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| author | Pjotr Prins | 2020-07-17 11:08:15 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2020-07-17 11:08:15 +0100 |
| commit | 16bb5df907c79cd0ce6bea0015821a2ce51fb992 (patch) | |
| tree | ddb9677cddcc463bb514300189cbd4300b9117ed /doc | |
| parent | 0be9983ef88fd3b925d8fa53e7f9ab2a28703bc0 (diff) | |
| parent | c69046ee9a5e24eadcd8cb885633328b0fd88011 (diff) | |
| download | bh20-seq-resource-16bb5df907c79cd0ce6bea0015821a2ce51fb992.tar.gz bh20-seq-resource-16bb5df907c79cd0ce6bea0015821a2ce51fb992.tar.lz bh20-seq-resource-16bb5df907c79cd0ce6bea0015821a2ce51fb992.zip | |
Merge branch 'master' into ebi-submit
Diffstat (limited to 'doc')
| -rw-r--r-- | doc/INSTALL.md | 6 | ||||
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part1.html | 192 | ||||
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part4.html | 44 | ||||
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part4.org | 6 | ||||
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part5.html | 194 | ||||
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part5.org | 49 | ||||
| -rw-r--r-- | doc/web/about.org | 3 |
7 files changed, 356 insertions, 138 deletions
diff --git a/doc/INSTALL.md b/doc/INSTALL.md index 6dcd72b..3b270dd 100644 --- a/doc/INSTALL.md +++ b/doc/INSTALL.md @@ -42,7 +42,7 @@ repository. ### Using the Web Uploader -To run the web uploader in a GNU Guix environment/container +To run the web uploader in a GNU Guix environment/container run it with something like ``` guix environment guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs --network openssl -- env FLASK_ENV=development PYTHONPATH=$PYTHONPATH:./bh20sequploader FLASK_APP=bh20simplewebuploader/main.py flask run @@ -59,7 +59,7 @@ WIP: add gunicorn container Currently the full webserver container deploy command looks like ``` -penguin2:~/iwrk/opensource/code/vg/bh20-seq-resource$ env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-bioinformatics/ ~/iwrk/opensource/guix/guix/pre-inst-env guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs python-pyshex python-pyyaml --network openssl python-pyshex python-pyshexc clustalw python-schema-salad python-arvados-python-client --share=/export/tmp -- env TMPDIR=/export/tmp FLASK_ENV=development FLASK_APP=bh20simplewebuploader/main.py flask run -`` +penguin2:~/iwrk/opensource/code/vg/bh20-seq-resource$ env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-oinformatics/ ~/iwrk/opensource/guix/guix/pre-inst-env guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs python-pyshex python-pyyaml --network openssl python-pyshex python-pyshexc clustalw python-schema-salad python-arvados-python-client --share=/export/tmp -- env TMPDIR=/export/tmp FLASK_ENV=development FLASK_APP=bh20simplewebuploader/main.py flask run +``` Note: see above on GUIX_PACKAGE_PATH. diff --git a/doc/blog/using-covid-19-pubseq-part1.html b/doc/blog/using-covid-19-pubseq-part1.html index 1959fac..0e6136c 100644 --- a/doc/blog/using-covid-19-pubseq-part1.html +++ b/doc/blog/using-covid-19-pubseq-part1.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <head> -<!-- 2020-05-29 Fri 12:06 --> +<!-- 2020-07-17 Fri 05:05 --> <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 1)</title> @@ -248,20 +248,20 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#org9afe6ab">1. What does this mean?</a></li> -<li><a href="#orgf4bc3d4">2. Fetch sequence data</a></li> -<li><a href="#org9d7d482">3. Predicates</a></li> -<li><a href="#orgc6046bb">4. Fetch submitter info and other metadata</a></li> -<li><a href="#orgdcb216b">5. Fetch all sequences from Washington state</a></li> -<li><a href="#org7060f51">6. Discussion</a></li> -<li><a href="#orgdc51ccc">7. Acknowledgements</a></li> +<li><a href="#org0db5db0">1. What does this mean?</a></li> +<li><a href="#orge5267fd">2. Fetch sequence data</a></li> +<li><a href="#orgfbd3adc">3. Predicates</a></li> +<li><a href="#org08e70e1">4. Fetch submitter info and other metadata</a></li> +<li><a href="#org9194557">5. Fetch all sequences from Washington state</a></li> +<li><a href="#org76317ad">6. Discussion</a></li> +<li><a href="#orgeb871a1">7. Acknowledgements</a></li> </ul> </div> </div> -<div id="outline-container-org9afe6ab" class="outline-2"> -<h2 id="org9afe6ab"><span class="section-number-2">1</span> What does this mean?