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A LARGE INTEGRATED KNOWLEDGE GRAPH OF ECNOMICS, FINANCE AND BANKING

Creating the first release to obtain a DOI on Zenodo

opencc-by-4.0Dec 2023View details →

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The TU Delft Urbanism Integrated Knowledge Paradigm

TU Delft Urbanism Integrated Knowledge Paradigm Model Logics of inquiry are underlying epistemological frameworks or approaches researchers adopt when conducting their studies (Stainton-Rogers, 2006). They represent different perspectives on how we acquire, justify, and evaluate knowledge. This speaks to the importance of interdisciplinary knowledge in addressing complex urban challenges. At the Delft University of Technology (and in the Netherlands more broadly), Urbanism is an interdisciplinary activity that involves planning and designing sustainable, inclusive urban spaces through the integration of design, social sciences, and physical sciences (Rocco et al., 2009). The Physical Sciences (Positivist paradigm) address the environmental and technical aspects of urbanism. They involve the application of principles from disciplines such as geography, ecology, and engineering to understand and manage the physical underpinnings of urban spaces (Rosenberg, 2005). The Social Sciences (Constructivist or critical paradigm) entail understanding the human and societal factors that shape urban environments. They include the study of social dynamics, governance, policy-making, and the economic and cultural contexts of urban development (Giddens, 1993).  Finally, the Design Paradigm (Pragmatic or Creative paradigm) speaks to the creative and practical aspects of urban planning and design that are propositional and future-oriented. It involves the conceptualisation and visualisation of spatial interventions and processes to improve urban environments (Biggs et al., 2009; Biggs & Büchler, 2008; Roggema, 2017). These logics of inquiry reflect diverse philosophical orientations and worldviews, leading researchers to formulate research questions and choose methodologies that align with their chosen approach. For example, let us look at these three different research questions stemming from the canals of Amsterdam: 1. ”How can the efficiency of water management in the canals of Amsterdam be improved to better serve the city's flood prevention needs?” (Positivist/ Pragmatic) 2. "How does the municipality of Amsterdam organise the governance of its canals, and who are the main stakeholders involved?” (Constructivist) 3. “What are competing claims over the canals of Amsterdam in terms of mobility, water management, leisure and identity? How can urban planning and policy address these competing claims?” (Critical) It is obvious that each of the Research Questions stems from a different logic of inquiry and that they consequently require different methods to be answered. This connection between logic of enquiry, research questions and methods employed to answer them is absolutely crucial. Positivism is the prevalent logic of enquiry in engineering (Romero et al., 2013). It is rooted in the belief that objective knowledge can be obtained through empirical observation and quantitative methods. Research under this logic inquiry aims to identify causal relationships and generalisable patterns in the data. Quantitative methods such as surveys, experiments and statistical analyses are commonly employed to collect and analyse data in a controlled manner (Rosenberg, 2005). The critique of the positivist logic of inquiry centres on its pretence neutrality (Bird, 2018). Positivism generally assumes a single “universal” perspective (male, Eurocentric, patriarchal). The positivist paradigm pretends culture, gender, values, and politics don’t influence real-world issues, hiding biases & conflict under the guise of “neutrality” (Okasha, 2002). Positivism generally doesn’t take alternative ways of knowing into account (feminist/ black/ queer/Indigenous/anti-capitalist/migrant, etc.). As a consequence, it commonly disdains non-expert knowledge. The Constructivist logic of inquiry is prevalent in the political sciences, economics, governance studies and, more recently, in the understanding of socio-technical systems that address the interrelationships between actors, institutions and technologies (Giddens, 1993; Okasha, 2002; Shannon-Baker, 2023). In this perspective, knowledge is actively constructed by individuals and influenced by their experiences and interpretations. It resonates with understanding the complex interplay between actors, institutions, spaces, and technologies. From this perspective, research explores how individuals and societies conceive, interact with, and shape real-world issues. This perspective commonly uses qualitative methods, case studies, and narrative analysis. It often emphasises stakeholders' expectations, behaviours, skills, and perspectives (Creswell & Plano Clark, 2007). Critics point out that constructivists often pay insufficient attention to causality and may underestimate the power of technology to shape behaviour. The Critical logic of inquiry draws heavily from sociology, ethnography, and political economy, as well as from critical theory (Hartimo et al., 2019).  