</span> Specimen source</h4> +<div id="outline-container-orge03eb0c" class="outline-4"> +<h4 id="orge03eb0c"><span class="section-number-4">3.2.3</span> Specimen source</h4> <div class="outline-text-4" id="text-3-2-3"> <p> We have that: nasopharyngeal swab @@ -461,8 +461,8 @@ We have that: nasopharyngeal swab </div> </div> -<div id="outline-container-org86b21b2" class="outline-4"> -<h4 id="org86b21b2"><span class="section-number-4">3.2.4</span> Source database accession</h4> +<div id="outline-container-org6815a6e" class="outline-4"> +<h4 id="org6815a6e"><span class="section-number-4">3.2.4</span> Source database accession</h4> <div class="outline-text-4" id="text-3-2-4"> <p> Genbank which is <a href="http://identifiers.org/insdc/MT536190.1#sequence">http://identifiers.org/insdc/MT536190.1#sequence</a>. @@ -471,8 +471,8 @@ Note we plug in our own identifier MT536190.1. </div> </div> -<div id="outline-container-org771ea66" class="outline-4"> -<h4 id="org771ea66"><span class="section-number-4">3.2.5</span> Strain name</h4> +<div id="outline-container-org51b37e8" class="outline-4"> +<h4 id="org51b37e8"><span class="section-number-4">3.2.5</span> Strain name</h4> <div class="outline-text-4" id="text-3-2-5"> <p> SARS-CoV-2/human/USA/LA-BIE-070/2020 @@ -482,8 +482,8 @@ SARS-CoV-2/human/USA/LA-BIE-070/2020 </div> </div> -<div id="outline-container-org7d281f5" class="outline-2"> -<h2 id="org7d281f5"><span class="section-number-2">4</span> Step 3: Submit to COVID-19 PubSeq</h2> +<div id="outline-container-org5778da6" class="outline-2"> +<h2 id="org5778da6"><span class="section-number-2">4</span> Step 3: Submit to COVID-19 PubSeq</h2> <div class="outline-text-2" id="text-4"> <p> Once you have the sequence and the metadata together, hit @@ -493,8 +493,8 @@ submitted and the workflows should kick in! </div> -<div id="outline-container-orgdf0f02d" class="outline-3"> -<h3 id="orgdf0f02d"><span class="section-number-3">4.1</span> Trouble shooting</h3> +<div id="outline-container-orge803d65" class="outline-3"> +<h3 id="orge803d65"><span class="section-number-3">4.1</span> Trouble shooting</h3> <div class="outline-text-3" id="text-4-1"> <p> We got an error saying: {"stem": "<a href="http://www.wikidata.org/entity/">http://www.wikidata.org/entity/</a>",… @@ -508,9 +508,8 @@ submit button. </div> </div> - -<div id="outline-container-org29f8a92" class="outline-2"> -<h2 id="org29f8a92"><span class="section-number-2">5</span> Step 4: Check output</h2> +<div id="outline-container-org540cfdf" class="outline-2"> +<h2 id="org540cfdf"><span class="section-number-2">5</span> Step 4: Check output</h2> <div class="outline-text-2" id="text-5"> <p> The current pipeline takes 5.5 hours to complete! Once it completes @@ -521,8 +520,8 @@ in. </div> </div> -<div id="outline-container-orgf493854" class="outline-2"> -<h2 id="orgf493854"><span class="section-number-2">6</span> Bulk sequence uploader</h2> +<div id="outline-container-org6c43ab3" class="outline-2"> +<h2 id="org6c43ab3"><span class="section-number-2">6</span> Bulk sequence uploader</h2> <div class="outline-text-2" id="text-6"> <p> Above steps require a manual upload of one sequence with metadata. @@ -544,8 +543,8 @@ host: host_age: <span style="color: #8bc34a;">20</span> host_age_unit: http://purl.obolibrary.org/obo/UO_<span style="color: #8bc34a;">0000036</span> host_health_status: http://purl.obolibrary.org/obo/NCIT_C<span style="color: #8bc34a;">25269</span> - host_treatment: Process in which the act is intended to modify or alter host status <span style="color: #e91e63;">(</span>Compounds<span style="color: #e91e63;">)</span> - host_vaccination: <span style="color: #e91e63;">[</span>vaccines<span style="color: #8bc34a;">1</span>,vaccine<span style="color: #8bc34a;">2</span><span style="color: #e91e63;">]</span> + host_treatment: Process in which the act is intended to modify or alter host status (Compounds) + host_vaccination: [vaccines<span style="color: #8bc34a;">1</span>,vaccine<span style="color: #8bc34a;">2</span>] ethnicity: http://purl.obolibrary.org/obo/HANCESTRO_<span style="color: #8bc34a;">0010</span> additional_host_information: Optional free text field for additional information @@ -553,11 +552,11 @@ sample: sample_id: Id of the sample as defined by the submitter collector_name: Name of the person that took the sample collecting_institution: Institute that was responsible of sampling - specimen_source: <span style="color: #e91e63;">[</span>http://purl.obolibrary.org/obo/NCIT_C<span style="color: #8bc34a;">155831</span>,http://purl.obolibrary.org/obo/NCIT_C<span style="color: #8bc34a;">155835</span>] + specimen_source: [http://purl.obolibrary.org/obo/NCIT_C<span style="color: #8bc34a;">155831</span>,http://purl.obolibrary.org/obo/NCIT_C<span style="color: #8bc34a;">155835</span>] collection_date: <span style="color: #9ccc65;">"2020-01-01"</span> collection_location: http://www.wikidata.org/entity/Q<span style="color: #8bc34a;">148</span> sample_storage_conditions: frozen specimen - source_database_accession: <span style="color: #2196F3;">[</span>http://identifiers.org/insdc/LC<span style="color: #8bc34a;">522350.1</span>#sequence] + source_database_accession: [http://identifiers.org/insdc/LC<span style="color: #8bc34a;">522350.1</span>#sequence] additional_collection_information: Optional free text field for additional information virus: @@ -565,28 +564,28 @@ virus: virus_strain: SARS-CoV-<span style="color: #8bc34a;">2</span>/human/CHN/HS_<span style="color: #8bc34a;">8</span>/<span style="color: #8bc34a;">2020</span> technology: - sample_sequencing_technology: <span style="color: #EF6C00;">[</span>http://www.ebi.ac.uk/efo/EFO_<span style="color: #8bc34a;">0009173</span>,http://www.ebi.ac.uk/efo/EFO_<span style="color: #8bc34a;">0009173</span>] + sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_<span style="color: #8bc34a;">0009173</span>,http://www.ebi.ac.uk/efo/EFO_<span style="color: #8bc34a;">0009173</span>] sequence_assembly_method: Protocol used for assembly - sequencing_coverage: <span style="color: #B388FF;">[</span><span style="color: #8bc34a;">70.0</span>, <span style="color: #8bc34a;">100.0</span><span style="color: #B388FF;">]</span> + sequencing_coverage: [<span style="color: #8bc34a;">70.0</span>, <span style="color: #8bc34a;">100.0</span>] additional_technology_information: Optional free text field for additional information submitter: - authors: <span style="color: #B388FF;">[</span>John Doe, Joe Boe, Jonny Oe<span style="color: #B388FF;">]</span> - submitter_name: <span style="color: #B388FF;">[</span>John Doe<span style="color: #B388FF;">]</span> + authors: [John Doe, Joe Boe, Jonny Oe] + submitter_name: [John Doe] submitter_address: John Doe's address originating_lab: John Doe kitchen lab_address: John Doe's address provider_sample_id: XXX<span style="color: #8bc34a;">1</span> submitter_sample_id: XXX<span style="color: #8bc34a;">2</span> publication: PMID<span style="color: #8bc34a;">00001113</span> - submitter_orcid: <span style="color: #B388FF;">[</span>https://orcid.org/<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>,https://orcid.org/<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0001</span>] + submitter_orcid: [https://orcid.org/<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>,https://orcid.org/<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0001</span>] additional_submitter_information: Optional free text field for additional information </pre> </div> </div> -<div id="outline-container-org37fadbc" class="outline-3"> -<h3 id="org37fadbc"><span class="section-number-3">6.1</span> Run the uploader (CLI)</h3> +<div id="outline-container-org99bb8b7" class="outline-3"> +<h3 id="org99bb8b7"><span class="section-number-3">6.1</span> Run the uploader (CLI)</h3> <div class="outline-text-3" id="text-6-1"> <p> Installing with pip you should be @@ -621,20 +620,35 @@ The web interface using this exact same script so it should just work </div> </div> -<div id="outline-container-org39adf09" class="outline-3"> -<h3 id="org39adf09"><span class="section-number-3">6.2</span> Example: uploading bulk GenBank sequences</h3> +<div id="outline-container-orga88593f" class="outline-3"> +<h3 id="orga88593f"><span class="section-number-3">6.2</span> Example: uploading bulk GenBank sequences</h3> <div class="outline-text-3" id="text-6-2"> <p> We also use above script to bulk upload GenBank sequences with a <a href="https://github.com/arvados/bh20-seq-resource/blob/master/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py">FASTA and YAML</a> extractor specific for GenBank. This means that the steps we took above for uploading a GenBank sequence are already automated. </p> + +<p> +The steps are: from the +<code>bh20-seq-resource/scripts/download_genbank_data/</code> directory +</p> + +<div class="org-src-container"> +<pre class="src src-sh">python3 from_genbank_to_fasta_and_yaml.py +<span style="color: #ffcc80;">dir_fasta_and_yaml</span>=~/bh20-seq-resource/scripts/download_genbank_data/fasta_and_yaml +ls $<span style="color: #ffcc80;">dir_fasta_and_yaml</span>/*.yaml | <span style="color: #fff59d;">while </span><span style="color: #ff8A65;">read</span> path_code_yaml; <span style="color: #fff59d;">do</span> + <span style="color: #ffcc80;">path_code_fasta</span>=${<span style="color: #ffcc80;">path_code_yaml</span>%.*}.fasta + bh20-seq-uploader --skip-qc $<span style="color: #ffcc80;">path_code_yaml</span> $<span style="color: #ffcc80;">path_code_fasta</span> +<span style="color: #fff59d;">done</span> +</pre> +</div> </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 2020-05-30 Sat 18:12</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 2020-08-24 Mon 04:31</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 e8fee36..fda7be8 100644 --- a/doc/blog/using-covid-19-pubseq-part3.org +++ b/doc/blog/using-covid-19-pubseq-part3.org @@ -146,7 +146,6 @@ 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. - * Step 4: Check output The current pipeline takes 5.5 hours to complete! Once it completes @@ -237,3 +236,15 @@ The web interface using this exact same script so it should just work We also use above script to bulk upload GenBank sequences with a [[https://github.com/arvados/bh20-seq-resource/blob/master/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py][FASTA and YAML]] extractor specific for GenBank. This means that the steps we took above for uploading a GenBank sequence are already automated. + +The steps are: from the +~bh20-seq-resource/scripts/download_genbank_data/~ directory + +#+BEGIN_SRC sh +python3 from_genbank_to_fasta_and_yaml.py +dir_fasta_and_yaml=~/bh20-seq-resource/scripts/download_genbank_data/fasta_and_yaml +ls $dir_fasta_and_yaml/*.yaml | while read path_code_yaml; do + path_code_fasta=${path_code_yaml%.