Provenance Information Research Articles

Soft rumor control in mobile instant messengers

Mobile Instant Messengers (MIMs) are vastly used for communication and information sharing in recent years. However, interesting features of these applications such as group-based communication and broadcasting in channels cause rumors also to be spread in MIM networks more quickly than ordinary social networks. Although there are lots of works on modeling, analysis, and controlling rumor dissemination in social networks, the mentioned features of MIMs are not almost considered. In this paper we propose a new model for soft rumor control in MIMs that considers rumor propagation in groups and channels. By soft rumor control we mean measures for enhancing the people’s knowledge and awareness against the rumor to persuade them avoiding rumor dissemination. We suggest two soft rumor control mechanisms including a provenance based decision making process and making anti-rumor campaigns. In the first mechanism, in order to improve the ability of users to take proper actions against rumors, they are equipped with rumor provenance information including the level of trust to rumor spreader, reputation of the source of rumor and the degree of credibility of the rumor. In the second mechanism, some MIM users who have more serious concerns about the rumor effects try making an anti-rumor campaign to fight spreading the rumor. The proposed model is formalized as an extended Partially Observable Markov Decision Process (POMDP) to capture the dynamics of rumor propagation and the control mechanisms. To evaluate the proposed model, we conduct a number of extensive agent-based simulation experiments on a synthesized MIM network that show the effectiveness of the proposed mechanisms to control rumor propagation. We also conduct interesting sensitivity analysis to see the effects of different model parameters on the dynamics of the rumor propagation with control mechanisms. The proposed model helps MIM developers to provide facilities to control rumor by collective wisdom. Furthermore, it helps people, NGOs, political parties, and so on to improve their rumor fighting strategies by making properly designed anti-rumor campaigns.

The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

BackgroundThe NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for “suspect screening” lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide.ResultsThe NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https://zenodo.org/communities/norman-sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard/), enabling further access to these lists, along with the additional functionality and calculated properties these resources offer. PubChem has also integrated significant annotation content from the NORMAN-SLE, including a classification browser (https://pubchem.ncbi.nlm.nih.gov/classification/#hid=101).ConclusionsThe NORMAN-SLE offers a specialized service for hosting suspect screening lists of relevance for the environmental community in an open, FAIR manner that allows integration with other major chemical resources. These efforts foster the exchange of information between scientists and regulators, supporting the paradigm shift to the “one substance, one assessment” approach. New submissions are welcome via the contacts provided on the NORMAN-SLE website (https://www.norman-network.com/nds/SLE/).

Undergraduate Learning and Research with Provenance Information

Objects in multiple formats can comprise both the subjects and the approach making up “material culture”: a mode of investigating and understanding culture. Some colleges and universities steward millions of objects in academic galleries, libraries, archives, and museums (GLAM institutions). Convergence among such information professionals has led to recent offerings of an undergraduate honors seminar around campus material culture which is the focus of analysis in this paper. Students in that setting interrogated and applied the concept of provenance in reflecting on their object-based interactions. We analyze three categories of provenance lessons from the students to inform future teaching: (1) an object’s origins and pathways, (2) what provenance is and helps people do, and (3) new storytelling contributions.

Biospecimens in FDO world

Biospecimens in FDO world

Facing the Challenges in simulation-based Earth System Sciences and the Role of FAIR Digital Objects

Facing the Challenges in simulation-based Earth System Sciences and the Role of FAIR Digital Objects

