[GOAL] COVID-19 and access to knowledge

[Peter Murray-Rust]

We've launched a site https://github.com/petermr/openVirus to search the
whole open literature for content  which could help tackle the pandemic.
We're looking for volunteers (tech, biblio/library, documenters to help).

Background
=
It's now clear that knowledge is one of the key tools in tackling this
COVID-19 epidemic, and also that citizens across the world are desperate
for knowledge. To address this some organizations are releasing
restrictions on all IP as long as the epidemic lasts + 1 year.
https://opencovidpledge.org/

Immediate action is required to halt the COVID-19 Pandemic and treat
those it has affected. It is a practical and moral imperative that every
tool we have at our disposal be applied to develop and deploy technologies
on a massive scale without impediment.

We therefore pledge to make all intellectual property under our control
available to any group or individual for use in ending the COVID-19
pandemic and minimizing the impact of the disease, free of charge and
without encumbrances.

We will implement this pledge expeditiously in accordance with the rules
and regulations under which we operate.


The COVID-19 outbreak has drawn a minimal response from Scholarly
publishing, both commercial and academic (e.g. repositories). One
publisher, The Royal Society, has made ALL its publications freely
accessible without restriction. This is the minimum that makes any
difference.
The only other response I know of is CORD-19 dataset (
https://cset.georgetown.edu/covid-19-open-research-dataset-cord-19/)


CORD-19 contains 29,000 full-text articles with a wealth of information
about the novel coronavirus (SARS-CoV-2), the associated illness COVID-19,
and related viruses. The collection will be updated as new research is
published in peer-reviewed publications and archival services like bioRxiv
, medRxiv , and others.

At the request of the White House Office of Science and Technology Policy,
CSET leads this effort in partnership with the Allen Institute for AI, Chan
Zuckerberg Initiative, Microsoft Research and the National Library of
Medicine of the National Institutes of Health.

I have worked with this dataset and had helpful discussions with Allen AI.
But I believe this response is minimal and can be only used by a very small
proportion of the world. (I have no criticism of Allen AI, but  I have a
major criticism of the scholarly publishing industry).

This dataset (29 K) is a minute fraction of scholarly publication relevant
to epidemics, between 0.1-1% . Half of it is public anyway in Europe/PMC
and *rxiv so the amount contributed by publishers is even less. It assumes
that (a) the publishers know what people want (they don't) and (b) that the
only people who need to get help are datamining AI academics. The data set
is not readable by humans (the papers have been cast into JSON and the
metadata removed into a separate CSV file).

The terms "COVID", "SARS", "coronavirus" only reach a small amount of the
literature. I'm on a Cambridge Slack where my colleagues are discussing
many different aspects of tackling the epidemic. Here are some:
* aerosols
* communications
* early detection
* epidemic modelling
* law
* masks
* molecular modelling
* strategy
* surfaces
* ventilators

None of these will be in CORD-19.

It's clear that some strategies depend heavily on human behaviour and
political systems. We need papers on history, law, psychology, economics,
literature, maths, statistics, education, politics ...
... in fact everything

Every subject researched in University is relevant to this fight.
And the majority of citizens will be able to understand and use a large
amount of the scholarly literature. You don't need to know quantum
mechanics to read papers on how previous epidemics have been controlled.

Humans now must have a basic right to read any publicly funded research
without restriction. Charging them 35-50 USD to read a single paper for one
day is an insult. CEO's trumpeting what a great contribution CORD-19 is is
unbearably arrogant. People are losing their livelihoods and lives, yet
they are being charged exorbitant amounts to read about how to stay alive.

"food rationing" is a possible strategy in compliance.  I've searched
Elsevier and Taylor and Francis for this and of the top 20/25 hits there is
ZERO access to citizens, even for papers 50 years old. It's time we started
thinking about READERS, not authors.

It's also critical that we use machines to read the ALL literature as it is
published - perhaps 10K / day. And also theses. It's not a huge task, it's
just horribly messy because we don't have tradition of wanting the output
to be read or used. (If we had, the Ebola outbreak prediction would have
been made public many years ago).

The only modern way to use the fruits of public scholarship are:
* create all material openly
* with a semantic version
* review as necessary in public
* remove any access

[GOAL] COVID-19, open access and open research: good progress, and what is missing

[Heather Morrison]

Major publishers are making research and data directly related to COVID-19 
freely available. This is good news, and may reflect progress towards open 
access over the past two decades, because the arguments for free sharing of 
information in the context of pandemic are so compelling, as I touched on in 
this 
post.