*}.fasta + bh20-seq-uploader --skip-qc $path_code_yaml $path_code_fasta +done +#+END_SRC diff --git a/doc/blog/using-covid-19-pubseq-part5.html b/doc/blog/using-covid-19-pubseq-part5.html index 4caa5ac..5d640f9 100644 --- a/doc/blog/using-covid-19-pubseq-part5.html +++ b/doc/blog/using-covid-19-pubseq-part5.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> -<!-- 2020-07-17 Fri 05:03 --> +<!-- 2020-08-22 Sat 07:43 --> <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 (part 4)</title> @@ -248,19 +248,28 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#org758b923">1. Modify Metadata</a></li> -<li><a href="#orgec32c13">2. What is the schema?</a></li> -<li><a href="#org2e487b2">3. How is the website generated?</a></li> -<li><a href="#orge4dfe84">4. Modifying the schema</a></li> -<li><a href="#org564a7a8">5. Adding fields to the form</a></li> -<li><a href="#org633781a">6. <span class="todo TODO">TODO</span> Testing the license fields</a></li> +<li><a href="#org935d151">1. Modify Metadata</a></li> +<li><a href="#orgfb70872">2. What is the schema?</a></li> +<li><a href="#orga76b489">3. How is the website generated?</a></li> +<li><a href="#org80bb905">4. Changing the license field</a> +<ul> +<li><a href="#org3689b60">4.1. Modifying the schema</a></li> +<li><a href="#org07e0c66">4.2. Adding fields to the form</a></li> +<li><a href="#org1cfb94a">4.3. <span class="todo TODO">TODO</span> Testing the license fields</a></li> +</ul> +</li> +<li><a href="#org88d4555">5. Changing GEO or location field</a> +<ul> +<li><a href="#org063bcfa">5.1. Relaxing the shex constraint</a></li> +</ul> +</li> </ul> </div> </div> -<div id="outline-container-org758b923" class="outline-2"> -<h2 id="org758b923"><span class="section-number-2">1</span> Modify Metadata</h2> +<div id="outline-container-org935d151" class="outline-2"> +<h2 id="org935d151"><span class="section-number-2">1</span> Modify Metadata</h2> <div class="outline-text-2" id="text-1"> <p> The public sequence resource uses multiple data formats listed on the @@ -268,8 +277,8 @@ The public sequence resource uses multiple data formats listed on the for RDF and semantic web/linked data ontologies. This technology allows for querying data in unprescribed ways - that is, you can formulate your own queries without dealing with a preset model of that -data (so typical of CSV files and SQL tables). Examples of exploring -data are listed <a href="http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part1">here</a>. +data (which is how one has to approach CSV files and SQL +tables). Examples of exploring data are listed <a href="http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part1">here</a>. </p> <p> @@ -280,8 +289,8 @@ understand that anyone, including you, can change that information! </div> </div> -<div id="outline-container-orgec32c13" class="outline-2"> -<h2 id="orgec32c13"><span class="section-number-2">2</span> What is the schema?</h2> +<div id="outline-container-orgfb70872" class="outline-2"> +<h2 id="orgfb70872"><span class="section-number-2">2</span> What is the schema?</h2> <div class="outline-text-2" id="text-2"> <p> The default metadata schema is listed <a href="https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml">here</a>. @@ -289,8 +298,8 @@ The default metadata schema is listed <a href="https://github.com/arvados/bh20-s </div> </div> -<div id="outline-container-org2e487b2" class="outline-2"> -<h2 id="org2e487b2"><span class="section-number-2">3</span> How is the website generated?</h2> +<div id="outline-container-orga76b489" class="outline-2"> +<h2 id="orga76b489"><span class="section-number-2">3</span> How is the website generated?</h2> <div class="outline-text-2" id="text-3"> <p> Using the schema we use <a href="https://pypi.org/project/PyShEx/">pyshex</a> shex expressions and <a href="https://github.com/common-workflow-language/schema_salad">schema salad</a> to @@ -300,9 +309,13 @@ All from that one metadata schema. </div> </div> -<div id="outline-container-orge4dfe84" class="outline-2"> -<h2 id="orge4dfe84"><span class="section-number-2">4</span> Modifying the schema</h2> +<div id="outline-container-org80bb905" class="outline-2"> +<h2 id="org80bb905"><span class="section-number-2">4</span> Changing the license field</h2> <div class="outline-text-2" id="text-4"> +</div> +<div id="outline-container-org3689b60" class="outline-3"> +<h3 id="org3689b60"><span class="section-number-3">4.1</span> Modifying the schema</h3> +<div class="outline-text-3" id="text-4-1"> <p> One of the first things we want to do is to add a field for the data license. Initially we only supported CC-4.0 as a license, but @@ -380,25 +393,25 @@ So, we'll add it simply as a title field. Now the draft schema is type: record fields: license_type: - doc: License types as refined in https://wiki.creativecommons.org/images/d/d6/Ccrel-1.0.pdf + doc: License types as refined <span style="color: #fff59d;">in</span> https:<span style="color: #b0bec5;">//</span><span style="color: #b0bec5;">wiki.creativecommons.org/images/d/d6/Ccrel-1.0.pdf</span> type: string? jsonldPredicate: - _id: https://creativecommons.org/ns#License + _id: https:<span style="color: #b0bec5;">//</span><span style="color: #b0bec5;">creativecommons.org/ns#License</span> title: doc: Attribution title related to license type: string? jsonldPredicate: - _id: http://semanticscience.org/resource/SIO_001167 + _id: http:<span style="color: #b0bec5;">//</span><span style="color: #b0bec5;">semanticscience.org/resource/SIO_001167</span> attribution_url: doc: Attribution URL related to license type: string? jsonldPredicate: - _id: https://creativecommons.org/ns#Work + _id: https:<span style="color: #b0bec5;">//</span><span style="color: #b0bec5;">creativecommons.org/ns#Work</span> attribution_source: doc: Attribution source URL type: string? jsonldPredicate: - _id: https://creativecommons.org/ns#Work + _id: https:<span style="color: #b0bec5;">//</span><span style="color: #b0bec5;">creativecommons.org/ns#Work</span> </pre> </div> @@ -411,13 +424,13 @@ gitter channel and I merged it. </div> </div> -<div id="outline-container-org564a7a8" class="outline-2"> -<h2 id="org564a7a8"><span class="section-number-2">5</span> Adding fields to the form</h2> -<div class="outline-text-2" id="text-5"> +<div id="outline-container-org07e0c66" class="outline-3"> +<h3 id="org07e0c66"><span class="section-number-3">4.2</span> Adding fields to the form</h3> +<div class="outline-text-3" id="text-4-2"> <p> To add the new fields to the form we have to modify it a little. If we go to the upload form we need to add the license box. The schema is -loaded in <a href="https://github.com/arvados/bh20-seq-resource/blob/a0c8ebd57b875f265e8b0efec4abfaf892eb6c45/bh20simplewebuploader/main.py#L229">main.py</a> in the 'generate<sub>form</sub>' function. +loaded in <a href="https://github.com/arvados/bh20-seq-resource/blob/a0c8ebd57b875f265e8b0efec4abfaf892eb6c45/bh20simplewebuploader/main.py#L229">main.py</a> in the 'generate-form' function. </p> <p> @@ -453,12 +466,71 @@ field to be optional - a missing license assumes it is CC-BY-4.0. </div> </div> -<div id="outline-container-org633781a" class="outline-2"> -<h2 id="org633781a"><span class="section-number-2">6</span> <span class="todo TODO">TODO</span> Testing the license fields</h2> +<div id="outline-container-org1cfb94a" class="outline-3"> +<h3 id="org1cfb94a"><span class="section-number-3">4.3</span> <span class="todo TODO">TODO</span> Testing the license fields</h3> +</div> +</div> + +<div id="outline-container-org88d4555" class="outline-2"> +<h2 id="org88d4555"><span class="section-number-2">5</span> Changing GEO or location field</h2> +<div class="outline-text-2" id="text-5"> +<p> +When fetching information from GenBank and EBI/ENA we also translate +the location into an unambiguous identifier. We opted for the wikidata +tag. E.g. for New York city it is <a href="https://www.wikidata.org/wiki/Q60">https://www.wikidata.org/wiki/Q60</a> +and for New York state it is <a href="https://www.wikidata.org/wiki/Q1384">https://www.wikidata.org/wiki/Q1384</a>. If +everyone uses these metadata URIs it is easy to group when making +queries. Note that we should be using +<a href="http://www.wikidata.org/entity/Q60">http://www.wikidata.org/entity/Q60</a> in the dataset (http instead of +https and entitity instead of wiki). +</p> + +<p> +Unfortunately the main repositories of SARS-CoV-2 have variable +strings of text for location and/or GPS coordinates. For us to support +our schema we had to translate all options and this proves expensive. +</p> +</div> + +<div id="outline-container-org063bcfa" class="outline-3"> +<h3 id="org063bcfa"><span class="section-number-3">5.1</span> Relaxing the shex constraint</h3> +<div class="outline-text-3" id="text-5-1"> +<p> +So we decide to relax the enforcement of this type of metadata and to +allow for a free form string. +</p> + +<p> +The schema already used <a href="http://purl.obolibrary.org/obo/GAZ_00000448">http://purl.obolibrary.org/obo/GAZ_00000448</a> +which states: +</p> + +<div class="org-src-container"> +<pre class="src src-js">Class: geographic + location + Term IRI: http:<span style="color: #b0bec5;">//</span><span style="color: #b0bec5;">purl.obolibrary.org/obo/GAZ_00000448</span> +Definition: A reference to a place on + the Earth, by its name or by its geographical location. +</pre> +</div> + +<p> +and when you check count by location in the <a href="./demo">DEMO</a> it lists a free +format. +</p> + +<p> +So, why does the validation step balk when importing GenBank? +The problem was in the <a href="https://github.com/arvados/bh20-seq-resource/blob/46d4b7a3a31f6605f81d43ecd6651d60a5782364/bh20sequploader/bh20seq-shex.rdf#L39">shex check</a> for RDF generation. +Removing the wikidata requirement relaxed the imports with this +<a href="https://github.com/arvados/bh20-seq-resource/commit/f776816ee2b1af7ccc84afb494f68a81a51f5a76">patch</a>. +</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 2020-07-16 Thu 03:27</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 2020-08-22 Sat 07:42</small>. </div> </body> </html> diff --git a/doc/blog/using-covid-19-pubseq-part5.org b/doc/blog/using-covid-19-pubseq-part5.org index 78eea66..e260078 100644 --- a/doc/blog/using-covid-19-pubseq-part5.org +++ b/doc/blog/using-covid-19-pubseq-part5.org @@ -12,9 +12,12 @@ - [[#modify-metadata][Modify Metadata]] - [[#what-is-the-schema][What is the schema?]] - [[#how-is-the-website-generated][How is the website generated?]] - - [[#modifying-the-schema][Modifying