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1

Raymond, Carolyn A., and M. Henson. "Genetic Variation Amongst and Within The Native Provenances of Pinus radiata D. Don in South-eastern Australia. 1. Growth and form to age 26 years." Silvae Genetica 58, no. 1-6 (December 1, 2009): 242–52. http://dx.doi.org/10.1515/sg-2009-0031.

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Abstract Four hundred and sixty individual families of Pinus radiata, representing all provenances and populations in a 1978 seed collection, plus a local seed orchard control, were planted together in 1980 in a large trial in southern New South Wales, Australia. Provenance means and genetic parameters for growth measured at ages 3, 8 and 26 years plus stem straightness, branch angle and nodality at age 26 years are reported. Large provenance differences were apparent for all traits. The two island provenances, Cedros and Guadalupe, were significantly inferior to the mainland provenances and, due to competition effects, very few trees survived to age 26. Within the mainland provenances, the performance of Año Nuevo and Monterey was almost identical, with Cambria being less vigorous. The best performing seedlot for all traits was the local control. Differences between populations within the mainland provenances were apparent for diameter at age 26 within Año Nuevo and Cambria but not Monterey. Año Nuevo also showed population differences for stem straightness. Heritabilities for early growth were similar within Año Nuevo and Monterey but by age 26, the heritability for diameter was higher in Monterey. Within Cambria, heritabilities for growth and tree form at age 26 were close to zero. Genetic correlations between traits showed similar patterns for each of the mainland provenances, with the exception of correlations with stem straightness within Año Nuevo. Results are discussed in light of recent molecular studies of genetic architecture, levels of inbreeding in the native stands and possible effects of this inbreeding.
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2

Hasham, Khawar, Kamran Munir, and Richard McClatchey. "Cloud infrastructure provenance collection and management to reproduce scientific workflows execution." Future Generation Computer Systems 86 (September 2018): 799–820. http://dx.doi.org/10.1016/j.future.2017.07.015.

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Pourvahab, Mehran, and Gholamhossein Ekbatanifard. "Digital Forensics Architecture for Evidence Collection and Provenance Preservation in IaaS Cloud Environment Using SDN and Blockchain Technology." IEEE Access 7 (2019): 153349–64. http://dx.doi.org/10.1109/access.2019.2946978.

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4

Balis, Bartosz, Marian Bubak, and Bartłomiej Łabno. "Monitoring of Grid Scientific Workflows." Scientific Programming 16, no. 2-3 (2008): 205–16. http://dx.doi.org/10.1155/2008/849354.

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Scientific workflows are a means of conducting in silico experiments in modern computing infrastructures for e-Science, often built on top of Grids. Monitoring of Grid scientific workflows is essential not only for performance analysis but also to collect provenance data and gather feedback useful in future decisions, e.g., related to optimization of resource usage. In this paper, basic problems related to monitoring of Grid scientific workflows are discussed. Being highly distributed, loosely coupled in space and time, heterogeneous, and heavily using legacy codes, workflows are exceptionally challenging from the monitoring point of view. We propose a Grid monitoring architecture for scientific workflows. Monitoring data correlation problem is described and an algorithm for on-line distributed collection of monitoring data is proposed. We demonstrate a prototype implementation of the proposed workflow monitoring architecture, the GEMINI monitoring system, and its use for monitoring of a real-life scientific workflow.
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5

Giovannini, E. C., M. Lo Turco, and N. Mafrici. "DOCUMENTING HISTORICAL RESEARCH FOR A COLLECTION INFORMATION MODELLING. A PROPOSAL FOR A DIGITAL ASSET MANAGEMENT SYSTEM." ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XLII-2/W15 (August 22, 2019): 519–25. http://dx.doi.org/10.5194/isprs-archives-xlii-2-w15-519-2019.

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<p><strong>Abstract.</strong> The paper describes part of the conceptual structure produced within the still ongoing project B.A.C.K. TO T.H.E. F.U.T.U.RE. (BIM Acquisition as Cultural Key TO Transfer Heritage of ancient Egypt For many Uses To many Users REplayed). The aim of the project was to use a semantic web infrastructure to describe archival research and tracking informations related to a hidden museum collection <q>expedition models of Egyptian architecture</q> partially stored in the depots of the Museo Egizio of Turin. The outcome will be an interactive web-presentation portal of high-resolution 3D models enriched by historical and archival set of content, from the digitization procedure applied to collection objects, to the digitization process of related data and information. The development of the collection documentation of the project illustrates how is crucial to declare the semantic description underlying narrative contents. Data about single collection objects were conceptually modelled using generalizable formulas already known by CIDOC-CRM community. The description of provenance of knowledge related to the historical investigation process was modelled using CRMinf extension, exploring the possibility of making beliefs based on the available documentation and validating the results of the assumptions made during the research.</p>
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6

Martinez, Katharine. "The Research Libraries Group: new initiatives to improve access to art and architecture information." Art Libraries Journal 23, no. 1 (1998): 30–37. http://dx.doi.org/10.1017/s0307472200010798.

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This survey of the achievements of the Research Libraries Group (RLG) and its Art and Architecture Group shows the effectiveness of a collaborative approach in developing best practices and standards, and implementing new methodologies and technologies, to benefit the international art library and research communities. RLG members in Europe, North America and Australia include many of the major art research libraries. RLG offers services such as the RLIN bibliographic database and the MARCADIA retrospective conversion service in conjunction with projects documenting sales catalogue records (SCIPIO), preserving serials (the Art Serials Preservation Project) and facilitating the interloan of material between members. More recently the partnership between the RLG and the Getty Information Institute has made available an enormous range of art documentation work carried out by the Getty: standards and authority control work such as the Art & Architecture Thesaurus, the Union List of Artists’ Names and the Thesaurus of Geographic Names. In the 1980s the RLG conducted a survey identifying information needs in the humanities, which has led to resources such as the Bibliography of the History of Art becoming widely accessible, with the Provenance Index to follow shortly. This partnership is now active in the museum field, attempting to bridge the gap between the domains of secondary and primary materials in the field of art research. The REACH project (Record Export for Art and Cultural Heritage) is experimenting with the export of existing machine-readable data from heterogeneous museum collection systems, and testing the feasibility of designing a common interface for access which will complement RLG’s other resources.
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Shaikh, Zaffar Ahmed, Abdullah Ayub Khan, Lin Teng, Asif Ali Wagan, and Asif Ali Laghari. "BIoMT Modular Infrastructure: The Recent Challenges, Issues, and Limitations in Blockchain Hyperledger-Enabled E-Healthcare Application." Wireless Communications and Mobile Computing 2022 (September 21, 2022): 1–14. http://dx.doi.org/10.1155/2022/3813841.

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This paper presents a layered hierarchy that depicts the progressive relationship between data, information, knowledge, and wisdom. To begin with, data is gathered and organized into information. Information is gathered, filtered, refined, and put through an investigation process to create knowledge. Wisdom is attained after knowledge discovery through the process of filtration and aggregation through experience. The layered hierarchy in the domain of e-healthcare necessitates higher scheduling costs for data collection, processing wisdom, and management, which is also an insecure and untrustworthy process for progressive medical service. The medical industry faces a difficult problem in providing collected data integrity, information reliability, and knowledge trustworthiness for the service of progressive medical relationships in the face of an increasing number of day-to-day records. The blockchain consortium hyperledger (fabric) has been used in this paper to act as a bridge that bridges the gap between electronic data, information, knowledge, and wisdom (DIKW) movement and processes by enabling the process of the layered hierarchy of schedule information and management and providing security and transparency. For e-healthcare information management and privacy, the DIKW-ledger, such as patients’ consultancy information, availing medical services, personal records, appointments, treatment details, and other health-related transactions, a consortium hyperledger fabric-enabled efficient architecture is proposed. This proposed architecture creates two networks: a public network for medical stakeholders to exchange and agree on specific medical activities before being preserved on distributed storage (read-only after record registration) and a private network for complete DIKW process scheduling and management. We designed and created smart contracts for this purpose, as well as use-case diagrams to describe the overall execution process. The proposed architectural solution provides more efficient information integrity, provenance, and storage procedures to immutably preserve the medical ledger in a permissioned hash-encrypted structure.
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8

Hobern, Donald, Andrea Hahn, and Tim Robertson. "Options to streamline and enrich biodiversity data aggregation." Biodiversity Information Science and Standards 2 (May 21, 2018): e26808. http://dx.doi.org/10.3897/biss.2.26808.

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The success of Darwin Core and ABCD Schema as flexible standards for sharing specimen data and species occurrence records has enabled GBIF to aggregate around one billion data records. At the same time, other thematic, national or regional aggregators have developed a wide range of other data indexes and portals, many of which enrich the data by interpreting and normalising elements not currently handled by GBIF or by linking other data from geospatial layers, trait databases, etc. Unfortunately, although each of these aggregators has specific strengths and supports particular audiences, this diversification produces many weaknesses and deficiencies for data publishers and for data users, including: incomplete and inconsistent inclusion of relevant datasets; proliferation of record identifiers; inconsistent and bespoke workflows to interpret and standardise data; absence of any shared basis for linked open data and annotations; divergent data formats and APIs; lack of clarity around provenance and impact; etc. The time is ripe for the global community to review these processes. From a technical standpoint, it would be feasible to develop a shared, integrated pipeline which harvested, validated and normalised all relevant biodiversity data records on behalf of all stakeholders. Such a system could build on TDWG expertise to standardise data checks and all stages in data transformation. It could incorporate a modular structure that allowed thematic, national or regional networks to generate additional data elements appropriate to the needs of their users, but for all of these elements to remain part of a single record with a single identifier, facilitating a much more rigorous approach to linked open data. Most of the other issues we currently face around fitness-for-use, predictability and repeatability, transparency and provenance could be supported much more readily under such a model. The key challenges that would need to be overcome would be around social factors, particularly to deliver a flexible and appropriate governance model and to allow research networks, national agencies, etc. to embed modular components within a shared workflow. Given the urgent need to improve data management to support Essential Biodiversity Variables and to deliver an effective global virtual natural history collection, we should review these challenges and seek to establish a data management and aggregation architecture that will support us for the coming decades.
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9

Gouru, Navya, and NagaLakshmi Vadlamani. "CoPS - Cooperative Provenance System with ZKP using Ethereum Blockchain Smart Contracts." International Journal of Distributed Systems and Technologies 9, no. 4 (October 2018): 40–53. http://dx.doi.org/10.4018/ijdst.2018100103.

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The redesign of cloud storage with the amalgamation of cooperative cloud and an immutable and unhackable distributed database blockchain thrives towards a strong CIA triad and secured data provenance. The conspiracy ideology associated with the traditional cloud has economized with cooperative cloud storage like Storj and Sia, decentralized storage, which allows renting the unused hard drive space and getting monetary compensation in an exchange with cryptocurrency. In this article, the authors explain how confidentiality, integrity and availability can be progressed with cooperative cloud storage along with tamper-proof data provenance management with ethereum smart contracts using zero-knowledge proof (ZKP). A contemporary architecture is proposed with regards to storing data on the cooperative cloud and collecting and verifying the provenance data from the cloud and publishing the provenance data into blockchain network as transactions.
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10

Walker, Annalise K. "Canadian Architectural Archives at the University of Calgary Libraries." Research Notes 12, no. 3 (October 21, 2013): 63–70. http://dx.doi.org/10.7202/1018943ar.

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The Canadian Architectural Archives at the University of Calgary Libraries were established in 1974; first major collections were donated in 1975 and, by 1983, the Archives has grown significantly. Collections consist mostly of drawings, file material and photographs, with some models. The purpose of the Archives is support of study and research and preservation of documents. Major collections include those of John B. Parkin Associates, Arthur Erickson, and Ron Thorn, as well as other large collections from the Toronto, Calgary and Vancouver area. Organization of collections is based on archival principles of original order and provenance, and access to individual building projects is facilitated through various indices and inventories. An Oral History programme provides some additional biographical background. With a few exceptions, all materials are accessible for research in the Archives reader area; limited research assistance can be given to persons from out of town or out of province. Copies of individual items can be provided for research, exhibition or publication under strict copyright regulations.
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11

Mariz, Vera, Rosário Salema de Carvalho, Fernando Cabral, Maria Neto, Clara Moura Soares, and Natália Jorge. "ORION—Art Collections and Collectors in Portugal." Heritage 2, no. 2 (April 2, 2019): 1045–59. http://dx.doi.org/10.3390/heritage2020068.

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ORION is a digital art history research-oriented project focused on the study of art collections and collectors in Portugal, supported on a relational database management system. Besides the obvious advantage of organizing and systematizing an enormous amount of information, promoting its analysis, this database was specifically designed to highlight the relationships between data. Its relational capacity is not only one of the most relevant features of ORION, but a differentiating quality, one step forward in comparison to other international databases and studies that use digital methodologies. This article discusses the methods and the advantages of using ORION in research related to the history of collecting, art markets and provenance of art objects in Portugal, where it is the very first time that an approach such as this is intended, looking for a systematization of data that paves the way to the emergence of new research questions. Furthermore, and because ORION aims to share the data and knowledge with other projects, institutions and researchers, the database uses different international standards, such as data structure (CIDOC-OIC and Getty-CDWA), controlled vocabulary (Iconclass, Art and Architecture Thesaurus (AAT), Thesaurus of Geographic Names (TGN), and Union List of Artist Names (ULAN)) and communication and exchange of information (CIDOC-CRM).
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Janjua, Kanwal, Munam Ali Shah, Ahmad Almogren, Hasan Ali Khattak, Carsten Maple, and Ikram Ud Din. "Proactive Forensics in IoT: Privacy-Aware Log-Preservation Architecture in Fog-Enabled-Cloud Using Holochain and Containerization Technologies." Electronics 9, no. 7 (July 19, 2020): 1172. http://dx.doi.org/10.3390/electronics9071172.

