From 4167c87ece222f07b8a7cf4e56f71d8256ab5839 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sun, 12 Jul 2020 12:29:52 +0100 Subject: Generate About page --- doc/web/about.html | 143 +++++++++++++++++++++++++---------------------------- 1 file changed, 68 insertions(+), 75 deletions(-) diff --git a/doc/web/about.html b/doc/web/about.html index c907e6c..9b16c92 100644 --- a/doc/web/about.html +++ b/doc/web/about.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + About/FAQ @@ -161,19 +161,6 @@ .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; @@ -198,7 +185,7 @@ @licstart The following is the entire license notice for the JavaScript code in this tag. -Copyright (C) 2012-2020 Free Software Foundation, Inc. +Copyright (C) 2012-2018 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 @@ -247,29 +234,29 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 What is the 'public sequence resource' about?

+
+

1 What is the 'public sequence resource' about?

The public sequence resource aims to provide a generic and useful @@ -280,17 +267,18 @@ sequence comparison and protein prediction.

-
-

2 Who created the public sequence resource?

+
+

2 Who created the public sequence resource?

The public sequence resource is an initiative by bioinformatics 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), Michael Crusoe (Common -Workflow Language), Thomas Liener (consultant, formerly EBI) and -Jerven Bolleman (Swiss Institute of Bioinformatics). +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).

@@ -301,8 +289,8 @@ wrangling experts. Thank you everyone!

-
-

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

+
+

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

The short version is that we use state-of-the-art practices in @@ -312,17 +300,18 @@ to building out this resource!

-Importantly: all data is published under the Creative Commons 4.0 -attribution license 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, including GISAID. +Importantly: all data is published under either the Creative Commons +4.0 attribution license or the CC0 “No Rights Reserved” license 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, +including GISAID.

-
-

4 Why should I upload my data here?

+
+

4 Why should I upload my data here?

  1. We champion truly shareable data without licensing restrictions - with proper @@ -353,8 +342,8 @@ multiple resources.
-
-

5 Why should I not upload by data here?

+
+

5 Why should I not upload by data here?

Funny question. There are only good reasons to upload your data here @@ -376,8 +365,8 @@ for bulk uploads!

-
-

6 How does the public sequence resource work?

+
+

6 How does the public sequence resource work?

On uploading a sequence with metadata it will automatically be @@ -388,14 +377,18 @@ using workflows from the High Performance Open Biology Lab defined

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-

7 Who uses the public sequence resource?

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+

7 Who uses the public sequence resource?

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

+

+The Pantograph viewer uses PubSeq data for their visualisations. +

+

UTHSC and ORNL use COVID-19 PubSeq data for protein prediction and drug development. @@ -403,8 +396,8 @@ drug development.

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-

8 Is this about open data?

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+

8 Is this about open data?

All data is published under a Creative Commons 4.0 attribution license @@ -414,8 +407,8 @@ data and store it for further processing.

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-

9 Is this about free software?

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+

9 Is this about free software?

Absolutely. Free software allows for fully reproducible pipelines. You @@ -424,8 +417,8 @@ can take our workflows and data and run it elsewhere!

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-

10 How do I upload raw data?

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+

10 How do I upload raw data?

We are preparing raw sequence data pipelines (fastq and BAM). The @@ -440,8 +433,8 @@ assembly variations into consideration. This is all work in progress.

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-

11 How do I change metadata?

+
+

11 How do I change metadata?

See the http://covid19.genenetwork.org/blog! @@ -449,8 +442,8 @@ See the http://covid19.genenetwork

-
-

12 How do I change the work flows?

+ -
-

13 How do I change the source code?

+
+

13 How do I change the source code?

Go to our source code repositories, fork/clone the repository, change @@ -469,8 +462,8 @@ many PRs we already merged.

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-

14 Should I choose CC-BY or CC0?

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+

14 Should I choose CC-BY or CC0?

Restrictive data licenses are hampering data sharing and reproducible @@ -486,8 +479,8 @@ In all honesty: we prefer both data and software to be free.

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-

15 How do I deal with private data and privacy?

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+

15 How do I deal with private data and privacy?

A public sequence resource is about public data. Metadata can refer to @@ -498,8 +491,8 @@ plan to combine identifiers with clinical data stored securely at

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-

16 How do I communicate with you?

+
+

16 How do I communicate with you?

We use a gitter channel you can join. @@ -507,8 +500,8 @@ We use a -

17 Who are the sponsors?

+
+

17 Who are the sponsors?

The main sponsors are listed in the footer. In addition to the time @@ -519,7 +512,7 @@ for donating COVID-19 related compute time.