the schema]] - - [[#adding-fields-to-the-form][Adding fields to the form]] - - [[#testing-the-license-fields][Testing the license fields]] + - [[#changing-the-license-field][Changing the license field]] + - [[#modifying-the-schema][Modifying the schema]] + - [[#adding-fields-to-the-form][Adding fields to the form]] + - [[#testing-the-license-fields][Testing the license fields]] + - [[#changing-geo-or-location-field][Changing GEO or location field]] + - [[#relaxing-the-shex-constraint][Relaxing the shex constraint]] * Modify Metadata @@ -23,8 +26,8 @@ The public sequence resource uses multiple data formats listed on the for RDF and semantic web/linked data ontologies. This technology allows for querying data in unprescribed ways - that is, you can formulate your own queries without dealing with a preset model of that -data (so typical of CSV files and SQL tables). Examples of exploring -data are listed [[http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part1][here]]. +data (which is how one has to approach CSV files and SQL +tables). Examples of exploring data are listed [[http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part1][here]]. In this BLOG we are going to look at the metadata entered on the COVID-19 PubSeq website (or command line client). It is important to @@ -40,7 +43,9 @@ Using the schema we use [[https://pypi.org/project/PyShEx/][pyshex]] shex expres generate the [[https://github.com/arvados/bh20-seq-resource/blob/edb17e7f7caebfa1e76b21006b1772a33f4f7887/bh20simplewebuploader/templates/form.html#L47][input form]], [[https://github.com/arvados/bh20-seq-resource/blob/edb17e7f7caebfa1e76b21006b1772a33f4f7887/bh20sequploader/qc_metadata.py#L13][validate]] the user input and to build [[https://github.com/arvados/bh20-seq-resource/blob/edb17e7f7caebfa1e76b21006b1772a33f4f7887/workflows/pangenome-generate/merge-metadata.py#L24][RDF]]! All from that one metadata schema. -* Modifying the schema +* Changing the license field + +** Modifying the schema One of the first things we want to do is to add a field for the data license. Initially we only supported CC-4.0 as a license, but @@ -120,11 +125,11 @@ our source tree and ask for feedback before wiring it up in the data entry form. The pull request was submitted [[https://github.com/arvados/bh20-seq-resource/pull/97][here]] and reviewed on the gitter channel and I merged it. -* Adding fields to the form +** Adding fields to the form To add the new fields to the form we have to modify it a little. If we go to the upload form we need to add the license box. The schema is -loaded in [[https://github.com/arvados/bh20-seq-resource/blob/a0c8ebd57b875f265e8b0efec4abfaf892eb6c45/bh20simplewebuploader/main.py#L229][main.py]] in the 'generate_form' function. +loaded in [[https://github.com/arvados/bh20-seq-resource/blob/a0c8ebd57b875f265e8b0efec4abfaf892eb6c45/bh20simplewebuploader/main.py#L229][main.py]] in the 'generate-form' function. With this [[https://github.com/arvados/bh20-seq-resource/commit/b9691c7deae30bd6422fb7b0681572b7b6f78ae3][patch]] the website adds the license input fields on the form. @@ -148,4 +153,43 @@ When pushing the license info we discovered the workflow broke because the existing data had no licensing info. So we changed the license field to be optional - a missing license assumes it is CC-BY-4.0. -* TODO Testing the license fields +** TODO Testing the license fields + +* Changing GEO or location field + +When fetching information from GenBank and EBI/ENA we also translate +the location into an unambiguous identifier. We opted for the wikidata +tag. E.g. for New York city it is https://www.wikidata.org/wiki/Q60 +and for New York state it is https://www.wikidata.org/wiki/Q1384. If +everyone uses these metadata URIs it is easy to group when making +queries. Note that we should be using +http://www.wikidata.org/entity/Q60 in the dataset (http instead of +https and entitity instead of wiki). + +Unfortunately the main repositories of SARS-CoV-2 have variable +strings of text for location and/or GPS coordinates. For us to support +our schema we had to translate all options and this proves expensive. + +** Relaxing the shex constraint + +So we decide to relax the enforcement of this type of metadata and to +allow for a free form string. + +The schema already used http://purl.obolibrary.org/obo/GAZ_00000448 +which states: + +#+BEGIN_SRC js +Class: geographic + location + Term IRI: http://purl.obolibrary.org/obo/GAZ_00000448 +Definition: A reference to a place on + the Earth, by its name or by its geographical location. +#+END_SRC + +and when you check count by location in the [[./demo][DEMO]] it lists a free +format. + +So, why does the validation step balk when importing GenBank? +The problem was in the [[https://github.com/arvados/bh20-seq-resource/blob/46d4b7a3a31f6605f81d43ecd6651d60a5782364/bh20sequploader/bh20seq-shex.rdf#L39][shex check]] for RDF generation. +Removing the wikidata requirement relaxed the imports with this +[[https://github.com/arvados/bh20-seq-resource/commit/f776816ee2b1af7ccc84afb494f68a81a51f5a76][patch]]. diff --git a/doc/web/about.html b/doc/web/about.html index c971a4e..2d1f51d 100644 --- a/doc/web/about.html +++ b/doc/web/about.html @@ -1,964 +1,649 @@ <?xml version="1.0" encoding="utf-8"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" - "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> +"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <head> - <!-- 2020-07-18 Sat 03:27 --> - <meta http-equiv="Content-Type" content="text/html;charset=utf-8"/> - <meta name="viewport" content="width=device-width, initial-scale=1"/> - <title>About/FAQ</title> - <meta name="generator" content="Org mode"/> - <meta name="author" content="Pjotr Prins"/> - <style type="text/css"> - <!-- /*--><![CDATA[/*><!--*/ - .title { - text-align: center; 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The code is distributed WITHOUT ANY WARRANTY; +without even the implied warranty of MERCHANTABILITY or FITNESS +FOR A PARTICULAR PURPOSE. See the GNU GPL for more details. + +As additional permission under GNU GPL version 3 section 7, you +may distribute non-source (e.g., minimized or compacted) forms of +that code without the copy of the GNU GPL normally required by +section 4, provided you include this license notice and a URL +through which recipients can access the Corresponding Source. + + +@licend The above is the entire license notice +for the JavaScript code in this tag. +*/ +<!--/*--><![CDATA[/*><!--*/ + function CodeHighlightOn(elem, id) + { + var target = document.getElementById(id); + if(null != target) { + elem.cacheClassElem = elem.className; + elem.cacheClassTarget = target.className; + target.className = "code-highlighted"; + elem.className = "code-highlighted"; + } + } + function CodeHighlightOff(elem, id) + { + var target = document.getElementById(id); + if(elem.cacheClassElem) + elem.className = elem.cacheClassElem; + if(elem.cacheClassTarget) + target.className = elem.cacheClassTarget; + } +/*]]>*///--> +</script> </head> <body> <div id="content"> - <h1 class="title">About/FAQ</h1> - <div id="table-of-contents"> - <h2>Table of Contents</h2> - <div id="text-table-of-contents"> - <ul> - <li><a href="#org0db9061">1. What is the 'public sequence resource' about?</a></li> - <li><a href="#org983877d">2. Who created the public sequence resource?</a></li> - <li><a href="#org83093c3">3. How does the public sequence resource compare to other data resources?</a> - </li> - <li><a href="#org9b31fd4">4. Why should I upload my data here?</a></li> - <li><a href="#org4e92cb5">5. Why should I not upload by data here?</a></li> - <li><a href="#orgdfe72f6">6. How does the public sequence resource work?</a></li> - <li><a href="#orgd0c5abb">7. Who uses the public sequence resource?</a></li> - <li><a href="#org56f4a54">8. How can I contribute?</a></li> - <li><a href="#org2240ef7">9. Is this about open data?</a></li> - <li><a href="#orgbb655e0">10. Is this about free software?</a></li> - <li><a href="#org4e779f4">11. How do I upload raw data?</a></li> - <li><a href="#org83f6b7b">12. How do I change metadata?</a></li> - <li><a href="#org1bc6dab">13. How do I change the work flows?</a></li> - <li><a href="#org1140d62">14. How do I change the source code?</a></li> - <li><a href="#orge182714">15. Should I choose CC-BY or CC0?</a></li> - <li><a href="#orgf4a692b">16. How do I deal with private data and privacy?</a></li> - <li><a href="#org7757574">17. How do I communicate with you?</a></li> - <li><a href="#org194006f">18. Who are the sponsors?</a></li> - </ul> - </div> - </div> - - <div id="outline-container-org0db9061" class="outline-2"> - <h2 id="org0db9061"><span class="section-number-2">1</span> What is the 'public sequence resource' about?</h2> - <div class="outline-text-2" id="text-1"> - <p> - The <b>public sequence resource</b> aims to provide a generic and useful - resource for COVID-19 research. The focus is on providing the best - possible sequence data with associated metadata that can be used for - sequence comparison and protein prediction. - </p> - <p> - We were at the <strong>Bioinformatics Community Conference 2020</strong>! Have a look at the - <a href="https://bcc2020.sched.com/event/coLw">video talk</a></li> - (<a href="https://drive.google.com/file/d/1skXHwVKM_gl73-_4giYIOQ1IlC5X5uBo/view?usp=sharing">alternative link</a>) - and the <a href="https://drive.google.com/file/d/1vyEgfvSqhM9yIwWZ6Iys-QxhxtVxPSdp/view?usp=sharing">poster</a>. - </p> - </div> - </div> - - <div id="outline-container-org983877d" class="outline-2"> - <h2 id="org983877d"><span class="section-number-2">2</span> Who created the public sequence resource?</h2> - <div class="outline-text-2" id="text-2"> - <p> - The <b>public sequence resource</b> is an initiative by <a - href="https://github.com/arvados/bh20-seq-resource/graphs/contributors">bioinformatics</a> and - ontology experts who want to create something agile and useful for the - wider research community. The initiative started at the COVID-19 - biohackathon in April 2020 and is ongoing. The main project drivers - are Pjotr Prins (UTHSC), Peter Amstutz (Curii), Andrea Guarracino - (University of Rome Tor Vergata), Michael Crusoe (Common Workflow - Language), Thomas Liener (consultant, formerly EBI), Erik Garrison - (UCSC) and Jerven Bolleman (Swiss Institute of Bioinformatics). - </p> - - <p> - Notably, as this is a free software initiative, the project represents - major work by hundreds of software developers and ontology and data - wrangling experts. Thank you everyone! - </p> - </div> - </div> - - <div id="outline-container-org83093c3" class="outline-2"> - <h2 id="org83093c3"><span class="section-number-2">3</span> How does the public sequence resource compare to - other data resources?