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Collecting and preserving the smart environment logs connected to cloud storage is challenging due to the black-box nature and the multi-tenant cloud models which can pervade log secrecy and privacy. The existing work for log secrecy and confidentiality depends on cloud-assisted models, but these models are prone to multi-stakeholder collusion problems. This study proposes ’PLAF,’ a holistic and automated architecture for proactive forensics in the Internet of Things (IoT) that considers the security and privacy-aware distributed edge node log preservation by tackling the multi-stakeholder issue in a fog enabled cloud. We have developed a test-bed to implement the specification, as mentioned earlier, by incorporating many state-of-the-art technologies in one place. We used Holochain to preserve log integrity, provenance, log verifiability, trust admissibility, and ownership non-repudiation. We introduced the privacy preservation automation of log probing via non-malicious command and control botnets in the container environment. For continuous and robust integration of IoT microservices, we used docker containerization technology. For secure storage and session establishment for logs validation, Paillier Homomorphic Encryption, and SSL with Curve25519 is used respectively. We performed the security and performance analysis of the proposed PLAF architecture and showed that, in stress conditions, the automatic log harvesting running in containers gives a 95% confidence interval. Moreover, we show that log preservation via Holochain can be performed on ARM-Based architectures such as Raspberry Pi in a very less amount of time when compared with RSA and blockchain.
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13

Lane, Andrew. "The ruins at Virginia Water (part 1)." Libyan Studies 35 (2004): 67–94. http://dx.doi.org/10.1017/s0263718900003721.

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AbstractOne of the more unusual attractions in Windsor Great Park is the folly beside the lake at Virginia Water. Built in the 1820's in the form of an idealised Classical ruin, it incorporates a large collection of Roman antiquities from the site of Lepcis Magna in Libya. Considering the importance of this monument, not only as one of the most elaborate follies, but one of largest assemblages of Roman architectural fragments in the country, it has received relatively little scholarly attention. As a consequence, in the summer of 2003 a thorough survey and partial excavation of the site were undertaken. The results of this work, a detailed plan of the ruins, a catalogue of the items remaining and new evidence for the origin, construction and history of the site, are presented. The provenance of the Roman elements will be examined in greater detail in part 2.
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Andritsos, Leslie A., Michael R. Grever, Mirela Anghelina, Claire E. Dearden, Monica Else, James S. Blachly, Omkar Lele, et al. "A Distributed International Patient Data Registry for Hairy Cell Leukemia." Blood 128, no. 22 (December 2, 2016): 5986. http://dx.doi.org/10.1182/blood.v128.22.5986.5986.

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Abstract BACKGROUND: The study of rare diseases is limited by the uncommon nature of the conditions as well as the widely dispersed patient populations. Current rare disease registries such as the National Organization of Rare Diseases utilize centralized platforms for data collection; however because of their broad nature, these do not always capture unique, disease specific elements. Hairy Cell Leukemia (HCL) is a rare leukemia globally with approximately 900 new cases diagnosed in the US each year. The HCL Foundation undertook creation of a Patient Data Registry that collects data from multiple HCL Centers of Excellence (COE) around the globe to better understand the complications, treatment outcomes, disease subtypes, comorbid conditions, epidemiology, and quality of life of patients with HCL. METHODS: Investigators at The Ohio State University Department of Biomedical Informatics and Division of Hematology in collaboration with the HCL Foundation developed a Patient Data Registry (PDR) for the longitudinal capture of high quality research data. This system differs from other registries in that it uses a federated( rather than centralized) architecture, wherein data is queried and integrated in an on-demand manner from local registry databases at each participating site. Further, the data collected for use in the registry combines both automated exports from existing electronic health records (EHRs) as well as additional data entered via a set of web-based forms. All manually entered data comes from source documents, and data provenance spanning electronic and manually entered data is maintained via multiple technical measures. Patients may be enrolled at HCL COE, or, if they do not have access to a COE they may enroll via a web-based portal (www.hairycellleukemia.org). At this time due to regulatory requirements the web-based portal is available to US patients only. All data are de-identified (see Figure 1: De-Identification Workflow) which reduces regulatory burden and increases opportunities for data access and re-use. End users have access to data via a project-specific query portal. RESULTS: The Patient Data Registry has been deployed at The Ohio State University, Royal Marsden Hospital, and MD Anderson Cancer Center, and is undergoing deployment at the University of Rochester. Up to 25 international HCL COE may participate. In addition, US patients are actively entering the registry via the web-based portal. To date, 227 patients have been consented to the registry with 119 of these being via the web-based entry point. CONCLUSION: We created an international and web-based patient data registry which will enable researchers to study outcomes in HCL in ways not previously possible given the rarity of the disease. This work was made possible by research funding from the Hairy Cell Leukemia Foundation. Figure De-Identification Workflow Figure. De-Identification Workflow Disclosures Andritsos: Hairy Cell Leukemia Foundation: Research Funding. Anghelina:Hairy Cell Leukemia Foundation: Research Funding. Lele:Hairy Cell Leukemia Foundation: Research Funding. Burger:Pharmacyclics: Research Funding. Delgado:Gilead: Consultancy, Honoraria; Novartis/GSK: Consultancy, Honoraria; Janssen: Consultancy, Honoraria; Roche: Consultancy, Honoraria, Research Funding; Infinity: Research Funding. Jones:AbbVie: Membership on an entity's Board of Directors or advisory committees, Research Funding; Janssen: Membership on an entity's Board of Directors or advisory committees, Research Funding; Pharmacyclics, LLC, an AbbVie Company: Membership on an entity's Board of Directors or advisory committees, Research Funding. Lozanski:Beckman Coulter: Research Funding; Genentech: Research Funding; Stemline Therapeutics Inc.: Research Funding; Boehringer Ingelheim: Research Funding. Montserrat:Morphosys: Other: Expert Testimony; Vivia Biotech: Equity Ownership; Gilead: Consultancy, Other: Expert Testimony; Pharmacyclics: Consultancy; Janssen: Honoraria, Other: travel, accommodations, expenses. Parikh:Pharmacyclics: Honoraria, Research Funding. Park:Genentech/Roche: Research Funding; Amgen: Consultancy; Juno Therapeutics: Consultancy, Research Funding. Robak:Pharmacyclics, LLC, an AbbVie Company: Consultancy, Honoraria, Research Funding; Janssen: Consultancy, Honoraria, Research Funding; AbbVie: Consultancy, Honoraria, Research Funding. Tam:janssen: Honoraria, Research Funding; Roche: Honoraria, Membership on an entity's Board of Directors or advisory committees; AbbVie: Honoraria, Membership on an entity's Board of Directors or advisory committees. Heckler:Hairy Cell Leukemia Foundation: Research Funding. Payne:Hairy Cell Leukemia Foundation: Research Funding.
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Gouripeddi, Ram, Katherine Sward, Mollie Cummins, Karen Eilbeck, Bernie LaSalle, and Julio C. Facelli. "4549 Reproducible Informatics for Reproducible Translational Research." Journal of Clinical and Translational Science 4, s1 (June 2020): 66–67. http://dx.doi.org/10.1017/cts.2020.221.

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OBJECTIVES/GOALS: Characterize formal informatics methods and approaches for enabling reproducible translational research. Education of reproducible methods to translational researchers and informaticians. METHODS/STUDY POPULATION: We performed a scoping review [1] of selected informatics literature (e.g. [2,3]) from PubMed and Scopus. In addition we reviewed literature and documentation of translational research informatics projects [4–21] at the University of Utah. RESULTS/ANTICIPATED RESULTS: The example informatics projects we identified in our literature covered a broad spectrum of translational research. These include research recruitment, research data requisition, study design and statistical analysis, biomedical vocabularies and metadata for data integration, data provenance and quality, and uncertainty. Elements impacting reproducibility of research include (1) Research Data: its semantics, quality, metadata and provenance; and (2) Research Processes: study conduct including activities and interventions undertaken, collections of biospecimens and data, and data integration. The informatics methods and approaches we identified as enablers of reproducibility include the use of templates, management of workflows and processes, scalable methods for managing data, metadata and semantics, appropriate software architectures and containerization, convergence methods and uncertainty quantification. In addition these methods need to be open and shareable and should be quantifiable to measure their ability to achieve reproducibility. DISCUSSION/SIGNIFICANCE OF IMPACT: The ability to collect large volumes of data collection has ballooned in nearly every area of science, while the ability to capturing research processes hasn’t kept with this pace. Potential for problematic research practices and irreproducible results are concerns.Reproducibility is a core essentially of translational research. Translational research informatics provides methods and means for enabling reproducibility and FAIRness [22] in translational research. In addition there is a need for translational informatics itself to be reproducible to make research reproducible so that methods developed for one study or biomedical domain can be applied elsewhere. Such informatics research and development requires a mindset for meta-research [23].The informatics methods we identified covers the spectrum of reproducibility (computational, empirical and statistical) and across different levels of reproducibility (reviewable, replicable, confirmable, auditable, and open or complete) [24–29]. While there are existing and ongoing efforts in developing informatics methods for translational research reproducibility in Utah and elsewhere, there is a need to further develop formal informatics methods and approaches: the Informatics of Research Reproducibility.In this presentation, we summarize the studies and literature we identified and discuss our key findings and gaps in informatics methods for research reproducibility. We conclude by discussing how we are covering these topics in a translational research informatics course.1.Pham MT, Rajić A, Greig JD, Sargeant JM, Papadopoulos A, McEwen SA. A scoping review of scoping reviews: advancing the approach and enhancing the consistency. Res Synth Methods. 2014 Dec;5(4):371–85.2.McIntosh LD, Juehne A, Vitale CRH, Liu X, Alcoser R, Lukas JC, Evanoff B. Repeat: a framework to assess empirical reproducibility in biomedical research. BMC Med Res Methodol [Internet]. 2017 Sep 18 [cited 2018 Nov 30];17. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5604503/3.Denaxas S, Direk K, Gonzalez-Izquierdo A, Pikoula M, Cakiroglu A, Moore J, Hemingway H, Smeeth L. Methods for enhancing the reproducibility of biomedical research findings using electronic health records. BioData Min. 2017;10:31.4.Burnett N, Gouripeddi R, Wen J, Mo P, Madsen R, Butcher R, Sward K, Facelli JC. Harmonization of Sensor Metadata and Measurements to Support Exposomic Research. In: 2016 International Society of Exposure Science [Internet]. Research Triangle Park, NC, USA; 2017 [cited 2017 Jun 17]. Available from: http://www.intlexposurescience.org/ISES20175.Butcher R, Gouripeddi RK, Madsen R, Mo P, LaSalle B. CCTS Biomedical Informatics Core Research Data Service. In Salt Lake City; 2016.6.Cummins M, Gouripeddi R, Facelli J. A low-cost, low-barrier clinical trials registry to support effective recruitment. In Salt Lake City, Utah, USA; 2016 [cited 2018 Nov 30]. Available from: //campusguides.lib.utah.edu/UtahRR16/abstracts7.Gouripeddi R, Warner P, Madsen R, Mo P, Burnett N, Wen J, Lund A, Butcher R, Cummins MR, Facelli J, Sward K. An Infrastructure for Reproducibile Exposomic Research. In: Research Reproducibility 2016 [Internet]. Salt Lake City, Utah, USA; 2016 [cited 2018 Nov 30]. Available from: //campusguides.lib.utah.edu/UtahRR16/abstracts8.Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M. The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol. 2005;6:R44.9.Gouripeddi R, Cummins M, Madsen R, LaSalle B, Redd AM, Presson AP, Ye X, Facelli JC, Green T, Harper S. Streamlining study design and statistical analysis for quality improvement and research reproducibility. J Clin Transl Sci. 2017 Sep;1(S1):18–9.10.Gouripeddi R, Eilbeck K, Cummins M, Sward K, LaSalle B, Peterson K, Madsen R, Warner P, Dere W, Facelli JC. A Conceptual Architecture for Reproducible On-demand Data Integration for Complex Diseases. In: Research Reproducibility 2016 (UtahRR16) [Internet]. Salt Lake City, Utah, USA; 2016 [cited 2017 Apr 25]. Available from: https://zenodo.org/record/16806711.Gouripeddi R, Lane E, Madsen R, Butcher R, LaSalle B, Sward K, Fritz J, Facelli JC, Cummins M, Shao J, Singleton R. Towards a scalable informatics platform for enhancing accrual into clinical research studies. J Clin Transl Sci. 2017 Sep;1(S1):20–20.12.Gouripeddi R, Deka R, Reese T, Butcher R, Martin B, Talbert J, LaSalle B, Facelli J, Brixner D. Reproducibility of Electronic Health Record Research Data Requests. In Washington, DC, USA; 2018 [cited 2018 Apr 21]. Available from: https://zenodo.org/record/1226602#.WtvvyZch27013.Gouripeddi R, Mo P, Madsen R, Warner P, Butcher R, Wen J, Shao J, Burnett N, Rajan NS, LaSalle B, Facelli JC. A Framework for Metadata Management and Automated Discovery for Heterogeneous Data Integration. In: 2016 BD2K All Hands Meeting [Internet]. Bethesda, MD; November 29-30 [cited 2017 Apr 25]. Available from: https://zenodo.org/record/16788514.Groat D, Gouripeddi R, Lin YK, Dere W, Murray M, Madsen R, Gestaland P, Facelli J. Identification of High-Level Formalisms that Support Translational Research Reproducibility. In: Research Reproducibility 2018 [Internet]. Salt Lake City, Utah, USA; 2018 [cited 2018 Oct 30]. Available from: //campusguides.lib.utah.edu/UtahRR18/abstracts15.Huser V, Kahn MG, Brown JS, Gouripeddi R. Methods for examining data quality in healthcare integrated data repositories. Pac Symp Biocomput Pac Symp Biocomput. 2018;23:628–33.16.Lund A, Gouripeddi R, Burnett N, Tran L-T, Mo P, Madsen R, Cummins M, Sward K, Facelli J. Enabling Reproducible Computational Modeling: The Utah PRISMS Ecosystem. In Salt Lake City, Utah, USA; 2018 [cited 2018 Oct 30]. Available from: //campusguides.lib.utah.edu/UtahRR18/abstracts17.Pflieger LT, Mason CC, Facelli JC. Uncertainty quantification in breast cancer risk prediction models using self-reported family health history. J Clin Transl Sci. 2017 Feb;1(1):53–9.18.Shao J, Gouripeddi R, Facelli J. Improving Clinical Trial Research Reproducibility using Reproducible Informatics Methods. In Salt Lake City, Utah, USA; 2018 [cited 2018 Oct 30]. Available from: //campusguides.lib.utah.edu/UtahRR18/abstracts19.Shao J, Gouripeddi R, Facelli JC. Semantic characterization of clinical trial descriptions from ClincalTrials.gov and patient notes from MIMIC-III. J Clin Transl Sci. 2017 Sep;1(S1):12–12.20.Tiase V, Gouripeddi R, Burnett N, Butcher R, Mo P, Cummins M, Sward K. Advancing Study Metadata Models to Support an Exposomic Informatics Infrastructure. In Ottawa, Canada; 2018 [cited 2018 Oct 30]. Available from: = http://www.eiseverywhere.com/ehome/294696/638649/?&t=8c531cecd4bb0a5efc6a0045f5bec0c321.Wen J, Gouripeddi R, Facelli JC. Metadata Discovery of Heterogeneous Biomedical Datasets Using Token-Based Features. In: IT Convergence and Security 2017 [Internet]. Springer, Singapore; 2017 [cited 2017 Sep 6]. p. 60–7. (Lecture Notes in Electrical Engineering). Available from: https://link.springer.com/chapter/10.1007/978-981-10-6451-7_822.Wilkinson MD, Dumontier M, Aalbersberg IjJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten J-W, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJG, Groth P, Goble C, Grethe JS, Heringa J, ’t Hoen PAC, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone S-A, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016 Mar 15;3:160018.23.Ioannidis JPA. Meta-research: Why research on research matters. PLOS Biol. 2018 Mar 13;16(3):e2005468.24.Stodden V, Borwein J, Bailey DH. Setting the default to reproducible. Comput Sci Res SIAM News. 2013;46(5):4–6.25.Stodden V, McNutt M, Bailey DH, Deelman E, Gil Y, Hanson B, Heroux MA, Ioannidis JPA, Taufer M. Enhancing reproducibility for computational methods. Science. 2016 Dec 9;354(6317):1240–1.26.Stodden V, McNutt M, Bailey DH, Deelman E, Gil Y, Hanson B, Heroux MA, Ioannidis JPA, Taufer M. Enhancing reproducibility for computational methods. Science. 2016 Dec 9;354(6317):1240–1.27.Stodden V. Reproducible Research for Scientific Computing: Tools and Strategies for Changing the Culture. Comput Sci Eng. 2012 Jul 1;14(4):13–7.28.Baker M. Muddled meanings hamper efforts to fix reproducibility crisis. Nat News Available from: http://www.nature.com/news/muddled-meanings-hamper-efforts-to-fix-reproducibility-crisis-1.2007629.Barba LA. Terminologies for Reproducible Research. ArXiv180203311 Cs 2018 Feb 9; Available from: http://arxiv.org/abs/1802.03311
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16

