fairdataihub/poster-sentry-training-data huggingface dataset:
WSY HERBARIUM- OUR DIGITAL FUTURE Mrs Mandeep Matharu1, Mrs Lydia Walles1, Mrs Sian Tyrrell1 1Royal Horticultural Society Gardens, Surrey, United Kingdom In 2011 with a capacity of 60,000 specimens, a herb scan and one staff member, the Royal Horticultural Society’s herbarium (now known as The 1851 Royal Commission Herbarium, and with the official abbreviation WSY) started its digitisation journey with the goal of creating a ‘Virtual Herbarium’. In the Winter of 2020-2021, amidst a pandemic, the team moved the collection to a state of the art facility based in our new building ‘RHS Hilltop – The Home of Gardening Science’. The new facility includes a space for 400,000 herbarium specimens in a temperature and humidity controlled environment and a digitisation suite with a high spec camera. All rooms within the herbarium suite have windows through which our visitors can glimpse into our fascinating collections and the herbarium’s curation and research work. With around 90,000 (and growing) digitised specimens, thanks in part to sponsorship by the Society’s members, the 1851 Royal Commission, the Mellon Foundation and the National Lottery Heritage Fund, the herbarium is ready to share the world’s largest ornamental plant collection with a wider audience through the Libnova Open Access online portal. The RHS has adopted the Libsafe digital preservation platform for the long-term preservation and public sharing of its digital herbarium and library collections. This new platform will safeguard the digitised herbarium specimens and their metadata in a cloud based solution whilst allowing the team to share specially curated collections and themed sets with the public alongside items from the RHS’s botanical art, photography and library collection
BioSharing works to map the landscape of community developed content standards, ensuring they are registered, informative and discoverable, monitoring their: development, evolution and integration; implementation and use in databases; and adoption by data policies by funders and journals. Progressively, BioSharing will monitor the maturity of content standards, collecting metrics of usage, and the level of endorsement. BioSharing is also being further developed as content- provider for standards-driven metadata templates for data collection and curation. BioSharing works to serve those seeking information on existing standards and databases, and to identify areas where duplications or gaps in coverage exist, promoting harmonization to avoid wasteful reinvention. Team Funded By Philippe Rocca-Serra Eamonn Maguire Alejandra Gonzalez-Beltran Milo Thurston Susanna-Assunta Sansone STANDARDS & DATABASE DEVELOPERS & MAINTAINERS FUNDERS, JOURNAL EDITORS & LIBRARIANS RESEARCHERS, TOOL DEVELOPERS & CURATORS e.g. seek guidance to find data- bases that implement standards to deposit their data; or identify appropriate data standards to be implemented in an annotation tool e.g. gather enough infor- mation to make informed decisions on which content stand- ards should be funded, implemented or recom- mended in their policies A catalogue of data preservation, management and sharing policies from international funding agencies and regulators. Call for collaborators If you have catalogues you would like us to link to, contact us. A catalogue of reporting standards and organizations that develop these. Partly compiled by linking to A catalogue of databases, described according to the BioDBcore guidelines, along with the standards used within them. Partly compiled with the support of NAR Database Issue and DATABASE journals User profiles Faceted search Database Details Standard Details a web-based curated and searchable registry of content standards, databases and policies in the life sciences e.g. need a central place to register their work, claiming ownership and getting credit; make standards visible and re-usable Advisory Board and RDA working group members Jessica Tenenbaum (Duke University, USA), Co-Chair of the Advisory Board Melissa Haendel (OHSU, USA; Force 11; Monarch Initiative), Co-Chair of the Advisory Board Susanna-Assunta Sansone (University of Oxford, UK; NPG Scientiﬁc Data), Co-Chair of the RDA WG Simon Hodson (CODATA), Co-Chair of the RDA WG Rebecca Lawrence (F1000), Co-Chair of the RDA WG Michael Ball (BBSRC) Theo Bloom (BMJ) Jennifer Boyd (OUP) Scott Edmunds (GigaScience, BGI) Rafael Jimenez (ELIXIR) Amye Kenall (BMC) Varsha Khodiyar (NPG) Thomas Lemberger (EMBO Press) Jennifer Lin (PLoS) Jonathan Tedds (Ubiquity Press Open Health Data Journal, University of Leicester, UK) Todd Vision (UNC Chapel Hill & NESCent, USA) Michael Witt (re3data, Purdue University Libraries) Communities (see more on the website)