</h2> - <div class="outline-text-2" id="text-3"> - <p> - The short version is that we use state-of-the-art practices in - bioinformatics using agile methods. Unlike the resources from large - institutes we can improve things on a dime and anyone can contribute - to building out this resource! Sequences from GenBank, EBI/ENA and - others are regularly added to PubSeq. We encourage people to everyone - to submit on PubSeq because of its superior live tooling and metadata - support (see the next question). - </p> - - <p> - Importantly: all data is published under either the <a - href="https://creativecommons.org/licenses/by/4.0/">Creative Commons - 4.0 attribution license</a> or the <a - href="https://creativecommons.org/share-your-work/public-domain/cc0/">CC0 “No Rights Reserved” - license</a> which - means it data can be published and workflows can run in public - environments allowing for improved access for research and - reproducible results. This contrasts with some other public resources, - such as GISAID. - </p> - </div> - </div> - - <div id="outline-container-org9b31fd4" class="outline-2"> - <h2 id="org9b31fd4"><span class="section-number-2">4</span> Why should I upload my data here?</h2> - <div class="outline-text-2" id="text-4"> - <ol class="org-ol"> - <li>We champion truly shareable data without licensing restrictions - with proper - attribution - </li> - <li>We provide full metadata support using state-of-the-art ontology's</li> - <li>We provide a web-based sequence uploader and a command-line version - for bulk uploads - </li> - <li>We provide a live SPARQL end-point for all metadata</li> - <li>We provide free data analysis and sequence comparison triggered on data upload</li> - <li>We do real work for you, with this <a - href="https://workbench.lugli.arvadosapi.com/container_requests/lugli-xvhdp-bhhk4nxx1lch5od">link</a> - you can see the last - run took 5.5 hours! - </li> - <li>We provide free downloads of all computed output</li> - <li>There is no need to set up pipelines and/or compute clusters</li> - <li>All workflows get triggered on uploading a new sequence</li> - <li>When someone (you?) improves the software/workflows and everyone benefits</li> - <li>Your data gets automatically integrated with the Swiss Institure of - Bioinformatics COVID-19 knowledge base - <a href="https://covid-19-sparql.expasy.org/">https://covid-19-sparql.expasy.org/</a> (Elixir - Switzerland) - </li> - <li>Your data will be used to develop drug targets</li> - </ol> - - <p> - Finally, if you upload your data here we have workflows that output - formatted data suitable for <a - href="http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part6">uploading to EBI - resources</a> (and soon - others). Uploading your data here get your data ready for upload to - multiple resources. - </p> - </div> - </div> - - <div id="outline-container-org4e92cb5" class="outline-2"> - <h2 id="org4e92cb5"><span class="section-number-2">5</span> Why should I not upload by data here?</h2> - <div class="outline-text-2" id="text-5"> - <p> - Funny question. There are only good reasons to upload your data here - and make it available to the widest audience possible. - </p> - - <p> - In fact, you can upload your data here as well as to other - resources. It is your data after all. No one can prevent you from - uploading your data to multiple resources. - </p> - - <p> - We recommend uploading to EBI and NCBI resources using our data - conversion tools. It means you only enter data once and make the - process smooth. You can also use our command line data uploader - for bulk uploads! - </p> - </div> - </div> - - <div id="outline-container-orgdfe72f6" class="outline-2"> - <h2 id="orgdfe72f6"><span class="section-number-2">6</span> How does the public sequence resource work?</h2> - <div class="outline-text-2" id="text-6"> - <p> - On uploading a sequence with metadata it will automatically be - processed and incorporated into the public pangenome with metadata - using workflows from the High Performance Open Biology Lab defined - <a href="https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate">here</a>. - </p> - </div> - </div> - - <div id="outline-container-orgd0c5abb" class="outline-2"> - <h2 id="orgd0c5abb"><span class="section-number-2">7</span> Who uses the public sequence resource?</h2> - <div class="outline-text-2" id="text-7"> - <p> - The Swiss Institute of Bioinformatics has included this data in - <a href="https://covid-19-sparql.expasy.org/">https://covid-19-sparql.expasy.org/</a> and made it part - of <a href="https://www.uniprot.org/">Uniprot</a>. - </p> - - <p> - The Pantograph <a href="https://graph-genome.github.io/">viewer</a> uses PubSeq data for their - visualisations. - </p> - - <p> - <a href="https://uthsc.edu">UTHSC</a> (USA), <a href="https://www.esr.cri.nz/">ESR</a> (New Zealand) and - <a href="https://www.ornl.gov/news/ornl-fight-against-covid-19">ORNL</a> (USA) use COVID-19 PubSeq data - for monitoring, protein prediction and drug development. - </p> - </div> - </div> - - <div id="outline-container-org56f4a54" class="outline-2"> - <h2 id="org56f4a54"><span class="section-number-2">8</span> How can I contribute?</h2> - <div class="outline-text-2" id="text-8"> - <p> - You can contribute by submitting sequences, updating metadata, submit - issues on our issue tracker, and more importantly add functionality. - See 'How do I change the source code' below. Read through our online - documentation at <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a> - as a starting - point. - </p> - </div> - </div> - - <div id="outline-container-org2240ef7" class="outline-2"> - <h2 id="org2240ef7"><span class="section-number-2">9</span> Is this about open data?</h2> - <div class="outline-text-2" id="text-9"> - <p> - All data is published under a <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons - 4.0 attribution license</a> - (CC-BY-4.0). You can download the raw and published (GFA/RDF/FASTA) - data and store it for further processing. - </p> - </div> - </div> - - <div id="outline-container-orgbb655e0" class="outline-2"> - <h2 id="orgbb655e0"><span class="section-number-2">10</span> Is this about free software?</h2> - <div class="outline-text-2" id="text-10"> - <p> - Absolutely. Free software allows for fully reproducible pipelines. You - can take our workflows and data and run it elsewhere! - </p> - </div> - </div> - - <div id="outline-container-org4e779f4" class="outline-2"> - <h2 id="org4e779f4"><span class="section-number-2">11</span> How do I upload raw data?</h2> - <div class="outline-text-2" id="text-11"> - <p> - We are preparing raw sequence data pipelines (fastq and BAM). The - reason is that we want the best data possible for downstream analysis - (including protein prediction and test development). The current - approach where people publish final sequences of SARS-CoV-2 is lacking - because it hides how this sequence was created. For reasons of - reproducible and improved results we want/need to work with the raw - sequence reads (both short reads and long reads) and take alternative - assembly variations into consideration. This is all work in progress. - </p> - </div> - </div> - - <div id="outline-container-org83f6b7b" class="outline-2"> - <h2 id="org83f6b7b"><span class="section-number-2">12</span> How do I change metadata?</h2> - <div class="outline-text-2" id="text-12"> - <p> - See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a>! - </p> - </div> - </div> - - <div id="outline-container-org1bc6dab" class="outline-2"> - <h2 id="org1bc6dab"><span class="section-number-2">13</span> How do I change the work flows?</h2> - <div class="outline-text-2" id="text-13"> - <p> - Workflows are on <a href="https://github.com/arvados/bh20-seq-resource/tree/master/workflows">github</a> - and can be modified. See also the BLOG - <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a> on workflows. - </p> - </div> - </div> - - <div id="outline-container-org1140d62" class="outline-2"> - <h2 id="org1140d62"><span class="section-number-2">14</span> How do I change the source code?</h2> - <div class="outline-text-2" id="text-14"> - <p> - Go to our <a href="https://github.com/arvados/bh20-seq-resource">source code repositories</a>, - fork/clone the repository, change - something and submit a <a href="https://github.com/arvados/bh20-seq-resource/pulls">pull request</a> - (PR). That easy! Check out how - many PRs we already merged. - </p> - </div> - </div> - - <div id="outline-container-orge182714" class="outline-2"> - <h2 id="orge182714"><span class="section-number-2">15</span> Should I choose CC-BY or CC0?</h2> - <div class="outline-text-2" id="text-15"> - <p> - Restrictive data licenses are hampering data sharing and reproducible - research. CC0 is the preferred license because it gives researchers - the most freedom. Since we provide metadata there is no reason for - others not to honour your work. We also provide CC-BY as an option - because we know people like the attribution clause. - </p> - - <p> - In all honesty: we prefer both data and software to be free. - </p> - </div> - </div> - - <div id="outline-container-orgf4a692b" class="outline-2"> - <h2 id="orgf4a692b"><span class="section-number-2">16</span> How do I deal with private data and privacy?</h2> - <div class="outline-text-2" id="text-16"> - <p> - A public sequence resource is about public data. Metadata can refer to - private data. You can use your own (anonymous) identifiers. We also - plan to combine identifiers with clinical data stored securely at - <a href="https://redcap-covid19.elixir-luxembourg.org/redcap/">REDCap</a>. See the relevant <a - href="https://github.com/arvados/bh20-seq-resource/issues/21">tracker</a> for more information and - contributing. - </p> - </div> - </div> - - <div id="outline-container-org7757574" class="outline-2"> - <h2 id="org7757574"><span class="section-number-2">17</span> How do I communicate with you?</h2> - <div class="outline-text-2" id="text-17"> - <p> - We use a <a - href="https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link">gitter - channel</a> you can join. - </p> - </div> - </div> - - <div id="outline-container-org194006f" class="outline-2"> - <h2 id="org194006f"><span class="section-number-2">18</span> Who are the sponsors?