This perspective seeks to uncover and challenge prevailing social arrangements, structures, and institutions. This paradigm addresses issues of power, governance, and justice (Giddens, 1993). It utilises qualitative methods, critical discourse analysis, and participatory action research. It prioritises addressing social and spatial inequalities through changes in process, governance, and political action. The main critique of this logic of inquiry is that it may remain in the diagnosis phase, often failing to advance solutions (Stainton-Rogers, 2006). The Pragmatic logic of inquiry is expressed in design and engineering disciplines (Duram, 2010). It emphasises practical problem-solving and seeks suitable methods for addressing real-world issues. It deals with understanding and managing systems, including their interrelationships and the impacts of human activities. It commonly uses a mix of quantitative and qualitative methods (surveys, modelling, and interdisciplinary approaches integrating natural and social sciences) and makes ample use of case studies. Issues with the pragmatic logic of inquiry involve the common overlooking of culture, governance and values, with little concern for real-world implementation to which a constructivist approach would contribute (Biggs & Buchler, 2008). It is beyond the scope of this exercise to define Design, as it involves a wide variety of activities and areas of application (urban design being only one of them) (Biggs & Büchler, 2008; Jong & Duin, 2002; Marchand & Walker, 2009; Oosterhuis, 2009). Design can be understood in its broader conceptualisation as not only the physical design of artefacts or spaces but also process design, institutional design, user interface design, service design and more. A common characteristic of all areas of design is being future-oriented, problem-solving, and propositional For the purpose of the discussion here, I will define design as the creative process of conceptualising and creating solutions that address specific needs or challenges based on evidence and research, integrating functionality, aesthetics, and usability within cultural, social, and environmental contexts (Biggs et al., 2009). Design could be said to be creative and pragmatic, often going from problem to solution (sometimes too quickly). However, a "good" design (and there are many conceptions of "good" we could employ) can be said to address all the logics of enquiry mentioned here. "Good" design is technically sound, functional and rooted in data (Positivism). "Good" design is concerned with the material chains necessary for the production of the design and its reuse, recycling, upcycling and the overall ethical and political implications of its production, use, and discharge (Critical). It is also informed by the rich array of human experiences, perspectives and cultures (Constructivist). "Good" design addresses real-world issues and is environmentally sustainable (Pragmatic). "Good" design is innovative, creative, and often aesthetically attractive (Creative). Urban design, for instance, aims to transform urban spaces into more equitable, sustainable, and livable environments (Pragmatic+Critical+Constructivist) (Roggema, 2017). The Creative paradigm or logic of inquiry, particularly in the context of design disciplines, propels design forward due to its inherent flexibility and capacity for innovation. It allows for the integration of diverse perspectives, fostering interdisciplinary collaboration that can lead to holistic and innovative solutions to complex challenges. This paradigm encourages thinking outside of the box, enabling the exploration of novel ideas and approaches that are both practical and forward-thinking. It values the synthesis of functionality, aesthetics, and usability, ensuring that solutions are not only effective but also culturally and contextually relevant (Rocco et al., 2009). However, this creative approach is also deeply challenging from a scientific perspective (DeWitt, 2004). Its emphasis on rapid problem-solving and future-oriented solutions can sometimes lead to a superficial understanding of underlying issues, bypassing thorough empirical analysis and theoretical rigour . This rush to solutions may overlook the nuances of cultural, social, and environmental contexts, potentially leading to interventions that are not sustainable or that fail to address root causes. Moreover, the subjective nature of creative processes can introduce biases, making it challenging to ensure replicability and objectivity, which are core tenets of scientific inquiry. Thus, while the creative paradigm fosters innovation and practical application, it must be balanced with rigorous empirical methods and a critical approach to ensure comprehensive and scientifically sound outcomes (Stainton-Rogers, 2006). This is not for nothing; this is the very point of the model proposed here. These challenges are particularly pronounced when these processes are solitary, leading to solutions that reflect a single perspective rather than a collective, plural and comprehensive understanding of the issue at hand (Biggs et al., 2010). Such an approach can result in irrational confidence in the effectiveness of designs, neglecting the complexity and diversity of real-world contexts. To address this shortcoming, designers can integrate rigorous research methods and embrace co-design