arXiv subjects

Carole Goble

Publications and source records attributed to Carole Goble.

25 records · Page 2Linked to original sources

arXiv2021

Workflows Community Summit: Bringing the Scientific Workflows Community Together

Scientific workflows have been used almost universally across scientific domains, and have underpinned some of the most significant discoveries of the past several decades. Many of these workflows have high computational, storage, and/or communication demands, and thus must execute on a wide range of large-scale platforms, from large clouds to upcoming exascale high-performance computing (HPC) platforms. These executions must be managed using some software infrastructure. Due to the popularity of workflows, workflow management systems (WMSs) have been developed to provide abstractions for creating and executing workflows conveniently, efficiently, and portably. While these efforts are all worthwhile, there are now hundreds of independent WMSs, many of which are moribund. As a result, the WMS landscape is segmented and presents significant barriers to entry due to the hundreds of seemingly comparable, yet incompatible, systems that exist. As a result, many teams, small and large, still elect to build their own custom workflow solution rather than adopt, or build upon, existing WMSs. This current state of the WMS landscape negatively impacts workflow users, developers, and researchers. The "Workflows Community Summit" was held online on January 13, 2021. The overarching goal of the summit was to develop a view of the state of the art and identify crucial research challenges in the workflow community. Prior to the summit, a survey sent to stakeholders in the workflow community (including both developers of WMSs and users of workflows) helped to identify key challenges in this community that were translated into 6 broad themes for the summit, each of them being the object of a focused discussion led by a volunteer member of the community. This report documents and organizes the wealth of information provided by the participants before, during, and after the summit.

cs.DC↗

arXiv2021

A Fresh Look at FAIR for Research Software

This document captures the discussion and deliberation of the FAIR for Research Software (FAIR4RS) subgroup that took a fresh look at the applicability of the FAIR Guiding Principles for scientific data management and stewardship for research software. We discuss the vision of research software as ideally reproducible, open, usable, recognized, sustained and robust, and then review both the characteristic and practiced differences of research software and data. This vision and understanding of initial conditions serves as a backdrop for an attempt at translating and interpreting the guiding principles to more fully align with research software. We have found that many of the principles remained relatively intact as written, as long as considerable interpretation was provided. This was particularly the case for the "Findable" and "Accessible" foundational principles. We found that "Interoperability" and "Reusability" are particularly prone to a broad and sometimes opposing set of interpretations as written. We propose two new principles modeled on existing ones, and provide modified guiding text for these principles to help clarify our final interpretation. A series of gaps in translation were captured during this process, and these remain to be addressed. We finish with a consideration of where these translated principles fall short of the vision laid out in the opening.

cs.SE↗

arXiv2015

Taverna Mobile: Taverna workflows on Android

Researchers are often on the move, say at conferences or projects meetings, and as workflows are becoming ubiquitous in the scientific process, having access to scientific workflows from a mobile device would be a significant advantage. We therefore have developed Taverna Mobile, an application for Android phones which allows browsing of existing workflows, executing them, and reviewing the results. Taverna Mobile does not aim to reproduce the full experience of building workflows in the Taverna Workbench, rather it focuses on tasks we have deemed relevant to a scientist that is not at her desk. For instance, when visiting a conference she might hear about someone's workflow, which she can quickly locate and mark for later exploration. When in the biology lab, faced with updated scientific data, the scientist can rerun her own workflow with new inputs. While commuting, she can monitor the status of a long-running job.

cs.SE↗

arXiv2014

Structuring research methods and data with the Research Object model: genomics workflows as a case study

One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for understanding an experiment, and this is increasingly recognized in the bioinformatics community. Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results of an experiment. To support this we explored a model for the semantic description of a workflow-centric Research Object (RO), where an RO is defined as a resource that aggregates other resources, e.g., datasets, software, spreadsheets, text, etc. We applied this model to a case study where we analysed human metabolite variation by workflows.

q-bio.GN↗

arXiv2014

The Research Object Suite of Ontologies: Sharing and Exchanging Research Data and Methods on the Open Web

