JASM2014 talk - "Phinch: An interactive, exploratory data visualization for enviornmental sequence data"
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Phinch is a web-based, interactive data visualization framework for analyzing environmental sequence data and metadata in standard formats like BIOM and tab-delimited files. It allows users to explore patterns in large datasets and export or share visualizations. Future work will add phylogenetic visualizations, more analysis tools, and an open source developer community to expand the framework's capabilities.
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The document discusses the future of Cochrane Reviews and scientific articles moving away from static documents toward structured linked data and interfaces. It argues that the focus should shift from the documents themselves to the things they are about (e.g. populations, interventions, outcomes), which can be connected as a web of data. This would allow content to be more nimble, traveling freely across datasets while retaining context. Interfaces could provide better access than documents by enabling smart search and filtering of this linked data graph. The future is making content and delivery more important than the containers (documents/articles) themselves.
The Rhetoric of Research Objects
Keynote: SemSci 2017: Enabling Open Semantic Science
1st International Workshop co-located with ISWC 2017, October 2017, Vienna, Austria,
https://semsci.github.io/semSci2017/
Abstract
We have all grown up with the research article and article collections (let’s call them libraries) as the prime means of scientific discourse. But research output is more than just the rhetorical narrative. The experimental methods, computational codes, data, algorithms, workflows, Standard Operating Procedures, samples and so on are the objects of research that enable reuse and reproduction of scientific experiments, and they too need to be examined and exchanged as research knowledge.
We can think of “Research Objects” as different types and as packages all the components of an investigation. If we stop thinking of publishing papers and start thinking of releasing Research Objects (software), then scholar exchange is a new game: ROs and their content evolve; they are multi-authored and their authorship evolves; they are a mix of virtual and embedded, and so on.
But first, some baby steps before we get carried away with a new vision of scholarly communication. Many journals (e.g. eLife, F1000, Elsevier) are just figuring out how to package together the supplementary materials of a paper. Data catalogues are figuring out how to virtually package multiple datasets scattered across many repositories to keep the integrated experimental context.
Research Objects [1] (http://researchobject.org/) is a framework by which the many, nested and contributed components of research can be packaged together in a systematic way, and their context, provenance and relationships richly described. The brave new world of containerisation provides the containers and Linked Data provides the metadata framework for the container manifest construction and profiles. It’s not just theory, but also in practice with examples in Systems Biology modelling, Bioinformatics computational workflows, and Health Informatics data exchange. I’ll talk about why and how we got here, the framework and examples, and what we need to do.
[1] Sean Bechhofer, Iain Buchan, David De Roure, Paolo Missier, John Ainsworth, Jiten Bhagat, Philip Couch, Don Cruickshank, Mark Delderfield, Ian Dunlop, Matthew Gamble, Danius Michaelides, Stuart Owen, David Newman, Shoaib Sufi, Carole Goble, Why linked data is not enough for scientists, In Future Generation Computer Systems, Volume 29, Issue 2, 2013, Pages 599-611, ISSN 0167-739X, https://doi.org/10.1016/j.future.2011.08.004
Mtsr2015 goble-keynote
Metadata and Semantics Research Conference, Manchester, UK 2015
Research Objects: why, what and how,
In practice the exchange, reuse and reproduction of scientific experiments is hard, dependent on bundling and exchanging the experimental methods, computational codes, data, algorithms, workflows and so on along with the narrative. These "Research Objects" are not fixed, just as research is not “finished”: codes fork, data is updated, algorithms are revised, workflows break, service updates are released. Neither should they be viewed just as second-class artifacts tethered to publications, but the focus of research outcomes in their own right: articles clustered around datasets, methods with citation profiles. Many funders and publishers have come to acknowledge this, moving to data sharing policies and provisioning e-infrastructure platforms. Many researchers recognise the importance of working with Research Objects. The term has become widespread. However. What is a Research Object? How do you mint one, exchange one, build a platform to support one, curate one? How do we introduce them in a lightweight way that platform developers can migrate to? What is the practical impact of a Research Object Commons on training, stewardship, scholarship, sharing? How do we address the scholarly and technological debt of making and maintaining Research Objects? Are there any examples
I’ll present our practical experiences of the why, what and how of Research Objects.