</h2> +<div id="outline-container-org0db5db0" class="outline-2"> +<h2 id="org0db5db0"><span class="section-number-2">1</span> What does this mean?</h2> <div class="outline-text-2" id="text-1"> <p> This means that when someone uploads a SARS-CoV-2 sequence using one @@ -274,24 +274,24 @@ expressed in a <a href="https://github.com/arvados/bh20-seq-resource/blob/master type: record fields: host_species: - doc: Host species as defined in NCBITaxon, e.g. http://purl.obolibrary.org/obo/NCBITaxon_<span style="color: #8bc34a;">9606</span> for Homo sapiens + doc: Host species as defined in NCBITaxon, e.g. http://purl.obolibrary.org/obo/NCBITaxon_9606 for Homo sapiens type: string jsonldPredicate: - _id: http://www.ebi.ac.uk/efo/EFO_<span style="color: #8bc34a;">0000532</span> - _type: <span style="color: #9ccc65;">"@id"</span> - noLinkCheck: <span style="color: #8bc34a;">true</span> + _id: http://www.ebi.ac.uk/efo/EFO_0000532 + _type: "@id" + noLinkCheck: true host_sex: - doc: Sex of the host as defined in PATO, expect male <span style="color: #e91e63;">()</span> or female <span style="color: #e91e63;">()</span> + doc: Sex of the host as defined in PATO, expect male () or female () type: string? jsonldPredicate: - _id: http://purl.obolibrary.org/obo/PATO_<span style="color: #8bc34a;">0000047</span> - _type: <span style="color: #9ccc65;">"@id"</span> - noLinkCheck: <span style="color: #8bc34a;">true</span> + _id: http://purl.obolibrary.org/obo/PATO_0000047 + _type: "@id" + noLinkCheck: true host_age: - doc: Age of the host as number <span style="color: #e91e63;">(</span>e.g. <span style="color: #8bc34a;">50</span><span style="color: #e91e63;">)</span> + doc: Age of the host as number (e.g. 50) type: int? jsonldPredicate: - _id: http://purl.obolibrary.org/obo/PATO_<span style="color: #8bc34a;">0000011</span> + _id: http://purl.obolibrary.org/obo/PATO_0000011 </pre> </div> @@ -314,8 +314,8 @@ initiative! </div> -<div id="outline-container-orgf4bc3d4" class="outline-2"> -<h2 id="orgf4bc3d4"><span class="section-number-2">2</span> Fetch sequence data</h2> +<div id="outline-container-orge5267fd" class="outline-2"> +<h2 id="orge5267fd"><span class="section-number-2">2</span> Fetch sequence data</h2> <div class="outline-text-2" id="text-2"> <p> The latest run of the pipeline can be viewed <a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca">here</a>. Each of these @@ -339,8 +339,8 @@ these identifiers throughout. </div> </div> -<div id="outline-container-org9d7d482" class="outline-2"> -<h2 id="org9d7d482"><span class="section-number-2">3</span> Predicates</h2> +<div id="outline-container-orgfbd3adc" class="outline-2"> +<h2 id="orgfbd3adc"><span class="section-number-2">3</span> Predicates</h2> <div class="outline-text-2" id="text-3"> <p> To explore an RDF dataset, the first query we can do is open and gets @@ -350,10 +350,10 @@ the following in a SPARQL end point </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?p -<span style="color: #e91e63;">{</span> +<pre class="src src-sql">select distinct ?p +{ ?o ?p ?s -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -364,10 +364,10 @@ To get a <a href="http://sparql.genenetwork.org/sparql/?default-graph-uri=&q </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?g -<span style="color: #e91e63;">{</span> - GRAPH ?g <span style="color: #2196F3;">{</span>?s ?p ?o<span style="color: #2196F3;">}</span> -<span style="color: #e91e63;">}</span> +<pre class="src src-sql">select distinct ?g +{ + GRAPH ?g {?s ?p ?o} +} </pre> </div> @@ -383,10 +383,10 @@ To list all submitters, try </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?s -<span style="color: #e91e63;">{</span> - ?o <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">#MainSchema/submitter></a> ?s -<span style="color: #e91e63;">}</span> +<pre class="src src-sql">select distinct ?s +{ + ?o <http://biohackathon.org/bh20-seq-schema#MainSchema/submitter> ?s +} </pre> </div> @@ -397,11 +397,11 @@ and by </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?s -<span style="color: #e91e63;">{</span> - ?o <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/submitter">#MainSchema/submitter></a> ?id . +<pre class="src src-sql">select distinct ?s +{ + ?o <http://biohackathon.org/bh20-seq-schema#MainSchema/submitter> ?id . ?id ?p ?s -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -415,12 +415,12 @@ To lift the full URL out of the query you can use a header like </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/></a> -<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?dataset ?submitter -<span style="color: #e91e63;">{</span> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +select distinct ?dataset ?submitter +{ ?dataset pubseq:submitter ?id . ?id ?p ?submitter -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -438,32 +438,32 @@ Now we got this far, lets <a href="http://sparql.genenetwork.org/sparql/?default </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/></a> -<span style="color: #fff59d;">select</span> <span style="color: #e91e63;">(</span><span style="color: #ff8A65;">COUNT</span><span style="color: #2196F3;">(</span><span style="color: #fff59d;">distinct</span> ?dataset<span style="color: #2196F3;">)</span> <span style="color: #fff59d;">as</span> ?num<span style="color: #e91e63;">)</span> -<span style="color: #e91e63;">{</span> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +select (COUNT(distinct ?dataset) as ?num) +{ ?dataset pubseq:submitter ?id . ?id ?p ?submitter -<span style="color: #e91e63;">}</span> +} </pre> </div> </div> </div> -<div id="outline-container-orgc6046bb" class="outline-2"> -<h2 id="orgc6046bb"><span class="section-number-2">4</span> Fetch submitter info and other metadata</h2> +<div id="outline-container-org08e70e1" class="outline-2"> +<h2 id="org08e70e1"><span class="section-number-2">4</span> Fetch submitter info and other metadata</h2> <div class="outline-text-2" id="text-4"> <p> To get dataests with submitters we can do the above </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/></a> -<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?dataset ?p ?submitter -<span style="color: #e91e63;">{</span> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +select distinct ?dataset ?p ?submitter +{ ?dataset pubseq:submitter ?id . ?id ?p ?submitter -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -480,13 +480,13 @@ Let's focus on one sample with </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/></a> -<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?dataset ?submitter -<span style="color: #e91e63;">{</span> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +select distinct ?dataset ?submitter +{ ?dataset pubseq:submitter ?id . ?id ?p ?submitter . - FILTER<span style="color: #2196F3;">(</span><span style="color: #fff59d;">CONTAINS</span><span style="color: #EF6C00;">(</span>?submitter,"Roychoudhury"<span style="color: #EF6C00;">)</span><span style="color: #2196F3;">)</span> . -<span style="color: #e91e63;">}</span> + FILTER(CONTAINS(?submitter,"Roychoudhury")) . +} </pre> </div> @@ -496,12 +496,12 @@ see if we can get a sample ID by listing sample predicates </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/></a> -<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?p -<span style="color: #e91e63;">{</span> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +select distinct ?p +{ ?dataset ?p ?o . ?dataset pubseq:submitter ?id . -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -513,15 +513,15 @@ Let's zoom in on those of Roychoudhury with <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/">#MainSchema/></a> -<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?sid ?sample ?p1 ?dataset ?submitter -<span style="color: #e91e63;">{</span> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +select distinct ?sid ?sample ?p1 ?dataset ?submitter +{ ?dataset pubseq:submitter ?id . ?id ?p ?submitter . - FILTER<span style="color: #2196F3;">(</span><span style="color: #fff59d;">CONTAINS</span><span style="color: #EF6C00;">(</span>?submitter,"Roychoudhury"<span style="color: #EF6C00;">)</span><span style="color: #2196F3;">)</span> . + FILTER(CONTAINS(?submitter,"Roychoudhury")) . ?dataset pubseq:sample ?sid . ?sid ?p1 ?sample -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -532,18 +532,13 @@ this database. Let's focus on one sample "MT326090.1" with predicate </p> <div class="org-src-container"> -<pre class="src src-sql"><span style="color: #fff59d;">PREFIX</span> pubseq: <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/> -PREFIX sio: <http://semanticscience.org/resource/"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/> -PREFIX sio: <http://semanticscience.org/resource/">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/> -PREFIX sio: <http://semanticscience.org/resource/">#MainSchema/> -</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/> -PREFIX sio: <http://semanticscience.org/resource/">PREFIX</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/> -PREFIX sio: <http://semanticscience.org/resource/"> sio: <http://semanticscience.org/resource/></a> -<span style="color: #fff59d;">select</span> <span style="color: #fff59d;">distinct</span> ?sample ?p ?o -<span style="color: #e91e63;">{</span> +<pre class="src src-sql">PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/> +PREFIX sio: <http://semanticscience.org/resource/> +select distinct ?sample ?p ?o +{ ?sample sio:SIO_000115 "MT326090.1" . ?sample ?p ?o . -<span style="color: #e91e63;">}</span> +} </pre> </div> @@ -561,8 +556,8 @@ to view/query the database. </div> </div> -<div id="outline-container-orgdcb216b" class="outline-2"> -<h2 id="orgdcb216b"><span class="section-number-2">5</span> Fetch all sequences from Washington state</h2> +<div id="outline-container-org9194557" class="outline-2"> +<h2 id="org9194557"><span class="section-number-2">5</span> Fetch all sequences from Washington state</h2> <div class="outline-text-2" id="text-5"> <p> Now we know how to get at the origin we can do it the other way round @@ -570,15 +565,11 @@ and fetch all sequences referring to Washington state </p> <div class="org-src-container"> -<pre class="src src-sql"> -<span style="color: #fff59d;">select</span> ?seq ?sample -<span style="color: #e91e63;">{</span> - ?seq <a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample> ?sample . - ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223"><http://biohackathon.org/bh20-seq-</a><span style="color: #fff59d;"><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample> ?sample . - ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223">schema</a></span><a href="http://biohackathon.org/bh20-seq-schema#MainSchema/sample> ?sample . - ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223">#MainSchema/sample> ?sample . - ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223></a> -<span style="color: #e91e63;">}</span> +<pre class="src src-sql">select ?seq ?sample +{ + ?seq <http://biohackathon.org/bh20-seq-schema#MainSchema/sample> ?sample . + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q1223> +} </pre> </div> @@ -586,11 +577,26 @@ and fetch all sequences referring to Washington state which lists 300 sequences originating from Washington state! Which is almost half of the set coming out of GenBank. </p> + +<p> +Likewise to list all sequences from Turkey we can find the wikidata +entity is <a href="https://www.wikidata.org/wiki/Q43">Q43</a>: +</p> + +<div class="org-src-container"> +<pre class="src src-sql">select ?seq ?sample +{ + ?seq <http://biohackathon.org/bh20-seq-schema#MainSchema/sample> ?sample . + ?sample <http://purl.obolibrary.org/obo/GAZ_00000448> <http://www.wikidata.org/entity/Q43> +} +</pre> </div> </div> +</div> + -<div id="outline-container-org7060f51" class="outline-2"> -<h2 id="org7060f51"><span class="section-number-2">6</span> Discussion</h2> +<div id="outline-container-org76317ad" class="outline-2"> +<h2 id="org76317ad"><span class="section-number-2">6</span> Discussion</h2> <div class="outline-text-2" id="text-6"> <p> The