- AgBioData-LIST - Main Bioinformatics Lab

AgBiodata monthly webinar - TOMORROW, May 4th

by Annarita Marrano

Hi everybody, This email is a gentle reminder of *tomorrow's webinar* with Karon Yook and Daniela Raciti from microPublication Biology <https://www.micropublication.org/>. We will start at *12 PM CT* as usual (find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…>) using the zoom link that you can see below. We also want to invite you to *vote for two new members of the AgBioData steering committee.* The steering committee members are the driving force of the AgBioData consortium, and your opinion can help us shape our future direction. As a member of AgBioData, you should have received an email from Election Runners with the link to vote. *Please vote by May 15!* I hope you'll be able to join us tomorrow. Regards, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: Presenters: Dr. Karen Yook and Dr. Daniela Raciti, California Institute of Technology, Wormbase <https://wormbase.org/#012-34-5>. Host: Leonore Reiser Abstract: *Bridging the gap between data production and database curation through microPublications* To solve a long-standing problem in data loss and accessibility, we developed a publishing platform, microPublication Biology, to bridge data publishing and database curation. Our journal accepts single experiment articles (microPublications) and embeds curation within the article submission/publishing workflow. microPublication Biology is an online, peer-reviewed, open-access journal published by the Caltech Library and discoverable in PubMed. Starting with articles focused on nematode biology, we continually expand to more organism communities, including Arabidopsis and most recently Dictyostelium, Maize, and Cotton. Our system is set up so that upon publication, atomized data is delivered directly to authoritative databases for each community (e.g., WormBase, Flybase, PomBase, TAIR), ensuring timely delivery to biological databases for deep data integration. We will give an overview of our journal and its integrated curation workflow and present our latest publishing metrics. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> Topic: AgBioData Monthly Webinar Time: This is a recurring meeting Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 One tap mobile +19292056099,,82038356125#,,,,*160683# US (New York) +13017158592,,82038356125#,,,,*160683# US (Washington DC) Dial by your location +1 929 205 6099 US (New York) +1 301 715 8592 US (Washington DC) +1 312 626 6799 US (Chicago) +1 669 900 6833 US (San Jose) +1 253 215 8782 US (Tacoma) +1 346 248 7799 US (Houston) Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

2 years, 6 months

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AgBiodata monthly webinar May 4th

by Annarita Marrano

Hi everybody, After a break in April, we are back with our monthly webinar! Next Wed, *May 4th*, we will have *Karen Yook* and *Daniela Raciti* from Wormbase talking about how to bridge data generation and database curation through microPublications. Below you can find more details about the webinar and the zoom link to attend the webinar. We hope you will join us. Best, Annarita :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-: Presenters: Dr. Karen Yook and Dr. Daniela Raciti, California Institute of Technology, Wormbase <https://wormbase.org/#012-34-5>. Host: Leonore Reiser Abstract: *Bridging the gap between data production and database curation through microPublications* To solve a long-standing problem in data loss and accessibility, we developed a publishing platform, microPublication Biology, to bridge data publishing and database curation. Our journal accepts single experiment articles (microPublications) and embeds curation within the article submission/publishing workflow. microPublication Biology is an online, peer-reviewed, open-access journal published by the Caltech Library and discoverable in PubMed. Starting with articles focused on nematode biology, we continually expand to more organism communities, including Arabidopsis and most recently Dictyostelium, Maize, and Cotton. Our system is set up so that upon publication, atomized data is delivered directly to authoritative databases for each community (e.g., WormBase, Flybase, PomBase, TAIR), ensuring timely delivery to biological databases for deep data integration. We will give an overview of our journal and its integrated curation workflow and present our latest publishing metrics. *| 1P ET | 12P CT | 11A MT | 10A PT |* Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Monthly…> Topic: AgBioData Monthly Webinar Time: This is a recurring meeting Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 One tap mobile +19292056099,,82038356125#,,,,*160683# US (New York) +13017158592,,82038356125#,,,,*160683# US (Washington DC) Dial by your location +1 929 205 6099 US (New York) +1 301 715 8592 US (Washington DC) +1 312 626 6799 US (Chicago) +1 669 900 6833 US (San Jose) +1 253 215 8782 US (Tacoma) +1 346 248 7799 US (Houston) Meeting ID: 820 3835 6125 Passcode: 160683 Find your local number: https://us06web.zoom.us/u/kF3akiFg7