practices. Co-design, also known as participatory design, involves collaborating with stakeholders, including users, community members, and other relevant parties, throughout the design process (Roggema, 2017). This approach ensures that multiple perspectives are considered, leading to more inclusive and contextually appropriate solutions. By engaging in co-design, designers can mitigate the risk of one-sided solutions, fostering a more democratic and effective design process that values the input and experiences of all participants. This collaborative effort not only enhances the relevance and sustainability of design outcomes but also builds trust and empowerment among stakeholders, making the design process more transparent and accountable. Note: I owe an awful lot to the <a href="https://www.delftdesignforvalues.nl/">Delft Design for Values Institute</a> and the Section of Ethics and Philosophy of Technology in my conceptualisation of "good design". I realise the discussion in this text was very brief, but scholars like Ibo van de Poel, Stefan Koller, and Peter Kroes have thought long and hard about these issues and have produced scholarship that helps us discuss what "good design" is. The issue of the academisation of design practice is ongoing, but advances have been made in the last decades, especially in England, Sweden and other countries where there is an established community of reflective design practitioners. I had the honour to integrate the Research Into Practice group at Hertfordshire University in the UK under the leadership of Professor Michael Biggs and Daniela Buchler, where these issues were discussed in depth. Please have a look at the references for some of the scholarship produced. References:  Biggs, M., & Buchler, D. (2008). Eight Criteria for practice-based research in the creative and cultural industries. Art, Design and Education in Higher Education, 7(1), 5-18. <a href="https://doi.org/https:/doi.org/10.1386/adch.7.1.5_1">https://doi.org/https://doi.org/10.1386/adch.7.1.5_1</a> Biggs, M., Buchler, D., & Rocco, R. (2009). Design Practice and Research: Interconnections and the criterion-based approach. European Academy of Design: Design Connexity, Aberdeen. Biggs, M., Buchler, D., Rocco, R., & Schjerven, C. (2010, 15-17 November 2010). The production of academic research and some barriers to academicisation in the creative and performing arts. ICERI 2010, Madrid. Biggs, M. A. R., & Büchler, D. (2008). Architectural Practice and Academic Research. Nordic Journal of Architectural Research, 20(1), 83-94. <a href="https://core.ac.uk/download/pdf/1640258.pdf">https://core.ac.uk/download/pdf/1640258.pdf</a> Bird, A. (2018). Thomas Kuhn. Stanford Encyclopedia of Philosophy. Retrieved 10 January 2025 from <a href="https://plato.stanford.edu/entries/thomas-kuhn/">https://plato.stanford.edu/entries/thomas-kuhn/</a> Creswell, J. W., & Plano Clark, V. L. (2007). Designing and conducting mixed methods research. SAGE. <a href="http://www.loc.gov/catdir/toc/ecip0610/2006008436.html">http://www.loc.gov/catdir/toc/ecip0610/2006008436.html</a> DeWitt, R. (2004). Worldviews : an introduction to the history and philosophy of science. Blackwell Pub. <a href="http://www.loc.gov/catdir/toc/ecip047/2003018208.html">http://www.loc.gov/catdir/toc/ecip047/2003018208.html</a> Duram, L. A. (2010). Pragmatic Study. In Encyclopedia of Research Design (pp. 1073-1075). SAGE. <a href="https://doi.org/10.4135/9781412961288.n326">https://doi.org/10.4135/9781412961288.n326</a> Giddens, A. (1993). New rules of sociological method : a positive critique of interpretative sociologies (2nd ed.). Stanford University Press. Hartimo, M., Kjosavik, F., & Linnebo, Ø. (2019). Introduction to special issue on ‘critical views of logic’. Inquiry, 65(6), 631-637. <a href="https://doi.org/10.1080/0020174X.2019.1651077">https://doi.org/10.1080/0020174X.2019.1651077</a> Jong, T. M. d., & Duin, L. v. (2002). Design research. In T. M. D. Jong & D. J. M. Voordt (Eds.), Ways to study and research. DUP Science. Marchand, A., & Walker, S. (2009). Designing in Design Research: From solving problems to exploring issues. European Academy of Design: Design Connexity, Aberdeen. Okasha, S. (2002). Philosophy of science : a very short introduction. Oxford University Press. Oosterhuis, R. (2009). The role of design in planning. TU Delft, Urbanism. Rocco, R., Biggs, M., & Buchler, D. (2009, 2009). A Pedagogical Proposal in an Area of Epistemological Uncertainty. PROJETAR, Sao Paulo. Roggema, R. (2017). Research by Design: Proposition for a Methodological Approach. Urban Science, 1(2), 1-19. Romero, P., Rojas, K., & Rojas, C. (2013). Postpositivism, Positivist and Engineering. International Journal of Engineering Research and Development, 9(1), 05-06. Rosenberg, A. (2005). Philosophy of Science: A Contemporary Introduction. Routledge. Shannon-Baker, P. (2023). Philosophical underpinnings of mixed methods research in education. In R. J. Tierney, F. Rizvi, & K. Ercikan (Eds.), International Encyclopedia of Education (Fourth Edition) (pp. 380-389). Elsevier. <a href="https://doi.org/10.1016/B978-0-12-818630-5.11037-1">https://doi.org/10.1016/B978-0-12-818630-5.11037-1</a> Stainton-Rogers, W. (2006). Logics of Enquiry. In S. Potter (Ed.), Doing Postgraduate Research, Volume 13 (pp. 73-91). Sage.