Creating lightweight FAIR Digital Objects with RO-Crate

Creating lightweight FAIR Digital Objects with RO-Crate

RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine

BackgroundBiomedical translational science is increasingly using computational reasoning on repositories of structured knowledge (such as UMLS, SemMedDB, ChEMBL, Reactome, DrugBank, and SMPDB in order to facilitate discovery of new therapeutic targets and modalities. The NCATS Biomedical Data Translator project is working to federate autonomous reasoning agents and knowledge providers within a distributed system for answering translational questions. Within that project and the broader field, there is a need for a framework that can efficiently and reproducibly build an integrated, standards-compliant, and comprehensive biomedical knowledge graph that can be downloaded in standard serialized form or queried via a public application programming interface (API).ResultsTo create a knowledge provider system within the Translator project, we have developed RTX-KG2, an open-source software system for building—and hosting a web API for querying—a biomedical knowledge graph that uses an Extract-Transform-Load approach to integrate 70 knowledge sources (including the aforementioned core six sources) into a knowledge graph with provenance information including (where available) citations. The semantic layer and schema for RTX-KG2 follow the standard Biolink model to maximize interoperability. RTX-KG2 is currently being used by multiple Translator reasoning agents, both in its downloadable form and via its SmartAPI-registered interface. Serializations of RTX-KG2 are available for download in both the pre-canonicalized form and in canonicalized form (in which synonyms are merged). The current canonicalized version (KG2.7.3) of RTX-KG2 contains 6.4M nodes and 39.3M edges with a hierarchy of 77 relationship types from Biolink.ConclusionRTX-KG2 is the first knowledge graph that integrates UMLS, SemMedDB, ChEMBL, DrugBank, Reactome, SMPDB, and 64 additional knowledge sources within a knowledge graph that conforms to the Biolink standard for its semantic layer and schema. RTX-KG2 is publicly available for querying via its API at arax.rtx.ai/api/rtxkg2/v1.2/openapi.json. The code to build RTX-KG2 is publicly available at github:RTXteam/RTX-KG2.

Studying Saraha: Technical and Multi-Analytical Investigation of the Painting Materials and Techniques in an 18th Century Tibetan Thangka

Scientific analyses of the traditional materials and methods in thangka production are uncommon, as thangkas are sacred objects, the sampling of which is discouraged, in order to preserve their integrity. This study builds on this important ethical challenge and presents a three-stage methodology that systematically delves deeper into each layer of the composition, successfully enabling the investigation of different phases of production. In the first stage, visual examination of the painting, including observations under magnification, was used to assess its condition. In the next step, the infrared reflected (IRR) and short-wave infrared (SWIR) images revealed the underdrawing and instances of modifications as well as colour notations. Additionally, ultraviolet-induced visible luminescence (UVL), infrared-reflected false colour (IRRFC) and X-ray images provided important preliminary information on the colourants present, the nature of the underdrawing, and the painting technique. In the final stages, fibre optic reflectance (FORS), Fourier-transform infrared (FTIR) and Raman spectroscopies confirmed the identity of many of the pigments (cinnabar/vermillion, minium, iron oxide, malachite, azurite, indigo, Indian lac), the ground and the binder used for the blue and green paint layers. In addition, key details of practices and materials were revealed, that may indicate provenance or other information of scholarly importance. These will constitute a helpful comparison to existing and future studies of other thangkas.

Benefit sharing: Why inclusive provenance metadata matter.

Fair and equitable benefit sharing of genetic resources is an expectation of the Nagoya Protocol. Although the Nagoya Protocol does not yet formally apply to Digital Sequence Information (“DSI”), discussions are currently underway regarding to include such data through ongoing Convention on Biological Diversity (“CBD”) negotiations. While Indigenous Peoples and Local Communities (“IPLC”) expect the value generated from genomic data to be subject to benefit sharing arrangements, a range of views are currently being expressed by Nation States, IPLC and other stakeholders. The use of DSI gives rise to unique considerations, creating a gray area as to how it should be considered under the Nagoya Protocol’s Access and Benefit Sharing (“ABS”) principles. One way for benefit sharing to be enhanced is through the connection of data to proper provenance information. A significant development is the use of digital labeling systems to ensure that the origin of samples is appropriately disclosed. The Traditional Knowledge and Biocultural Labels initiative offers a practical option for data provided to genomic databases. In particular, the BioCultural Labels (“BC Labels”) are a mechanism for Indigenous communities to identify and maintain provenance, origin and authority over biocultural material and data generated from Indigenous land and waters held in research, cultural institutions and data repositories. This form of cultural metadata adds value to the research endeavor and the creation of Indigenous fields within databases adds transparency and accountability to the research environment.

Envisioning networked provenance data storytelling with American cuneiform collections

Cuneiform tablets remain founding cornerstones of two hundred plus collections in American academic institutions, having been acquired a century or more ago under dynamic ethical norms and global networks. To foster data sharing, this contribution incorporates empirical data from interactive ArcGIS and reusable OpenContext maps to encourage tandem dialogues about using the inscribed works and learning their collecting histories. Such provenance research aids, on their own, initiate the narration of objects’ journeys over time while cultivating the digital inclusion of expert local knowledge relevant to an object biography. The paper annotates several approaches institutions are or might consider using to expand upon current provenance information in ways that encourage visitors’ critical thinking and learning about global journeys, travel archives, and such dispositions as virtual reunification, reconstructions, or restitution made possible by the provenance research.