Bölling, Christian, Satpal Bilkhu, Christian Gendreau, Falko Glöckler, James Macklin, and David Shorthouse. "Representation of Object Provenance for Research on Natural Science Objects: Samples, parts and derivatives in DINA-compliant collection data management." Biodiversity Information Science and Standards 6 (September 7, 2022). http://dx.doi.org/10.3897/biss.6.94531.

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Анотація:
Collection objects in natural science collections span a diverse set of object types of substantially different origin, physical composition, and relevance for different fields and methodologies of research and application. Object provenance is often characterized by elaborate series of interventions from collecting or observing originals in a natural state to generating derived objects that can be physically persistent or are suitable for a given use. This sequence of events gives rise to intermediate objects or object states that can be of a persistent or ephemeral nature in their own right. Detailed metadata on object provenance is vital to enable informed use of collection objects for research and other application areas. Providing the ability to generate, maintain, update and access such accounts is an important requirement for Collection Management Software (CMS). DINA (Digital Information System for Natural History Data, Glöckler et al. 2020)-compliant collection management software meets this challenge by using process- and state-based representation of object histories and modular application architecture as the main conceptual and architectural principles, respectively (Bölling et al. 2021). In applying these principles, we showcase how object provenance can be represented in the DINA system in cases where multiple objects, possibly of varying types, are derived from a single object, objects consist of parts of different biological individuals, object histories involve different types of objects such as living biological individuals, samples, and preserved specimens. multiple objects, possibly of varying types, are derived from a single object, objects consist of parts of different biological individuals, object histories involve different types of objects such as living biological individuals, samples, and preserved specimens. We highlight how the abstractions and categories used in the DINA model can be used to meet a variety of challenging use cases for representing collection object provenance. For instance, while the connections and relationships between living, preserved, and even destructively processed samples can be documented in DINA, these are ordinarily difficult to accommodate in a single information system.
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17

Ametepe, Wolali, Changda Wang, Selasi Kwame Ocansey, Xiaowei Li, and Fida Hussain. "Data provenance collection and security in a distributed environment: a survey." International Journal of Computers and Applications, August 25, 2018, 1–15. http://dx.doi.org/10.1080/1206212x.2018.1501937.

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18

Hardisty, Alex, Keping Ma, Gil Nelson, and Jose Fortes. "‘openDS’ – A New Standard for Digital Specimens and Other Natural Science Digital Object Types." Biodiversity Information Science and Standards 3 (June 18, 2019). http://dx.doi.org/10.3897/biss.3.37033.

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Анотація:
With projected lifespans of many decades, infrastructure initiatives such as Europe’s Distributed System of Scientific Collections (DiSSCo), USA’s Integrated Digitized Biocollections (iDigBio), National Specimen Information Infrastructure (NSII) of China and Australia’s digitisation of national research collections (NRCA Digital) aim at transforming today’s slow, inefficient and limited practices of working with natural science collections. The need to borrow specimens (plants, animals, fossils or rocks) or physically visit collections, and absence of linkages to other relevant information represent significant impediments to answering today’s scientific and societal questions. A logical extension of the Internet, Digital Object Architecture (Kahn and Wilensky 2006) offers a way of grouping, managing and processing fragments of information relating to a natural science specimen. A ‘digital specimen’ acts as a surrogate in cyberspace for a specific physical specimen, identifying its actual location and authoritatively saying something about its collection event (who, when, where) and taxonomy, as well as providing links to high-resolution images. A digital specimen exposes supplementary information about related literature, traits, tissue samples and DNA sequences, chemical analyses, environmental information, etc. stored elsewhere than in the natural science collection itself. By presenting digital specimens as a new layer between data infrastructure of natural science collections and user applications for processing and interacting with information about specimens and collections, it’s possible to seamlessly organise global access spanning multiple collection-holding institutions and sources. Virtual collections of digital specimens with unique identifiers offer possibilities for wider, more flexible, and ‘FAIR’ (Findable, Accessible, Interoperable, Reusable) access for varied research and policy uses: recognising curatorial work, annotating with latest taxonomic treatments, understanding variations, working with DNA sequences or chemical analyses, supporting regulatory processes for health, food, security, sustainability and environmental change, inventions/products critical to the bio-economy, and educational uses. Adopting a digital specimen approach is expected to lead to faster insights for lower cost on many fronts. We propose that realising this vision requires a new TDWG standard. OpenDS is a specification of digital specimen and other object types essential to mass digitisation of natural science collections and their digital use. For five principal digital object types corresponding to major categories of collections and specimens’ information, OpenDS defines structure and content, and behaviours that can act upon them: Digital specimen: Representing a digitised physical specimen, contains information about a single specimen with links to related supplementary information; Storage container: Representing groups of specimens stored within a single container, such as insect tray, drawer or sample jar; Collection: Information about characteristics of a collection; Organisation: Information about the legal-entity owning the specimen and collection to which it belongs; and, Interpretation: Assertion(s) made on or about the specimen such as determination of species and comments. Digital specimen: Representing a digitised physical specimen, contains information about a single specimen with links to related supplementary information; Storage container: Representing groups of specimens stored within a single container, such as insect tray, drawer or sample jar; Collection: Information about characteristics of a collection; Organisation: Information about the legal-entity owning the specimen and collection to which it belongs; and, Interpretation: Assertion(s) made on or about the specimen such as determination of species and comments. Secondary classes gather presentation/preservation characteristics (e.g., herbarium sheets, pinned insects, specimens in glass jars, etc.), the general classification of a specimen (i.e., plant, animal, fossil, rock, etc.) and history of actions on the object (provenance). Equivalencing concepts in ABCD 3.0 and EFG extension for geo-sciences, OpenDS is also an ontology extending OBO Foundry’s Biological Collection Ontology (BCO) (Walls et al. 2014) from bco:MaterialSample, which has preferred label dwc:specimen from Darwin Core, thus linking it also with that standard. OpenDS object content can be serialized to specific formats/representations (e.g. JSON) for different exchange and processing purposes.
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19

Pouchard, Line, Tanzima Islam, and Bogdan Nicolae. "Challenges for Implementing FAIR Digital Objects with High Performance Workflows." Research Ideas and Outcomes 8 (October 12, 2022). http://dx.doi.org/10.3897/rio.8.e94835.

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New types of workflows are being used in science that couple traditional distributed and high-performance computing (HPC) with data-intensive approaches, and orchestrate ensembles of numerical simulations and artificial intelligence (AI) models. Such workflows may use AI models to supplement computation where numerical simulations may be too computationally expensive, to automate trivial yet time consuming operations, to perform preliminary selections among intractable numbers of combinations in domains as diverse as protein binding, fine-grid climate simulations, and drug discovery. They offer renewed opportunities for scientific research but exhibit high computational, storage and communications requirements [Goble et al. 2020, Al-Saadi et al. 2021, da Silva et al. 2021]. These workflows can be orchestrated by workflow management systems (WMS) and built upon composable blocks that facilitate task placement and resource allocation for parallel executions on high performance systems [Lee et al. 2021, Merzky et al. 2021]. The scientific computing communities running these kinds of workflows have been slow to adopt Findable, Accessible, Interpretable, and Re-usable (FAIR) principles, in part due to the complexity of workflow life cycles, the numerous WMS, and the specificity of HPC systems with rapidly evolving architectures and software stacks, and execution modes that require resource managers and batch schedulers [Plale et al. 2021]. FAIR Digital Objects (FDO) that encapsulate bit sequences of data, metadata, types and persistent identifiers (PID) can help promote the adoption of FAIR, enable knowledge extraction and dissemination, and contribute to re-use [De Smedt et al. 2020]. As workflows typically use data and software during planning and execution, FDOs are particularly adapted to enable re-use [Wittenburg et al. 2020]. But the benefits of FDOs such as automating data processing and actionable DO collections cannot be realized without the main components of FAIR, rich metadata and clear identifiers, being universally adopted in the community. These components are still elusive for HPC digital objects. Some metadata are added after results have been produced, are not described by controlled vocabularies, and typically left unconstrained, resulting in inefficient processes and loss of knowledge. Persistent identifiers are added at the time of publication to data supporting conclusions, so only a very small amount of data are being shared outside a small community of researchers “in the know”. In this conceptual work, one can distinguish several kinds of FDOs for HPC workflows that present both common and specific challenges to the development of canonical DO infrastructure and the implementation of FDO workflows that we discuss below: result FDOs represent computational results obtained when program execution complete, performance FDOs that contain performance measures and results from code optimization on parallel, heterogeneous architectures, intermediate FDOs from intermediate states of workflow execution, obtained from HPC checkpointing. result FDOs represent computational results obtained when program execution complete, performance FDOs that contain performance measures and results from code optimization on parallel, heterogeneous architectures, intermediate FDOs from intermediate states of workflow execution, obtained from HPC checkpointing. All these FDOs for HPC workflows should include the computing environment and system specifications on which code was executed for metadata rich enough to enable re-usability [Pouchard et al. 2019]. Containers are often being used to capture dependencies between underlying libraries and versions in the execution environment for the installation and re-use of software code [Lofstead et al. 2015, Olaya et al. 2020]. But containers published in code repositories are made available without identifiers registered with resolvers. For instance, to attribute a Digital Object Identifier to software shared in github, one must perform the additional step of registering the code into Zenodo. FDOs extracted and built in the context of a canonical workflow framework including collections will help with the attribution of persistent identifiers and the linking of execution environment with data and workflow. Computational results may include machine learning predictions resulting form stochastic training of non-deterministic models. Neural networks and deep learning models present specific challenges to result FDOs related to provenance and the selection of quantities needed to include in an FDO for the re-use of results. What information needs to be included in a FAIR Digital Object encapsulating deep learning results to make it persistent and re-usable? The description of method, data and experiment recommended in [Gundersen and Kjensmo 2018] can be instantiated in a FDO collection. To make it re-usable, it should include the model architecture, the machine learning platform and its version, a submission script that contains hyperparameters, the loss function, batch size and number of epochs [Pouchard et al. 2020]. Challenges specific to digital objects containing performance measures for HPC workflows are those related to size, selection and reduction. Performance data at scale tends to be very large, thus a principled approach to selection is needed to determine which execution counters must be included in FDOs for performance reproducibility of an application [Patki et al. 2019]. Performance FDOs should include the variables selected to show their impact on performance and the methods used for selection: do such variables represent outliers in performance metrics? What methods and thresholds are used to qualify as outliers, what impact do these outliers have on overall performance of an execution? A key contributor to the failure to capture important information in HPC workflows is that metadata and provenance capture is often “bolted on” after the fact and in a piecemeal, cumbersome, inefficient manner that impedes further analysis. An FDO approach including DO collections at the appropriate level of abstraction and rich metadata is needed. Capturing metadata automatically must take into account the appropriate granularity level for re-use across system layers and abstraction levels. Intermediate FDOs capture and fuse metadata across multiple sources during the planning and execution stages [Nicolae 2022]. Some tools already exist. Darshan is a scalable tool summarizing Input/Output file characteristics [Dai et al. 2019], Radical Cybertools [Merzky et al. 2021] can produce the provenance task graph of an execution. Such tools could be included in a canonical workflow framework as they present a path forward for composable services for HPC and would guarantee a level of encapsulation into DOs favorable to re-use.
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20

Nieva de la Hidalga, Abraham, and Alex Hardisty. "Making Heterogeneous Specimen Data ‘FAIR’: Implementing a digital specimen repository." Biodiversity Information Science and Standards 3 (June 18, 2019). http://dx.doi.org/10.3897/biss.3.37163.