Nitrogen fractionation across the Galaxy Observations of the 14N/15N ratio in a large sample of high-mass star-forming cores L. Colzi1,2, F. Fontani2, V. M. Rivilla2, A. Sánchez-Monge3, L. Testi2,4, M. T. Beltrán2, P. Caselli5 1 Università degli studi di Firenze, Dipartimento di Fisica e Astronomia, Via Sansone, 1 - 50019 Sesto Fiorentino (Italy); 2 INAF-Osservatorio Astrofisico di Arcetri, L.go E. Fermi 5, I-50125 Firenze (Italy); 3 I. Physikalisches Institut of the Universität zu Köln, D-50937 – Cologne (Germany); 4 European ALMA Programme Scientist - ESO, Karl Schwarzschild str. 2, D-85748 Garching (Germany); 5 Max-Planck-Institute for Extraterrestrial Physics, Giessenbachstrasse 1, D-85748 Garching (Germany) Introduction 15N is the less abundant stable isotope of nitrogen and is enriched in comets and carbonaceous chondrites with respect to the value measured in the Protosolar Nebula (PSN) (Marty et al., 2010), but we still do not understand if this enrichment is a heritage of the past chemical history. Because our Sun was born in a rich cluster, possibly including massive stars (e.g. Adams 2010), observations of massive, dense star forming cores in different evolutionary stages, and in a statistically significant sample, are needed. Sample and observations - LINES: HN13C, H13CN, HC15N, H15NC (J=1-0) with the IRAM- 30m Telescope; - SOURCES: 87 high-mass star forming cores: 27 of these sources belong to the three main evolutionary categories of the high-mass star formation process (Colzi et al., 2017). This sample has been recently increased with 60 massive dense cores and do not have an evolutionary classification yet (Colzi et al., in prep). 1) 15N-Fractionation - 14N/15N 180-555 from HNC - 14N/15N 115-810 from HCN - Asymmetric distributions peaked around values <440 2) Galactocentric gradient With linear fit: HCN/HC15N = 21±9 kpc−1 × DGC + 250±67 HNC/H15NC = 20±6 kpc−1 × DGC + 221± 42 Consistent with that found by Adande & Ziurys (2012). 3) Comparison with models Non-Parametric fit can not reproduce the flattening trend of the Galactic Chemical Evolution model made by Romano et al. (2017) for DGC > 8 kpc. NEEDED MORE OBSERVATIONS IN THE OUTER GALAXY… BASED ON A LARGE STATISTICS!! References: Adams 2010, ARA&A, 48, 74 Adande & Ziurys 2012, ApJ, 744,194 Colzi et al., 2017, arXiv:1709.04237 Marty et al.: Geochimica et Cosmochimica Acta74, 340-355, 2010 Romano et al. 2017, MNRAS, 470, 401
Distributed Text Services (DTS) A Community-driven Text Interoperability API Linked Pasts 6, University of London and British Library, December 2-16, 2020 DTS Community 46 Members Communication via Google Group list Technical exchanges: GH issues Minutes: meeting notes GH repo Want to join? Subscribe to the Google Group Why DTS? DTS provides a standard way for clients to interact with collections of TEI documents. A standard API allows users to access many text collections using the same client software. It also allows editors to publish text collections in a usable way that existing clients can use. What is DTS? Goal: enable machine-actionable operations across a wide variety of TEI texts. As DTS strives for genericity, it does not dictate: - how collections should be organized - type of persistent identiﬁers to use - what ontologies to use for metadata - how the texts are structured. Classes of objects in DTS Collections: - Hold metadata - Serve as a catalog - May be: - nested - readable - chunked into citable textual elements References: hold identiﬁers & metadata for subsections of documents Passages: hold textual content Endpoints & Operations Collections endpoint: - List available collections - Support for pagination & virtual collections - Navigate between nested collections Navigation endpoint: - List available text passages Documents endpoint: - Retrieve the text of a document Specs: w3id.org/dts Demo: web + notebooks FAQ page DTS-compliant resources APIs ENC Alpheios Perseids EDH Beta maṣāḥǝft A Generic Text API DTS supports: - Multi-level/competing text hierarchies - Any identiﬁer scheme (*) - Non-homogeneous text hierarchies Implementations TEI publisher client/server Perseids DTS API Nautilus + MyCapytain