Context for Reproducibility and Replicability in Geospatial Unmanned Aircraft Systems

Multiple scientific disciplines face a so-called crisis of reproducibility and replicability (R&R) in which the validity of methodologies is questioned due to an inability to confirm experimental results. Trust in information technology (IT)-intensive workflows within geographic information science (GIScience), remote sensing, and photogrammetry depends on solutions to R&R challenges affecting multiple computationally driven disciplines. To date, there have only been very limited efforts to overcome R&R-related issues in remote sensing workflows in general, let alone those tied to unmanned aircraft systems (UAS) as a disruptive technology. This review identifies key barriers to, and suggests best practices for, R&R in geospatial UAS workflows as well as broader remote sensing applications. We examine both the relevance of R&R as well as existing support for R&R in remote sensing and photogrammetry assisted UAS workflows. Key barriers include: (1) awareness of time and resource requirements, (2) accessibility of provenance, metadata, and version control, (3) conceptualization of geographic problems, and (4) geographic variability between study areas. R&R in geospatial UAS applications can be facilitated through augmented access to provenance information for authorized stakeholders, and the establishment of R&R as an important aspect of UAS and related research design. Where ethically possible, future work should exemplify best practices for R&R research by publishing access to open data sets and workflows. Future work should also explore new avenues for access to source data, metadata, provenance, and methods to adapt principles of R&R according to geographic variability and stakeholder requirements.

Data provenance tracking and reporting in a high-security digital research environment.

ObjectiveTo protect privacy, routinely-collected data are processed and anonymised by third parties before being used for research. However, the methods used to do this are rarely shared, leaving the resulting research difficult to evaluate and liable to undetected errors. Here, we present a provenance-based approach for documenting and auditing such methods. ApproachWe designed the Safe Haven Provenance (SHP) ontology for representing provenance information about data, users, and activities within high-security environments as knowledge graphs. The work was based on a case study of the Grampian Data Safe Haven (DASH) which holds and processes medical records for 600,000 people in Scotland. The SHP ontology was designed as an extension to the standard W3C PROV-O ontology. The auditing capabilities of our approach were evaluated against a set of transparency requirements through a prototype interactive dashboard. ResultsWe demonstrated the ability of the SHP ontology to document the workflow within DASH: capturing the extraction and anonymisation process using a structured vocabulary of entities (e.g. datasets), activities (e.g. linkage, anonymisation) and agents (e.g. analysts, data owners). Two provenance reporting templates were designed following interviews with DASH staff and clinical researchers: 1) a detailed report for use within DASH for quality assurance, and 2) a summary report for researchers that was safe for public release. Using a prototype data-linkage project, we formalised queries for report generation, and demonstrated use of automated rules for error detection (e.g., data discrepancies) using the structure of the SHP knowledge graphs. All of the project outputs are available under an open-source license. ConclusionsThis project lays a foundation for more transparent high-quality research using public data for health care and innovation. The SHP ontology is extendible for different domains and potentially represents a key component for further automation of provenance capture and reporting in high-security research environments.

Novel blockchain transaction provenance model with graph attention mechanism

With the maturity of the blockchain technology, more and more blockchain digital currencies including the Bitcoin, the Ethereum and the Ripple have been developed. Meanwhile, the security problem of the blockchain digital currency has become increasingly serious. It is necessary to build a provenance model for a large number of blockchain transaction, which can be used to find out which link has trouble and who is responsible once a problem occurs. However, the existing blockchain transaction data analysis methods have low traceback accuracy for data provenance. Therefore, a novel blockchain transaction provenance model with graph attention mechanism is proposed in this paper. The graph attention mechanism is used to identify the traders. Then, a triplet data structure is built to record provenance information and express the relationship between transaction amount and traders. Finally, the smart contract is used to implement the proposed provenance model. The provenance information can be searched through the interface provided by the smart contract when the traceback is required. In addition, the real large-scale Bitcoin transaction dataset Elliptic is used to compare the proposed method with other existing methods. The experiment show that the proposed method achieves state of the art results of the traceback accuracy.