2 years, 7 months

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AgBioData 2022 Survey of Genomic, Genetic, and Breeding (GGB) Database Stakeholders

by Annarita Marrano

Dear AgBioData members, We are asking you to participate in a survey about standardized data curation principles and their implementation in data repositories for agricultural research and breeding programs. This survey was developed by the AgBioData consortium (https://www.agbiodata.org) in collaboration with Washington State University. Please disregard this email if you already received this survey and submitted your answers. The survey is anonymous, and your answers will be used to shape AgBioData's future goals and solutions for standardized data management in agriculture. If you are willing to participate, please submit your answers here <https://ncsu.qualtrics.com/jfe/form/SV_9Zv0sSXJhdz2bYO> by May 9th, 2022. Your opinion is valuable to us and can help AgBioData define better genomic, genetic, and breeding data curation practices. Best regards, Annarita Marrano On behalf of the AgBioData Steering Committee

2 years, 7 months

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Refresh AgBioData group of ontologies in AgroPortal

by Clement Jonquet

Dear AgBioData, A few years ago, after a review in the AgBioData community (at large, not only the ontology/metadata WG) we had produced a list of ontologies actively used by our databases. To my memory, except maybe CheBI we had them all in AgroPortal. So we created a « group » in AgroPortal for AgBioData. These ontologies can be visualized in AgroPortal here by filtering by group: http://agroportal.lirmm.fr/ontologies <http://agroportal.lirmm.fr/ontologies> We also setup a slice (i.e., a subset of the whole AgroPortal where all the UI and services are « restricted » to the AGBIODATA group): http://agbiodata.agroportal.lirmm.fr/ontologies <http://agbiodata.agroportal.lirmm.fr/ontologies> The meeting last week remind me that we should refresh/complete this list (looking at other ontologies available in AgroPortal or in other resources (BioPortal, OLS, ...). Also, at the same time I registered the « projects » using the ontologies… here : http://agroportal.lirmm.fr/projects <http://agroportal.lirmm.fr/projects> This page looks a bit « unattractive » (the UI will be refactored soon) but in fact this is the only place where the relation between a project and and ontology is formally (and machine actionably) represented e.g., http://data.agroportal.lirmm.fr/ontologies/PO/projects <http://data.agroportal.lirmm.fr/ontologies/PO/projects> (Add ?&apikey=528c4e4a-5c3e-4798-a2e2-11d96761b8ce at the end of the call in your Browser) This information allow us, for instance, to show « ontology in used » in the landscape page: So if you an take a minute to reply to this email with ONE sentence : I am XX, my database or project, YY, (still) uses ontologies/semantic resources ZZ, RR, TT, etc. I will then compile the data in AgroPortal. Bye Thanks Clement ------------------------------------------------------------------------------------------- Dr. Clement JONQUET – PhD in Informatics Senior Researcher – INRAE (MISTEA) Associate Researcher – University of Montpellier (LIRMM) Coordinator of the SIFR, AgroPortal and D2KAB projects clement.jonquet(a)inrae.fr or jonquet(a)lirmm.fr http://www.lirmm.fr/~jonquet @MISTEA (L,M,M,J): +33/0 4 99 61 22 77 @LIRMM (V): +33/0 4 67 14 97 43 -------------------------------------------------------------------------------------------

2 years, 8 months

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AG2PI Field Day: Integrating domain knowledge in genomic prediction models

by Scott, Nicole M [AGRON]

Dear AgBioData community members, The next AG2PI Field Day is on Wednesday, April 20 from 10:30 AM to 12:00 PM (Central Time, UTC-5). In this virtual field day, Drs. Christine Diepenbrock and Jack Dekkers will discuss how they integrate different types of models into their genomic prediction methods to improve predictions of crop or animal performance. Dr. Diepenbrock will describe a large maize breeding experiment she is conducting across several sites while Dr. Dekkers will share how he integrates models of physiological and biological processes to better predict pig growth. We invite you to register for this Zoom event at https://tinyurl.com/AG2PI-FD17, where you will also find additional information. Upon registration, you will receive a confirmation email with information about joining the meeting. If you are unable to attend the live session, then you will be able to find a recording at ag2pi.org/<https://www.ag2pi.org/>, at a later date. Please note: you do not need to register to view the recording; it is readily available on the AG2PI website soon after the close of the event (generally within 24 hours). Please share this message and attached flyer with colleagues at your institution. Kind regards, Nicole ------------------------ Nicole Scott, PhD Program Specialist Agricultural Genome to Phenome Initiative Iowa State University 1111 WOI Rd Ames, IA 50011 office: 1077 Roy J. Carver Co-Lab phone: 515-294-3945 ag2pi.org<https://www.ag2pi.org/> *** If you no longer wish to receive messages from AG2PI, then please visit https://www.ag2pi.org/join-ag2pi/unsubscribe/ to unsubscribe *** Please note, you cannot unsubscribe if you are receiving this message through a third party ***