public sequence uploader collects sequences, raw data and @@ -601,8 +607,8 @@ referenced in publications and origins are citeable. </div> </div> -<div id="outline-container-orgdc51ccc" class="outline-2"> -<h2 id="orgdc51ccc"><span class="section-number-2">7</span> Acknowledgements</h2> +<div id="outline-container-orgeb871a1" class="outline-2"> +<h2 id="orgeb871a1"><span class="section-number-2">7</span> Acknowledgements</h2> <div class="outline-text-2" id="text-7"> <p> The overall effort was due to magnificent freely donated input by a @@ -617,7 +623,7 @@ Garrison this initiative would not have existed! </div> </div> <div id="postamble" class="status"> -<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-05-29 Fri 12:06</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 2020-07-17 Fri 05:02</small>. </div> </body> </html> diff --git a/doc/blog/using-covid-19-pubseq-part4.html b/doc/blog/using-covid-19-pubseq-part4.html index b5a05ca..c975c21 100644 --- a/doc/blog/using-covid-19-pubseq-part4.html +++ b/doc/blog/using-covid-19-pubseq-part4.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> -<!-- 2020-07-12 Sun 06:24 --> +<!-- 2020-07-17 Fri 05:04 --> <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> @@ -161,6 +161,19 @@ .footdef { margin-bottom: 1em; } .figure { padding: 1em; } .figure p { text-align: center; } + .equation-container { + display: table; + text-align: center; + width: 100%; + } + .equation { + vertical-align: middle; + } + .equation-label { + display: table-cell; + text-align: right; + vertical-align: middle; + } .inlinetask { padding: 10px; border: 2px solid gray; @@ -186,7 +199,7 @@ @licstart The following is the entire license notice for the JavaScript code in this tag. -Copyright (C) 2012-2018 Free Software Foundation, Inc. +Copyright (C) 2012-2020 Free Software Foundation, Inc. The JavaScript code in this tag is free software: you can redistribute it and/or modify it under the terms of the GNU @@ -235,15 +248,16 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#org8f8b64a">1. What does this mean?</a></li> -<li><a href="#orgcc7a403">2. Modify Workflow</a></li> +<li><a href="#orgc2ee09f">1. What does this mean?</a></li> +<li><a href="#org0d37881">2. Where can I find the workflows?</a></li> +<li><a href="#orgddb0531">3. Modify Workflow</a></li> </ul> </div> </div> -<div id="outline-container-org8f8b64a" class="outline-2"> -<h2 id="org8f8b64a"><span class="section-number-2">1</span> What does this mean?</h2> +<div id="outline-container-orgc2ee09f" class="outline-2"> +<h2 id="orgc2ee09f"><span class="section-number-2">1</span> What does this mean?</h2> <div class="outline-text-2" id="text-1"> <p> This means that when someone uploads a SARS-CoV-2 sequence using one @@ -253,18 +267,28 @@ which triggers a rerun of our workflows. </div> </div> - -<div id="outline-container-orgcc7a403" class="outline-2"> -<h2 id="orgcc7a403"><span class="section-number-2">2</span> Modify Workflow</h2> +<div id="outline-container-org0d37881" class="outline-2"> +<h2 id="org0d37881"><span class="section-number-2">2</span> Where can I find the workflows?</h2> <div class="outline-text-2" id="text-2"> <p> +Workflows are written in the common workflow language (CWL) and listed +on <a href="https://github.com/arvados/bh20-seq-resource/tree/master/workflows">github</a>. PubSeq being an open project these workflows can be studied +and modified! +</p> +</div> +</div> + +<div id="outline-container-orgddb0531" class="outline-2"> +<h2 id="orgddb0531"><span class="section-number-2">3</span> Modify Workflow</h2> +<div class="outline-text-2" id="text-3"> +<p> <i>Work in progress!