</h2> - <div class="outline-text-2" id="text-18"> - <p> - The main sponsors are listed in the footer. In addition to the time - generously donated by many contributors we also acknowledge Amazon AWS - for donating COVID-19 related compute time. - </p> - </div> - </div> +<h1 class="title">About/FAQ</h1> +<div id="table-of-contents"> +<h2>Table of Contents</h2> +<div id="text-table-of-contents"> +<ul> +<li><a href="#orge0f47ff">1. What is the 'public sequence resource' about?</a></li> +<li><a href="#orgdf364dc">2. Presentations</a></li> +<li><a href="#org5fc8f04">3. Who created the public sequence resource?</a></li> +<li><a href="#org6f93b70">4. How does the public sequence resource compare to other data resources?</a></li> +<li><a href="#org8e3181a">5. Why should I upload my data here?</a></li> +<li><a href="#orgdf83b8b">6. Why should I not upload by data here?</a></li> +<li><a href="#org99d5e54">7. How does the public sequence resource work?</a></li> +<li><a href="#org8eac95c">8. Who uses the public sequence resource?</a></li> +<li><a href="#orgd5907cf">9. How can I contribute?</a></li> +<li><a href="#orgef93e3d">10. Is this about open data?</a></li> +<li><a href="#orgab39a73">11. Is this about free software?</a></li> +<li><a href="#orgad533ff">12. How do I upload raw data?</a></li> +<li><a href="#org4ca5ce9">13. How do I change metadata?</a></li> +<li><a href="#org2af2c45">14. How do I change the work flows?</a></li> +<li><a href="#org6a3ff30">15. How do I change the source code?</a></li> +<li><a href="#org3bdaa46">16. Should I choose CC-BY or CC0?</a></li> +<li><a href="#orge4cdab7">17. Are there also variant in the RDF databases?</a></li> +<li><a href="#org8a56c4c">18. How do I deal with private data and privacy?</a></li> +<li><a href="#orgf3ba61a">19. Do you have any checks or concerns if human sequence accidentally submitted to your service as part of a fastq? *</a></li> +<li><a href="#orgc693d03">20. Does PubSeq support only SARS-CoV-2 data?</a></li> +<li><a href="#org927057f">21. How do I communicate with you?</a></li> +<li><a href="#orgb05122d">22. Citing PubSeq</a></li> +<li><a href="#org16a19a4">23. Who are the sponsors?</a></li> +</ul> +</div> +</div> + +<div id="outline-container-orge0f47ff" class="outline-2"> +<h2 id="orge0f47ff"><span class="section-number-2">1</span> What is the 'public sequence resource' about?</h2> +<div class="outline-text-2" id="text-1"> +<p> +PubSeq, the <b>public sequence resource</b>, aims to provide a generic and +useful resource for COVID-19 research. The focus is on providing the +best possible sequence data with associated metadata that can be used +for sequence comparison and protein prediction. +</p> + +<p> +Just to avoid the notion that PubSeq is a biorepository: it is far +more than that. We are not competing with the likes of GenBank, +EBI/ENA and GISAID - in fact, PubSeq sources much of the data from +those and they get ours. +</p> + +<p> +There is no conflict of posting data to multiple repositories. +</p> + +<p> +It is better to view PubSeq as an <b>open precision medicine initiative</b> that +allows for early detection of new variants and strains; very valuable +for both testing and treatment. We have live analysis work flows that +run on uploading a new sequence. Contributing sequences helps the +overall detection. At this moment the output is limited. We will soon +add interactive discovery tools. Uploading data from a sequencer will +give researchers all information they want in 5 hours <b>without any +bioinformatics knowledge</b>. We may even provide workflows that take +data straight from the sequencer. In fact, you get very little out of +existing biorepositories, in our opinion, unless you have solid +bioinformatics support. And even then there is the question about +comparing data that was created using different technologies and +workflows. How do you deal with that? +</p> + +<p> +With PubSeq we are in a position to reanalyse that data from raw +material when new insights arise. It is likely that COVID19 will be +around for another year at least. After that we should prepare for +the next pandemic. PubSeq is meant for that. We take the long view and +it will only get more powerful. Who knows: maybe the live analysis +part of PubSeq will be an approach that other biorepositories will +follow. +</p> +</div> +</div> + +<div id="outline-container-orgdf364dc" class="outline-2"> +<h2 id="orgdf364dc"><span class="section-number-2">2</span> Presentations</h2> +<div class="outline-text-2" id="text-2"> +<p> +We presented at the BOSC 2020 Have a look at the <a href="https://bcc2020.sched.com/event/coLw">video</a> (<a href="https://drive.google.com/file/d/1skXHwVKM_gl73-_4giYIOQ1IlC5X5uBo/view?usp=sharing">alternative +link</a>) and the <a href="https://drive.google.com/file/d/1vyEgfvSqhM9yIwWZ6Iys-QxhxtVxPSdp/view?usp=sharing">poster</a>. +</p> +</div> +</div> + +<div id="outline-container-org5fc8f04" class="outline-2"> +<h2 id="org5fc8f04"><span class="section-number-2">3</span> Who created the public sequence resource?</h2> +<div class="outline-text-2" id="text-3"> +<p> +The <b>public sequence resource</b> is an initiative by <a href="https://github.com/arvados/bh20-seq-resource/graphs/contributors">bioinformatics</a> and +ontology experts who want to create something agile and useful for the +wider research community. The initiative started at the COVID-19 +biohackathon in April 2020 and is ongoing. The main project drivers +are Pjotr Prins (UTHSC), Peter Amstutz (Curii), Andrea Guarracino +(University of Rome Tor Vergata), Michael Crusoe (Common Workflow +Language), Thomas Liener (consultant, formerly EBI), Erik Garrison +(UCSC) and Jerven Bolleman (Swiss Institute of Bioinformatics). +</p> + +<p> +Notably, as this is a free software initiative, the project represents +major work by hundreds of software developers and ontology and data +wrangling experts. Thank you everyone! +</p> +</div> +</div> + +<div id="outline-container-org6f93b70" class="outline-2"> +<h2 id="org6f93b70"><span class="section-number-2">4</span> How does the public sequence resource compare to other data resources?</h2> +<div class="outline-text-2" id="text-4"> +<p> +The short version is that we use state-of-the-art practices in +bioinformatics using agile methods. Unlike the resources from large +institutes we can improve things on a dime and anyone can contribute +to building out this resource! Sequences from GenBank, EBI/ENA and +others are regularly added to PubSeq. We encourage people to everyone +to submit on PubSeq because of its superior live tooling and metadata +support (see the next question). +</p> + +<p> +Importantly: all data is published under either the <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons +4.0 attribution license</a> or the <a href="https://creativecommons.org/share-your-work/public-domain/cc0/">CC0 “No Rights Reserved” license</a> which +means it data can be published and workflows can run in public +environments allowing for improved access for research and +reproducible results. This contrasts with some other public resources, +such as GISAID. +</p> +</div> +</div> + +<div id="outline-container-org8e3181a" class="outline-2"> +<h2 id="org8e3181a"><span class="section-number-2">5</span> Why should I upload my data here?</h2> +<div class="outline-text-2" id="text-5"> +<ol class="org-ol"> +<li>We champion truly shareable data without licensing restrictions - with proper +attribution</li> +<li>We provide full metadata support using state-of-the-art ontology's</li> +<li>We provide a web-based sequence uploader and a command-line version +for bulk uploads</li> +<li>We provide a live SPARQL end-point for all metadata</li> +<li>We provide free data analysis and sequence comparison triggered on data upload</li> +<li>We do real work for you, with this <a href="https://workbench.lugli.arvadosapi.com/container_requests/lugli-xvhdp-bhhk4nxx1lch5od">link</a> you can see the last +run took 5.5 hours!</li> +<li>We provide free downloads of all computed output</li> +<li>There is no need to set up pipelines and/or compute clusters</li> +<li>All workflows get triggered on uploading a new sequence</li> +<li>When someone (you?) improves the software/workflows and everyone benefits</li> +<li>Your data gets automatically integrated with the Swiss Institure of +Bioinformatics COVID-19 knowledge base +<a href="https://covid-19-sparql.expasy.org/">https://covid-19-sparql.expasy.org/</a> (Elixir Switzerland)</li> +<li>Your data will be used to develop drug targets</li> +</ol> + +<p> +Finally, if you upload your data here we have workflows that output +formatted data suitable for <a href="http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part6">uploading to EBI resources</a> (and soon +others). Uploading your data here get your data ready for upload to +multiple resources. +</p> +</div> +</div> + +<div id="outline-container-orgdf83b8b" class="outline-2"> +<h2 id="orgdf83b8b"><span class="section-number-2">6</span> Why should I not upload by data here?</h2> +<div class="outline-text-2" id="text-6"> +<p> +Funny question. There are only good reasons to upload your data here +and make it available to the widest audience possible. +</p> + +<p> +In fact, you can upload your data here as well as to other +resources. It is your data after all. No one can prevent you from +uploading your data to multiple resources. +</p> + +<p> +We recommend uploading to EBI and NCBI resources using our data +conversion tools. It means you only enter data once and make the +process smooth. You can also use our command line data uploader +for bulk uploads! +</p> +</div> +</div> + +<div id="outline-container-org99d5e54" class="outline-2"> +<h2 id="org99d5e54"><span class="section-number-2">7</span> How does the public sequence resource work?</h2> +<div class="outline-text-2" id="text-7"> +<p> +On uploading a sequence with metadata it will automatically be +processed and incorporated into the public pangenome with metadata +using workflows from the High Performance Open Biology Lab defined +<a href="https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate">here</a>. +</p> +</div> +</div> + +<div id="outline-container-org8eac95c" class="outline-2"> +<h2 id="org8eac95c"><span class="section-number-2">8</span> Who uses the public sequence resource?</h2> +<div class="outline-text-2" id="text-8"> +<p> +The Swiss Institute of Bioinformatics has included this data in +<a href="https://covid-19-sparql.expasy.org/">https://covid-19-sparql.expasy.org/</a> and made it part of <a href="https://www.uniprot.org/">Uniprot</a>. +</p> + +<p> +The Pantograph <a href="https://graph-genome.github.io/">viewer</a> uses PubSeq data for their visualisations. +</p> + +<p> +<a href="https://uthsc.edu">UTHSC</a> (USA), <a href="https://www.esr.cri.nz/">ESR</a> (New Zealand) and <a href="https://www.ornl.gov/news/ornl-fight-against-covid-19">ORNL</a> (USA) use COVID-19 PubSeq data +for monitoring, protein prediction and drug development. +</p> +</div> +</div> + +<div id="outline-container-orgd5907cf" class="outline-2"> +<h2 id="orgd5907cf"><span class="section-number-2">9</span> How can I contribute?