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Анотація:
The definition of a digital specimen is proposed to encompass the digital representation(s) of physical specimens from natural science collections. The digital specimen concept is intended to define a representation (digital object) that brings together an array of heterogeneous data types, which are themselves alternative physical specimen representations. In this case, the digital specimen (DS) holds references to specimen data from a collection management system, images, 3D models, research articles, DNA sequences, collector information, among many other data types. The proposal is to create persistent relationships between the DS and other categories of digital objects (e.g. resource types mentioned above, collections, storage platforms, organisations, databases, and provenance data). Complying with FAIR data principles (findability, accessibility, interoperability, and reuse), i.e., achieving data ‘FAIRness’, eases data integration, which is needed for cross-disciplinary linking and combination of data from different domains, making the DS as a comprehensive package of information about a specimen. Implementation and access to a digital specimen repository (DSR) as a Digital Object Architecture (Sharp 2016) component demonstrates the alignment of the DS concept and FAIR data principles (Wilkinson et al. 2016, Kahn and Wilensky 2006). The DSR fulfills four roles: data producer, resource manager, data publisher, and collaboration space. As data producer, the DSR allows acquisition and curation (indexing, storage) of DSs linking primary data, models, analyses, and other digital object types. As resource manager, the DSR manages access to distributed platforms, ranging from acquisition networks (digitisation stations, museums, herbariums) to processing services, advanced computational resources, data asset storage systems, and specialised servers. As data publisher, the DSR provides access to data assets from national and transnational data archives. As collaboration space, the DSR supports users’ accessing, sharing and (re)using data assets, and derived data products and services. Adopting the collaboration space and data publisher roles, the DSR implements interfaces that expose the DSs to the research community, fulfilling the FAIR findability, accessibility, and reuse principles. Adopting the data producer and resource manager roles, the DSR creates meaningful and persistent relationships required to link DSs and other types of digital objects, fulfilling the FAIR interoperability principle. A prototype DSR based on the Cordra digital object repository has been deployed (Corporation for National Research Initiatives (CNRI) 2018, Reilly and Tupelo-Schneck 2010). The advantages of Cordra are: rapid deployment, customisable object model, creation of relations between digital objects, and application program interfaces for programmatic access. Rapid deployment of the DSR provides a tangible target for discussing the implementation of the DS concept. The customisable object model enables the refinement and enhancing of the definition of DS in response to feedback from colleagues who have accessed the DSR and used its contents. Creating relations between digital objects enables flexible linking to digital objects stored in different repositories. Accessing the DSR programmatically through APIs enables extending the use of the repository in different platforms (e.g. mobile devices) as well as integration with other repositories and services. As well as supporting a HTTP-oriented API, Cordra implements Digital Object Interface Protocol (DONA Foundation 2018), allowing the definition of operations to act directly on selected DSs in the repository. The DSR prototype has been demonstrated by providing access to the repository administrative interface and with a custom interface designed to facilitate access by different user groups, such as collection curators, researchers, teachers, and students. The client interface has been designed to demonstrate a subset of the functionalities derived from user stories, which describe software features from the end-user perspective. Demonstrating the DSR capabilities as proposed, will inform the refinement of the design of the DS model and provide early feedback about the needed software features.
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21

Holetschek, Jörg, Gabriele Droege, Anton Güntsch, Nils Köster, Jeannine Marquardt, and Thomas Borsch. "Gardens4Science: Setting Up a Trusted Network for German Botanic Gardens Using Open Source Technologies." Biodiversity Information Science and Standards 3 (June 13, 2019). http://dx.doi.org/10.3897/biss.3.35368.

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Анотація:
Botanic gardens are an invaluable refuge for plant diversity for conservation, education and research. Worldwide, they manage over 100,000 species, roughly 30% of all plant species diversity, and over 41% of known threatened species; the botanic gardens in Germany house approximately 50,000 different species (Marquardt et al. in press). Scientists in need of plant material rely upon these resources for their research; they require a pooled, up-to-date inventory of ideally all accessions of these gardens. Sharing data from (living) specimen collections online has become routine in the past years; initiatives like PlantSearch of Botanic Gardens Conservation International and the Global Biodiversity Information Facility (GBIF) allow requesting specimens of interest. However, these catalogues are accessible for everyone. Legitimate concerns about potential theft and legal issues keep curators of living collections from sharing their full catalogues; in most cases, only filtered views of the data will be fed into these networks. Gardens4Science (http://gardens4science.biocase.org) aims at overcoming this issue by creating a trusted network between botanic gardens that allows an unfiltered access on the constituents’ accession catalogues. This unified data pool needs to be automatically synchronized with the individual garden’s catalogues, irrespective of the collection management systems used locally. For the three-year construction phase of Gardens4Science, focus is on Cactaceae and Bromeliaceae, since these families are well-represented in the collections and ideal models for studying the origin of biodiversity on evolutionary time scale. Gardens4Science’s technical architecture (Fig. 1) is based on existing tools for setting up biodiversity networks: The BioCASe (Biological Collections Access Service) Provider Software acts as an interface to the local databases that shields the network from their peculiarities (database management systems and data models used). BioCASe transforms the data into the Access to Biological Collections Data schema (ABCD) and publishes them as a BioCASe-compliant web service (Holetschek and Döring 2008, Holetschek et al. 2012). The data portal is based on portal software from the Global Genome Biodiversity Network and provides a user-specific view on the data. Registered trusted users will be able to display full details of individual accessions, whereas guest users will see only an aggregated view (Droege et al. 2014). The Berlin Indexing and Harvesting Toolkit (B-HIT) is used for harvesting the BioCASe web services of the local catalogues and creating a unified index database (Kelbert et al. 2015). Harvesting is done in regular intervals in order to keep the index in sync with the source databases and does not require any action on the provider’s side. The BioCASe (Biological Collections Access Service) Provider Software acts as an interface to the local databases that shields the network from their peculiarities (database management systems and data models used). BioCASe transforms the data into the Access to Biological Collections Data schema (ABCD) and publishes them as a BioCASe-compliant web service (Holetschek and Döring 2008, Holetschek et al. 2012). The data portal is based on portal software from the Global Genome Biodiversity Network and provides a user-specific view on the data. Registered trusted users will be able to display full details of individual accessions, whereas guest users will see only an aggregated view (Droege et al. 2014). The Berlin Indexing and Harvesting Toolkit (B-HIT) is used for harvesting the BioCASe web services of the local catalogues and creating a unified index database (Kelbert et al. 2015). Harvesting is done in regular intervals in order to keep the index in sync with the source databases and does not require any action on the provider’s side. In addition to harvesting, B-HIT performs several data cleaning steps. Foremost, it reconciles scientific names from the source databases with a taxonomic backbone (currently caryophyllales.org for Cactaceae and the Butcher and Gouda checklist for Bromeliaceae), which allows harmonizing the taxonomies from the different sources and the correction of outdated species names and orthographic mistakes. Provenance information are validated (for example specified geographic coordinates versus country) and corrected, if possible; date values are parsed and converted into a standard format. The issues found and potential corrections are compiled in reports and send to the curators, so the mistakes can be rectified in the source databases. In the construction phase, Gardens4Science consists of seven German Botanic gardens that share their accessions of the Bromeliaceae and Cactaceae families. Up to now (March 2019), 19.539 records have been published in Evo-BoGa, with about 3,500 to be added until the end of the project in January 2020. After the construction phase, it is planned to extend the network to include more Botanic Gardens – both from Germany and other countries – as well as additional plant families.
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22

Ruiz-Olazar, Margarita, Evandro Santos Rocha, Claudia D. Vargas, and Kelly Rosa Braghetto. "The Neuroscience Experiments System (NES)–A Software Tool to Manage Experimental Data and Its Provenance." Frontiers in Neuroinformatics 15 (January 7, 2022). http://dx.doi.org/10.3389/fninf.2021.768615.

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Computational tools can transform the manner by which neuroscientists perform their experiments. More than helping researchers to manage the complexity of experimental data, these tools can increase the value of experiments by enabling reproducibility and supporting the sharing and reuse of data. Despite the remarkable advances made in the Neuroinformatics field in recent years, there is still a lack of open-source computational tools to cope with the heterogeneity and volume of neuroscientific data and the related metadata that needs to be collected during an experiment and stored for posterior analysis. In this work, we present the Neuroscience Experiments System (NES), a free software to assist researchers in data collecting routines of clinical, electrophysiological, and behavioral experiments. NES enables researchers to efficiently perform the management of their experimental data in a secure and user-friendly environment, providing a unified repository for the experimental data of an entire research group. Furthermore, its modular software architecture is aligned with several initiatives of the neuroscience community and promotes standardized data formats for experiments and analysis reporting.
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23

El-Gebali, Sara, Rory Macneil, Rorie Edmunds, Parul Tewatia, and Jens Klump. "Biospecimens in FDO world." Research Ideas and Outcomes 8 (October 12, 2022). http://dx.doi.org/10.3897/rio.8.e94544.

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Анотація:
With the advent of technological advances in research settings, scientific collections including sample material became on par with big data. Consequently there is a widespread need to highlight and recognise the inherent value of samples coupled with efforts in unlocking sample potential as resources for new scientific discovery. Samples with informative metadata can be more easily discoverable, more readily shared and reused, allowing reanalysis of associated datasets, avoiding duplicate efforts, and providing metaanalysis yielding considerably enhanced insight. Metadata provides the framework for a consistent, systematic and standardized collection of sample information, enabling users to identify the availability of research output from the samples, relevancy to their intended use, and a way to conveniently identify sample material as well as access provenance information related to the physical samples. Researchers need this essential information aiding their decision making process on the quality, usability and accessibility of the samples and associated datasets. We propose to explore the practical implementation of FAIR Digital Objects (FDO) for biological life science physical samples and practically how to create an FDO framework centralized around biospecimen samples, linked datasets, sample information and PIDs (Persistent Identifiers)Klump et al. 2021. This effort is highly relevant to enhancing the portability of sample information between multiple repositories and other kinds of resources (e.g. e-infrastructures). In this session we would like to present our current work in order to mobilize the community to define the FAIR Digital Object Architecture for biospecimen in life science including all infrastructure components e.g. metadata, PIDs and their integration with technical solutions. To that end, in our community of practice we aim to: What: Identify the minimum set of attributes required for describing biospecimen in biological life science (Minimal Information About a Biological Sample, MIABS) with ontological mapping for semantic unambiguity and machine actionability.Identify the required attributes for registering PIDs for biospecimens and how that will operate in an FDO ecosystem. This will pave the way for a framework of coupling the descriptive metadata to the digital object in a FAIR and comprehensive manner. How:Define a semantic FDO model for biospecimens.Define the role of biospecimen PIDs registration information and kernel attributes and how that translates to machine actionability and programmatic decisions.Define the implementation specifics for integration of biospecimen FDOs with operational infrastructure e.g. e-infrastructures, repositories and machines. What: Identify the minimum set of attributes required for describing biospecimen in biological life science (Minimal Information About a Biological Sample, MIABS) with ontological mapping for semantic unambiguity and machine actionability.Identify the required attributes for registering PIDs for biospecimens and how that will operate in an FDO ecosystem. This will pave the way for a framework of coupling the descriptive metadata to the digital object in a FAIR and comprehensive manner. Identify the minimum set of attributes required for describing biospecimen in biological life science (Minimal Information About a Biological Sample, MIABS) with ontological mapping for semantic unambiguity and machine actionability. Identify the required attributes for registering PIDs for biospecimens and how that will operate in an FDO ecosystem. This will pave the way for a framework of coupling the descriptive metadata to the digital object in a FAIR and comprehensive manner. How:Define a semantic FDO model for biospecimens.Define the role of biospecimen PIDs registration information and kernel attributes and how that translates to machine actionability and programmatic decisions.Define the implementation specifics for integration of biospecimen FDOs with operational infrastructure e.g. e-infrastructures, repositories and machines. Define a semantic FDO model for biospecimens. Define the role of biospecimen PIDs registration information and kernel attributes and how that translates to machine actionability and programmatic decisions. Define the implementation specifics for integration of biospecimen FDOs with operational infrastructure e.g. e-infrastructures, repositories and machines. Relevant technologies include: RO-Crate, Persistent identifiers, and metadata schemas Relevant technologies include: RO-Crate, Persistent identifiers, and metadata schemas The recent partnership between IGSN and DataCite described below is a catalyst in this call of action to the FDO community to build a Community of Practice (CoP) specifically focused on biospecimen samples. Community of practice: IGSN e.V. announced a partnership with DataCite, in which DataCite’s registration services and supporting technology for Digital Object Identifiers (another type of PID) are now being leveraged to register IGSN IDs, and thus ensure the ongoing sustainability of the IGSN ID infrastructure. Importantly, the two organizations are also focusing the community’s efforts on advocacy of PIDs for physical samples and expanding the global sample ecosystem. Assisted by the DataCite Samples Community Manager, the IGSN e.V. is establishing working groups (Communities of Practice) within different research domains to support development and promotion of standardized methods for identifying, citing, and locating physical samples. In particular, the partnership wishes to work with the Biosamples community to elaborate the necessary information (metadata) such that those within the community have a full understanding of a physical sample when its descriptive webpage is accessed via its PID, see this example.
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Kostandini, Silvia. "Rock With Lots Of Holes." Rangahau Aranga: AUT Graduate Review 1, no. 1 (April 12, 2022). http://dx.doi.org/10.24135/rangahau-aranga.v1i1.72.

