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RDA COVID Group – some things to note

  • Creator
    Discussion
  • #105099

    Hilary Hanahoe
    Participant

    Dear RDA COVID-19 Working Group Members,
    Thank you for joining this group and contributing to a very important, urgent initiative. As an international, consensus-driven, community-based organisation, the Research Data Alliance has been asked to leverage on the global RDA data community to support the urgent CoronaVirus COVID-19 pandemic. As a response, RDA has set up this fast track Working Group.
    This group will work at an unprecedented speed, to deliver the first set of recommendations in 4 weeks time (15th April 2020) and is co-chaired by:
    Juan Bicarregui, Head of Data Division, UKRI-STFC & EOSC Executive Board
    Anne Cambon Thomsen, Emeritus Research Director CNRS & RDA Ambassador for Health Sciences & Research Ethics
    Sarah Jones, Associate Director, Digital Curation Centre (DCC) & EOSC Executive Board
    Mark Leggott, Executive Director, Research Data Canada & RDA Council Co-Chair
    Priyanka Pillai, Health Informatics Specialist, University of Melbourne
    Online collaborative working documents, bi-weekly meetings and frequent updates will be communicated to you via the group web page and this mailing list over the coming days (***@***.***-groups.org). You are automatically subscribed to the mailing list once you join the group.
    The RDA COVID-19 Data Sharing Working Group is OPEN TO ALL – Log in to RDA (or sign up if you are not a member – FREE) and then join the group at https://www.rd-alliance.org/groups/rda-covid19
    Please pass this message on to colleagues, staff who you believe could provide some time and expertise to generating these recommendations in record time.
    If you would like further information, please feel free to contact me or Bridget Walker RDA [bridget.walker[at]rda-foundation.org] directly.
    Thank you, as always, for your support for RDA and being part of a truly reactive, global community.
    Hilary
    _____________________________________
    Hilary Hanahoe
    Secretary General Research Data Alliance
    Tel: +39-345-4719284
    email: ***@***.***-foundation.org
    skype: hilary.hanahoe
    Twitter: @hilaryhanahoe
    Orcid ID: 0000-0002-0328-3419
    Web: http://www.rd-alliance.org
    RDA Foundation: https://www.rd-alliance.org/about-rda/rda-foundation
    _____________________________________
    RDA 15th VIRTUAL PLENARY Meeting 18 March – 10 April 2020 – see Virtual Programme updates
    RDA 16th Plenary Meeting, 10 – 12 November 2020, San Jose, Costa Rica – see updates
    RDA 17th Plenary Meeting, April 2021, Edinburgh, Scotland – see updates
    _____________________________________
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    Replies
  • #130113

    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

  • #130110

    Katie Hannan
    Member

    Hi, I’m here in Australia working at CSIRO supporting our researchers at the Australian Animal and Health Laboratory as they work on a vaccine for COVID-19. Keen to get involved where I can.

  • #130108

    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

  • #130107

    Gayo Diallo
    Member

    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
    http://www.gayodiallo.org
    Le mer. 25 mars 2020 à 20:38, Hofmann-Apitius via RDA-COVID19 <
    ***@***.***-groups.org> a écrit :

  • #130106

    Brian Corrie
    Member

    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 (http://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 (http://www.ireceptor.org) and iReceptor Plus (an EU H2020/Can project – http://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

     

  • #130104

    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 | ***@***.*** |
    @susheelvarma
    On Wed, 25 Mar 2020 at 20:09, gayo via RDA-COVID19 <
    ***@***.***-groups.org> wrote:

  • #130102

    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
    Sent: 25 March 2020 19:38
    To: RDA-COVID19
    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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  • #130101

    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!

    —————————

    Sarah M. Champion
    Data Architect
    Technical Support Unit for the National Climate Assessment
     
     
    Research Scholar
     
    (828) 271-4135
  • #130100

    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. 

  • #130098

    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

  • #130082

    Patrick Dunn
    Member

    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. 🙁

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