A few examples, current best practices and gaps, will follow, but first, a few 
notes to explain why we need to move beyond open sharing of directly related 
resources to include all resources.

  *   Scientists working on COVID: while the greatest need is research and data 
directly on COVID per se, some pieces of the puzzle of solving any scientific 
problem can come from any branch of scientific inquiry. For example, basic 
research on how the respiratory system works, viruses and their transmission, 
may provide clues that will help COVID scientists. Some of this knowledge may 
be locked up in the print collections of libraries that are closed to limit 
spread of the virus.
  *   Practitioners dealing with the more severe cases are often dealing with 
patients who have other health issues. Clinical research on the other issues 
and relevant co-morbidity studies (e.g. when people with the other illness have 
other types of pneumonia) might save some lives.
  *   Educational institutions and governments that want to speed up training 
of health professionals to cope with the pandemic need the full range of 
knowledge relating to the health professions, in addition to COVID-specific 
resources. This includes all of the basic sciences (biology, chemistry, 
physics), much of the social sciences, as well as arts and humanities for a 
well-rounded education (e.g. foster creativity through arts, cultural 
understanding for clinical care through humanities).
  *   The pandemic per se raises a great many major secondary challenges, 
particularly the social challenges of helping entire populations cope with 
lock-down and the short and medium-term economic challenges. To address these 
challenges, we need all of our knowledge about communications, information, 
psychology, culture and history, along with classical and political economics. 
Part of the immediate solution to help people cope with lockdown is culture and 
arts. Like the COVID resources, many arts organizations and individual artists 
are making their works freely available. This is welcome and useful, but raises 
questions about economic support for artists and the arts so that this can 
continue; these are economic questions as well as challenges for the arts. We 
need open access to all of our knowledge to move forward with these secondary 
challenges. Right now is an excellent time to do this, because some of these 
secondary challenges are critical to dealing with the pandemic and limiting 
short and medium-term damage, and because so many researchers everywhere are 
working from home and would be able to benefit from this access.
  *   Libraries are an essential service and have been providing online 
services for many resources. In the short term, one way to contribute even 
further: It should be possible to have people work at scanning stations to 
digitize material not yet online while maintaining social distancing.

Examples of major publisher COVID-19 related initiatives for comparative 
purposes follow. Note that I use parent company names first as part of an 
ongoing effort to help people understand the nature of these organizations, 
whether publicly traded corporations or privately held businesses, often with 
multiple divisions of which scholarly publishing forms just one part.

RELX (Elsevier +): COVID responses across all company 
divisions, featured prominently on home page; Novel Coronavirus Center “;with 
the latest medical and scientific information on COVID-19. The center has been 
set up since the start of the outbreak and is in English and Mandarin. Elsevier 
has provided full access to this content for PubMed Central”; COVID-19 clinical 
toolkit; free institutional access to ClinicalKey student platform until the 
end of June; rapid publication (preprints and data) of COVID-19 related works; 
data visualization of the impact of the virus on the aviation industry; 
LexisNexis free, comprehensive COVID-19 related legal news coverage; turned 
exhibition space in Austria into a functional hospital.

SpringerNature:
 “As a leading research publisher, Springer Nature is committed to supporting 
the global response to emerging outbreaks by enabling fast and direct access to 
the latest available research, evidence, and data.”

informa (Taylor & Francis +): no mention of COVID on 
parent company home page; Taylor & Francis COVID-19 resource 
center: m

Re: [GOAL] COVID-19 and access to knowledge

[Stevan Harnad]