opencc-by-4.0Jun 2024View details →

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Integrated knowledge graphs and embeddings vectors for drug-drug interaction prediction

The associated Knowledge Graphs for predicting potential drug-drug interaction, which is used in our paper titled "Drug-Drug Interaction Prediction Based on Knowledge Graph Embeddings and Convolutional-LSTM Network".  Please consider citing the following paper if you plan or used our datasets. Md. Rezaul Karim, Michael Cochez, Joao Bosco Jares, Mamtaz Uddin, Oya Beyan, and Stefan Decker, "Drug-Drug Interaction Prediction Based on Knowledge Graph Embeddings and Convolutional-LSTM Network", In 10th ACM Int’l Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB ’19), September 7–10, 2019, Niagara Falls, NY, USA.

opencc-by-4.0Sep 2019View details →

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Data from: Building on 150 years of knowledge: the freshwater isopod Asellus aquaticus as an integrative eco-evolutionary model system

Introduction This is a literature database with reference information of all papers that use the freshwater isopod Asellus aquaticus; published between the years 1867 and 2020. This database is intended as a starting point for scientists interested in conducting research on and with this organism. The database is currently only available as a single CSV file; future versions may be made available through a more frequently updated SQL database. The database includes specific information about the subject area and content of each paper, as well as bibliographic information. This repository is associated with the paper "Building on 150 years of knowledge: the freshwater isopod Asellus aquaticus as an integrative eco-evolutionary model system", published in Frontiers in Ecology and Evolution. Details on Methods from the electronic supplement: We used the we online search tools of Web of Science (WOS; Clarivate analytics) by searching for the term "asellus aquaticus" in six relevant databases (BIOSIS, CABI, FSTA, Medline, WOS Core Collection and Zoological Records). The database was accessed with a University License (Lund University). We manually downloaded the results and combined them to a single CSV file in Excel (Microsoft). All further processing was done in the statistical programming language R, version 4.0.2 (R Core Team 2020). From the 1238 obtained records we discarded three papers that were published after the year 2020 to work with completed years only. We used the subject areas assigned by WOS to provide an overview of the fields of science in which A. aquaticus has been most studied. Each paper had between one and ten subject areas assigned by WOS (2845 assignments to 1235 papers, meaning 2.3 assignments per paper, on average). To represent these multiple assignments in relation to the actual number of papers per year, we calculated "fractional assignments" by adding up all assignments to a field per year, divided by the total number of assignments in that year, and then multiplied by the number of papers.  For example, if there were 12 assignments to "toxicology" in 1993, and 133 assignments in 1993, but only 21 papers published, "toxicology" would get a score of 1.9 papers in 1993 (as calculated by = (12/133)*21). In Figure 1, we represent these "fractional assignments" in the top panel, and the total number of assignments in the lower panel. Caption for figure (1) in publication: FIGURE 1 | Over 150 years of research on and with Asellus aquaticus. The figure summarizes published scientific literature on A. aquaticus. We conducted a quantitative literature survey with the search tools of Web of Science (WOS; Clarivate analytics) by searching for the term "asellus aquaticus" in six databases (i.e., BIOSIS, CABI, FSTA, Medline, WOS Core Collection, and Zoological Records). We found 1235 records, published between 1867 and 2020. (A) The graph shows the number of publications per year within a given subject area, as designated by WOS. (B) The graph shows the total number of publications assigned to a specific subject area. The top 10 fields account for 72.58% of all publications, and are indicated by color coding in A and B (multiple assignments are possible, summing up to 2845 assignments). The inset in B shows a wordcloud with the 100 most used keywords from all A. aquaticus’ publications. Furthermore, we compiled all records with relevant information (e.g., title, keywords, research areas, and abstract) to a single file which is available online. More details can be found in the Supplementary Material.

opencc-by-4.0Jun 2021View details →

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NTDs2RDF: A heterogeneous and integrated knowledge graph for the exploration of neglected tropical diseases

Neglected tropical diseases (NTDs) are a heterogeneous group of 20 bacterial, viral, parasitic, and fungal conditions that generally occur in developing tropical countries in the Americas, Africa, and Asia. NTDs mainly affect poor populations that do not have access to safe water, sanitation, and high-quality healthcare. Because of the severe effects of NTDs (i.e., they can cause long-lasting disabilities), they reinforce the cycle of poverty in vulnerable communities. The NTDs2RDF project aimed to create a knowledge graph (KG) of genes, proteins, metabolic pathways, gene ontologies, single nucleotide variants, drugs, and other relevant data for three NTDs (Chagas disease, leishmaniasis, and African trypanosomiasis), integrating all the information in a single data structure that can be explored through a query interface implemented with a Streamlit web application. This software provides a user-friendly platform to extract information from the KG using SPARQL queries. The project represents an initial step towards the creation of a heterogeneous database for different NTDs with several potential applications in advancing the understanding of NTDs biology and providing insights that cannot be obtained through alternative resources.