Engaging Information Professionals in the Process of Authoritative Interlinki...
Through the use of Linked Data (LD), Libraries, Archives and Museums (LAMs) have the potential to expose their collections to a larger audience and to allow for more efficient user searches. Despite this, relatively few LAMs have invested in LD projects and the majority of these display limited interlinking across datasets and institutions. A survey was conducted to understand Information Professionals' (IPs') position with regards to LD, with a particular focus on the interlinking problem. The survey was completed by 185 librarians, archivists, metadata cataloguers and researchers. Results indicated that, when interlinking, IPs find the process of ontology and property selection to be particularly challenging, and LD tooling to be technologically complex and unsuitable for their needs.
Our research is focused on developing an authoritative interlinking framework for LAMs with a view to increasing IP engagement in the linking process. Our framework will provide a set of standards to facilitate IPs in the selection of link types, specifically when linking local resources to authorities. The framework will include guidelines for authority, ontology and property selection, and for adding provenance data. A user-interface will be developed which will direct IPs through the resource interlinking process as per our framework. Although there are existing tools in this domain, our framework differs in that it will be designed with the needs and expertise of IPs in mind. This will be achieved by involving IPs in the design and evaluation of the framework. A mock-up of the interface has already been tested and adjustments have been made based on results. We are currently working on developing a minimal viable product so as to allow for further testing of the framework. We will present our updated framework, interface, and proposed interlinking solutions.
Preserving the Inputs and Outputs of Scholarship
Tim Babbitt discusses the changing context of research and scholarship due to digitization and the internet. The inputs and outputs of research are increasingly digital and complex, including data, code, presentations, and more. ProQuest has a history of preserving scholarship through microfilming and is exploring how to preserve the full range of digital scholarly outputs and their linkages in a sustainable way. Key questions include balancing new and old preservation methods and moving beyond preserving individual objects to also preserving networks and linkages between scholarly works.
Authors' and Publications' Citations knowledge base
It is our presentation during CEIT-2016 (Fourth Edition of the International Conference on Control Engineering and Information Technology) held at Hammamet, Tunisia, December 16-18 2016.
Being FAIR: FAIR data and model management SSBSS 2017 Summer School
Lecture 1:
Being FAIR: FAIR data and model management
In recent years we have seen a change in expectations for the management of all the outcomes of research – that is the “assets” of data, models, codes, SOPs, workflows. The “FAIR” (Findable, Accessible, Interoperable, Reusable) Guiding Principles for scientific data management and stewardship [1] have proved to be an effective rallying-cry. Funding agencies expect data (and increasingly software) management retention and access plans. Journals are raising their expectations of the availability of data and codes for pre- and post- publication. The multi-component, multi-disciplinary nature of Systems and Synthetic Biology demands the interlinking and exchange of assets and the systematic recording of metadata for their interpretation.
Our FAIRDOM project (http://www.fair-dom.org) supports Systems Biology research projects with their research data, methods and model management, with an emphasis on standards smuggled in by stealth and sensitivity to asset sharing and credit anxiety. The FAIRDOM Platform has been installed by over 30 labs or projects. Our public, centrally hosted Asset Commons, the FAIRDOMHub.org, supports the outcomes of 50+ projects.
Now established as a grassroots association, FAIRDOM has over 8 years of experience of practical asset sharing and data infrastructure at the researcher coal-face ranging across European programmes (SysMO and ERASysAPP ERANets), national initiatives (Germany's de.NBI and Systems Medicine of the Liver; Norway's Digital Life) and European Research Infrastructures (ISBE) as well as in PI's labs and Centres such as the SynBioChem Centre at Manchester.
In this talk I will show explore how FAIRDOM has been designed to support Systems Biology projects and show examples of its configuration and use. I will also explore the technical and social challenges we face.
I will also refer to European efforts to support public archives for the life sciences. ELIXIR (http:// http://www.elixir-europe.org/) the European Research Infrastructure of 21 national nodes and a hub funded by national agreements to coordinate and sustain key data repositories and archives for the Life Science community, improve access to them and related tools, support training and create a platform for dataset interoperability. As the Head of the ELIXIR-UK Node and co-lead of the ELIXIR Interoperability Platform I will show how this work relates to your projects.