Research in life sciences is increasingly being conducted in a digital and online environment. In particular, life scientists have been pioneers in embracing new computational tools to conduct their investigations. To support the sharing of digital objects produced during such research investigations, we have witnessed in the last few years the emergence of specialized repositories, e.g., DataVerse and FigShare. Such repositories provide users with the means to share and publish datasets that were used or generated in research investigations. While these repositories have proven their usefulness, interpreting and reusing evidence for most research results is a challenging task. Additional contextual descriptions are needed to understand how those results were generated and/or the circumstances under which they were concluded. Because of this, scientists are calling for models that go beyond the publication of datasets to systematically capture the life cycle of scientific investigations and provide a single entry point to access the information about the hypothesis investigated, the datasets used, the experiments carried out, the results of the experiments, the people involved in the research, etc. In this paper we present the Research Object (RO) suite of ontologies, which provide a structured container to encapsulate research data and methods along with essential metadata descriptions. Research Objects are portable units that enable the sharing, preservation, interpretation and reuse of research investigation results. The ontologies we present have been designed in the light of requirements that we gathered from life scientists. They have been built upon existing popular vocabularies to facilitate interoperability. Furthermore, we have developed tools to support the creation and sharing of Research Objects, thereby promoting and facilitating their adoption.

cs.DL↗

arXiv2013

PAV ontology: Provenance, Authoring and Versioning

Provenance is a critical ingredient for establishing trust of published scientific content. This is true whether we are considering a data set, a computational workflow, a peer-reviewed publication or a simple scientific claim with supportive evidence. Existing vocabularies such as DC Terms and the W3C PROV-O are domain-independent and general-purpose and they allow and encourage for extensions to cover more specific needs. We identify the specific need for identifying or distinguishing between the various roles assumed by agents manipulating digital artifacts, such as author, contributor and curator. We present the Provenance, Authoring and Versioning ontology (PAV): a lightweight ontology for capturing just enough descriptions essential for tracking the provenance, authoring and versioning of web resources. We argue that such descriptions are essential for digital scientific content. PAV distinguishes between contributors, authors and curators of content and creators of representations in addition to the provenance of originating resources that have been accessed, transformed and consumed. We explore five projects (and communities) that have adopted PAV illustrating their usage through concrete examples. Moreover, we present mappings that show how PAV extends the PROV-O ontology to support broader interoperability. The authors strived to keep PAV lightweight and compact by including only those terms that have demonstrated to be pragmatically useful in existing applications, and by recommending terms from existing ontologies when plausible. We analyze and compare PAV with related approaches, namely Provenance Vocabulary, DC Terms and BIBFRAME. We identify similarities and analyze their differences with PAV, outlining strengths and weaknesses of our proposed model. We specify SKOS mappings that align PAV with DC Terms.

cs.DL↗

arXiv2012

Theoretical And Technological Building Blocks For An Innovation Accelerator

The scientific system that we use today was devised centuries ago and is inadequate for our current ICT-based society: the peer review system encourages conservatism, journal publications are monolithic and slow, data is often not available to other scientists, and the independent validation of results is limited. Building on the Innovation Accelerator paper by Helbing and Balietti (2011) this paper takes the initial global vision and reviews the theoretical and technological building blocks that can be used for implementing an innovation (in first place: science) accelerator platform driven by re-imagining the science system. The envisioned platform would rest on four pillars: (i) Redesign the incentive scheme to reduce behavior such as conservatism, herding and hyping; (ii) Advance scientific publications by breaking up the monolithic paper unit and introducing other building blocks such as data, tools, experiment workflows, resources; (iii) Use machine readable semantics for publications, debate structures, provenance etc. in order to include the computer as a partner in the scientific process, and (iv) Build an online platform for collaboration, including a network of trust and reputation among the different types of stakeholders in the scientific system: scientists, educators, funding agencies, policy makers, students and industrial innovators among others. Any such improvements to the scientific system must support the entire scientific process (unlike current tools that chop up the scientific process into disconnected pieces), must facilitate and encourage collaboration and interdisciplinarity (again unlike current tools), must facilitate the inclusion of intelligent computing in the scientific process, must facilitate not only the core scientific process, but also accommodate other stakeholders such science policy makers, industrial innovators, and the general public.

cs.DL↗