2 years, 8 months

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FW: [CODATA-international] vocabulary update

by Daureen Nesdill

Hi, Looks like there has been some changes. CASRAI does not exist anymore. CODATA will be responsible for Research Data Management Glossary now called Research Data Management Terminology NISO will be responsible for Contributor Roles Taxonomy (CRediT) https://casrai.org will close down 20220623 Daureen Nesdill From: CODATA-international <codata-international-bounces(a)lists.codata.org> On Behalf Of Asha CODATA Sent: Wednesday, March 23, 2022 8:07 AM To: codata-international(a)lists.codata.org Subject: [CODATA-international] Stewarding ex-CASRAI Assets for the Future A joint statement from CODATA, euroCRIS and NISO [https://codata.org/wp-content/uploads/2022/03/codata-eurocris-niso.png]<mailto:nisohq@niso.org>CODATA<http://codata.org>, euroCRIS<https://eurocris.org/>, and NISO<https://www.niso.org/> are pleased to confirm arrangements for the future of selected key resources from the former CASRAI organisation. CASRAI as an organisation has ceased to exist. Before the organisation was closed down, CODATA, euroCRIS, and NISO were each approached to steward selected CASRAI resources of value to the research data, research information and information standards communities. We thank all the volunteers internationally who worked on CASRAI to make such important contributions to our fields, and are honoured to continue the stewardship and development of these valuable resources. CODATA is taking responsibility for the CASRAI Research Data Management Glossary, which will now be known as the Research Data Management Terminology. The Research Data Management Terminology is intended as a practical reference for individuals and groups concerned with the practice and improvement of research data management. The Terminology is being actively reviewed and improved through a voluntary Working Group of experts from the global RDM community and will remain freely available for community use. For more information, see https://codata.org/initiatives/data-science-and-stewardship/rdm-terminology…. euroCRIS is taking over the management and curation of the CASRAI Catalogue of Elements. The catalogue is the result of a joint effort of business owners that semantically described elements related to research and education, and placed them in a relational context. The original CASRAI Catalogue of Elements will be managed in a Github repository and the content will be used to enrich the CERIF format<https://eurocris.org/services/main-features-cerif>, the Common European Research Information Format used for exchanging research information in a semantically interoperable manner, stored in research information systems. For more information see: https://eurocris.org/casrai-domain-handover. NISO has taken over management of the CASRAI Contributor Roles Taxonomy (CRediT)<https://www.niso.org/publications/z39104-2022-credit> and has published the terminology as a formal ANSI/NISO standard. The work to formalise CRediT was launched in 2020, focusing first on the initial fourteen contributor roles in the existing CRediT taxonomy. Now that the formal approval process has been completed and the official standard has been published<https://www.niso.org/press-releases/contributor-roles-taxonomy-credit-forma…>, a NISO CRediT Standing Committee will be set up to provide a forum for discussion and community feedback, support further implementations and use cases for CRediT, and to consider how CRediT can be further developed and expanded to support contributions in a wider range of subject areas. The taxonomy remains freely available for community use. For more information, please visit: http://credit.niso.org/ The CASRAI website continues to be available at https://casrai.org/, but will finally close on 23 June 2022. We look forward to welcoming colleagues to use and contribute to the Research Data Management Terminology, the Catalogue of Elements and the CRediT taxonomy at their new locations. The three organisations have agreed to collaborate to ensure good communication and any necessary alignment at the points where the three resources connect. For more information, please contact the respective organisations for each resource. · CODATA: https://codata.org/, info(a)codata.org<mailto:info@codata.org> · EuroCris: https://eurocris.org/, eurocris(a)eurocris.org<mailto:eurocris@eurocris.org> · NISO: https://www.niso.org<https://www.niso.org/>/, nisohq(a)niso.org<mailto:nisohq@niso.org> Thanks, Asha -- ___________________________ GOSC DataIO Webinar on the emerging Core Interoperability Framework, 31 March 2022: REGISTER NOW<https://codata.org/registration-open-gosc-dataio-webinar-on-the-emerging-co…> Call for Presentations and Posters: SciDataCon/IDW 2022: deadline 25 April 2022<https://codata.org/call-for-presentations-and-posters-scidatacon-2022-part-…> International Data Week 2022: Registration Open!<https://codata.org/international-data-week-2022-registration-open/> February 2022 publications<https://codata.org/february-2022-publications-in-the-data-science-journal/> in the CODATA Data Science Journal<https://datascience.codata.org/> Stay in touch with CODATA: Stay up to date with CODATA activities: join the CODATA International News list<http://lists.codata.org/mailman/listinfo/codata-international_lists.codata.…> Looking for training and career opportunities in data science and data stewardship? Sign up to the CODATA early career community-run data science training and careers list<http://lists.codata.org/mailman/listinfo/data_science_training_lists.codata…> Follow us on social media! Twitter<https://twitter.com/CODATANews> - Facebook<https://www.facebook.com/codata.org/> - LinkedIn<https://www.linkedin.com/in/simon-hodson-b3711a11/> - Instagram<https://www.instagram.com/codatainternational/> ___________________________ Asha Law | Program Assistant, CODATA | http://www.codata.org<http://www.codata.org/> E-Mail: asha(a)codata.org<mailto:asha@codata.org> Tel (Office): +33 1 45 25 04 96 CODATA (Committee on Data of the International Council for Science), 5 rue Auguste Vacquerie, 75016 Paris, FRANCE