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We perceive our surroundings differently when fully engaged with them. Interactions with spaces begin to define our experience of the world. This research is a modern story of matter and philosophy, investigating the rock Scoria to produce a series of public architectural spaces that uniquely engage with the beholder. By taking part in the Material Imaginaries Research Collective - AUT Spatial Design department - I ask the following: 'What is our world made of? How might an expanded sense of 'material' and a focus on meaning, provenance, story, and performance recast how we make space?' With an imaginary read on the rock Scoria, the research explores both abstract and tangible ways to unfold a narrative of matter. Engaging with geographical, cultural, and social aspects that define the scoriaceous element and its connection to the “Tamaki Makaurau Volcanic landscape” (Tūpuna Maunga Authority). The exploration of Scoria's materiality becomes the driving aspect of the study, bridging learning and processes into practice-led research to uncover the existing history of the volcanic rock, challenging conventional methods and developing Le Mappe Del Mondo, Lavoro Manuale, and Il Giornale as a creative alternative to organize the various tools and techniques that shape the creative practice. The choice to incorporate Italian terminology becomes a playful way to acknowledge my background through the research. The project wishes to provide a set of interventions that engage with the geographical heritage features of Tāmaki Makarau in shaping a collection of public gathering spaces that activate unfurnished and unutilized areas around the territory. By celebrating the Tūpuna Maunga to showcase the heritage values associated with preserving those sites and considering the broader landscape's role in supporting our growth as a society. By providing a range of public spaces for the collective, such as gatherings and recreation, the designer considers all the components to ensure “sustainable” (Project for Public Spaces) city life engagement.
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Guarini, Beaux Fen. "Beyond Braille on Toilet Doors: Museum Curators and Audiences with Vision Impairment." M/C Journal 18, no. 4 (August 7, 2015). http://dx.doi.org/10.5204/mcj.1002.