opencc-by-4.0Mar 2023View details →

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Integrating Local and Traditional Ecological Knowledge into Anadromous Waters Cataloging and Fish Inventories of select drainages of the Tanana and Yukon rivers 2021-2023

***Funded by the Alaska Sustainable Salmon Fund #54007, a part of the Pacific Coastal Salmon Recovery Fund Synopsis During 2021 and 2022, staff from the Alaska Department of Fish and Game (ADF&G), Division of Sport Fish, Alaska Freshwater Fish Inventory (AFFI) program and the Yukon River Drainage Fisheries Association (YRDFA) will collaborate to integrate Local and Traditional Ecological Knowledge (LTK) ethnographic interviews into a rapid systematic inventory of fish communities and associated habitats in select drainages of the lower Tanana River and Upper Yukon River in the area of Tanana and Fairbanks. First, in 2021, LTK surveys in the communities of Tanana, Manley Hot Springs and Nenana will locate important subsistence areas that will be overlain on our GIS-selected target streams to assist in filling gaps in coverage of the State of Alaska's Catalog of Waters Important for the Spawning, Rearing or Migration of Anadromous Fishes (AWC) in freshwater habitats expected to support anadromous fish populations likely to be impacted by human activities. Then, in 2022, this project will seasonally sample target streams and record observations in the Alaska Freshwater Fish Inventory database (AFFID), nominate water bodies to the AWC when anadromous fish are observed, and provide publicly available data via the AFFID internet mapping service. Anticipated benefits of this project are multiple hundreds of kilometers and/or dozens of water bodies added to the AWC as well as a broader understanding of the importance of this region’s fish species to local human communities. 1.      Introduction In Alaska, habitats that support migrating, spawning, or rearing anadromous fish are protected under multiple administrative jurisdictions, including state, federal, and local habitat protection standards. Alaska Statute (AS) 16.05.871 (the Anadromous Fish Act) is a keystone statutory protection for freshwater habitats of anadromous fish in Alaska, requiring the ADF&G to "specify the various rivers, lakes, and streams or parts of them" of the state that are important to the spawning, rearing, or migration of anadromous fish.  The resulting atlas is known as the Anadromous Waters Catalog (AWC) which is adopted as regulation under 5 AAC 95.011. Under the Anadromous Fish Act, activities and uses conducted in or otherwise affecting water bodies specified in the AWC require permitting from the ADF&G Habitat Section. Many other federal, state, and local government policies specify additional protections for anadromous fish habitat in Alaska. To be listed in the AWC, water bodies must have site-specific, direct, unambiguous observations of anadromous fish by a qualified observer. This is a major reason the AFFI program targets areas with high potential to add water bodies to the AWC. Beginning in spring 2021, YRDFA and AFFI staff will conduct LTK interviews and mapping in the communities of Tanana, Manley Hot Springs, and Nenana. By spring 2022, the LTK contributions will be mapped and added to our site selection criteria prior to field work. Based on seasonality of some fishes in this area, we will establish certain seasonal site locations that are road accessible to determine spatiotemporal patterns in the fish community used by area residents. This will include target streams sampled in June, the main summer season (see following paragraph), and September. From July 10 to August 1, 2022, 4 crews, each with 2 members, will sample fish communities using AFFI protocols in selected streams draining into the Tanana and Yukon rivers within a general area upstream of the Kokrines (a historical settlement downstream of Tanana) and downstream of the city of Fairbanks. Target sites will include wadeable headwater streams and un-wadeable streams. Summer surveys will maximize detection of juvenile and spawning Chinook salmon, juvenile coho salmon, as well as spawning summer chum salmon. More opportunistic seasonal sampling for 5 days, tentatively in late-spring (e.g., early June) and fall (September or October), could enhance the likelihood of detecting multiple life history stages of rearing, migrating, or spawning whitefishes, Chinook salmon, coho salmon, and chum salmon.  Given the size and remoteness of the Yukon and Tanana river drainages, this AFFI proposal is for years 3 and 4 of a multiyear effort to sample the region and provides enough funding to conduct spring, summer, and fall sampling. AFFI staff will pursue additional funding sources to conduct more surveys if possible. Before this proposed study, AKSSF funded AFFI to survey the upper Yukon and Tanana River drainages in 2019 and 2020 (AKSSF projects 44375 and 53013, respectively). For example, 2019 surveys in the upper Yukon and Tanana river drainages documented >40 streams previously unlisted in the AWC for Chinook salmon. 2.      Location(s) Sampling will be done in select drainages of the Yukon and Tanana rivers bounded downstream near the old Yukon River village of Kokrines (N 64.9376, W -154.6944) and upstream to the Tanana River tributary Willow Creek (N 64.6719, W -148.2027). This includes the area and tributaries around the confluence of the Yukon and Tanana rivers (N 65.1682, W -151.9982) between the villages of Tanana and Manley Hot Springs. I.                   Objectives Objective 1: To maximize the spatial increase of documented anadromous fish habitats depicted in the AWC within the study area (sampling a minimum 80 headwater target streams, and 12 un-wadeable target streams) not including repeat sampling of select sites to document seasonal presence of some anadromous species. Objective 2: To use LTK to maximize the spatial increase of documented anadromous fish habitats depicted in the AWC within the study area while also corroborating and verifying the LTK with field surveys. Objective 3:  To record characteristics, using established protocols, of aquatic habitats (including riparian zone) at each sampling location. Objective 4:  To provide the fish distribution and associated aquatic habitat information to State & Federal agencies, participating communities, and the public. II.                