</h2> +<div class="outline-text-2" id="text-9"> +<p> +You can contribute by submitting sequences, updating metadata, submit +issues on our issue tracker, and more importantly add functionality. +See 'How do I change the source code' below. Read through our online +documentation at <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a> as a starting +point. +</p> +</div> +</div> + +<div id="outline-container-orgef93e3d" class="outline-2"> +<h2 id="orgef93e3d"><span class="section-number-2">10</span> Is this about open data?</h2> +<div class="outline-text-2" id="text-10"> +<p> +All data is published under a <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons 4.0 attribution license</a> +(CC-BY-4.0). You can download the raw and published (GFA/RDF/FASTA) +data and store it for further processing. +</p> +</div> +</div> + +<div id="outline-container-orgab39a73" class="outline-2"> +<h2 id="orgab39a73"><span class="section-number-2">11</span> Is this about free software?</h2> +<div class="outline-text-2" id="text-11"> +<p> +Absolutely. Free software allows for fully reproducible pipelines. You +can take our workflows and data and run it elsewhere! +</p> +</div> +</div> + +<div id="outline-container-orgad533ff" class="outline-2"> +<h2 id="orgad533ff"><span class="section-number-2">12</span> How do I upload raw data?</h2> +<div class="outline-text-2" id="text-12"> +<p> +We are preparing raw sequence data pipelines (fastq and BAM). The +reason is that we want the best data possible for downstream analysis +(including protein prediction and test development). The current +approach where people publish final sequences of SARS-CoV-2 is lacking +because it hides how this sequence was created. For reasons of +reproducible and improved results we want/need to work with the raw +sequence reads (both short reads and long reads) and take alternative +assembly variations into consideration. This is all work in progress. +</p> +</div> +</div> + +<div id="outline-container-org4ca5ce9" class="outline-2"> +<h2 id="org4ca5ce9"><span class="section-number-2">13</span> How do I change metadata?</h2> +<div class="outline-text-2" id="text-13"> +<p> +See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a>! +</p> +</div> +</div> + +<div id="outline-container-org2af2c45" class="outline-2"> +<h2 id="org2af2c45"><span class="section-number-2">14</span> How do I change the work flows?</h2> +<div class="outline-text-2" id="text-14"> +<p> +Workflows are on <a href="https://github.com/arvados/bh20-seq-resource/tree/master/workflows">github</a> and can be modified. See also the BLOG +<a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a> on workflows. +</p> +</div> +</div> + +<div id="outline-container-org6a3ff30" class="outline-2"> +<h2 id="org6a3ff30"><span class="section-number-2">15</span> How do I change the source code?</h2> +<div class="outline-text-2" id="text-15"> +<p> +Go to our <a href="https://github.com/arvados/bh20-seq-resource">source code repositories</a>, fork/clone the repository, change +something and submit a <a href="https://github.com/arvados/bh20-seq-resource/pulls">pull request</a> (PR). That easy! Check out how +many PRs we already merged. +</p> +</div> +</div> + +<div id="outline-container-org3bdaa46" class="outline-2"> +<h2 id="org3bdaa46"><span class="section-number-2">16</span> Should I choose CC-BY or CC0?</h2> +<div class="outline-text-2" id="text-16"> +<p> +Restrictive data licenses are hampering data sharing and reproducible +research. CC0 is the preferred license because it gives researchers +the most freedom. Since we provide metadata there is no reason for +others not to honour your work. We also provide CC-BY as an option +because we know people like the attribution clause. +</p> + +<p> +In all honesty: we prefer both data and software to be free. +</p> +</div> +</div> + +<div id="outline-container-orge4cdab7" class="outline-2"> +<h2 id="orge4cdab7"><span class="section-number-2">17</span> Are there also variant in the RDF databases?</h2> +<div class="outline-text-2" id="text-17"> +<p> +We do output a RDF file with the pangenome built in, and you can parse it because it has variants implicitly. +</p> + +<p> +We are also writing tools to generate VCF files directly from the pangenome. +</p> +</div> +</div> + +<div id="outline-container-org8a56c4c" class="outline-2"> +<h2 id="org8a56c4c"><span class="section-number-2">18</span> How do I deal with private data and privacy?</h2> +<div class="outline-text-2" id="text-18"> +<p> +A public sequence resource is about public data. Metadata can refer to +private data. You can use your own (anonymous) identifiers. We also +plan to combine identifiers with clinical data stored securely at +<a href="https://redcap-covid19.elixir-luxembourg.org/redcap/">REDCap</a>. See the relevant <a href="https://github.com/arvados/bh20-seq-resource/issues/21">tracker</a> for more information and contributing. +</p> +</div> +</div> + +<div id="outline-container-orgf3ba61a" class="outline-2"> +<h2 id="orgf3ba61a"><span class="section-number-2">19</span> Do you have any checks or concerns if human sequence accidentally submitted to your service as part of a fastq? *</h2> +<div class="outline-text-2" id="text-19"> +<p> +We are planning to remove reads that match the human reference. +</p> +</div> +</div> + +<div id="outline-container-orgc693d03" class="outline-2"> +<h2 id="orgc693d03"><span class="section-number-2">20</span> Does PubSeq support only SARS-CoV-2 data?</h2> +<div class="outline-text-2" id="text-20"> +<p> +To date, PubSeq is a resource specific to SARS-CoV-2, but we are designing it to be able to support other species in the future. +</p> +</div> +</div> + + +<div id="outline-container-org927057f" class="outline-2"> +<h2 id="org927057f"><span class="section-number-2">21</span> How do I communicate with you?</h2> +<div class="outline-text-2" id="text-21"> +<p> +We use a <a href="https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link">gitter channel</a> you can join. See also <a href="./contact">contact</a>. +</p> +</div> +</div> + +<div id="outline-container-orgb05122d" class="outline-2"> +<h2 id="orgb05122d"><span class="section-number-2">22</span> Citing PubSeq</h2> +<div class="outline-text-2" id="text-22"> +<p> +We have two publications in the works. Until we have a DOI please cite +PubSeq in the following way: +</p> + +<p> +We made use of the COVID-19 public sequence (PubSeq) resources hosted +at <a href="http://covid19.genenetwork.org/">http://covid19.genenetwork.org/</a>. +</p> +</div> +</div> + + +<div id="outline-container-org16a19a4" class="outline-2"> +<h2 id="org16a19a4"><span class="section-number-2">23</span> Who are the sponsors?</h2> +<div class="outline-text-2" id="text-23"> +<p> +The main sponsors are listed in the footer. In addition to the time +generously donated by many contributors we also acknowledge Amazon AWS +for donating COVID-19 related compute time. +</p> +</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 2020-07-18 Sat 03:27</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 2020-08-24 Mon 03:12</small>. </div> </body> </html> diff --git a/doc/web/about.org b/doc/web/about.org index 29a80bf..d8d7f73 100644 --- a/doc/web/about.org +++ b/doc/web/about.org @@ -3,6 +3,7 @@ * Table of Contents :TOC:noexport: - [[#what-is-the-public-sequence-resource-about][What is the 'public sequence resource' about?]] + - [[#presentations][Presentations]] - [[#who-created-the-public-sequence-resource][Who created the public sequence resource?]] - [[#how-does-the-public-sequence-resource-compare-to-other-data-resources][How does the public sequence resource compare to other data resources?]] - [[#why-should-i-upload-my-data-here][Why should I upload my data here?]] @@ -17,21 +18,54 @@ - [[#how-do-i-change-the-work-flows][How do I change the work flows?]] - [[#how-do-i-change-the-source-code][How do I change the source code?]] - [[#should-i-choose-cc-by-or-cc0][Should I choose CC-BY or CC0?]] - - [[#are-there-also-variant-in-the-RDF-databases]][Are there also variant in the RDF databases?] + - [[#are-there-also-variant-in-the-rdf-databases][Are there also variant in the RDF databases?]] - [[#how-do-i-deal-with-private-data-and-privacy][How do I deal with private data and privacy?]] - - [[#do-you-have-any-checks-or-concerns-if-human-sequence-accidentally-submitted-to-your-service-as-part-of-a-fastq][Do you have any checks or concerns if human sequence accidentally submitted to your service as part of a fastq?] - - [[#does-PubSeq-support-only-SARS-CoV-2=data]][Does PubSeq support only SARS-CoV-2 data?] + - [[#do-you-have-any-checks-or-concerns-if-human-sequence-accidentally-submitted-to-your-service-as-part-of-a-fastq-][Do you have any checks or concerns if human sequence accidentally submitted to your service as part of a fastq? *]] + - [[#does-pubseq-support-only-sars-cov-2-data][Does PubSeq support only SARS-CoV-2 data?]] - [[#how-do-i-communicate-with-you][How do I communicate with you?]] + - [[#citing-pubseq][Citing PubSeq]] - [[#who-are-the-sponsors][Who are the sponsors?]] * What is the 'public sequence resource' about? -The *public sequence resource* aims to provide a generic and useful -resource for COVID-19 research. The focus is on providing the best -possible sequence data with associated metadata that can be used for -sequence comparison and protein prediction. - -We were at the *Bioinformatics Community Conference 2020*! Have a look at the [[https://bcc2020.sched.com/event/coLw]][video talk] ([[https://drive.google.com/file/d/1skXHwVKM_gl73-_4giYIOQ1IlC5X5uBo/view?usp=sharing]][alternative link]) and the [[https://drive.google.com/file/d/1vyEgfvSqhM9yIwWZ6Iys-QxhxtVxPSdp/view?usp=sharing]][poster]. +PubSeq, the *public sequence resource*, aims to provide a generic and +useful resource for COVID-19 research. The focus is on providing the +best possible sequence data with associated metadata that can be used +for sequence comparison and protein prediction. + +Just to avoid the notion that PubSeq is a biorepository: it is far +more than that. We are not competing with the likes of GenBank, +EBI/ENA and GISAID - in fact, PubSeq sources much of the data from +those and they get ours. + +There is no conflict of posting data to multiple repositories. + +It is better to view PubSeq as an *open precision medicine initiative* that +allows for early detection