-
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-05-29 Fri 08:26. +
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-07-12 Sun 04:54.
-- cgit v1.2.3 From b5e38b960c380f0f7868d8fc4038ea3c3a0c52ee Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 13 Jul 2020 08:50:25 +0100 Subject: Add ontology and schema for license information. For review. --- bh20sequploader/bh20seq-options.yml | 4 ++ bh20sequploader/bh20seq-schema.yml | 25 ++++++++++++ doc/blog/using-covid-19-pubseq-part5.org | 68 +++++++++++++++++++++++++++++++- example/maximum_metadata_example.yaml | 10 ++++- 4 files changed, 104 insertions(+), 3 deletions(-) diff --git a/bh20sequploader/bh20seq-options.yml b/bh20sequploader/bh20seq-options.yml index c553f41..d1ea398 100644 --- a/bh20sequploader/bh20seq-options.yml +++ b/bh20sequploader/bh20seq-options.yml @@ -3,6 +3,10 @@ # being unique or at least using the same options in different containing # types. +license_type: + CC0 Public Domain Dedication: http://creativecommons.org/publicdomain/zero/1.0/ + CC-BY-4.0 Attribution 4.0 International: http://creativecommons.org/licenses/by/4.0/ + host_age_unit: Years: http://purl.obolibrary.org/obo/UO_0000036 Months: http://purl.obolibrary.org/obo/UO_0000035 diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index a8ab920..b3d4d12 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -1,5 +1,6 @@ $base: http://biohackathon.org/bh20-seq-schema $namespaces: + cc: http://creativecommons.org/ns# sch: https://schema.org/ efo: http://www.ebi.ac.uk/efo/ obo: http://purl.obolibrary.org/obo/ @@ -9,6 +10,30 @@ $namespaces: $graph: +- name: licenseSchema + type: record + fields: + license_type: + doc: License types as defined 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 data license + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_001167 + attribution_url: + doc: Attribution URL related to data license + type: string? + jsonldPredicate: + _id: https://creativecommons.org/ns#Work + attribution_source: + doc: Attribution source URL related to data license + type: string? + jsonldPredicate: + _id: https://creativecommons.org/ns#Work + - name: hostSchema type: record fields: diff --git a/doc/blog/using-covid-19-pubseq-part5.org b/doc/blog/using-covid-19-pubseq-part5.org index fe1908a..4b0ea64 100644 --- a/doc/blog/using-covid-19-pubseq-part5.org +++ b/doc/blog/using-covid-19-pubseq-part5.org @@ -40,7 +40,7 @@ All from that one metadata schema. * Modifying the schema -One of the first things we wanted to do is to add a field for the data +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 liberal CC0 license. The first step is to find a good ontology term @@ -51,4 +51,70 @@ attribution license https://creativecommons.org/licenses/by/4.0/. According to this [[https://wiki.creativecommons.org/images/d/d6/Ccrel-1.0.pdf][document]] we should really also add fields for attributionName and attributionURL. +A minimal triple should be + +: id xhtml:license . + +Other suggestions are + +: id dc:title "Description" . +: id cc:attributionName "Your Name" . +: id cc:attributionURL + +and 'dc:source' which indicates the original source of any modified +work, specified as a URI. +The prefix 'cc:' is an abbreviation for http://creativecommons.org/ns#. + +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 + + +id: placeholder + +: 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 + +So, let's update the example. Notice the license info is optional - if it is missing +we just assume the default CC-4.0. + +One thing that is interesting is that in the name space https://creativecommons.org/ns 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 + +#+BEGIN_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 +#+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. + /Note: work in progress/ diff --git a/example/maximum_metadata_example.yaml b/example/maximum_metadata_example.yaml index 432877c..54736f8 100644 --- a/example/maximum_metadata_example.yaml +++ b/example/maximum_metadata_example.yaml @@ -1,5 +1,11 @@ id: placeholder +license: + license_type: http://creativecommons.org/licenses/by/4.0/ + title: "Sample" + attribution_name: "John doe, Joe Boe, Jonny Oe" + attribution_url: http://covid19.genenetwork.org/id + host: host_id: XX1 host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606 @@ -13,9 +19,9 @@ host: additional_host_information: Optional free text field for additional information sample: - sample_id: Id of the sample as defined by the submitter + 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 + collecting_institution: Institute that was responsible of sampling specimen_source: [http://purl.obolibrary.org/obo/NCIT_C155831,http://purl.obolibrary.org/obo/NCIT_C155835] collection_date: "2020-01-01" collection_location: http://www.wikidata.org/entity/Q148 -- cgit v1.2.3