Methods This collaborative project is designed to contribute to the AWC using social and biological methods. Prior to field work, a YRDFA anthropologist and ADF&G staff will contact the Tribal Councils of Tanana, Manley Hot Springs, and Nenana to schedule community meetings (in-person or online, as able) and ethnographic interviews between late spring 2021 and spring 2022. These interviews and mapping activities will establish what is known about the timing and distribution of resident and anadromous fishes and create maps that can be overlain on the AWC with other AFFI site selection criteria to identify streams to sample the following year. The next year, project staff will seek to verify LTK surveys and add to the AWC through seasonal sampling. The proposed study area for 2020 has a road system along the Tanana River which will allow access via truck and boat to certain streams during 5 days each in spring (June) and fall (September). This will likely raise the number of sites this project can sample while avoiding excess helicopter expenses. Additionally, this will allow better seasonal sampling efforts to maximize the ability to document seasonally variable fish distributions such as summer salmon spawning and fall whitefish spawning seasons. Summer sampling will be more expansive and follow ADF&G's AFFI protocols (Giefer and Cathcart 2019) where 4 crews, each with 2 members, will use helicopters to sample fish communities in selected study stream reaches for approximately 21 days in summer of 2022. Target survey sites will include wadeable headwater streams sampled with a backpack electrofisher, and un-wadeable streams sampled with a raft-mounted electrofisher. Sites within the study area that are identified as being anadromous fish rearing from LTK surveys and currently unlisted in the AWC will be prioritized for verification.           Study area selection The long-term goal of the AFFI program is to complete a statewide baseline inventory of fish assemblages and associated aquatic and riparian habitats. At its inception, the AFFI program developed a systematic approach to rank and prioritize Alaska’s 139 subbasin level hydrologic units. At the time of this proposal, the AFFI program has surveyed 81 of the 139 subbasins that were originally prioritized. This project’s 99,099 square kilometer study area includes subbasins of the lower Tanana River between the city Fairbanks and the mouth of the Tanana River, tributaries draining the south side of the Tanana upstream of Fairbanks but west of Clear Creek, and in select subbasins of the Yukon River near the community of Tanana but upstream of Kokrines.  Target stream selection Target stream selection will be performed by integrating LTK survey information with our conventional method of using GIS to identify previously unsampled (or not rigorously sampled) streams that can be safely accessed while maximizing potential additions to the AWC. The number of headwater streams in the study area will exceed the project’s limited sampling effort capacity; therefore, a subset of streams comprising the longest stream segments not listed in the AWC will be selected as targets. The headwater team will sample approximately six to eight headwater streams per day and, when operating, the raft or riverboat team will float and sample one un-wadeable stream per day. Based on past AFFI projects, it is estimated that a minimum of 80 headwater target streams will be sampled, and 12 un-wadeable target streams could be rafted and sampled during the 21 field days (not including the 5 field days in each of June and September).  However, these estimates are contingent upon weather and logistics. Reference sites for seasonal sampling will be prioritized depending on spatial and temporal observations from LTK surveys where we will select road or boat accessible locations to target fishes in spring, summer, and fall. We will seek to access all LTK-identified subbasins for subsistence fishes but they will be prioritized according to logistics (i.e., fuel and time needed to reach location) and potential addition to the AWC. Sampling methods Ideally, the fish community and habitat will be sampled with standardized methods per AFFI protocols. Fish will be collected by single-pass electrofishing standardized by stream width (i.e., 40 or 120 wetted-channel-widths in wadeable and un-wadeable target streams, respectively). Captured fish will be identified, measured, and released. Other gear types (such as beach seines, angling, or minnow traps) may be deployed if conditions prohibit electrofishing. Standard water chemistry, channel morphology, and riparian habitat parameters will be recorded at each sample site in addition to longer-term water temperature or eDNA sampling efforts in reference streams.   III.             Benefits Updated and more comprehensive AWC coverage will be the primary regulatory or fish habitat benefit of this project toward sustaining salmon habitat. Enhanced communication and partnerships with tribal communities will be established through interviews to gather LTK. Based on summer AFFI sampling since 2016, sampling at least 80 headwater target streams and 12 un-wadeable target streams, this project will add many (likely >300) previously unlisted kilometers of salmon habitat among several distinct streams to the AWC. Only anadromous fish habitat listed in the AWC receives protection under the Anadromous Fish Act and various other policies that provide additional protections to specified anadromous fish habitat. Also, providing more complete (e.g., seasonal) and accessible fish community and habitat information will benefit ADF&G, as well as help other federal, state, and local resource agencies better implement their respective fish habitat management, protection, and research missions.  Better protection and management of salmon habitat will benefit salmon fisheries and the communities they sustain by safeguarding critical salmon habitat thereby ensuring the long-term productivity of habitats and salmon populations.