of new variants and strains; very valuable +for both testing and treatment. We have live analysis work flows that +run on uploading a new sequence. Contributing sequences helps the +overall detection. At this moment the output is limited. We will soon +add interactive discovery tools. Uploading data from a sequencer will +give researchers all information they want in 5 hours *without any +bioinformatics knowledge*. We may even provide workflows that take +data straight from the sequencer. In fact, you get very little out of +existing biorepositories, in our opinion, unless you have solid +bioinformatics support. And even then there is the question about +comparing data that was created using different technologies and +workflows. How do you deal with that? + +With PubSeq we are in a position to reanalyse that data from raw +material when new insights arise. It is likely that COVID19 will be +around for another year at least. After that we should prepare for +the next pandemic. PubSeq is meant for that. We take the long view and +it will only get more powerful. Who knows: maybe the live analysis +part of PubSeq will be an approach that other biorepositories will +follow. + +* Presentations + +We presented at the BOSC 2020 Have a look at the [[https://bcc2020.sched.com/event/coLw][video]] ([[https://drive.google.com/file/d/1skXHwVKM_gl73-_4giYIOQ1IlC5X5uBo/view?usp=sharing][alternative +link]]) and the [[https://drive.google.com/file/d/1vyEgfvSqhM9yIwWZ6Iys-QxhxtVxPSdp/view?usp=sharing][poster]]. * Who created the public sequence resource? @@ -176,7 +210,7 @@ because we know people like the attribution clause. In all honesty: we prefer both data and software to be free. -* Are there also variant in the RDF databases? * +* Are there also variant in the RDF databases? We do output a RDF file with the pangenome built in, and you can parse it because it has variants implicitly. @@ -193,14 +227,23 @@ plan to combine identifiers with clinical data stored securely at We are planning to remove reads that match the human reference. -* Does PubSeq support only SARS-CoV-2 data? * +* Does PubSeq support only SARS-CoV-2 data? To date, PubSeq is a resource specific to SARS-CoV-2, but we are designing it to be able to support other species in the future. * How do I communicate with you? -We use a [[https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link][gitter channel]] you can join. +We use a [[https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link][gitter channel]] you can join. See also [[./contact][contact]]. + +* Citing PubSeq + +We have two publications in the works. Until we have a DOI please cite +PubSeq in the following way: + +We made use of the COVID-19 public sequence (PubSeq) resources hosted +at http://covid19.genenetwork.org/. + * Who are the sponsors? diff --git a/doc/web/contact.html b/doc/web/contact.html new file mode 100644 index 0000000..bdd838d --- /dev/null +++ b/doc/web/contact.html @@ -0,0 +1,336 @@ +<?xml version="1.0" encoding="utf-8"?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" +"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> +<head> +<!-- 2020-08-23 Sun 05:13 --> +<meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> +<meta name="viewport" content="width=device-width, initial-scale=1" /> +<title>CONTACT</title> +<meta name="generator" content="Org mode" /> +<meta name="author" content="Pjotr Prins" /> +<style type="text/css"> + <!--/*--><![CDATA[/*><!--*/ + .title { text-align: center; + margin-bottom: .2em; } + .subtitle { text-align: center; 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The code is distributed WITHOUT ANY WARRANTY; +without even the implied warranty of MERCHANTABILITY or FITNESS +FOR A PARTICULAR PURPOSE. See the GNU GPL for more details. + +As additional permission under GNU GPL version 3 section 7, you +may distribute non-source (e.g., minimized or compacted) forms of +that code without the copy of the GNU GPL normally required by +section 4, provided you include this license notice and a URL +through which recipients can access the Corresponding Source. + + +@licend The above is the entire license notice +for the JavaScript code in this tag. +*/ +<!--/*--><![CDATA[/*><!--*/ + function CodeHighlightOn(elem, id) + { + var target = document.getElementById(id); + if(null != target) { + elem.cacheClassElem = elem.className; + elem.cacheClassTarget = target.className; + target.className = "code-highlighted"; + elem.className = "code-highlighted"; + } + } + function CodeHighlightOff(elem, id) + { + var target = document.getElementById(id); + if(elem.cacheClassElem) + elem.className = elem.cacheClassElem; + if(elem.cacheClassTarget) + target.className = elem.cacheClassTarget; + } +/*]]>*///--> +</script> +</head> +<body> +<div id="content"> +<h1 class="title">CONTACT</h1> +<div id="table-of-contents"> +<h2>Table of Contents</h2> +<div id="text-table-of-contents"> +<ul> +<li><a href="#org56be096">1. CONTACT and SUPPORT</a> +<ul> +<li><a href="#orgad45632">1.1. Oxford Nanopore Analysis</a></li> +<li><a href="#org9249189">1.2. Data from other sequencers</a></li> +<li><a href="#orga2650ba">1.3. Professional support</a></li> +<li><a href="#orgaf18932">1.4. E-mail</a></li> +</ul> +</li> +</ul> +</div> +</div> + +<div id="outline-container-org56be096" class="outline-2"> +<h2 id="org56be096"><span class="section-number-2">1</span> CONTACT and SUPPORT</h2> +<div class="outline-text-2" id="text-1"> +<p> +COVID-19 PubSeq was created by a group of <a href="https://github.com/arvados/bh20-seq-resource/graphs/contributors">bioinformaticians</a> and +software developers working at leading institutes (see sponsors below) +with the goal of making online analysis available to everyone. You can +talk with us directly on a <a href="https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link">gitter channel</a>. We are open to improving +work flows and analysis. +</p> +</div> + +<div id="outline-container-orgad45632" class="outline-3"> +<h3 id="orgad45632"><span class="section-number-3">1.1</span> Oxford Nanopore Analysis</h3> +<div class="outline-text-3" id="text-1-1"> +<p> + <img class="img-right" src="static/image/oxford-nanopore.jpg" /> +</p> + +<p> +We run <a href="https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies">Oxford Nanopore</a> ourselves. It is an exaciting technology +because it gives us an accurate SARS-CoV-2 sequencer for a few +thousand dollars which can be run in a living room! With PubSeq we aim +to make it easy to analyse Nanopore material using our <b>free</b> Cloud +infrastructure. If you need help in using the online workflows don't +hesitate to contact us. +</p> + +<p> + </br></br></br> +</p> +</div> +</div> + +<div id="outline-container-org9249189" class="outline-3"> +<h3 id="org9249189"><span class="section-number-3">1.2</span> Data from other sequencers</h3> +<div class="outline-text-3" id="text-1-2"> +<p> +We accept FASTA sequences of SARS-CoV-2. Simply upload them using the +web form and/or REST API. No sign-up required! If you have large scale +short read data and require support we can discuss that. We also run +Illumina sequencing in several places. +</p> +</div> +</div> + +<div id="outline-container-orga2650ba" class="outline-3"> +<h3 id="orga2650ba"><span class="section-number-3">1.3</span> Professional support</h3> +<div class="outline-text-3" id="text-1-3"> +<p> +To use COVID-19 PubSeq solutions for professional purposes you can +contact Boston based <a href="mailto:info@curii.com">Curii</a>, the creators of <a href="https://arvados.org/">Arvados</a>, directly. +</p> + +<p> +COVID-19 is built on Arvados using CWL workflows. +</p> +</div> +</div> + +<div id="outline-container-orgaf18932" class="outline-3"> +<h3 id="orgaf18932"><span class="section-number-3">1.4</span> E-mail</h3> +<div class="outline-text-3" id="text-1-4"> +<p> +For questions feel free to write directly to <a href="mailto:pjotr.public821@thebird.nl">Pjotr Prins</a>. +</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 2020-08-23 Sun 05:13</small>. +</div> +</body> +</html> diff --git a/doc/web/contact.org b/doc/web/contact.org new file mode 100644 index 0000000..3e2c6b4 --- /dev/null +++ b/doc/web/contact.org @@ -0,0 +1,41 @@ +#+TITLE: CONTACT +#+AUTHOR: Pjotr Prins + +* CONTACT and SUPPORT + +COVID-19 PubSeq was created by a group of [[https://github.com/arvados/bh20-seq-resource/graphs/contributors][bioinformaticians]] and +software developers working at leading institutes (see sponsors below) +with the goal of making online analysis available to everyone. You can +talk with us directly on a [[https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link][gitter channel]]. We are open to improving +work flows and analysis. + +** Oxford Nanopore Analysis + +@@html: <img class="img-right" src="static/image/oxford-nanopore.jpg" />@@ + +We run [[https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies][Oxford Nanopore]] ourselves. It is an exaciting technology +because it gives us an accurate SARS-CoV-2 sequencer for a few +thousand dollars which can be run in a living room! With PubSeq we aim +to make it easy to analyse Nanopore material using our *free* Cloud +infrastructure. If you need help in using the online workflows don't +hesitate to contact us. + +@@html: </br></br></br>@@ + +** Data from other sequencers + +We accept FASTA sequences of SARS-CoV-2. Simply upload them using the +web form and/or REST API. No sign-up required! If you have large scale +short read data and require support we can discuss that. We also run +Illumina sequencing in several places. + +** Professional support + +To use COVID-19 PubSeq solutions for professional purposes you can +contact Boston based [[mailto:info@curii.com][Curii]], the creators of [[https://arvados.org/][Arvados]], directly. + +COVID-19 is built on Arvados using CWL workflows. + +** E-mail + +For questions feel free to write directly to [[mailto:pjotr.public821@thebird.nl][Pjotr Prins]]. diff --git a/doc/web/download.html b/doc/web/download.html index 1d196a0..998c87b 100644 --- a/doc/web/download.html +++ b/doc/web/download.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> -<!-- 2020-06-12 Fri 04:41 --> +<!