Bravo for this initiative, Peter! -- Stevan

> On Mar 30, 2020, at 12:45 PM, Peter Murray-Rust  wrote:
> 
> We've launched a site 
> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fpetermr%2FopenVirus&data=01%7C01%7C%7Cf53891ffaa584aaf561b08d7d4d5a1b0%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=gBSxe3jz6MphEALt%2BxbOeg2XEyOQlkhEcx0l%2BKfq%2FDE%3D&reserved=0
>  
> 
>  to search the whole open literature for content  which could help tackle the 
> pandemic. We're looking for volunteers (tech, biblio/library, documenters to 
> help).
> 
> Background
> =
> It's now clear that knowledge is one of the key tools in tackling this 
> COVID-19 epidemic, and also that citizens across the world are desperate for 
> knowledge. To address this some organizations are releasing restrictions on 
> all IP as long as the epidemic lasts + 1 year.
> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopencovidpledge.org%2F&data=01%7C01%7C%7Cf53891ffaa584aaf561b08d7d4d5a1b0%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=12RMSHkX8s%2FWzXnjp9VsYeZopJQXysaBqSSYtk7Kkic%3D&reserved=0
>  
> 
> 
> Immediate action is required to halt the COVID-19 Pandemic and treat 
> those it has affected. It is a practical and moral imperative that every 
> tool we have at our disposal be applied to develop and deploy 
> technologies on a massive scale without impediment.
> We therefore pledge to make all intellectual property under our control 
> available to any group or individual for use in ending the COVID-19 pandemic 
> and minimizing the impact of the disease, free of charge and without 
> encumbrances.
> 
> We will implement this pledge expeditiously in accordance with the rules and 
> regulations under which we operate.
> 
> 
> 
> The COVID-19 outbreak has drawn a minimal response from Scholarly publishing, 
> both commercial and academic (e.g. repositories). One publisher, The Royal 
> Society, has made ALL its publications freely accessible without restriction. 
> This is the minimum that makes any difference.
> The only other response I know of is CORD-19 dataset 
> (https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcset.georgetown.edu%2Fcovid-19-open-research-dataset-cord-19%2F&data=01%7C01%7C%7Cf53891ffaa584aaf561b08d7d4d5a1b0%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&sdata=yI%2F9%2BK%2BIVqMLlsPe5iJb1%2Fo0VEiJO%2FCWNIzKkzVp%2Fkw%3D&reserved=0
>  
> )
>  
> 
> CORD-19 contains 29,000 full-text articles with a wealth of information about 
> the novel coronavirus (SARS-CoV-2), the associated illness COVID-19, and 
> related viruses. The collection will be updated as new research is published 
> in peer-reviewed publications and archival services like bioRxiv 
> ,
>  medRxiv 
> ,
>  and others.
> 
> At the request of the White House Office of Science and Technology Policy, 
> CSET leads this effort in partnership with the Allen Institute for AI, Chan 
> Zuckerberg Initiative, Microsoft Research and the National Library of 
> Medicine of the National Institutes of Health. 
> 
> 
> I have worked with this dataset and had helpful discussions with Allen AI. 
> But I believe this response is minimal and can be only used by a very small 
> proportion of the world. (I have no criticism of Allen AI, but  I have a 
> major criticism of the scholarly publishing industry).
> 
> This dataset (29 K) is a minute fraction of scholarly publication relevant to 
> epidemics, between 0.1-1% . Half of it is public anyway in Europe/PMC and 
> *rxiv so the amount contributed by publishers is even less. It assumes that 
> (a) the publishers know what people want (they don't) and (b) that the only 
> people wh

Re: [GOAL] COVID-19 and access to knowledge

[Éric Archambault]

Peter,

Two months ago, that is, on January 27, we started work at Elsevier to make 
available as much as possible of the scholarly literature on coronavirus 
research easily discoverable and freely accessible.

At 1science, we created the Coronavirus Research Hub:

https://coronavirus.1science.com/search

This hub contains more than 36,000 bibliographic records from scholarly 
journals on coronavirus research which we are harvesting from all around the 
world. Like all papers in 1findr, they cover every fields of knowledge and all 
language. We’re working continuously to expand the collection yet we are 
concerned to keep it a tight collection to make the literature as relevant as 
possible.

Of these, a full 20,000 articles are freely downloadable. Everyone concerned at 
Elsevier from the top to the bottom, and the bottom to the top has work to make 
all Elsevier coronavirus-related literature freely available. Elsevier is not 
alone and many other publishers have unlocked their articles.

If we can help further, please let us know, we have been on it for two months 
and we continue to evaluate options to help the research community.

Yours sincerely

Éric

Eric Archambault
Vice-Président | ELSEVIER | Vice-President
Directeur général | 1science | General Manager
3863 St-Laurent, suite 206  | Montréal, QC, Canada  | H2W 1Y1
e.archamba...@elsevier.com
+1.438.356.4619
[cid:image001.png@01D60699.FE45D280]  
[cid:image002.png@01D60699.FE45D280] 


From: goal-boun...@eprints.org  On Behalf Of Peter 
Murray-Rust
Sent: March 30, 2020 12:45 PM
To: Global Open Access List (Successor of AmSci) 
Subject: [GOAL] COVID-19 and access to knowledge

We've launched a site https://github.com/petermr/openVirus to search the whole 
open literature for content  which could help tackle the pandemic. We're 
looking for volunteers (tech, biblio/library, documenters to help).