</i> </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 2020-07-12 Sun 06:24</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 2020-07-17 Fri 01:47</small>. </div> </body> </html> diff --git a/doc/blog/using-covid-19-pubseq-part4.org b/doc/blog/using-covid-19-pubseq-part4.org index 5fe71d1..8ad5e2d 100644 --- a/doc/blog/using-covid-19-pubseq-part4.org +++ b/doc/blog/using-covid-19-pubseq-part4.org @@ -10,6 +10,7 @@ * Table of Contents :TOC:noexport: - [[#what-does-this-mean][What does this mean?]] + - [[#where-can-i-find-the-workflows][Where can I find the workflows?]] - [[#modify-workflow][Modify Workflow]] * What does this mean? @@ -18,6 +19,11 @@ This means that when someone uploads a SARS-CoV-2 sequence using one of our tools (CLI or web-based) they add a sequence and some metadata which triggers a rerun of our workflows. +* Where can I find the workflows? + +Workflows are written in the common workflow language (CWL) and listed +on [[https://github.com/arvados/bh20-seq-resource/tree/master/workflows][github]]. PubSeq being an open project these workflows can be studied +and modified! * Modify Workflow diff --git a/doc/blog/using-covid-19-pubseq-part5.html b/doc/blog/using-covid-19-pubseq-part5.html index 80bf559..4caa5ac 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> -<!-- 2020-07-12 Sun 06:24 --> +<!-- 2020-07-17 Fri 05:03 --> <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> @@ -161,6 +161,19 @@ .footdef { margin-bottom: 1em; } .figure { padding: 1em; } .figure p { text-align: center; } + .equation-container { + display: table; + text-align: center; + width: 100%; + } + .equation { + vertical-align: middle; + } + .equation-label { + display: table-cell; + text-align: right; + vertical-align: middle; + } .inlinetask { padding: 10px; border: 2px solid gray; @@ -186,7 +199,7 @@ @licstart The following is the entire license notice for the JavaScript code in this tag. -Copyright (C) 2012-2018 Free Software Foundation, Inc. +Copyright (C) 2012-2020 Free Software Foundation, Inc. The JavaScript code in this tag is free software: you can redistribute it and/or modify it under the terms of the GNU @@ -235,38 +248,40 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#org871ad58">1. Modify Metadata</a></li> -<li><a href="#org07e8755">2. What is the schema?</a></li> -<li><a href="#org4857280">3. How is the website generated?</a></li> -<li><a href="#orge709ae2">4. Modifying the schema</a></li> +<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> </ul> </div> </div> -<div id="outline-container-org871ad58" class="outline-2"> -<h2 id="org871ad58"><span class="section-number-2">1</span> Modify Metadata</h2> +<div id="outline-container-org758b923" class="outline-2"> +<h2 id="org758b923"><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 -<a href="./download">DOWNLOAD</a> page. One of the most exciting features is the full support +<a href="http://covid19.genenetwork.org/download">download</a> page. One of the most exciting features is the full support 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="./blog?id=using-covid-19-pubseq-part1">here</a>. +data are listed <a href="http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part1">here</a>. </p> <p> In this BLOG we are going to look at the metadata entered on the -<a href="./">COVID-19 PubSeq</a> website (or command line client). It is important to +COVID-19 PubSeq website (or command line client). It is important to understand that anyone, including you, can change that information! </p> </div> </div> -<div id="outline-container-org07e8755" class="outline-2"> -<h2 id="org07e8755"><span class="section-number-2">2</span> What is the schema?</h2> +<div id="outline-container-orgec32c13" class="outline-2"> +<h2 id="orgec32c13"><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>. @@ -274,8 +289,8 @@ The default metadata schema is listed <a href="https://github.com/arvados/bh20-s </div> </div> -<div id="outline-container-org4857280" class="outline-2"> -<h2 id="org4857280"><span class="section-number-2">3</span> How is the website generated?