-- 2020-08-24 Mon 03:08 --> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <title>Download</title> @@ -247,34 +247,35 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#orgcd3d82f">1. Workflow runs</a></li> -<li><a href="#org9aff936">2. FASTA files</a></li> -<li><a href="#orgc3e953c">3. Metadata</a></li> -<li><a href="#orgc9c55c4">4. Pangenome</a> +<li><a href="#orgc7d7db3">1. Workflow runs</a></li> +<li><a href="#org3b6bb40">2. FASTA files</a></li> +<li><a href="#orgef20a06">3. Metadata</a></li> +<li><a href="#orgaabb9da">4. Pangenome</a> <ul> -<li><a href="#org82c3ce9">4.1. Pangenome GFA format</a></li> -<li><a href="#orgf63e9f7">4.2. Pangenome in ODGI format</a></li> -<li><a href="#org8faf32f">4.3. Pangenome RDF format</a></li> -<li><a href="#org0c452f6">4.4. Pangenome Browser format</a></li> +<li><a href="#org1171db3">4.1. Pangenome GFA format</a></li> +<li><a href="#orgfc74439">4.2. Pangenome in ODGI format</a></li> +<li><a href="#orge6bb923">4.3. Pangenome RDF format</a></li> +<li><a href="#org5978f5c">4.4. Pangenome Browser format</a></li> </ul> </li> -<li><a href="#org4707094">5. Log of workflow output</a></li> -<li><a href="#orgd4d8f91">6. All files</a></li> -<li><a href="#org237b3cf">7. Planned</a> +<li><a href="#orgae23127">5. Log of workflow output</a></li> +<li><a href="#org88613e5">6. All files</a></li> +<li><a href="#org97e0327">7. Planned</a> <ul> -<li><a href="#org66e03ac">7.1. Raw sequence data</a></li> -<li><a href="#orgdfae1b9">7.2. Multiple Sequence Alignment (MSA)</a></li> -<li><a href="#orgaedc43e">7.3. Phylogenetic tree</a></li> -<li><a href="#org19a6a11">7.4. Protein prediction</a></li> +<li><a href="#org35758f9">7.1. Raw sequence data</a></li> +<li><a href="#orgab1c848">7.2. Multiple Sequence Alignment (MSA)</a></li> +<li><a href="#orgadb7ade">7.3. Phylogenetic tree</a></li> +<li><a href="#org3ec62c4">7.4. Protein prediction</a></li> </ul> </li> -<li><a href="#org49778b7">8. Source code</a></li> +<li><a href="#orga430457">8. Source code</a></li> +<li><a href="#org768f91e">9. Citing PubSeq</a></li> </ul> </div> </div> -<div id="outline-container-orgcd3d82f" class="outline-2"> -<h2 id="orgcd3d82f"><span class="section-number-2">1</span> Workflow runs</h2> +<div id="outline-container-orgc7d7db3" class="outline-2"> +<h2 id="orgc7d7db3"><span class="section-number-2">1</span> Workflow runs</h2> <div class="outline-text-2" id="text-1"> <p> The last runs can be viewed <a href="https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-y4k4uswcqi3ku56#Subprojects">here</a>. If you click on a run you can see @@ -285,8 +286,8 @@ is listed under <code>Data collections</code>. All current data is listed </div> </div> -<div id="outline-container-org9aff936" class="outline-2"> -<h2 id="org9aff936"><span class="section-number-2">2</span> FASTA files</h2> +<div id="outline-container-org3b6bb40" class="outline-2"> +<h2 id="org3b6bb40"><span class="section-number-2">2</span> FASTA files</h2> <div class="outline-text-2" id="text-2"> <p> The <b>public sequence resource</b> provides all uploaded sequences as @@ -296,8 +297,8 @@ also provide a single file <a href="https://collections.lugli.arvadosapi.com/c=l </div> </div> -<div id="outline-container-orgc3e953c" class="outline-2"> -<h2 id="orgc3e953c"><span class="section-number-2">3</span> Metadata</h2> +<div id="outline-container-orgef20a06" class="outline-2"> +<h2 id="orgef20a06"><span class="section-number-2">3</span> Metadata</h2> <div class="outline-text-2" id="text-3"> <p> Metadata can be downloaded as <a href="https://www.w3.org/TR/turtle/">Turtle RDF</a> as a <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/mergedmetadata.ttl">mergedmetadat.ttl</a> which @@ -319,8 +320,8 @@ graph can be downloaded from below Pangenome RDF format. </div> </div> -<div id="outline-container-orgc9c55c4" class="outline-2"> -<h2 id="orgc9c55c4"><span class="section-number-2">4</span> Pangenome</h2> +<div id="outline-container-orgaabb9da" class="outline-2"> +<h2 id="orgaabb9da"><span class="section-number-2">4</span> Pangenome</h2> <div class="outline-text-2" id="text-4"> <p> Pangenome data is made available in multiple guises. Variation graphs @@ -328,8 +329,8 @@ Pangenome data is made available in multiple guises. Variation graphs </p> </div> -<div id="outline-container-org82c3ce9" class="outline-3"> -<h3 id="org82c3ce9"><span class="section-number-3">4.1</span> Pangenome GFA format</h3> +<div id="outline-container-org1171db3" class="outline-3"> +<h3 id="org1171db3"><span class="section-number-3">4.1</span> Pangenome GFA format</h3> <div class="outline-text-3" id="text-4-1"> <p> <a href="https://github.com/GFA-spec/GFA-spec">GFA</a> is a standard for graphical fragment assembly and consumed @@ -338,8 +339,8 @@ by tools such as <a href="https://github.com/vgteam/vg">vgtools</a>. </div> </div> -<div id="outline-container-orgf63e9f7" class="outline-3"> -<h3 id="orgf63e9f7"><span class="section-number-3">4.2</span> Pangenome in ODGI format</h3> +<div id="outline-container-orgfc74439" class="outline-3"> +<h3 id="orgfc74439"><span class="section-number-3">4.2</span> Pangenome in ODGI format</h3> <div class="outline-text-3" id="text-4-2"> <p> <a href="https://github.com/vgteam/odgi">ODGI</a> is a format that supports an optimised dynamic genome/graph @@ -348,8 +349,8 @@ implementation. </div> </div> -<div id="outline-container-org8faf32f" class="outline-3"> -<h3 id="org8faf32f"><span class="section-number-3">4.3</span> Pangenome RDF format</h3> +<div id="outline-container-orge6bb923" class="outline-3"> +<h3 id="orge6bb923"><span class="section-number-3">4.3</span> Pangenome RDF format</h3> <div class="outline-text-3" id="text-4-3"> <p> An RDF file that includes the sequences themselves in a variation @@ -360,8 +361,8 @@ graph can be downloaded from </div> -<div id="outline-container-org0c452f6" class="outline-3"> -<h3 id="org0c452f6"><span class="section-number-3">4.4</span> Pangenome Browser format</h3> +<div id="outline-container-org5978f5c" class="outline-3"> +<h3 id="org5978f5c"><span class="section-number-3">4.4</span> Pangenome Browser format</h3> <div class="outline-text-3" id="text-4-4"> <p> The many JSON files that are named as @@ -372,8 +373,8 @@ Pangenome browser. </div> </div> -<div id="outline-container-org4707094" class="outline-2"> -<h2 id="org4707094"><span class="section-number-2">5</span> Log of workflow output</h2> +<div id="outline-container-orgae23127" class="outline-2"> +<h2 id="orgae23127"><span class="section-number-2">5</span> Log of workflow output</h2> <div class="outline-text-2" id="text-5"> <p> Including in below link is a log file of the last workflow runs. @@ -381,8 +382,8 @@ Including in below link is a log file of the last workflow runs. </div> </div> -<div id="outline-container-orgd4d8f91" class="outline-2"> -<h2 id="orgd4d8f91"><span class="section-number-2">6</span> All files</h2> +<div id="outline-container-org88613e5" class="outline-2"> +<h2 id="org88613e5"><span class="section-number-2">6</span> All files</h2> <div class="outline-text-2" id="text-6"> <p> <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/</a> @@ -390,16 +391,16 @@ Including in below link is a log file of the last workflow runs. </div> </div> -<div id="outline-container-org237b3cf" class="outline-2"> -<h2 id="org237b3cf"><span class="section-number-2">7</span> Planned</h2> +<div id="outline-container-org97e0327" class="outline-2"> +<h2 id="org97e0327"><span class="section-number-2">7</span> Planned</h2> <div class="outline-text-2" id="text-7"> <p> We are planning the add the following output (see also </p> </div> -<div id="outline-container-org66e03ac" class="outline-3"> -<h3 id="org66e03ac"><span class="section-number-3">7.1</span> Raw sequence data</h3> +<div id="outline-container-org35758f9" class="outline-3"> +<h3 id="org35758f9"><span class="section-number-3">7.1</span> Raw sequence data</h3> <div class="outline-text-3" id="text-7-1"> <p> See <a href="https://github.com/arvados/bh20-seq-resource/issues/16">fastq tracker</a> and <a href="https://github.com/arvados/bh20-seq-resource/issues/63">BAM tracker</a>. @@ -407,8 +408,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/16">fastq track </div> </div> -<div id="outline-container-orgdfae1b9" class="outline-3"> -<h3 id="orgdfae1b9"><span class="section-number-3">7.2</span> Multiple Sequence Alignment (MSA)</h3> +<div id="outline-container-orgab1c848" class="outline-3"> +<h3 id="orgab1c848"><span class="section-number-3">7.2</span> Multiple Sequence Alignment (MSA)</h3> <div class="outline-text-3" id="text-7-2"> <p> See <a href="https://github.com/arvados/bh20-seq-resource/issues/11">MSA tracker</a>. @@ -416,8 +417,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/11">MSA tracker </div> </div> -<div id="outline-container-orgaedc43e" class="outline-3"> -<h3 id="orgaedc43e"><span class="section-number-3">7.3</span> Phylogenetic tree</h3> +<div id="outline-container-orgadb7ade" class="outline-3"> +<h3 id="orgadb7ade"><span class="section-number-3">7.3</span> Phylogenetic tree</h3> <div class="outline-text-3" id="text-7-3"> <p> See <a href="https://github.com/arvados/bh20-seq-resource/issues/43">Phylo tracker</a>. @@ -425,8 +426,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/43">Phylo track </div> </div> -<div id="outline-container-org19a6a11" class="outline-3"> -<h3 id="org19a6a11"><span class="section-number-3">7.4</span> Protein prediction</h3> +<div id="outline-container-org3ec62c4" class="outline-3"> +<h3 id="org3ec62c4"><span class="section-number-3">7.4</span> Protein prediction</h3> <div class="outline-text-3" id="text-7-4"> <p> We aim to make protein predictions available. @@ -435,8 +436,8 @@ We aim to make protein predictions available. </div> </div> -<div id="outline-container-org49778b7" class="outline-2"> -<h2 id="org49778b7"><span class="section-number-2">8</span> Source code</h2> +<div id="outline-container-orga430457" class="outline-2"> +<h2 id="orga430457"><span class="section-number-2">8</span> Source code</h2> <div class="outline-text-2" id="text-8"> <p> All source code for this website and tooling is available @@ -445,9 +446,18 @@ from </p> </div> </div> + +<div id="outline-container-org768f91e" class="outline-2"> +<h2 id="org768f91e"><span class="section-number-2">9</span> Citing PubSeq</h2> +<div class="outline-text-2" id="text-9"> +<p> +See the <a href="./about">FAQ</a>. +</p> +</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 2020-06-12 Fri 04:41</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 2020-08-24 Mon 03:07</small>. </div> </body> </html> diff --git a/doc/web/download.org b/doc/web/download.org index 7614c60..a3f1949 100644 --- a/doc/web/download.org +++ b/doc/web/download.org @@ -18,6 +18,7 @@ - [[#phylogenetic-tree][Phylogenetic tree]] - [[#protein-prediction][Protein prediction]] - [[#source-code][Source code]] + - [[#citing-pubseq][Citing PubSeq]] * Workflow runs @@ -107,3 +108,7 @@ We aim to make protein predictions available. All source code for this website and tooling is available from https://github.com/arvados/bh20-seq-resource + +* Citing PubSeq + +See the [[./about][FAQ]]. |