RDA COVID Group - some things to note

Hi, as I am probably a rather strange animal here, may I introduce myself: My name is Nikolaus Forgó, the specific expertise I can (try to) bring is law, in particular data protection and intellectual property. Very much looking forward to learning from you! Kind regards Nikolaus

Dear All,

I do have some experience to organize data and knowledge for an entire indication area; my team at Fraunhofer SCAI has - in collaboration with colleagues at Fraunhofer IME in Hamburg - started to create a MindMap that captures various aspects of SARS-CoV-2 biology, epidemiology and information about the drug-target space. Another team (lead by Alpha Tom Kodamullil) in my Department has started to work on a terminology for COVID concepts and terms. Ultimately, we will generate a knowledge-based model of SARS-CoV-2; the network models recently published help us to move fast in this area.

Furthermore, under the guidance of Juliane Fluck (Information Center Life Sciences, ZBMED, Cologne), we have started to generate a text mining machine for COVID. This text mining machine has a focus on the identification and extraction of chemical entities in relevant publications; the idea is that we want to systematically extract all potential repurposing candidate compounds from the literature (and there is a strong need for this, as everywhere in the world, supercomputer folks are running docking-MD like crazy and they need promising input structures).

Colleagues from Fraunhofer IME are currently looking into clinical studies in this area; as usual, they identified challenges with respect to variable names, spelling, lack of reference mappings .... the usual mess. If anybody here is already working on harmonizing the clinical study data available (including "related" studies like MERS and SARS CoV-1); I am happy to mediate contacts.

@Wei (Luxembourg): are you working on a text mining pipeline for COVID-19 ? Would be cool to align efforts ...

best wishes

Martin

Dear Martin,
If you are not aware of, you may be interested in a recent NLM LitCovid
initiative (Zhiyong Lu lab) which provides a Coronavirus related curated
literature from PubMed
https://www.ncbi.nlm.nih.gov/research/coronavirus/
Best regards,
Gayo
*Gayo DIALLO, HDR, PHD*
Associate Professor
Head of the ERIAS research group

,
Univ Bordeaux/ISPED, INSERM 1219 & LaBRI
www.gayodiallo.org
Le mer. 25 mars 2020 à 20:38, Hofmann-Apitius via RDA-COVID19 <
***@***.***-groups.org> a écrit :

Hello All,

Just wanted to say Hi and introduce myself. I and my colleagues are working in the world of the Adaptive Immune Response from an immuno-genetics perspective. We use modern sequencing technologies to deep sequence B and T cell immune repsonse. I am joining this group repersenting a couple of organizations.

Recently, the Adaptive Immune Receptor Repertoire Community (www.airr-community.org) put out a call for sharing of  AIRR-seq data in support of research fighting COVID-19 (https://www.antibodysociety.org/covid-19-demands-increased-public-sharing-of-biomedical-research-data/ and https://b-t.cr/t/any-covid-19-airr-seq-data/841/5). The AIRR Community is discussing establishing a community initiative to create a COVID-19 focussed public AIRR-seq data repository for sharing such data. I am the co-chair of the AIRR Community Common Repository Working Group, which is trying to establish an AIRR Data Commons for AIRR-seq data.

Through my work with the iReceptor (www.ireceptor.org) and iReceptor Plus (an EU H2020/Can project - www.ireceptorplus.org) projects, we are working with the AIRR Community to establish a publicly available COVID-19 focussed AIRR-seq repository. Our current problem - there isn't any public AIRR-seq data yet! Lots of research (https://www.zotero.org/groups/2468565/dkfz_-_fightcovid/items/KL8C45FD/library), but no public data as of yet.

Very keen to be involved in this initiative!

Brian

Dear All,
Glad to see this working group started under the RDA. I have been a
long-time member of the RDA as part of EMBL-EBI, ELIXIR and EOSC-Life and a
new member of the COVID-19 WG. Looking forward to collaborating with some
of you.
This email is just to introduce Health Data Research UK
, which is the national data science institute for
health data in the UK.
Understandably we are currently on a war footing and the national lead to
collect, assimilate and distribute relevant national health datasets for
the COVID19 challenge. We have set up a landing page for all our activities
here: https://www.hdruk.ac.uk/covid-19/ including a strategy doc here:
https://hdruk.box.com/s/01x3rf1yc1ps5kcpv3durglu3vhgquiv
We have started collecting any useful national and international resources
for COVID-19 research in an open Github repo:
https://github.com/hdruk/covid-19 and international COVID-19 Slack channel:
https://healthdataresearchuk.slack.com/archives/CV5B38SF3 (with over 357
members) and signup link here:
https://hdruk.us18.list-manage.com/subscribe?u=aebfef05d173a4888d1cde535....
We coordinate our efforts with the NHS in all four nations (NO, there is no
one NHS :), NHS Digital, NHSX, and UK Health Data Alliance Members -
https://ukhealthdata.org/members/ which is comprised of many large data
custodians in the UK.
We also had previously released our national health data registry via our
Innovation Gateway MVP - https://healthdatagateway.org which contain
general (no COVID-19 yet) health datasets available for researchers to
request access. The next phase of the Gateway will aim to streamline the
discovery and access process of requesting datasets for research, including
access to secure trusted research environments by Oct 2020 (probably
accelerated due to COVID-19)
Let me know how we could be involved in the RDA Working Group and how we
can help. We are extremely keen to make sure the resources we collect are
standardised and interoperable across worldwide health care efforts. Please
feel free to reach out to me, if you think we could collaborate and
harmonise work across the national clinical care pathways.
Best wishes
§ Susheel
--
*Dr Susheel Varma
| Director of Engineering |
Health Data Research UK *
Health Data Research UK, Gibbs Building, 215 Euston Road, London, NW1 2BE
+44 (0)7545 399 129 <00447545399129> | ***@***.*** |
@susheelvarma
On Wed, 25 Mar 2020 at 20:09, gayo via RDA-COVID19 <
***@***.***-groups.org> wrote:

Hi All,
With regards to text mining, and in case you missed it, Kaggle are currently running a research challenge (https://www.kaggle.com/allen-institute-for-ai/CORD-19-research-challenge) on the CORD-19 dataset (https://registry.opendata.aws/cord-19/)
All the best,
Sarah
- Show quoted text -From: ***@***.***-groups.org <***@***.***-groups.org>
Sent: 25 March 2020 19:38
To: RDA-COVID19 <***@***.***-groups.org>
Subject: Re: [rda-covid19] RDA COVID Group - some things to note
Dear All,
I do have some experience to organize data and knowledge for an entire indication area; my team at Fraunhofer SCAI has - in collaboration with colleagues at Fraunhofer IME in Hamburg - started to create a MindMap that captures various aspects of SARS-CoV-2 biology, epidemiology and information about the drug-target space. Another team (lead by Alpha Tom Kodamullil) in my Department has started to work on a terminology for COVID concepts and terms. Ultimately, we will generate a knowledge-based model of SARS-CoV-2; the network models recently published help us to move fast in this area.
Furthermore, under the guidance of Juliane Fluck (Information Center Life Sciences, ZBMED, Cologne), we have started to generate a text mining machine for COVID. This text mining machine has a focus on the identification and extraction of chemical entities in relevant publications; the idea is that we want to systematically extract all potential repurposing candidate compounds from the literature (and there is a strong need for this, as everywhere in the world, supercomputer folks are running docking-MD like crazy and they need promising input structures).
Colleagues from Fraunhofer IME are currently looking into clinical studies in this area; as usual, they identified challenges with respect to variable names, spelling, lack of reference mappings .... the usual mess. If anybody here is already working on harmonizing the clinical study data available (including "related" studies like MERS and SARS CoV-1); I am happy to mediate contacts.
@Wei (Luxembourg): are you working on a text mining pipeline for COVID-19 ? Would be cool to align efforts ...
best wishes
Martin
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Good Morning All!

I am excited to find a place to land professionally amidst all of the very important activity going on with COVID-19. I write to you from the U.S., as the Data Architect for the U.S. National Climate Assessment. I am responsible for ensuring Assessment data and information are transparent, accessible, and reproducible. I work hand in hand with legal counsel to ensure Intellectual Property Rights have been protected, data are open and accessible, and guidelines are drafted for our several hundred authors to follow and understand. We have produced a national government report relating a changing climate to human health, and continue to draw connections between the changing climate and social sciences as well. I work directly with authors and policymakers for access, understanding, and re-use of these important conclusions, and I hope to provide valuable contributions in this working group; I look forward to working together!

---------------------------

Hi all, nice to see the creation of such a group. I am currently working on a platform for sharing scientific data sustained by ontologies to describe the data and their scientific context. My scientific field is around Web services interoperability and the use of ontologies to ensure this interoperability. Looking forward to the discussions and see if I may be of any help.

Best wishes,

Thierry. 

Dear All,

nice to meet you! I am a researcher and legal consultant for CyberEthics Lab., an Italian SME active (inter alia) in EU Founded Projects. My field of expertise is EU data protection, and I am more than thrilled to help you and provide my assistance where it possible.

Best wishes,

Elena Sartini

Researcher & Legal Consultant

Via Antonio Salandra, 18 - 00187 Rome, Italy

+39 333 6107312

http://www.cyberethicslab.com

Dear all,

This is a interesting and exciting collection of folks interested in data sharing.  I'm a data curator and data deposition guide for ImmPort (https://immport.org), a NIH NIAID funded data repository to collect, standardize and FAIR share host immunology data sets for researchers funded by NIH and other funding sources.  I serve as a liasion between standards groups, shared data users, data providers, software developers and database administrators.  I look forward to the discussions and development of data sharing standards.

Health and sanity,

Patrick

P.S. I'm working on adding RDA emails to my NIH email white list (many seem to be going to spam list by default). I'm try to reply to any emails as soon as I can see them. :-(