opencc-by-4.0Oct 2024View details →

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One Health EJP MATRIX video about the One Health Surveillance CODEX: The Knowledge Integration Platform (OHS Codex/KIP)

This video was recorded during the webinar about the One Health Surveillance CODEX: The Knowledge Integration Platform (OHS Codex/KIP) as part of the OHEJP MATRIX Webinar Series 2022 Solutions for One Health Surveillance in Europe. The webinar took place on November 10th from 14:00 to 15:15 CET and was hosted by the <a href="https://onehealthejp.eu/jip-matrix/">One Health EJP project MATRIX.</a> The One Health Surveillance CODEX: The Knowledge Integration Platform (OHS Codex/KIP) is a community resource supporting the adoption of the OH paradigm. The OHS Codex/KIP comprises five high-level “action principles”, which respectively support: i) planning and management; ii) collaboration; iii) knowledge exchange; iv) data interoperability; v) reporting and dissemination. These principles are applicable to any sector-specific or cross sectorial surveillance activity. Under each of these principles, the OHS Codex/KIP provides the users a collection of resources (e.g. tools, technical resources, guidance documents and experiences) that address specific OH-problems in the context of the corresponding principle. As an open community framework, it is continuously updated by and for the community. More information is available <a href="https://oh-surveillance-codex.readthedocs.io/en/latest/">here.</a> The OHS Codex/KIP has been initially devolped in <a href="https://onehealthejp.eu/jip-orion/">One Health EJP ORION</a> and was expanded and promoted within <a href="https://onehealthejp.eu/jip-matrix/">One Health EJP MATRIX.</a> The MATRIX and ORION projects are part of the One Health European Joint Programme (OHEJP). They received funding from the European Union’s Horizon 2020 research and innovation programme under Grant Agreement No 773830. Leading MATRIX partner of the OHS Codex/KIP: German Federal Institute for Risk Assessment (BfR). Contact: Matthias Filter (Matthias.Filter@bfr.bund.de) Webinar agenda: Welcome and general overview of the MATRIX solutions for One Health Surveillance Guido Benedetti, Statens Serum Institut (SSI), Denmark One Health Surveillance CODEX: Knowledge Integration Platform – ORION perspective and MATRIX extension Matthias Filter, German Federal Institute for Risk Assessment (BfR), Germany Live Demo and special features of the One Health Surveillance CODEX: Knowledge Integration Platform Yvonne Mensching, German Federal Institute for Risk Assessment (BfR), Germany

opencc-by-4.0Nov 2022View details →

ClinicalTrials.gov32/100

Integrating Inuit Knowledge Principles in Multi-Level Mental Health Clinical Trials

ClinicalTrials.gov study NCT07014852. IPD Sharing: NO. Countries: 1. Publications: 9.

closedIPD-NOFeb 2026View details →

ClinicalTrials.gov32/100

Hill-grade Knowledge Via Integrated Neural-network for Gastroscopy

ClinicalTrials.gov study NCT06040723. IPD Sharing: NO. Countries: 1. Publications: 1.

closedIPD-NOFeb 2026View details →

ClinicalTrials.gov32/100

Cluster Randomized Trial of Knowledge Brokering to Integrate Mood and Smoking Cessation in Ontario Primary Care

ClinicalTrials.gov study NCT03130998. IPD Sharing: NO. Countries: 1. Publications: 2.

closedIPD-NOFeb 2026View details →

dryad32/100

Data from: Integrating local knowledge and research to refine the management of an invasive non-native grass in critically endangered grassy woodlands