The Forger’s tale: an insider’s account of corrupting the corpus of Cycladic figures

AbstractMany of the known Cycladic figures – the late prehistoric human-shaped sculptures from the Aegean archipelago – came from twentieth-century illicit excavations, especially in the 1960s and 1970s. It is also known that figures were being faked at the time and perhaps also earlier: a few fakes have been identified, whilst other figures are under suspicion. Interviews with a man who faked Cycladic figures in the 1980s and 1990s give us a first insider’s autobiographical account of the forging business. This article offers, step-by-step, the method that two forgers developed to create fake figures, to treat them so that they appeared ancient, and to sell them on. The forger has identified a few of these forgeries from photographs of figures; his story is consistent with other information and seems to ring true. By verifying various elements in the forger’s testimony – from names of well-known figures in the modern antiquities market to small details and dates – we have been able to evaluate the validity of the narrative; to use it in order to uncover the true paths that fake objects followed into various collections; and to highlight valuable provenance information that no one involved in trading these objects was ever willing to provide.

Re-purposing Excavation Database Content as Paradata

Although data reusers request information about how research data was created and curated, this information is often non-existent or only briefly covered in data descriptions. The need for such contextual information is particularly critical in fields like archaeology, where old legacy data created during different time periods and through varying methodological framings and fieldwork documentation practices retains its value as an important information source. This article explores the presence of contextual information in archaeological data with a specific focus on data provenance and processing information, i.e., paradata. The purpose of the article is to identify and explicate types of paradata in field observation documentation. The method used is an explorative close reading of field data from an archaeological excavation enriched with geographical metadata. The analysis covers technical and epistemological challenges and opportunities in paradata identification, and discusses the possibility of using identified paradata in data descriptions and for data reliability assessments. Results show that it is possible to identify both knowledge organisation paradata (KOP) relating to data structuring and knowledge-making paradata (KMP) relating to fieldwork methods and interpretative processes. However, while the data contains many traces of the research process, there is an uneven and, in some categories, low level of structure and systematicity that complicates automated metadata and paradata identification and extraction. The results show a need to broaden the understanding of how structure and systematicity are used and how they impact research data in archaeology and in comparable field sciences. The insights into how a dataset’s KOP and KMP can be read is also a methodological contribution to data literacy research and practice development. On a repository level, the results underline the need to include paradata about dataset creation, purpose, terminology, dataset internal and external relations, and eventual data colloquialisms that require explanation to reusers.

Motivating and Maintaining Ethics, Equity, Effectiveness, Efficiency, and Expertise in Peer Review

Scientists who engage in science and the scientific endeavor should seek truth with conviction of morals and commitment to ethics. While the number of publications continues to increase, the number of retractions has increased at a faster rate. Journals publish fraudulent research papers despite claims of peer review and adherence to publishing ethics. Nevertheless, appropriate ethical peer review will remain a gatekeeper when selecting research manuscripts in scholarly publishing and approving research applications for grant funding. However, this peer review must become more open, fair, transparent, equitable, and just with new recommendations and guidelines for reproducible and accountable reviews that support and promote fair citation and citational justice. We should engineer this new peer-review process with modern informatics technology and information science to provide and defend better safeguards for truth and integrity, to clarify and maintain the provenance of information and ideas, and to rebuild and restore trust in scholarly research institutions. Indeed, this new approach will be necessary in the current post-truth era to counter the ease and speed with which mis-information, dis-information, anti-information, caco-information, and mal-information spread through the internet, web, news, and social media. The most important question for application of new peer-review methods to these information wars should be ‘Who does what when?’ in support of reproducible and accountable reviews. Who refers to the authors, reviewers, editors, and publishers as participants in the review process. What refers to disclosure of the participants' identities, the material content of author manuscripts and reviewer commentaries, and other communications between authors and reviewers. When refers to tracking the sequential points in time for which disclosure of whose identity, which content, and which communication at which step of the peer-review process for which audience of readers and reviewers. We believe that quality peer review, and peer review of peer review, must be motivated and maintained by elevating their status and prestige to an art and a science. Both peer review itself and peer review analyses of peer reviews should be incentivised by publishing peer reviews as citable references separately from the research report reviewed while crossreferenced and crosslinked to the report reviewed.