2 years, 8 months

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FW: [RDA Newsletter] Registration Open For Improving Global Agricultural Data Community Of Practice 2nd Annual Virtual Meeting From 22 March To 8 April 2022

by Daureen Nesdill

Is anyone attending? Daureen Nesdill From: no-reply(a)rd-alliance.org <no-reply(a)rd-alliance.org> Sent: Saturday, March 19, 2022 10:04 AM To: Daureen Nesdill <daureen.nesdill(a)utah.edu> Subject: [RDA Newsletter] Registration Open For Improving Global Agricultural Data Community Of Practice 2nd Annual Virtual Meeting From 22 March To 8 April 2022 Click here to view this message on the web.<https://www.rd-alliance.org/registration-open-improving-global-agricultural…> Saturday 19 March 2022 [RDA] [https://www.rd-alliance.org/sites/all/themes/rdalliance/img/facebook_icon.p…]<https://www.rd-alliance.org/track/click/d25b3a30385397/e35f397aec1242> [https://www.rd-alliance.org/sites/all/themes/rdalliance/img/twitter_icon.png]<https://www.rd-alliance.org/track/click/bbb839d7ad5398/e35f397aec1242> [https://www.rd-alliance.org/sites/all/themes/rdalliance/img/linkedin_icon.p…]<https://www.rd-alliance.org/track/click/6b378dd3e95399/e35f397aec1242> [https://www.rd-alliance.org/sites/all/themes/rdalliance/img/slideshare_icon…]<https://www.rd-alliance.org/track/click/5ea51acdf55400/e35f397aec1242> Registration Open For Improving Global Agricultural Data Community Of Practice 2nd Annual Virtual Meeting From 22 March To 8 April 2022 After the success of the first Research Data Alliance (RDA) Improving Global Agricultural Data annual meeting in 2020, the IGAD co-chairs are thrilled to host the second annual meeting between March 22 and April 8, 2022. In place of an annual meeting in 2021, the IGAD Coffee Break webinar series worked to transition the Interest Group on Agricultural Data, to the new Improving Global Agricultural Data Community of Practice (CoP), which will provide better alignment with global practice, ability to impact stakeholders via improved data systems and practices, and mutual learning from exchanging experiences. It will also increase opportunities to form partnerships on specific projects. There are individual registration links for each virtual session. Interested participants are encouraged to register for multiple days based on interests and needs. Formed in 2013, the Interest Group on Agricultural Data has grown in community strength to over 200 members, becoming one of the RDA’s most prominent Thematic Groups. IGAD is a domain-oriented group working on all issues related to global agriculture data. It represents stakeholders in managing data for agricultural research and innovation, including producing, aggregating and consuming data. Beyond this, IGAD promotes good practices in research with regard to data sharing policies, data management plans, and data interoperability, and it is a forum for sharing experience and providing visibility to research and work in agricultural data. One of IGAD’s main roles is to serve as a platform that leads to the creation of domain-specific Working Groups. Learn more<https://www.rd-alliance.org/track/click/bfa7943fb05401/e35f397aec1242>. DISCLAIMER This targeted communication is brought to you by RDA. As we respect your time and privacy, if you wish to be removed from our mailing list, please click on Unsubscribe from this newsletter<https://www.rd-alliance.org/newsletter/confirm/remove/37ce5bad081242t24>.