Very high broadsense heritability for the root angle in both species = 0,82. WEB LINK : HTTPS://WWW.SOLACE-EU.NET GENETIC VARIATION OF WHEAT SEEDLING ROOT ANGLE C. COLLET, B. MOTTOULLE, T. DAGBERT, G. LOBET AND X. DRAYE EARTH AND LIFE INSTITUTE, UNIVERSITÉ CATHOLIQUE DE LOUVAIN, BELGIUM. CONTACT: clothilde.collet@uclouvain.be Below-ground parts of plants play a significant role in water and nitrogen extraction, and adaptation to changing environments. BELOW-GROUND PARTS OF PLANTS, OUR KEY PLAYERS ! Seminal root angles of cereal seedlings are good predictors of top soil exploration during crop establishment. PHENOTYPING ROOT GROWTH DYNAMICS Seedlings growing at different matric potentials (height above the water level) displayed a significant root angle plasticity in the two panels, despite the very small amplitude of potential (25 cm). This plasticity is genetically variable only in bread wheat. à The mean seminal root angle is 96° à The mean seminal root angle is 125° ^^^^ Water ^^^^ Illustration of extreme bread wheat varieties SEMINAL ROOT ANGLE EXPERIMENT This research is part of the European project SolACE : • Two diversity panels (bread wheat panel and durum wheat panel) for association genetics. • Advanced phenotyping experiments in equipped fields and controlled conditions platforms. • Emphasis on a combined deficit of water and nitrogen. Knowing the variability and heritability of root angle is a preliminary step towards improvement of seedling root architecture. à 2 experiments presented here as part of SolACE project. Identification and tracking of root tips in image sequences : • Root growth rate. • Emergence. • Maximum length. • Apical diameter. RootPhAir : • Aeroponics. • High throughput phenotyping. • Time-lapse image sequences with 2h resolution. • Affordable and non- invasive technique. CONCLUSIONS & PERSPECTIVES Seminal root angle experiment : • The large heritability of root angle suggests QTLs will be detected. • Wheat seminal root angle responds to small differences of water deficit. • In bread wheat, this response is genotype-dependent and may lead to unexplored adaptation possibilities. Further analyses : • Characterisation of genetic determinism for the root traits. © Laure Beff Other data sources will be mobilised : • Aeroponics (RootPhAir) : dynamic root traits. • 4PMI platform (INRA Dijon). • Field data (Syngenta, Arvalis, INRA). Albidum Zitnica
Gaia DR3 determination of the Galactic bar pattern speed Romero-Gomez M1, Jiménez-Arranz, Ó4, Chemin L3, Hunt J5, Khanna S2, Drimmel R2, Poggio E2, Ramos P6, Andrae, R7 1 Institut de Ciències del Cosmos (ICCUB), Universitat de Barcelona (IEEC-UB), Barcelona, Spain 2 INAF - Osservatorio Astrofisico di Torino, Torino, Italy 3 Instituto de Astrofisica, Universidad Andres Bello, Santiago RM, Chile 4 Division of Astrophysics, Lund Observatory, Sweden 5 University of Surrey, United Kingdom 6 National Astronomical Observatory of Japan, Tokyo, Japan 7 Max-Planck-Institut fur Astronomie, Konigstuhl 17, D-69117 Heidelberg, Germany Previously, in Gaia Collaboration, Drimmel+2023... ●We selected RGB stars in the Galactic plane using Gaia gspphot astrophysical parameters. We used the 6D (positions and velocities) sample, including about 5.7M RGB stars towards the inner disc. ●3D velocity maps in cylindrical coordinates show the outstanding signature of the Galactic bar. ●Using a bisymmetric model of the tangential velocity component, we derive the position of the corotation radius of the bar, and from the tangential velocity curve, an estimate of the bar pattern speed. In the present study… ●We select RGB stars from Andrae, Rix & Chandra (2023) using XGBoost algorithm, which derives metallicities, effective temperatures and gravities trained using APOGEE stellar parameters and including CatWISE magnitudes. ●The catalogue now contains about 12M RGB stars in the Galactic plane. ●We make NEW 3D velocity maps in cylindrical coordinates, now taking into consideration the correlations between the astrometric variables and propagated to the galactocentric coordinates. ●New velocity correlation maps show vertex deviation of the local velocity elipsoid. In the present study… ●Alternatively to the experimental method used in the Gaia Collaboration, Drimmel+2023 paper, we use the Tremaine-Weinberg version of the code in Bovy+2019 to estimate the pattern speed of the Galactic bar from this new dataset. Results of the corotation radius and bar pattern speed are consistent with the ones found in the Gaia Collaboration paper. Note that… The estimated values of the pattern speed using the TW method show a strong dependence on the assumed angular orientation of the Galactic bar, and the maximum galactocentric radius defining the bar region. Some inherent to the method might not apply. Preliminary results ●A thorough analysis of the method when applied to simulated data shows a high sensitivity of the pattern speed with the estimation of the bar region or orientation angle. The hypothesis of a density gradient following an exponentially decreasing elliptical pattern might not be realistic.