[1] Wilkinson et al, The FAIR Guiding Principles for scientific data management and stewardship Scientific Data 3, doi:10.1038/sdata.2016.18
An Open Context for Archaeology
The common use by archaeologists of ubiquitous technologies such as computers and digital cameras means that archaeological research projects now produce huge amounts of diverse, digital documentation. However, while the technology is available to collect this documentation, we still largely lack community accepted dissemination channels appropriate for such torrents of data. Open Context (http://www.opencontext.org) aims to help fill this gap by providing open access data publication services for archaeology. Open Context has a flexible and generalized technical architecture that can accommodate most archaeological datasets, despite the lack of common recording systems or other documentation standards. Open Context includes a variety of tools to make data dissemination easier and more worthwhile. Authorship is clearly identified through citation tools, a web-based publication systems enables individuals upload their own data for review, and collaboration is facilitated through easy download and other features. While we have demonstrated a potentially valuable approach for data sharing, we face significant challenges in scaling Open Context up for serving large quantities of data from multiple projects.
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BIBFLOW and the Libhub Initiative: Leveraging our past to define our future
Eric Miller, President, Zepheira
Jeff Penka, Director of Channel and Product Development, ZepheiraBw dave pattern lidp
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NHM Data Portal: first steps toward the Graph-of-Life
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NHM Data Portal: first steps toward the Graph-of-Life
Presented by Vince Smith at the Society for the Preservation of Natural History Collections Conference in Berlin on the 23 June 2016
COPO - Collaborative Open Plant Omics, by Rob Davey
COPO - Collaborative Open Plant Omics, by Rob DaveyAIMS (Agricultural Information Management Standards)
Agricultural Data Interest Group (IGAD)
Pre-Meeting Agenda
Research Data Alliance
21st to 22nd September 2015
INRA, Paris (France)FAIR Software (and Data) Citation: Europe, Research Object Systems, Networks ...
NSF Workshop Data and Software Citation, 6-7 June 2016, Boston USA, Software Panel
FIndable, Accessible, Interoperable, Reusable Software and Data Citation: Europe, Research Objects, and BioSchemas.org
Oxford DTP - Sansone - Data publications and Scientific Data - Dec 2014
- The document discusses the need for open and accessible data in research. It notes that over 50% of studies are not published due to selective reporting of results.
- There is a movement for "FAIR data" in life and medical sciences, where data is findable, accessible, interoperable, and reusable. However, not much data currently meets these standards.
- Publishers can play a role in incentivizing data sharing by implementing policies requiring data availability and format standards for publishing research. This includes supporting data citations and data journals.
SEEK for Science: A Data and Model Management Platform to support Open and Re...
SEEK for Science: A Data and Model Management Platform to support Open and Reproducible Science in Systems Biology
Linked Data (1st Linked Data Meetup Malmö)
This document discusses Linked Data and outlines its key principles and benefits. It describes how Linked Data extends the traditional web by creating a single global data space using RDF to publish structured data on the web and by setting links between data items from different sources. The document outlines the growth of Linked Data on the web, with over 31 billion triples from 295 datasets as of 2011. It provides examples of large Linked Data sources like DBpedia and discusses best practices for publishing, consuming, and working with Linked Data.
The Emergence of Research Information Management (RIM) within US Libraries
Presented by Rebecca Bryant, Maliaca Oxnam, and Paolo Mangiafico, at the CNI Spring 2017 Membership Meeting, 3 April 2017, Albuquerque, New Mexico (USA).
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- 1. ! #Phinch: An interactive, exploratory data visualization framework for environmental sequence data @hollybik University of California, Davis (now) University of Birmingham, UK (soon)
- 2. VERY DIFFICULT Bik et al. 2012, Trends in Ecology and Evolution
- 4. “A Research-Driven Data Visualization Framework for High-Throughput Environmental Sequence Data”
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- 24. Acknowledgements : : Jonathan Eisen Aaron Darling Guillaume Jospin Dongying Wu David Coil : : Further Information • hbik@ucdavis.edu • @Dr_Bik – updates posted to Twitter Wesley Grubbs, Shujian Bu (Pitch Interactive) Acknowledgements