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The debate on the social role of museums trundles along in an age where complex associations between community, collections, and cultural norms are highly contested (Silverman 3–4; Sandell, Inequality 3–23). This article questions whether, in the case of community groups whose aspirations often go unrecognised (in this case people with either blindness or low vision), there is a need to discuss and debate institutionalised approaches that often reinforce social exclusion and impede cultural access. If “access is [indeed] an entry point to experience” (Papalia), then the privileging of visual encounters in museums is clearly a barrier for people who experience sight loss or low vision (Levent and Pursley). In contrast, a multisensory aesthetic to exhibition display respects the gamut of human sensory experience (Dudley 161–63; Drobnick 268–69; Feld 184; James 136; McGlone 41–60) as do discursive gateways including “lectures, symposia, workshops, educational programs, audio guides, and websites” (Cachia). Independent access to information extends beyond Braille on toilet doors.Underpinning this article is an ongoing qualitative case study undertaken by the author involving participant observation, workshops, and interviews with eight adults who experience vision impairment. The primary research site has been the National Museum of Australia. Reflecting on the role of curators as storytellers and the historical development of museums and their practitioners as agents for social development, the article explores the opportunities latent in museum collections as they relate to community members with vision impairment. The outcomes of this investigation offer insights into emerging issues as they relate to the International Council of Museums (ICOM) definitions of the museum program. Curators as Storytellers“The ways in which objects are selected, put together, and written or spoken about have political effects” (Eilean Hooper-Greenhill qtd. in Sandell, Inequality 8). Curators can therefore open or close doors to discrete communities of people. The traditional role of curators has been to collect, care for, research, and interpret collections (Desvallées and Mairesse 68): they are characterised as information specialists with a penchant for research (Belcher 78). While commonly possessing an intimate knowledge of their institution’s collection, their mode of knowledge production results from a culturally mediated process which ensures that resulting products, such as cultural significance assessments and provenance determinations (Russell and Winkworth), privilege the knowing systems of dominant social groups (Fleming 213). Such ways of seeing can obstruct the access prospects of underserved audiences.When it comes to exhibition display—arguably the most public of work by museums—curators conventionally collaborate within a constellation of other practitioners (Belcher 78–79). Curators liaise with museum directors, converse with conservators, negotiate with exhibition designers, consult with graphics designers, confer with marketing boffins, seek advice from security, chat with editors, and engage with external contractors. I question the extent that curators engage with community groups who may harbour aspirations to participate in the exhibition experience—a sticking point soon to be addressed. Despite the team based ethos of exhibition design, it is nonetheless the content knowledge of curators on public display. The art of curatorial interpretation sets out not to instruct audiences but, in part, to provoke a response with narratives designed to reveal meanings and relationships (Freeman Tilden qtd. in Alexander and Alexander 258). Recognised within the institution as experts (Sandell, Inclusion 53), curators have agency—they decide upon the stories told. In a recent television campaign by the National Museum of Australia, a voiceover announces: a storyteller holds incredible power to connect and to heal, because stories bring us together (emphasis added). (National Museum of Australia 2015)Storytelling in the space of the museum often shares the histories, perspectives, and experiences of people past as well as living cultures—and these stories are situated in space and time. If that physical space is not fit-for-purpose—that is, it does not accommodate an individual’s physical, intellectual, psychiatric, sensory, or neurological needs (Disability Discrimination Act 1992, Cwlth)—then the story reaches only long-established patrons. The museum’s opportunity to contribute to social development, and thus the curator’s as the primary storyteller, will have been missed. A Latin-American PerspectiveICOM’s commitment to social development could be interpreted merely as a pledge to make use of collections to benefit the public through scholarship, learning, and pleasure (ICOM 15). If this interpretation is accepted, however, then any museum’s contribution to social development is somewhat paltry. To accept such a limited and limiting role for museums is to overlook the historical efforts by advocates to change the very nature of museums. The ascendancy of the social potential of museums first blossomed during the late 1960s at a time where, globally, overlapping social movements espoused civil rights and the recognition of minority groups (Silverman 12; de Varine 3). Simultaneously but independently, neighbourhood museums arose in the United States, ecomuseums in France and Quebec, and the integral museum in Latin America, notably in Mexico (Hauenschild; Silverman 12–13). The Latin-American commitment to the ideals of the integral museum developed out of the 1972 round table of Santiago, Chile, sponsored by the United Nations Educational, Scientific and Cultural Organization (Giménez-Cassina 25–26). The Latin-American signatories urged the local and regional museums of their respective countries to collaborate with their communities to resolve issues of social inequality (Round Table Santiago 13–21). The influence of Brazilian educator Paulo Freire should be acknowledged. In 1970, Freire ushered in the concept of conscientization, defined by Catherine Campbell and Sandra Jovchelovitch as:the process whereby critical thinking develops … [and results in a] … thinker [who] feels empowered to think and to act on the conditions that shape her living. (259–260)This model for empowerment lent inspiration to the ideals of the Santiago signatories in realising their sociopolitical goal of the integral museum (Assunção dos Santos 20). Reframing the museum as an institution in the service of society, the champions of the integral museum sought to redefine the thinking and practices of museums and their practitioners (United Nations Educational, Scientific and Cultural Organization 37–39). The signatories successfully lobbied ICOM to introduce an explicitly social purpose to the work of museums (Assunção dos Santos 6). In 1974, in the wake of the Santiago round table, ICOM modified their definition of a museum to “a permanent non-profit institution, open to the public, in the service of society and its development” (emphasis added) (Hauenschild). Museums had been transformed into “problem solvers” (Judite Primo qtd. in Giménez-Cassina 26). With that spirit in mind, museum practitioners, including curators, can develop opportunities for reciprocity with the many faces of the public (Guarini). Response to Social Development InitiativesStarting in the 1970s, the “second museum revolution” (van Mensch 6–7) saw the transition away from: traditional roles of museums [of] collecting, conservation, curatorship, research and communication … [and toward the] … potential role of museums in society, in education and cultural action. (van Mensch 6–7)Arguably, this potential remains a work in progress some 50 years later. Writing in the tradition of museums as agents of social development, Mariana Lamas states:when we talk about “in the service of society and its development”, it’s quite different. It is like the drunk uncle at the Christmas party that the family pretends is not there, because if they pretend long enough, he might pass out on the couch. (Lamas 47–48)That is not to say that museums have neglected to initiate services and programs that acknowledge the aspirations of people with disabilities (refer to Cachia and Krantz as examples). Without discounting such efforts, but with the refreshing analogy of the drunken uncle still fresh in memory, Lamas answers her own rhetorical question:how can traditional museums promote community development? At first the word “development” may seem too much for the museum to do, but there are several ways a museum can promote community development. (Lamas 52) Legitimising CommunitiesThe first way that museums can foster community or social development is to:help the community to over come [sic] a problem, coming up with different solutions, putting things into a new perspective; providing confidence to the community and legitimizing it. (Lamas 52)As a response, my doctoral investigation legitimises the right of people with vision impairment to participate in the social and cultural aspects of publicly funded museums. The Australian Government upheld this right in 2008 by ratifying the United Nations Convention on the Rights of Persons with Disabilities (and Optional Protocol), which enshrines the right of people with disability to participate in the cultural life of the nation (United Nations).At least 840,700 people in Australia (a minimum of four per cent of the population) experiences either blindness or low vision (Australian Bureau of Statistics 2009). For every one person in the Australian community who is blind, nearly five other people experience low vision. The medical model of disability identifies the impairment as the key feature of a person and seeks out a corrective intervention. In contrast, the social model of disability strives to remove the attitudinal, social, and physical barriers enacted by people or institutions (Landman, Fishburn, and Tonkin 14). Therein lies the opportunity and challenge for museums—modifying layouts and practices that privilege the visual. Consequently, there is scope for museums to partner with people with vision impairment to identify their aspirations rather than respond as a problem to be fixed. Common fixes in the museums for people with disabilities include physical alterations such as ramps and, less often, special tours (Cachia). I posit that curators, as co-creators and major contributors to exhibitions, can be part of a far wider discussion. In the course of doctoral research, I accompanied adults with a wide array of sight impairments into exhibitions at the Museum of Australian Democracy at Old Parliament House, the Australian War Memorial, and the National Museum of Australia. Within the space of the exhibition, the most commonly identified barrier has been the omission of access opportunities to interpreted materials: that is, information about objects on display as well as the wider narratives driving exhibitions. Often, the participant has had to work backwards, from the object itself, to understand the wider topic of the exhibition. If aesthetics is “the way we communicate through the senses” (Thrift 291), then the vast majority of exhibits have been inaccessible from a sensory perspective. For people with low vision (that is, they retain some degree of functioning sight), objects’ labels have often been too small to be read or, at times, poorly contrasted or positioned. Objects have often been set too deep into display cabinets or too far behind safety barriers. If individuals must use personal magnifiers to read text or look in vain at objects, then that is an indicator that there are issues with exhibition design. For people who experience blindness (that is, they cannot see), neither the vast majority of exhibits nor their interpretations have been made accessible. There has been minimal access across all museums to accessioned objects, handling collections, or replicas to tease out exhibits and their stories. Object labels must be read by family or friends—a tiring experience. Without motivated peers, the stories told by curators are silenced by a dearth of alternative options.Rather than presume to know what works for people with disabilities, my research ethos respects the “nothing about us without us” (Charlton 2000; Werner 1997) maxim of disability advocates. To paraphrase Lamas, we have collaborated to come up with different solutions by putting things into new perspectives. In turn, “person-centred” practices based on rapport, warmth, and respect (Arigho 206–07) provide confidence to a diverse community of people by legitimising their right to participate in the museum space. Incentivising Communities Museums can also nurture social or community development by providing incentives to “the community to take action to improve its quality of life” (Lamas 52). It typically falls to (enthusiastic) public education and community outreach teams to engage underserved communities through targeted programs. This approach continues the trend of curators as advocates for the collection, and educators as advocates for the public (Kaitavouri xi). If the exhibition briefs normally written by curators (Belcher 83) reinforced the importance of access, then exhibition designers would be compelled to offer fit-for-purpose solutions. Better still, if curators (and other exhibition team members) regularly met with community based organisations (perhaps in the form of a disability reference group), then museums would be better positioned to accommodate a wider spectrum of community members. The National Standards for Australian Museums and Galleries already encourages museums to collaborate with disability organisations (40). Such initiatives offer a way forward for improving a community’s sense of itself and its quality of life. The World Health Organization defines health as a “state of complete physical, mental and social well-being and not merely the absence of disease or infirmity”. While I am not using quality of life indicators for my doctoral study, the value of facilitating social and cultural opportunities for my target audience is evident in participant statements. At the conclusion of one sensory based workshop, Mara, a female participant who experiences low vision in one eye and blindness in the other, stated:I think it was interesting in that we could talk together about what we were experiencing and that really is the social aspect of it. I mean if I was left to go to a whole lot of museums on my own, I probably wouldn’t. You know, I like going with kids or a friend visiting from interstate—that sort of thing. And so this group, in a way, replicates that experience in that you’ve got someone else to talk about your impressions with—much better than going on your own or doing this alone.Mara’s statement was in response to one of two workshops I held with the support of the Learning Services team at the National Museum of Australia in May 2015. Selected objects from the museum’s accessioned collection and handling collection were explored, as well as replicas in the form of 3D printed objects. For example, participants gazed upon and handled a tuckerbox, smelt and tasted macadamia nuts in wattle seed syrup, and listened to a genesis story about the more-ish nut recorded by the Butchulla people—the traditional owners of Fraser Island. We sat around a table while I, as the workshop mediator, sought to facilitate free-flowing discussions about their experiences and, in turn, mused on the capacity of objects to spark social connection and opportunities for cultural access. While the workshop provided the opportunity for reciprocal exchanges amongst participants as well as between participants and me, what was highly valued by most participants was the direct contact with members of the museum’s Learning Services team. I observed that participants welcomed the opportunity to talk with real museum workers. Their experience of museum practitioners, to date, had been largely confined to the welcome desk of respective institutions or through special events or tours where they were talked at. The opportunity to communicate directly with the museum allowed some participants to share their thoughts and feelings about the services that museums provide. I suggest that curators open themselves up to such exchanges on a more frequent basis—it may result in reciprocal benefits for all stakeholders. Fortifying IdentityA third way museums can contribute to social or community development is by:fortify[ing] the bonds between the members of the community and reaffirm their identities making them feel more secure about who they are; and give them a chance to tell their own version of their history to “outsiders” which empowers them. (Lamas 52)Identity informs us and others of who we are and where we belong in the world (Silverman 54). However, the process of identity marking and making can be fraught: “some communities are ours by choice … [and] … some are ours because of the ways that others see us” (Watson 4). Communities are formed by identifying who is in and who is out (Francois Dubet qtd. in Bessant and Watts 260). In other words, the construction of collective identity is reinforced through means of social inclusion and social exclusion. The participants of my study, as members or clients of the Royal Society for the Blind | Canberra Blind Society, clearly value participating in events with empathetic peers. People with vision impairment are not a homogenous group, however. Reinforcing the cultural influences on the formation of identity, Fiona Candlin asserts that “to state the obvious but often ignored fact, blind people … [come] … from all social classes, all cultural, racial, religious and educational backgrounds” (101). Irrespective of whether blindness or low vision arises congenitally, adventitiously, or through unexpected illness, injury, or trauma, the end result is an assortment of individuals with differing perceptual characteristics who construct meaning in often divergent ways (De Coster and Loots 326–34). They also hold differing world views. Therefore, “participation [at the museum] is not an end in itself. It is a means for creating a better world” (Assunção dos Santos 9). According to the Australian Human Rights Commissioner, Professor Gillian Triggs, a better world is: a society for all, in which every individual has an active role to play. Such a society is based on fundamental values of equity, equality, social justice, and human rights and freedoms, as well as on the principles of tolerance and embracing diversity. (Triggs)Publicly funded museums can play a fundamental role in the cultural lives of societies. For example, the Powerhouse Museum (Museum of Applied Arts and Sciences) in Sydney partnered with Vision Australia to host an exhibition in 2010 titled Living in a Sensory World: it offered “visitors an understanding of the world of the blindness and low vision community and celebrates their achievements” (Powerhouse Museum). With similar intent, my doctoral research seeks to validate the world of my participants by inviting museums to appreciate their aspirations as a distinct but diverse community of people. ConclusionIn conclusion, the challenge for museum curators and other museum practitioners is balancing what Richard Sennett (qtd. in Bessant and Watts 265) identifies as opportunities for enhancing social cohesion and a sense of belonging while mitigating parochialism and community divisiveness. Therefore, curators, as the primary focus of this article, are indeed challenged when asked to contribute to serving the public through social development—a public which is anything but homogenous. Mindful of cultural and social differences in an ever-changing world, museums are called to respect the cultural and natural heritage of the communities they serve and collaborate with (ICOM 10). It is a position I wholeheartedly support. This is not to say that museums or indeed curators are capable of solving the ills of society. However, inviting people who are frequently excluded from social and cultural events to multisensory encounters with museum collections acknowledges their cultural rights. I suggest that this would be a seismic shift from the current experiences of adults with blindness or low vision at most museums.ReferencesAlexander, Edward, and Mary Alexander. Museums in Motion: An Introduction to the History and Functions of Museums. 2nd ed. Lanham, Maryland: AltaMira Press, 2008.Arigho, Bernie. “Getting a Handle on the Past: The Use of Objects in Reminiscence Work.” Touch in Museums: Policy and Practice in Object Handling. Ed. Helen Chatterjee. Oxford: Berg, 2008. 205–12.Assunção dos Santos, Paula. Introduction. Sociomuseology 4: To Think Sociomuseologically. Eds. Paula Assunção dos Santos and Judite Primo. Lisbon: Universidade Lusófona de Humanidades e Tecnologias, 2010. 5–12.Australian Bureau of Statistics. “National Health Survey: Summary of Results (2007- 2008) (Reissue), Cat. No. 4364.0. 2009.” Australian Bureau of Statistics. 12 Feb. 2015 ‹http://www.abs.gov.au/ausstats/abs@.nsf/mf/4364.0›.Belcher, Michael. Exhibitions in Museums. Leicester: Leicester UP, 1991.Bessant, Judith, and Rob Watts. Sociology Australia. 3rd ed. Crows Nest: Allen & Unwin, 2007.Cachia, Amanda. “Talking Blind: Disability, Access, and the Discursive Turn.” Disability Studies Quarterly 33.3 (2013). 23 July 2015 ‹http://dsq-sds.org/article/view/3758›.Campbell, Catherine, and Sandra Jovchelovitch. "Health, Community and Development: Towards a Social Psychology of Participation." Journal of Community & Applied Social Psychology 10.4 (2000): 255–70.Candlin, Fiona. "Blindness, Art and Exclusion in Museums and Galleries." International Journal of Art & Design Education 22.1 (2003): 100–10.Charlton, James. Nothing about Us without Us: Disability Oppression and Empowerment. Berkeley: U of California P, 2000.De Coster, Karin, and Gerrit Loots. "Somewhere in between Touch and Vision: In Search of a Meaningful Art Education for Blind Individuals." International Journal of Art & Design Education 23.3 (2004): 32634.De Varine, Hugues. “Decolonising Museology.” ICOM News 58.3 (2005): 3.Desvallées, André, and François Mairesse. Key Concepts of Museology. Paris: Armand Colin, 2010. 16 Jun. 2015 ‹http://icom.museum/professional-standards/key-concepts-of-museology/›.Disability Discrimination Act 1992 (Cwlth). 14 June 2015 ‹https://www.comlaw.gov.au/Series/C2004A04426›.Drobnick, Jim. “Volatile Effects: Olfactory Dimensions of Art and Architecture.” Empire of the Senses: The Sensual Culture Reader. Ed. David Howes. New York: Berg, 2005. 265–80.Dudley, Sandra. “Sensory Exile in the Field.” Museums Objects: Experiencing the Properties of Things. Ed. Sandra H. Dudley. Abingdon, UK: Routledge, 2012. 161–63.Feld, Steven. “Places Sensed, Senses Placed: Toward a Sensuous Epistemology of Environments.” Empire of the Senses: The Sensual Culture Reader. Ed. David Howes. New York: Berg, 2005. 179–91.Fleming, David. “Positioning the Museum for Social Inclusion.” Museums, Society, Inequality. Ed. Richard Sandell. London: Routledge, 2002. 213–24.Giménez-Cassina, Eduardo. “Who Am I? An Identity Crisis. Identity in the New Museologies and the Role of the Museum Professional.” Sociomuseology 3: To Understand New Museology in the XXI Century. Eds. Paula Assunção dos Santos and Judite Primo. Lisbon: Universidade Lusófona de Humanidades e Tecnologias, 2010. 25–42. Guarini, Beaux. Up Close and Personal: Engaging Collections alongside Adults with Vision Impairment. 2015. 17 June 2015 ‹http://nma.gov.au/blogs/education/2015/06/17/4802/›.Hauenschild, Andrea. Claims and Reality of New Museology: Case Studies in Canada, the United States and Mexico. 1988. 21 June 2015 ‹http://museumstudies.si.edu/claims2000.htm›.Hoyt, Bridget O’Brien. “Emphasizing Observation in a Gallery Program for Blind and Low-Vision Visitors: Art beyond Sight at the Museum of Fine Arts, Houston.” Disability Studies Quarterly 33.3 (2013). 23 July 2015 ‹http://dsq-sds.org/article/view/3737›.International Council of Museums. ICOM Code of Ethics for Museums. Paris: International Council of Museums, 2013. 6 June 2015 ‹http://icom.museum/the-vision/code-of-ethics/›.James, Liz. “Senses and Sensibility in Byzantium.” Museums Objects: Experiencing the Properties of Things. Ed. Sandra H. Dudley. Abingdon, UK: Routledge, 2012. 134–149.Kaitavouri, Kaija. Introduction. It’s All Mediating: Outlining and Incorporating the Roles of Curating and Education in the Exhibit Context. Eds. Kaija Kaitavouri, Laura Kokkonen, and Nora Sternfeld. Newcastle upon Tyne: Cambridge Scholars Publishing, 2013. x–xxi.Lamas, Mariana. “Lost in the Supermarket – The Traditional Museums Challenges.” Sociomuseology 3: To Understand New Museology in the XXI Century. Eds. Paula Assunção dos Santos and Judite Primo. Lisbon: Universidade Lusófona de Humanidades e Tecnologias, 2010. 42–58. Landman, Peta, Kiersten Fishburn, Lynda Kelly, and Susan Tonkin. Many Voices Making Choices: Museum Audiences with Disabilities. Sydney: Australian Museum and National Museum of Australia, 2005. Levent, Nina, and Joan Muyskens Pursley. “Sustainable Museum Acess: A Two-Way Street.” Disability Studies Quarterly 33.3 (2013). 22 July 2015 ‹http://dsq-sds.org/article/view/3742›.McGlone, Francis. “The Two Sides of Touch: Sensing and Feeling.” Touch in Museums: Policy and Practice in Object Handling. Ed. Helen Chatterjee. Oxford: Berg, 2008. 41–60.National Museum of Australia. “Stories Can Unite Us as One.” YouTube 28 May 2015. 16 Jun. 2015 ‹https://www.youtube.com/watch?v=Qwxj_rC57zM›.National Standards Taskforce. National Standards for Australian Museums and Galleries (Version 1.4, October 2014). Melbourne: The National Standards Taskforce, 2014. 20 June 2015 ‹http://www.mavic.asn.au/assets/NSFAMG_v1_4_2014.pdf›.Papalia, Carmen. “A New Model for Access in the Museum.” Disability Studies Quarterly 33.3 (2013). 23 July 2015 ‹http://dsq-sds.org/article/view/3757›.Powerhouse Museum. Living in a Sensory World: Stories from People with Blindness and Low Vision. nd. 18 Feb. 2015 ‹http://www.powerhousemuseum.com/previous/living/›.“Round Table Santiago do Chile ICOM, 1972.” Sociomuseology 4: To Think Sociomuseologically. Eds. Paula Assunção dos Santos and Judite Primo. Lisbon: Universidade Lusófona de Humanidades e Tecnologias, 2010.Royal Society for the Blind | Canberra Blind Society. Canberra Blind Society. nd. 14 Mar. 2015 ‹http://www.canberrablindsociety.org.au/›.Russell, Rosyln, and Kylie Winkworth. Significance 2.0: A Guide to Assessing the Significance of Collections. Adelaide: Collections Council of Australia, 2009. 15 June 2015 ‹http://arts.gov.au/sites/default/files/resources-publications/significance-2.0/pdfs/significance-2.0.pdf›.Sandell, Richard. “Museums and the Combatting of Social Inequality: Roles, Responsibities, Resistance.” Museums, Society, Inequality. Ed. Richard Sandell. London: Routledge, 2002. 3–23.———. "Social Inclusion, the Museum and the Dynamics of Sectoral Change." Museum and Society 1.1 (2003): 45–62.Silverman, Lois. The Social Work of Museums. London: Routledge, 2010.Thrift, Nigel. “Understanding the Material Practices of Glamour.” The Affect Theory Reader. Eds. Melissa Gregg and Gregory Seigworth. Durham: Duke UP, 2010. 289–308.Triggs, Gillian. Social Inclusion and Human Rights in Australia. 2013. 6 June 2015 ‹https://www.humanrights.gov.au/news/speeches/social-inclusion-and-human-rights-australia›. United Nations. Convention on the Rights of Persons with Disabilities. 2006. 16 Mar. 2015 ‹http://www.un.org/disabilities/default.asp?id=150?›.United Nations Educational Scientific and Cultural Organization. United Nations Educational Scientific and Cultural Organisation Round Table on the Development and the Role of Museums in the Contemporary World - Santiago de Chile, Chile 20-31 May 1972. 1973. 18 June 2015 ‹http://unesdoc.unesco.org/images/0002/000236/023679EB.pdf›.Van Mensch, Peter. Towards a Methodology of Museology. Diss. U of Zagreb, 1992. 16 June 2015 ‹http://www.muzeologie.net/downloads/mat_lit/mensch_phd.pdf›.Watson, Sheila. “Museum Communities in Theory and Practice.” Museums and Their Communities. Ed. Sheila Watson. Abingdon, UK: Routledge, 2007. 1–24.Werner, David. Nothing about Us without Us: Developing Innovative Technologies for, vy, and with Disabled Persons. Palo Alto, CA: Healthwrights, 1997.World Health Organization. Mental Health: Strengthening Our Response, Fact Sheet No. 220, Updated April 2014. 2014. 2 June 2015 ‹http://www.who.int/mediacentre/factsheets/fs220/en/›.
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Soiland-Reyes, Stian, Leyla Jael Castro, Daniel Garijo, Marc Portier, Carole Goble, and Paul Groth. "Updating Linked Data practices for FAIR Digital Object principles." Research Ideas and Outcomes 8 (October 12, 2022). http://dx.doi.org/10.3897/rio.8.e94501.