A ﬁrst look into Gollum’s cave: Are we hoarding data because of legal uncertainties? Lea Sophie Singson (FIZ Karlsruhe), Jannes Uhlott (JKI), Constantin Bress (FIZ Karlsruhe), Sophie Boße (ZB MED), Anne Sennhenn (ATB Potsdam) We asked the agro science community a catalogue of questions regarding their experiences and reservations regarding the sharing of their data. Emphasis here was to gather insight from a legal perspective with questions surrounding the license landscape in institutions and familiarity of the community with licenses, the Good Scientiﬁc Practice and more. Here is what we know… We gathered that scientists are hesitant to publish research data, especially under a CC0 license or a public domain mark. One of the reasons for that seems to be the perceived risk of not being attributed by their peers. This was surprising, considering the participants also stated, that they are familiar with the Good Scientiﬁc Practice. It seems that although the name rings a bell, scientists do not know that the Good Scientiﬁc Practice forces attribution by other scientists. Also, the use of CC-BY licenses, which require citing, is widespread. In the survey, the scientists were asked if they had an understanding of what a CC-BY and a publication into the public domain legally means. The answers suggest that quite a few are conﬁdent in what the licenses do while many others either answered that they don’t know at all or that they are unsure. Those who answered “yes” or “I’m not sure” where then also asked to write down what exactly they think the licenses mean. Misunderstandings about the meaning of CC-BY seem to be common, however. Thus, training on data publication and licenses is required … and wanted! What do you think? Do you agree with this ﬁrst look? Would you answer differently? Take the Survey! Get the Poster!
Further Reading General Info ● Arbetarrörelsens Arkiv och Bibliotek - https://www.arbark.se/ ● Folkrörelsearkivet för Uppsala Län - https://www.fauppsala.se/ ● Archiv der sozialen Demokratie - https://www.fes.de/archiv-der-sozialen-demokratie ● International Institute of Social History - https://iisg.amsterdam/ ● Riksbankens Jubileumsfond - https://www.rj.se/ ● Grant Information - https://www.rj.se/en/grants/2020/labours-memory.-digitization-of-annual-and-financial -reports-of-blue-collar-worker-unions-1880-2020/ Technology ● International Image Interoperability Framework (IIIF) - https://iiif.io/ ● Omeka S - https://omeka.org/s/ ● Archival IIIF server - https://github.com/archival-IIIF/server ● Archivematica - https://www.archivematica.org/ ● Archival Resource Key (ARK) - https://arks.org/ ● handle - http://www.handle.net/ ● Named Entity Recognition: Crina Tudor and Eva Pettersson. 2024. People and Places of the Past - Named Entity Recognition in Swedish Labour Movement Documents from Historical Sources. In Proceedings of the 8th Joint SIGHUM Workshop on Computational Linguistics for Cultural Heritage, Social Sciences, Humanities and Literature (LaTeCH-CLfL 2024). https://aclanthology.org/2024.latechclfl-1.17 ● Handwritten Text Recognition: "Loghi" - https://github.com/knaw-huc/loghi
Statement of need Collec'ng, aggrega'ng, and analyzing data to produce metrics is easier than ever before. In the realm of academic research, data on the digital distribu'on of scholarly content provides new opportuni'es to understand the publishing ecosystem. A range of stakeholders currently generates and collects this data, o?en as products of content usage or sales. There is growing concern about the ownership of, access to, and analysis of this data for “predic've bibliometrics.” Despite the growing demand for rich data and predic've analy'cs, the high costs of providing or purchasing data-­‐ related services are reinforcing inequi'es in the academic publishing landscape. Furthermore, the challenges associated with gathering, integra'ng, interpre'ng, and repor'ng usage data limit the ability of individual publishers, libraries, and other stakeholders to iden'fy— much less predict—important usage trends and opportuni'es through which these organiza'ons might extend their impact. Based on ins'tu'onal contribu'ons that would be used to seed-­‐fund this