</h2> +<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 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 @@ -285,13 +300,13 @@ All from that one metadata schema. </div> </div> -<div id="outline-container-orge709ae2" class="outline-2"> -<h2 id="orge709ae2"><span class="section-number-2">4</span> Modifying the schema</h2> +<div id="outline-container-orge4dfe84" class="outline-2"> +<h2 id="orge4dfe84"><span class="section-number-2">4</span> Modifying the schema</h2> <div class="outline-text-2" id="text-4"> <p> -One of the first things we wanted to do is to add a field for the data -license. Initially we only support CC-4.0 as a license by default, but -now we want to give uploaders the option to make it an even more +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 +we wanted to give uploaders the option to use an even more liberal CC0 license. The first step is to find a good ontology term for the field. Searching for `creative commons cc0 rdf' rendered this useful <a href="https://creativecommons.org/ns">page</a>. We also find an <a href="https://wiki.creativecommons.org/wiki/CC_License_Rdf_Overview">overview</a> where CC0 is represented as URI @@ -302,13 +317,148 @@ attributionName and attributionURL. </p> <p> -<i>Note: work in progress</i> +A minimal triple should be +</p> + +<pre class="example"> +id xhtml:license <http://creativecommons.org/licenses/by/4.0/> . +</pre> + + +<p> +Other suggestions are +</p> + +<pre class="example"> +id dc:title "Description" . +id cc:attributionName "Your Name" . +id cc:attributionURL <http://resource.org/id> +</pre> + + +<p> +and 'dc:source' which indicates the original source of any modified +work, specified as a URI. +The prefix 'cc:' is an abbreviation for <a href="http://creativecommons.org/ns">http://creativecommons.org/ns</a>#. +</p> + +<p> +Going back to the schema, where does it fit? Under host, sample, +virus, technology or submitter block? It could fit under sample, but +actually the license concerns the whole metadata block and sequence, +so I think we can fit under its own license tag. For example +</p> + + +<p> +id: placeholder +</p> + +<pre class="example"> +license: + license_type: http://creativecommons.org/licenses/by/4.0/ + attribution_title: "Sample ID" + attribution_name: "John doe, Joe Boe, Jonny Oe" + attribution_url: http://covid19.genenetwork.org/id + attribution_source: https://www.ncbi.nlm.nih.gov/pubmed/323088888 +</pre> + + +<p> +So, let's update the example. Notice the license info is optional - if it is missing +we just assume the default CC-4.0. +</p> + +<p> +One thing that is interesting is that in the name space <a href="https://creativecommons.org/ns">https://creativecommons.org/ns</a> there +is no mention of a title. I think it is useful, however, because we have no such field. +So, we'll add it simply as a title field. Now the draft schema is </p> + +<div class="org-src-container"> +<pre class="src src-js">- name: licenseSchema + type: record + fields: + license_type: + doc: License types as refined in https://wiki.creativecommons.org/images/d/d6/Ccrel-1.0.pdf + type: string? + jsonldPredicate: + _id: https://creativecommons.org/ns#License + title: + doc: Attribution title related to license + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_001167 + attribution_url: + doc: Attribution URL related to license + type: string? + jsonldPredicate: + _id: https://creativecommons.org/ns#Work + attribution_source: + doc: Attribution source URL + type: string? + jsonldPredicate: + _id: https://creativecommons.org/ns#Work +</pre> +</div> + +<p> +Now, we are no ontology experts, right? So, next we submit a patch to +our source tree and ask for feedback before wiring it up in the data +entry form. The pull request was submitted <a href="https://github.com/arvados/bh20-seq-resource/pull/97">here</a> and reviewed on the +gitter channel and I merged it. +</p> +</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"> +<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. +</p> + +<p> +With this <a href="https://github.com/arvados/bh20-seq-resource/commit/b9691c7deae30bd6422fb7b0681572b7b6f78ae3">patch</a> the website adds the license input fields on the form. +</p> + +<p> +Finally, to make RDF output work we need to add expressions to bh20seq-shex.rdf. This +was done with this <a href="https://github.com/arvados/bh20-seq-resource/commit/f4ed46dae20abe5147871495ede2d6ac2b0854bc">patch</a>. In the end we decided to use the Dublin core title, +<a href="http://purl.org/metadata/dublin_core_elements#Title">http://purl.org/metadata/dublin_core_elements#Title</a>: +</p> + +<div class="org-src-container"> +<pre class="src src-js">:licenseShape{ + cc:License xsd:string; + dc:Title xsd:string ?; + cc:attributionName xsd:string ?; + cc:attributionURL xsd:string ?; + cc:attributionSource xsd:string ?; +} +</pre> +</div> + +<p> +Note that cc:AttributionSource is not really defined in the cc standard. +</p> + +<p> +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. +</p> +</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> </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 2020-07-12 Sun 06:24</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 2020-07-16 Thu 03:27</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 4b0ea64..78eea66 100644 --- a/doc/blog/using-covid-19-pubseq-part5.org +++ b/doc/blog/using-covid-19-pubseq-part5.org @@ -13,19 +13,21 @@ - [[#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]] * Modify Metadata The public sequence resource uses multiple data formats listed on the -[[./download][DOWNLOAD]] page. One of the most exciting features is the full support +[[http://covid19.genenetwork.org/download][download]] page. One of the most exciting features is the full support 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 [[./blog?id=using-covid-19-pubseq-part1][here]]. +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 +COVID-19 PubSeq website (or command line client). It is important to understand that anyone, including you, can change that information! * What is the schema? @@ -41,8 +43,8 @@ All from that one metadata schema. * Modifying the schema One of the first things we want to do is to add a field for the data -license. Initially we only support CC-4.0 as a license by default, but -now we want to give uploaders the option to make it an even more +license. Initially we only supported CC-4.0 as a license, but +we wanted to give uploaders the option to use an even more liberal CC0 license. The first step is to find a good ontology term for the field. Searching for `creative commons cc0 rdf' rendered this useful [[https://creativecommons.org/ns][page]]. We also find an [[https://wiki.creativecommons.org/wiki/CC_License_Rdf_Overview][overview]] where CC0 is represented as URI @@ -113,8 +115,37 @@ So, we'll add it simply as a title field. Now the draft schema is _id: https://creativecommons.org/ns#Work #+END_SRC -Now, we are no ontology experts, right? So, next we submit a patch to our source tree and -ask for feedback before wiring it up in the data entry form. The pull request was -submitted here FIXME. +Now, we are no ontology experts, right? So, next we submit a patch to +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. -/Note: work in progress/ +* 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. + +With this [[https://github.com/arvados/bh20-seq-resource/commit/b9691c7deae30bd6422fb7b0681572b7b6f78ae3][patch]] the website adds the license input fields on the form. + +Finally, to make RDF output work we need to add expressions to bh20seq-shex.rdf. This +was done with this [[https://github.com/arvados/bh20-seq-resource/commit/f4ed46dae20abe5147871495ede2d6ac2b0854bc][patch]]. In the end we decided to use the Dublin core title, +http://purl.org/metadata/dublin_core_elements#Title: + +#+BEGIN_SRC js +:licenseShape{ + cc:License xsd:string; + dc:Title xsd:string ?; + cc:attributionName xsd:string ?; + cc:attributionURL xsd:string ?; + cc:attributionSource xsd:string ?; +} +#+END_SRC + +Note that cc:AttributionSource is not really defined in the cc standard. + +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 diff --git a/doc/web/about.org b/doc/web/about.org index ad13bc3..1949e2d 100644 --- a/doc/web/about.org +++ b/doc/web/about.org @@ -140,7 +140,8 @@ See the [[http://covid19.genenetwork.org/blog]]! * How do I change the work flows? -See the [[http://covid19.genenetwork.org/blog]]! +Workflows are on [[https://github.com/arvados/bh20-seq-resource/tree/master/workflows][github]] and can be modified. See also the +[[[[http://covid19.genenetwork.org/blog]]][workflow blog]]. * How do I change the source code? |