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Background The FAIR principles (Wilkinson et al. 2016) are fundamental for data discovery, sharing, consumption and reuse; however their broad interpretation and many ways to implement can lead to inconsistencies and incompatibility (Jacobsen et al. 2020). The European Open Science Cloud (EOSC) has been instrumental in maturing and encouraging FAIR practices across a wide range of research areas. Linked Data in the form of RDF (Resource Description Framework) is the common way to implement machine-readability in FAIR, however the principles do not prescribe RDF or any particular technology (Mons et al. 2017). FAIR Digital Object FAIR Digital Object (FDO) (Schultes and Wittenburg 2019) has been proposed to improve researcher’s access to digital objects through formalising their metadata, types, identifiers and exposing their computational operations, making them actionable FAIR objects rather than passive data sources. FDO is a set of principles (Bonino et al. 2019), implementable in multiple ways. Current realisations mostly use Digital Object Interface Protocol (DOIPv2) (DONA Foundation 2018), with the main implementation CORDRA. We can consider DOIPv2 as a simplified combination of object-oriented (CORBA, SOAP) and document-based (HTTP, FTP) approaches. More recently, the FDO Forum has prepared detailed recommendations, currently open for comments, including a DOIP endorsement and updated FDO requirements. These point out Linked Data as another possible technology stack, which is the focus of this work. Linked Data Linked Data standards (LD), based on the Web architecture, are commonplace in sciences like bioinformatics, chemistry and medical informatics – in particular to publish Open Data as machine-readable resources. LD has become ubiquitous on the general Web, the schema.org vocabulary is used by over 10 million sites for indexing by search engines – 43% of all websites use JSON-LD. Although LD practices align to FAIR (Hasnain and Rebholz-Schuhmann 2018), they do not fully encompass active aspects of FDOs. The HTTP protocol is used heavily for applications (e.g. mobile apps and cloud services), with REST APIs of customised JSON structures. Approaches that merge the LD and REST worlds include Linked Data Platform (LDP), Hydra and Web Payments. Meeting FDO principles using Linked Data standards Considering the potential of FDOs when combined with the mature technology stack of LD, here we briefly discuss how FDO principles in Bonino et al. (2019) can be achieved using existing standards. The general principles (G1–G9) apply well: Open standards with HTTP being stable for 30 years, JSON-LD is widely used, FAIR practitioners mainly use RDF, and a clear abstraction between the RDF model with stable bindings available in multiple serialisations. However, when considering the specific principles (FDOF1–FDOF12) we find that additional constraints and best practices need to be established – arbitrary LD resources cannot be assumed to follow FDO principles. This is equivalent to how existing use of DOIP is not FDO-compliant without additional constraints. Namely, persistent identifiers (PIDs) (McMurry et al. 2017) (FDOF1) are common in LD world (e.g. using http://purl.org/ or https://w3id.org/), however they don’t always have a declared type (FDOF2), or the PID may not even appear in the metadata. URL-based PIDs are resolvable (FDOF3), typically over HTTP using redirections and content-negotiation. One great advantage of RDF is that all attributes are defined semantic artefacts with PIDs (FDOF4), and attributes can be reused across vocabularies. While CRUD operations (FDOF6) are supported by native HTTP operations (GET/PUT/POST/DELETE) as in LDP , there is little consistency on how to define operation interfaces in LD (FDOF5). Existing REST approaches like OpenAPI and URI templates are mature and good candidates, and should be related to defined types to support machine-actionable composition (FDOF7). HTTP error code 410 Gone is used in tombstone pages for removed resources (FDOF12), although more frequent is 404 Not Found. Metadata is resolved to HTTP documents with their own URIs, but these frequently don’t have their own PID (FDOF8). RDF-Star and nanopublications (Kuhn et al. 2021) give ways to identify and trace provenance of individual assertions. Different metadata levels (FDOF9) are frequently developed for LD vocabularies across different communities (FDOF10), such as FHIR for health data, Bioschemas for bioinformatics and &gt;1000 more specific bioontologies. Increased declaration and navigation of profiles is therefore essential for machine-actionability and consistent consumption across FAIR endpoints. Several standards exist for rich collections (FDOF11), e.g. OAI-ORE, DCAT, RO-Crate, LDP. These are used and extended heterogeneously across the Web, but consistent machine-actionable FDOs will need specific choices of core standards and vocabularies. Another challenge is when multiple PIDs refer to “almost the same” concept in different collections – significant effort have created manual and automated semantic mappings (Baker et al. 2013, de Mello et al. 2022). Currently the FDO Forum has suggested the use of LDP as a possible alternative for implementing FAIR Digital Objects (Bonino da Silva Santos 2021), which proposes a novel approach of content-negotiation with custom media types. Discussion The Linked Data stack provides a set of specifications, tools and guidelines in order to help the FDO principles become a reality. This mature approach can accelerate uptake of FDO by scholars and existing research infrastructures such as the European Open Science Cloud (EOSC). However, the amount of standards and existing metadata vocabularies poses a potential threat for adoption and interoperability. Yet, the challenges for agreeing on usage profiles apply equally to DOIP as LD approaches. We have worked with different scientific communities to define RO-Crate (Soiland-Reyes et al. 2022), a lightweight method to package research outputs along with their metadata. While RO-Crate’s use of schema.org shows just one possible metadata model, it's powerful enough to be able to express FDOs, and familiar to web developers. We have also used FAIR Signposting (Van de Sompel et al. 2022) with HTTP Link: headers as a way to support navigation to the individual core properties of an FDO (PID, type, metadata, licence, bytestream) that does not require heuristics of content-negotiation and is agnostic to particular metadata vocabularies and serialisations. We believe that by adopting Linked Data principles, we can accelerate FDO today – and even start building practical ways to assist scientists in efficiently answering topical questions based on knowledge graphs.
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Cashman, Dorothy Ann. "“This receipt is as safe as the Bank”: Reading Irish Culinary Manuscripts." M/C Journal 16, no. 3 (June 23, 2013). http://dx.doi.org/10.5204/mcj.616.