Facilitating Asynchronous Collaboration in Scientific Workflow Composition Using Provenance

Advances in scientific domains are led to an increase in the complexity of the experiments. To address this growing complexity, scientists from different domains require to work collaboratively. Scientific Workflow Management Systems (SWfMSs) are popular tools for data-intensive experiments. To the best of our knowledge, very few of the existing SWfMSs support collaboration, and it is not efficient in many cases. Researchers share a single version of the workflow in existing collaborative data analysis systems, which increases the chance of interference as the number of collaborators grows. Moreover, for effective collaboration, contributors require a clear view of the project's status, the information that existing SWfMSs do not provide. Another significant problem is most scientists are not capable of adding collaborative tools to existing SWfMSs, and they need software engineers to take on this responsibility. Even for software engineers such tasks could be challenging and time consuming. In this paper, we attempted to address this crucial issue in scientific workflow composition and doing so in a collaborative setting. Hence, we propose a tool to facilitate collaborative workflow composition. This tool provides branching and versioning, which are standard version control system features to allow multiple researchers to contribute to the project asynchronously. We also suggest some visualizations and a variety of reports to increase group awareness and help the scientists to realize the project's status and issues. As a proof of concept, we developed an API to capture the provenance data and provide collaborative tools. This API is developed as an example for software engineers to help them understand how to integrate collaborative tools into any SWfMS. We collect provenance information during workflow composition and then employ it to track workflow versions using the proposed collaborative tool. Prior to implementing the visualizations, we surveyed to discover how much the proposed visualizations could contribute to group awareness. Moreover, in the survey we investigated to what extent the proposed version control system could help address shortcomings in collaborative experiments. The survey participants provided us with valuable feedback. In future, we will use the survey responses to enhance the proposed version control system and visualizations.

A Geospatial Dashboard Prototype for Evaluating Spatial Datasets by using Semantic Data Concepts and Open Source Libraries

Abstract. In today’s research data management, experts discuss datasets to be FAIR, as they should become findable, accessible, interoperable and reusable (Lacagnia et al. 2021). In recent years, quality information and provenance information as well as dataset’s general metadata have become important aspects to evaluate a dataset's fitness for use. In order to capture and process this meta-information in a systematic way, users need frameworks and meaningful user interfaces that allow them to interact with the information and to visualize them. Therefore, we provide a user-friendly and interactive geodashboard implementation as first prototype that supports the evaluation of spatial datasets with linked widgets by applying semantic concepts and using open source libraries.

Między lekturą a notatnikiem. Noty rękopiśmienne w książce drukowanej jako materiał badawczy

The subject of the article is the phenomenon of handwritten notes on the pages of old prints. Due to their astonishing variety, these notes constitute source material with great research potential, well beyond the history of reading and the history of the book as such. Using the previous observations obtained in the autopsy research with the use of the provenance method, the author presents a study of three examples and conclusions regarding the types of writing activity of owners and users of an antique book in the context of their individual approach to the book and reading. The issues were presented based on old prints materials from the collections of the Polish Academy of Sciences of the Gdańsk Library, taking into account the methodological issues related to obtaining provenance information from the collection of old prints, which in the discussed aspect are still insufficiently developed source data resources.

Managing virtual factory artifacts in the extended PLM context

Virtual engineering increases the rate of and diversity of models being created; hence requires maintenance in a product lifecycle management (PLM) system. This also induces the need to understand their creation contexts, known as historical or provenance information, to reuse the models in other engineering projects. PLM systems are specifically designed to manage product- and production-related data. However, they are less capable of handling the knowledge about the contexts of the models without an appropriate extension. Therefore, this research proposes an extension to PLM systems by designing a new information model to contain virtual models, their related data and knowledge generated from them through various engineering activities so that they can be effectively used to manage historical information related to all these virtual factory artifacts. Such an information model is designed to support a new Virtual Engineering ontology for capturing and representing virtual models and engineering activities, tightly integrated with an extended provenance model based on the W7 model. In addition, this paper presents how an application prototype, called Manage-Links, has been implemented with these extended PLM concepts and then used in several virtual manufacturing activities in an automotive company.