2 years, 8 months

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collaborations opportunities with the Midwest Big Data Innovation Hub and USDA NIFA

by Annarita Marrano

Hi AgBioData members, Please see below the collaborative activities offered by the MBDH and USDA NIFA. Best regards, Annarita The Midwest Big Data Innovation Hub is participating in the interagency Open Knowledge Network (OKN) Sprint workshop led by NSF. This is a series of collaborative activities between February and June 2022. MBDH is working with USDA NIFA program director Ann Stapleton and others on developing an OKN use case focused on food/ag/nutrition + climate resilience that would look across agencies' award portfolios and identify opportunities for future investments. Please contact John MacMullen (wjohn(a)illinois.edu) if you have interest in participating on this working group. More information: https://apply.hub.ki/okn/ <https://urldefense.com/v3/__https:/apply.hub.ki/okn/__;!!PvXuogZ4sRB2p-tU!R…> Jennifer Clarke on behalf of the MBDH Digital Agriculture Community

2 years, 8 months

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Call for nomination for new members of the AgBioData steering committee!

by Annarita Marrano

Dear AgBioData community, AgBioData is looking for candidates to serve as members of the AgBioData steering committee <https://www.agbiodata.org/steering-committee-members> (SC) for a term of 3 years. The SC is a vibrant, collaborative, and inclusive environment that offers plenty of opportunities to expand leadership skills, network with agricultural research community stakeholders, and help achieve a FAIR agricultural data ecosystem. *If you are interested or want to nominate someone else that you think will fit the position, please submit your application here <https://docs.google.com/forms/d/1e1o8SVA2zklg-_hZ_V_y2Yjlj0iKa9pKJOpB07qb19…>. * *Applications are due by April 1st.* You can find more details about the election process and the general duties of an SC member in the application form. Best regards, Annarita

2 years, 8 months

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AG2PI Field Day: National Institute of Food and Agriculture

by Scott, Nicole M [AGRON]

Dear AgBioData community members, The next AG2PI Field Day is on Wednesday, March 16 from 10:30 AM to 12:00 PM (Central Time, UTC-5). This event will feature the USDA NIFA national program leaders for the agricultural genome to phenome initiative, Frank Siewerdt and Christian Tobias. Dr. Siewerdt will describe some of the current funding opportunities in animal breeding offered by NIFA while Dr. Tobias will describe opportunities in plant breeding. Each will also discuss what makes for a good proposal and provide some "best practices" for submitting proposals in these spaces. We invite you to register for this Zoom event at https://tinyurl.com/AG2PI-FD16, where you will also find additional information. Upon registration, you will receive a confirmation email with information about joining the meeting. If you are unable to attend the live session, then you will be able to find a recording at ag2pi.org/<https://www.ag2pi.org/>, at a later date. Please note: you do not need to register to view the recording; it is readily available on the AG2PI website soon after the close of the event (generally within 24 hours). Please share this message and attached flyer with colleagues at your institution. Kind regards, Nicole ------------------------ Nicole Scott, PhD Program Specialist Agricultural Genome to Phenome Initiative Iowa State University 1111 WOI Rd Ames, IA 50011 office: 1077 Roy J. Carver Co-Lab phone: 515-294-3945 ag2pi.org<https://www.ag2pi.org/> *** If you no longer wish to receive messages from AG2PI, then please visit https://www.ag2pi.org/join-ag2pi/unsubscribe/ to unsubscribe *** Please note, you cannot unsubscribe if you are receiving this message through a third party ***

2 years, 8 months

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