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Introduction Ireland did not have a tradition of printed cookbooks prior to the 20th century. As a consequence, Irish culinary manuscripts from before this period are an important primary source for historians. This paper makes the case that the manuscripts are a unique way of accessing voices that have quotidian concerns seldom heard above the dominant narratives of conquest, colonisation and famine (Higgins; Dawson). Three manuscripts are examined to see how they contribute to an understanding of Irish social and culinary history. The Irish banking crisis of 2008 is a reminder that comments such as the one in the title of this paper may be more then a casual remark, indicating rather an underlying anxiety. Equally important is the evidence in the manuscripts that Ireland had a domestic culinary tradition sited within the culinary traditions of the British Isles. The terms “vernacular”, representing localised needs and traditions, and “polite”, representing stylistic features incorporated for aesthetic reasons, are more usually applied in the architectural world. As terms, they reflect in a politically neutral way the culinary divide witnessed in the manuscripts under discussion here. Two of the three manuscripts are anonymous, but all are written from the perspective of a well-provisioned house. The class background is elite and as such these manuscripts are not representative of the vernacular, which in culinary terms is likely to be a tradition recorded orally (Gold). The first manuscript (NLI, Tervoe) and second manuscript (NLI, Limerick) show the levels of impact of French culinary influence through their recipes for “cullis”. The Limerick manuscript also opens the discussion to wider social concerns. The third manuscript (NLI, Baker) is unusual in that the author, Mrs. Baker, goes to great lengths to record the provenance of the recipes and as such the collection affords a glimpse into the private “polite” world of the landed gentry in Ireland with its multiplicity of familial and societal connections. Cookbooks and Cuisine in Ireland in the 19th Century During the course of the 18th century, there were 136 new cookery book titles and 287 reprints published in Britain (Lehmann, Housewife 383). From the start of the 18th to the end of the 19th century only three cookbooks of Irish, or Anglo-Irish, authorship have been identified. The Lady’s Companion: or Accomplish’d Director In the whole Art of Cookery was published in 1767 by John Mitchell in Skinner-Row, under the pseudonym “Ceres,” while the Countess of Caledon’s Cheap Receipts and Hints on Cookery: Collected for Distribution Amongst the Irish Peasantry was printed in Armagh by J. M. Watters for private circulation in 1847. The modern sounding Dinners at Home, published in London in 1878 under the pseudonym “Short”, appears to be of Irish authorship, a review in The Irish Times describing it as being written by a “Dublin lady”, the inference being that she was known to the reviewer (Farmer). English Copyright Law was extended to Ireland in July 1801 after the Act of Union between Great Britain and Ireland in 1800 (Ferguson). Prior to this, many titles were pirated in Ireland, a cause of confusion alluded to by Lehmann when she comments regarding the Ceres book that it “does not appear to be simply a Dublin-printed edition of an English book” (Housewife 403). This attribution is based on the dedication in the preface: “To The Ladies of Dublin.” From her statement that she had a “great deal of experience in business of this kind”, one may conclude that Ceres had worked as a housekeeper or cook. Cheap Receipts and Hints on Cookery was the second of two books by Catherine Alexander, Countess of Caledon. While many commentators were offering advice to Irish people on how to alleviate their poverty, in Friendly Advice to Irish Mothers on Training their Children, Alexander was unusual in addressing her book specifically to its intended audience (Bourke). In this cookbook, the tone is of a practical didactic nature, the philosophy that of enablement. Given the paucity of printed material, manuscripts provide the main primary source regarding the existence of an indigenous culinary tradition. Attitudes regarding this tradition lie along the spectrum exemplified by the comments of an Irish journalist, Kevin Myers, and an eminent Irish historian, Louis Cullen. Myers describes Irish cuisine as a “travesty” and claims that the cuisine of “Old Ireland, in texture and in flavour, generally resembles the cinders after the suttee of a very large, but not very tasty widow”, Cullen makes the case that Irish cuisine is “one of the most interesting culinary traditions in Europe” (141). It is not proposed to investigate the ideological standpoints behind the various comments on Irish food. Indeed, the use of the term “Irish” in this context is fraught with difficulty and it should be noted that in the three manuscripts proposed here, the cuisine is that of the gentry class and representative of a particular stratum of society more accurately described as belonging to the Anglo-Irish tradition. It is also questionable how the authors of the three manuscripts discussed would have described themselves in terms of nationality. The anxiety surrounding this issue of identity is abating as scholarship has moved from viewing the cultural artifacts and buildings inherited from this class, not as symbols of an alien heritage, but rather as part of the narrative of a complex country (Rees). The antagonistic attitude towards this heritage could be seen as reaching its apogee in the late 1950s when the then Government minister, Kevin Boland, greeted the decision to demolish a row of Georgian houses in Dublin with jubilation, saying that they stood for everything that he despised, and describing the Georgian Society, who had campaigned for their preservation, as “the preserve of the idle rich and belted earls” (Foster 160). Mac Con Iomaire notes that there has been no comprehensive study of the history of Irish food, and the implications this has for opinions held, drawing attention to the lack of recognition that a “parallel Anglo-Irish cuisine existed among the Protestant elite” (43). To this must be added the observation that Myrtle Allen, the doyenne of the Irish culinary world, made when she observed that while we have an Irish identity in food, “we belong to a geographical and culinary group with Wales, England, and Scotland as all counties share their traditions with their next door neighbour” (1983). Three Irish Culinary Manuscripts The three manuscripts discussed here are held in the National Library of Ireland (NLI). The manuscript known as Tervoe has 402 folio pages with a 22-page index. The National Library purchased the manuscript at auction in December 2011. Although unattributed, it is believed to come from Tervoe House in County Limerick (O’Daly). Built in 1776 by Colonel W.T. Monsell (b.1754), the Monsell family lived there until 1951 (see, Fig. 1). The house was demolished in 1953 (Bence-Jones). William Monsell, 1st Lord Emly (1812–94) could be described as the most distinguished of the family. Raised in an atmosphere of devotion to the Union (with Great Britain), loyalty to the Church of Ireland, and adherence to the Tory Party, he converted in 1850 to the Roman Catholic religion, under the influence of Cardinal Newman and the Oxford Movement, changing his political allegiance from Tory to Whig. It is believed that this change took place as a result of the events surrounding the Great Irish Famine of 1845–50 (Potter). The Tervoe manuscript is catalogued as 18th century, and as the house was built in the last quarter of the century, it would be reasonable to surmise that its conception coincided with that period. It is a handsome volume with original green vellum binding, which has been conserved. Fig. 1. Tervoe House, home of the Monsell family. In terms of culinary prowess, the scope of the Tervoe manuscript is extensive. For the purpose of this discussion, one recipe is of particular interest. The recipe, To make a Cullis for Flesh Soups, instructs the reader to take the fat off four pounds of the best beef, roast the beef, pound it to a paste with crusts of bread and the carcasses of partridges or other fowl “that you have by you” (NLI, Tervoe). This mixture should then be moistened with best gravy, and strong broth, and seasoned with pepper, thyme, cloves, and lemon, then sieved for use with the soup. In 1747 Hannah Glasse published The Art of Cookery, Made Plain and Easy. The 1983 facsimile edition explains the term “cullis” as an Anglicisation of the French word coulis, “a preparation for thickening soups and stews” (182). The coulis was one of the essential components of the nouvelle cuisine of the 18th century. This movement sought to separate itself from “the conspicuous consumption of profusion” to one where the impression created was one of refinement and elegance (Lehmann, Housewife 210). Reactions in England to this French culinary innovation were strong, if not strident. Glasse derides French “tricks”, along with French cooks, and the coulis was singled out for particular opprobrium. In reality, Glasse bestrides both sides of the divide by giving the much-hated recipe and commenting on it. She provides another example of this in her recipe for The French Way of Dressing Partridges to which she adds the comment: “this dish I do not recommend; for I think it an odd jumble of thrash, by that time the Cullis, the Essence of Ham, and all other Ingredients are reckoned, the Partridges will come to a fine penny; but such Receipts as this, is what you have in most Books of Cookery yet printed” (53). When Daniel Defoe in The Complete English Tradesman of 1726 criticised French tradesmen for spending so much on the facades of their shops that they were unable to offer their customers a varied stock within, we can see the antipathy spilling over into other creative fields (Craske). As a critical strategy, it is not dissimilar to Glasse when she comments “now compute the expense, and see if this dish cannot be dressed full as well without this expense” at the end of a recipe for the supposedly despised Cullis for all Sorts of Ragoo (53). Food had become part of the defining image of Britain as an aggressively Protestant culture in opposition to Catholic France (Lehmann Politics 75). The author of the Tervoe manuscript makes no comment about the dish other than “A Cullis is a mixture of things, strained off.” This is in marked contrast to the second manuscript (NLI, Limerick). The author of this anonymous manuscript, from which the title of this paper is taken, is considerably perplexed by the term cullis, despite the manuscript dating 1811 (Fig. 2). Of Limerick provenance also, but considerably more modest in binding and scope, the manuscript was added to for twenty years, entries terminating around 1831. The recipe for Beef Stake (sic) Pie is an exact transcription of a recipe in John Simpson’s A Complete System of Cookery, published in 1806, and reads Cut some beef steaks thin, butter a pan (or as Lord Buckingham’s cook, from whom these rects are taken, calls it a soutis pan, ? [sic] (what does he mean, is it a saucepan) [sic] sprinkle the pan with pepper and salt, shallots thyme and parsley, put the beef steaks in and the pan on the fire for a few minutes then put them to cool, when quite cold put them in the fire, scrape all the herbs in over the fire and ornament as you please, it will take an hour and half, when done take the top off and put in some coulis (what is that?) [sic]. Fig. 2. Beef Stake Pie (NLI, Limerick). Courtesy of the National Library of Ireland. Simpson was cook to Lord Buckingham for at least a year in 1796, and may indeed have travelled to Ireland with the Duke who had several connections there. A feature of this manuscript are the number of Cholera remedies that it contains, including the “Rect for the cholera sent by Dr Shanfer from Warsaw to the Brussels Government”. Cholera had reached Germany by 1830, and England by 1831. By March 1832, it had struck Belfast and Dublin, the following month being noted in Cork, in the south of the country. Lasting a year, the epidemic claimed 50,000 lives in Ireland (Fenning). On 29 April 1832, the diarist Amhlaoibh Ó Súilleabháin notes, “we had a meeting today to keep the cholera from Callan. May God help us” (De Bhaldraithe 132). By 18 June, the cholera is “wrecking destruction in Ennis, Limerick and Tullamore” (135) and on 26 November, “Seed being sown. The end of the month wet and windy. The cholera came to Callan at the beginning of the month. Twenty people went down with it and it left the town then” (139). This situation was obviously of great concern and this is registered in the manuscript. Another concern is that highlighted by the recommendation that “this receipt is as good as the bank. It has been obligingly given to Mrs Hawkesworth by the chief book keeper at the Bank of Ireland” (NLI, Limerick). The Bank of Ireland commenced business at St. Mary’s Abbey in Dublin in June 1783, having been established under the protection of the Irish Parliament as a chartered rather then a central bank. As such, it supplied a currency of solidity. The charter establishing the bank, however, contained a prohibitory clause preventing (until 1824 when it was repealed) more then six persons forming themselves into a company to carry on the business of banking. This led to the formation, especially outside Dublin, of many “small private banks whose failure was the cause of immense wretchedness to all classes of the population” (Gilbert 19). The collapse that caused the most distress was that of the Ffrench bank in 1814, founded eleven years previously by the family of Lord Ffrench, one of the leading Catholic peers, based in Connacht in the west of Ireland. The bank issued notes in exchange for Bank of Ireland notes. Loans from Irish banks were in the form of paper money which were essentially printed promises to pay the amount stated and these notes were used in ordinary transactions. So great was the confidence in the Ffrench bank that their notes were held by the public in preference to Bank of Ireland notes, most particularly in Connacht. On 27 June 1814, there was a run on the bank leading to collapse. The devastation spread through society, from business through tenant farmers to the great estates, and notably so in Galway. Lord Ffrench shot himself in despair (Tennison). Williams and Finn, founded in Kilkenny in 1805, entered bankruptcy proceedings in 1816, and the last private bank outside Dublin, Delacours in Mallow, failed in 1835 (Barrow). The issue of bank failure is commented on by writers of the period, notably so in Dickens, Thackery, and Gaskill, and Edgeworth in Ireland. Following on the Ffrench collapse, notes from the Bank of Ireland were accorded increased respect, reflected in the comment in this recipe. The receipt in question is one for making White Currant Wine, with the unusual addition of a slice of bacon suspended from the bunghole when the wine is turned, for the purpose of enriching it. The recipe was provided to “Mrs Hawkesworth by the chief book keeper of the bank” (NLI, Limerick). In 1812, a John Hawkesworth, agent to Lord CastleCoote, was living at Forest Lodge, Mountrath, County Laois (Ennis Chronicle). The Coote family, although settling in County Laois in the seventeenth century, had strong connections with Limerick through a descendent of the younger brother of the first Earl of Mountrath (Landed Estates). The last manuscript for discussion is the manuscript book of Mrs Abraham Whyte Baker of Ballytobin House, County Kilkenny, 1810 (NLI, Baker). Ballytobin, or more correctly Ballaghtobin, is a townland in the barony of Kells, four miles from the previously mentioned Callan. The land was confiscated from the Tobin family during the Cromwellian campaign in Ireland of 1649–52, and was reputedly purchased by a Captain Baker, to establish what became the estate of Ballaghtobin (Fig. 3) To this day, it is a functioning estate, remaining in the family, twice passing down through the female line. In its heyday, there were two acres of walled gardens from which the house would have drawn for its own provisions (Ballaghtobin). Fig. 3. Ballaghtobin 2013. At the time of writing the manuscript, Mrs. Sophia Baker was widowed and living at Ballaghtobin with her son and daughter-in-law, Charity who was “no beauty, but tall, slight” (Herbert 414). On the succession of her husband to the estate, Charity became mistress of Ballaghtobin, leaving Sophia with time on what were her obviously very capable hands (Nevin). Sophia Baker was the daughter of Sir John Blunden of Castle Blunden and Lucinda Cuffe, daughter of the first Baron Desart. Sophia was also first cousin of the diarist Dorothea Herbert, whose mother was Lucinda’s sister, Martha. Sophia Baker and Dorothea Herbert have left for posterity a record of life in the landed gentry class in rural Georgian Ireland, Dorothea describing Mrs. Baker as “full of life and spirits” (Herbert 70). Their close relationship allows the two manuscripts to converse with each other in a unique way. Mrs. Baker’s detailing of the provenance of her recipes goes beyond the norm, so that what she has left us is not just a remarkable work of culinary history but also a palimpsest of her family and social circle. Among the people she references are: “my grandmother”; Dorothea Beresford, half sister to the Earl of Tyrone, who lived in the nearby Curraghmore House; Lady Tyrone; and Aunt Howth, the sister of Dorothea Beresford, married to William St Lawrence, Lord Howth, and described by Johnathan Swift as “his blue eyed nymph” (195). Other attributions include Lady Anne Fitzgerald, wife of Maurice Fitzgerald, 16th knight of Kerry, Sir William Parsons, Major Labilen, and a Mrs. Beaufort (Fig. 4). Fig. 4. Mrs. Beauforts Rect. (NLI, Baker). Courtesy of the National Library of Ireland. That this Mrs. Beaufort was the wife of Daniel Augustus Beaufort, mother of the hydrographer Sir Francis Beaufort, may be deduced from the succeeding recipe supplied by a Mrs. Waller. Mrs. Beaufort’s maiden name was Waller. Fanny Beaufort, the elder sister of Sir Francis, was Richard Edgeworth’s fourth wife and close friend and confidante of his daughter Maria, the novelist. There are also entries for “Miss Herbert” and “Aunt Herbert.” While the Baker manuscript is of interest for the fact that it intersects the worlds of the novelist Maria Edgeworth and the diarist Dorothea Herbert, and for the societal references that it documents, it is also a fine collection of recipes that date back to the mid-18th century. An example of this is a recipe for Sligo pickled salmon that Mrs. Baker, nee Blunden, refers to in an index that she gives to a second volume. Unfortunately this second volume is not known to be extant. This recipe features in a Blunden family manuscript of 1760 as referred to in Anelecta Hibernica (McLysaght). The recipe has also appeared in Cookery and Cures of Old Kilkenny (St. Canices’s 24). Unlike the Tervoe and Limerick manuscripts, Mrs. Baker is unconcerned with recipes for “cullis”. Conclusion The three manuscripts that have been examined here are from the period before the famine of 1845–50, known as An Gorta Mór, translated as “the big hunger”. The famine preceding this, Bliain an Áir (the year of carnage) in 1740–1 was caused by extremely cold and rainy weather that wiped out the harvest (Ó Gráda 15). This earlier famine, almost forgotten today, was more severe than the subsequent one, causing the death of an eight of the population of the island over one and a half years (McBride). These manuscripts are written in living memory of both events. Within the world that they inhabit, it may appear there is little said about hunger or social conditions beyond the walls of their estates. Subjected to closer analysis, however, it is evident that they are loquacious in their own unique way, and make an important contribution to the narrative of cookbooks. Through the three manuscripts discussed here, we find evidence of the culinary hegemony of France and how practitioners in Ireland commented on this in comparatively neutral fashion. An awareness of cholera and bank collapses have been communicated in a singular fashion, while a conversation between diarist and culinary networker has allowed a glimpse into the world of the landed gentry in Ireland during the Georgian period. References Allen, M. “Statement by Myrtle Allen at the opening of Ballymaloe Cookery School.” 14 Nov. 1983. Ballaghtobin. “The Grounds”. nd. 13 Mar. 2013. ‹http://www.ballaghtobin.com/gardens.html›. Barrow, G.L. “Some Dublin Private Banks.” Dublin Historical Record 25.2 (1972): 38–53. Bence-Jones, M. A Guide to Irish Country Houses. London: Constable, 1988. Bourke, A. Ed. Field Day Anthology of Irish Writing Vol V. Cork: Cork UP, 2002. Craske, M. “Design and the Competitive Spirit in Early and Mid 18th Century England”, Journal of Design History 12.3 (1999): 187–216. Cullen, L. The Emergence of Modern Ireland. London: Batsford, 1981. Dawson, Graham. “Trauma, Memory, Politics. The Irish Troubles.” Trauma: Life Stories of Survivors. Ed. Kim Lacy Rogers, Selma Leydesdorff and Graham Dawson. New Jersey: Transaction P, 2004. De Bhaldraithe,T. Ed. Cín Lae Amhlaoibh. Cork: Mercier P, 1979. Ennis Chronicle. 12–23 Feb 1812. 10 Feb. 2013 ‹http://astheywere.blogspot.ie/2012/12/ennis-chronicle-1812-feb-23-feb-12.html› Farmar, A. E-mail correspondence between Farmar and Dr M. Mac Con Iomaire, 26 Jan. 2011. Fenning, H. “The Cholera Epidemic in Ireland 1832–3: Priests, Ministers, Doctors”. Archivium Hibernicum 57 (2003): 77–125. Ferguson, F. “The Industrialisation of Irish Book Production 1790-1900.” The Oxford History of the Irish Book, Vol. IV The Irish Book in English 1800-1891. Ed. J. Murphy. Oxford: Oxford UP, 2011. Foster, R.F. Luck and the Irish: A Brief History of Change from 1970. Oxford: Oxford UP, 2008. Gilbert, James William. The History of Banking in Ireland. London: Longman, Rees, Orme, Brown, Green, and Longman, 1836. Glasse, Hannah. The Art of Cookery Made Plain and Easy by a Lady: Facsimile Edition. Devon: Prospect, 1983. Gold, C. Danish Cookbooks. Seattle: U of Washington P, 2007. Herbert, D. Retrospections of an Outcast or the Life of Dorothea Herbert. London: Gerald Howe, 1929. Higgins, Michael D. “Remarks by President Michael D. Higgins reflecting on the Gorta Mór: the Great famine of Ireland.” Famine Commemoration, Boston, 12 May 2012. 18 Feb. 2013 ‹http://www.president.ie/speeches/ › Landed Estates Database, National University of Galway, Moore Institute for Research, 10 Feb. 2013 ‹http://landedestates.nuigalway.ie/LandedEstates/jsp/family-show.jsp?id=633.› Lehmann, G. The British Housewife: Cookery books, cooking and society in eighteenth-century Britain. Totnes: Prospect, 1993. ---. “Politics in the Kitchen.” 18th Century Life 23.2 (1999): 71–83. Mac Con Iomaire, M. “The Emergence, Development and Influence of French Haute Cuisine on Public Dining in Dublin Restaurants 1900-2000: An Oral History”. Vol. 2. PhD thesis. Dublin Institute of Technology. 2009. 8 Mar. 2013 ‹http://arrow.dit.ie/tourdoc/12›. McBride, Ian. Eighteenth Century Ireland: The Isle of Slaves. Dublin: Gill and Macmillan, 2009. McLysaght, E.A. Anelecta Hibernica 15. Dublin: Irish Manuscripts Commission, 1944. Myers, K. “Dinner is served ... But in Our Culinary Dessert it may be Korean.” The Irish Independent 30 Jun. 2006. Nevin, M. “A County Kilkenny Georgian Household Notebook.” Journal of the Royal Society of Antiquaries of Ireland 109 (1979): 5–18. (NLI) National Library of Ireland. Baker. 19th century manuscript. MS 34,952. ---. Limerick. 19th century manuscript. MS 42,105. ---. Tervoe. 18th century manuscript. MS 42,134. Ó Gráda, C. Famine: A Short History. New Jersey: Princeton UP, 2009. O’Daly, C. E-mail correspondence between Colette O’Daly, Assistant Keeper, Dept. of Manuscripts, National Library of Ireland and Dorothy Cashman. 8 Dec. 2011. Potter, M. William Monsell of Tervoe 1812-1894. Dublin: Irish Academic P, 2009. Rees, Catherine. “Irish Anxiety, Identity and Narrative in the Plays of McDonagh and Jones.” Redefinitions of Irish Identity: A Postnationalist Approach. Eds. Irene Gilsenan Nordin and Carmen Zamorano Llena. Bern: Peter Lang, 2010. St. Canice’s. Cookery and Cures of Old Kilkenny. Kilkenny: Boethius P, 1983. Swift, J. The Works of the Rev Dr J Swift Vol. XIX Dublin: Faulkner, 1772. 8 Feb. 2013. ‹http://www.google.ie/search?tbm=bks&hl=en&q=works+of+jonathan+swift+Vol+XIX+&btnG=› Tennison, C.M. “The Old Dublin Bankers.” Journal of the Cork Historical and Archeological Society 1.2 (1895): 36–9.
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