project (at $1K and $5K levels), Project Meerkat will gather a diverse community of scholarly communica'on stakeholders, including authors and editors, to jointly develop governance, sustainability, and ethical frameworks for how usage data is gathered, analyzed, and shared, building upon the NISO Privacy Principles. The project team will also scope and develop analy'c and benchmark reports to meet the iden'ﬁed needs of libraries, publishers, aggregators, and other stakeholders. The resul'ng Publishing Analy'cs Data Alliance will work to sustain the outcomes of Project Meerkat, providing its members with shared governance of collected data. Member organiza'ons will agree to a code of prac'ce as a condi'on of membership. Developing tools and protocols rela5ng to the collec5on, aggrega5on, and dissemina5on of usage data about digital monograph publica5ons A Publishing Analy'cs Data Alliance We invite publishers, libraries, research centers, socie7es, funders, aggregators, and other scholarly communica7on stakeholders to join Project Meerkat to develop guidelines and standards for digital scholarly monograph usage data and to construct a neutral organiza7onal apparatus for the ongoing collec7on and aggrega7on of data about these scholarly publica7ons. Current conveners for Project Meerkat Chris7na Drummond (Educopia Ins'tute) Mar7n Paul Eve (Birbeck, University of London & Open Library of Humani'es) Kevin Hawkins (University of North Texas) Sarah Melton (Emory University) Lucy Montgomery (Cur'n University & Knowledge Unlatched) Cameron Neylon (Cur'n University) Lisa Schiﬀ (California Digital Library) Katherine Skinner (Educopia Ins'tute) Es7mated budget Project Meerkat (2017–2020): $480,500 To cover the costs of project facilita'on, development, and in-­‐person convenings of experts to complement virtual working groups. Publishing Analy7cs Data Alliance (2020 forward) On-­‐going revenue streams will be established to cover the costs associated with con'nued support of shared infrastructure and services.
CSSI Frameworks: Re-engineering Galaxy for Performance, Scalability and Energy Efficiency Award #: OAC-1931531 NSF CSSI PI Meeting, Seattle, WA, Feb. 13-14, 2020 II. Our Objective Re-engineer the Galaxy framework to enable GPUs and accelerators like FPGAs as "first-class" compute engines. Enlarge the Galaxy community by bringing GPU and FPGA supported tools. Enable Galaxy tools to take better advantage of emerging cluster scheduling capabilities. Achieve significant improvements in performance scalability and energy efficiency. I. What is the Problem? Galaxy is an open source, web-based framework that is extensively used by more than 20,000 researchers world-wide in many areas. Current galaxy implementation does not support GPU and accelerators like FPGAs. There is no support for dynamic resource scheduling and management in Galaxy. Galaxy Centers Galaxy Popularity IV. Current Developments Identified existing GPU based tools such as Racon. Integrated a GPU based implementation of RACON, a genomic consensus tool to Galaxy Toolshed . Integrated a GPU-version of Smith- Waterman sequencing tool to Galaxy. Deployed Galaxy on a Kubernetes managed cluster. V. Next Steps Develop GPU based implementation for existing ML tools for RNN sequencing, using Keras framework. Use GPU plugin in Kubernetes to enable GPU access for Galaxy pods. Expose GPU metrics to develop resource utilization-aware scheduling policies. Develop a Reinforcement-based Machine Learning scheduling framework. Develop a distributed data-store using Rook, to enable near data placement based scheduling policies. https://galaxyproject.org Get in Touch: mtk2@psu.edu Acknowledgments: Galaxy project is also supported by NSF grant #1661497 and other NIH grants. III. Our Vision for Galaxy 300k page views Deployed in 128 platforms 8915 publications > 7 million Research funds > 7800 supported tools 10000+ online subscribers 8000+ twitter followers Learn More PI: Mahmut Taylan Kandemir *, Co-PIs: Chita R. Das *, Anton NekrutenkoΨ, Paul Medvedev * * Dept. of Computer Science and Engineering, Ψ Dept. of Biochemistry and Molecular Biology Institution: The Pennsylvania State University, University Park