Background
=
It's now clear that knowledge is one of the key tools in tackling this COVID-19 
epidemic, and also that citizens across the world are desperate for knowledge. 
To address this some organizations are releasing restrictions on all IP as long 
as the epidemic lasts + 1 year.
https://opencovidpledge.org/

Immediate action is required to halt the COVID-19 Pandemic and treat those 
it has affected. It is a practical and moral imperative that every tool we 
have at our disposal be applied to develop and deploy technologies on a 
massive scale without impediment.

We therefore pledge to make all intellectual property under our control 
available to any group or individual for use in ending the COVID-19 pandemic 
and minimizing the impact of the disease, free of charge and without 
encumbrances.

We will implement this pledge expeditiously in accordance with the rules and 
regulations under which we operate.


The COVID-19 outbreak has drawn a minimal response from Scholarly publishing, 
both commercial and academic (e.g. repositories). One publisher, The Royal 
Society, has made ALL its publications freely accessible without restriction. 
This is the minimum that makes any difference.
The only other response I know of is CORD-19 dataset 
(https://cset.georgetown.edu/covid-19-open-research-dataset-cord-19/)



CORD-19 contains 29,000 full-text articles with a wealth of information about 
the novel coronavirus (SARS-CoV-2), the associated illness COVID-19, and 
related viruses. The collection will be updated as new research is published in 
peer-reviewed publications and archival services like 
bioRxiv, medRxiv, and 
others.

At the request of the White House Office of Science and Technology Policy, CSET 
leads this effort in partnership with the Allen Institute for AI, Chan 
Zuckerberg Initiative, Microsoft Research and the National Library of Medicine 
of the National Institutes of Health.

I have worked with this dataset and had helpful discussions with Allen AI. But 
I believe this response is minimal and can be only used by a very small 
proportion of the world. (I have no criticism of Allen AI, but  I have a major 
criticism of the scholarly publishing industry).

This dataset (29 K) is a minute fraction of scholarly publication relevant to 
epidemics, between 0.1-1% . Half of it is public anyway in Europe/PMC and *rxiv 
so the amount contributed by publishers is even less. It assumes that (a) the 
publishers know what people want (they don't) and (b) that the only people who 
need to get help are datamining AI academics. The data set is not readable by 
humans (the papers have been cast into JSON and the metadata removed into a 
separate CSV file).

The terms "COVID", "SARS", "coronavirus" only reach a small amount of the 
literature. I'm on a Cambridge Slack where my colleagues are discussing many 
different aspects of tackling the epidemic. 

Re: [GOAL] COVID-19 and access to knowledge

[Peter Murray-Rust]

On Mon, Mar 30, 2020 at 7:48 PM Éric Archambault <
eric.archamba...@science-metrix.com> wrote:

> Peter,
>
>
>
> Two months ago, that is, on January 27, we started work at Elsevier to
> make available as much as possible of the scholarly literature on
> coronavirus research easily discoverable and freely accessible.
>
>
>
> At 1science, we created the Coronavirus Research Hub:
>
> Why does Elsevier not simply open all its content and let the scientific ,
medical and citizen community decide what they want? Elsevier can't guess
what we want.

The Royal Society has done this. Elsevier can afford to do it.


>
>
If we can help further, please let us know, we have been on it for two
> months and we continue to evaluate options to help the research community.
>
>
My colleague, a software developer, working for free on openVirus
software,  is spending most of his time working making masks in Cambridge
Makespace to ship to Addenbrooke's hospital. When he goes to the literature
to find literature on masks, their efficacy and use and construction he
finds paywall after paywall after paywall after paywall  Some are
1-page notes behind a 36 USD Elsevier paywall.

Do not tell us what we want. let us choose freely.

Peter Murray-Rust

Volunteer fighting for free scientific knowledge in a world crisias.


-- 
"I always retain copyright in my papers, and nothing in any contract I sign
with any publisher will override that fact. You should do the same".

Peter Murray-Rust
Reader Emeritus in Molecular Informatics
Unilever Centre, Dept. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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