Open the record for dataset details and reuse information.

publicApr 2018View details →

dryad32/100

Data from: Integrating local knowledge to prioritise invasive species management

Open the record for dataset details and reuse information.

publicMay 2019View details →

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Supplementary material 1 from: Dehnen-Schmutz K, Pescott OL, Booy O, Walker KJ (2022) Integrating expert knowledge at regional and national scales improves impact assessments of non-native species. NeoBiota 77: 79-100. https://doi.org/10.3897/neobiota.77.89448

Survey and Tables S1–S3

opencc-zeroOct 2022View details →

zenodo28/100

Supplementary material 3 from: Dehnen-Schmutz K, Pescott OL, Booy O, Walker KJ (2022) Integrating expert knowledge at regional and national scales improves impact assessments of non-native species. NeoBiota 77: 79-100. https://doi.org/10.3897/neobiota.77.89448

Figure S1

opencc-zeroOct 2022View details →

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Supplementary material 2 from: Dehnen-Schmutz K, Pescott OL, Booy O, Walker KJ (2022) Integrating expert knowledge at regional and national scales improves impact assessments of non-native species. NeoBiota 77: 79-100. https://doi.org/10.3897/neobiota.77.89448

Table S2

opencc-zeroOct 2022View details →

zenodo28/100

Figure 1 from: Neumann M, Ehnert F (2024) Knowledge re-integration in real-world laboratories to transform cities and communities: report on workshop designs. Research Ideas and Outcomes 10: e124018. https://doi.org/10.3897/rio.10.e124018

Figure 1 Zooming into phase C: the process of knowledge re-integration into societal practice in a TDR process.

opencc-by-4.0Apr 2024View details →

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Supplementary material 2 from: Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Hobern D, Banki O, Addink W, Kõljalg U, Copas K, Mergen P, Güntsch A, Benichou L, Benito Gonzalez Lopez J, Ruch P, Martin CS, Barov B, Demirova I, Hristova K (2022) Biodiversity Community Integrated Knowledge Library (BiCIKL). Research Ideas and Outcomes 8: e81136. https://doi.org/10.3897/rio.8.e81136

Letters of Support and Descriptions of the Collaborating Infrastructures

opencc-zeroFeb 2022View details →

zenodo28/100

Supplementary material 1 from: Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Hobern D, Banki O, Addink W, Kõljalg U, Copas K, Mergen P, Güntsch A, Benichou L, Benito Gonzalez Lopez J, Ruch P, Martin CS, Barov B, Demirova I, Hristova K (2022) Biodiversity Community Integrated Knowledge Library (BiCIKL). Research Ideas and Outcomes 8: e81136. https://doi.org/10.3897/rio.8.e81136

BiCIKL Gantt chart

opencc-zeroFeb 2022View details →

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Supplementary material 3 from: Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Hobern D, Banki O, Addink W, Kõljalg U, Copas K, Mergen P, Güntsch A, Benichou L, Benito Gonzalez Lopez J, Ruch P, Martin CS, Barov B, Demirova I, Hristova K (2022) Biodiversity Community Integrated Knowledge Library (BiCIKL). Research Ideas and Outcomes 8: e81136. https://doi.org/10.3897/rio.8.e81136

Use Cases

opencc-zeroFeb 2022View details →

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Figure 8 from: Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Hobern D, Banki O, Addink W, Kõljalg U, Copas K, Mergen P, Güntsch A, Benichou L, Benito Gonzalez Lopez J, Ruch P, Martin CS, Barov B, Demirova I, Hristova K (2022) Biodiversity Community Integrated Knowledge Library (BiCIKL). Research Ideas and Outcomes 8: e81136. https://doi.org/10.3897/rio.8.e81136

Figure 8 The FAIR Data Place (FDP) built by JRA-05 will provide a one-stop point for searching bi- and multi-directionally linked FAIR data across domains to serve multiple research purposes.

opencc-by-4.0Feb 2022View details →

ScienceDex guides

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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.

Compare curated datasets

Allen Brain Atlas

Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.

allen-brain-atlas

neuroscienceopenDocumentation, web resources, and API references are available online.

Last verified 2026-04-30Open record

Annotated Behaviour and Observability Dataset (ABODe)

ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.

abode-home-cage

behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.

Last verified 2026-04-30Open record

DANDI Archive for NWB datasets

DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.

dandi-nwb

electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

Last verified 2026-04-30Open record

International Brain Laboratory public data

The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.

ibl

behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

Last verified 2026-04-29Open record

OpenNeuro

OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.

openneuro

neuroscienceopenPublished datasets are available on demand over the internet.

Last verified 2026-04-29Open record