An ecosystem of contributions

Slides for opening of the openRIF workshop at Force2016. <div>There exists an ecosystem of different projects that aim to represent the different aspects of the research ecosystem. OpenRIF aims to bring these efforts together to help support interoperability, improved attribution, and use of research data for analytics and team science.</div

Attribution of Work in the Scholarly Ecosystem

In this project we have outlined a list of contributor roles identified by the Force 11 Attribution Working Group. Contributor roles from existing taxonomies were leveraged (CRediT) and further enhanced with more finely-resolved contributor roles based on an in-depth investigation of activities and outputs. We have also collated and reviewed existing efforts on scholarly contribution taxonomies to determine their unique aspects, and how they complement each other. We reviewed the landscape of taxonomies and systems in order to compare and contrast key types of contributions.  We also considered the objectives needed to create a contributorship model that is robust enough to cover various fields of research, and specific enough to adequately describe contribution in a meaningful way.<br><br>We found there to be a diverse landscape of projects and groups working in this area, though each with its own perspective. A brief outline of the coverage, goals and relevant factors of these projects or groups is provided. Several projects were identified as being relevant to this inquiry, including Contributor Roles Taxonomy Project (CRediT), VIVO-ISF ontology, Provenance (PROV), the Becker Model and other impact frameworks, Transitive Credit, Academic Careers Understood through Measurement and Norms (ACUMEN Project), and the Scholarly Contributions and Roles Ontology (SCoRO). Additionally, several working groups were identified: Global Alliance for Genomics and Health (GA4GH), National Information Standards Organization (NISO), and the Force 11 Attribution Working Group.<br><br>Through the in-depth study of different contribution roles in the scholarly process, we were able to better understand how these contributions might be structured – in terms of a particular output (manuscript, dataset, etc.) and also contributions to the project as a whole.  Moreover, we developed a 2-level hierarchy to enable more complete representation of these roles through major classes such as author, communication, data, IP, project and team management, regulatory administration, software development, and so on.<br><br>While there are projects and ongoing efforts to better understand the diverse roles that professionals take on when contributing to the scholarly ecosystem, it is clear that more work is needed to fully explore the area of contributorship roles. Several leaders in this area have proposed projects to define an informatics infrastructure that enables the collection and dissemination on contributor attribution data to various stakeholder audiences. Projects of that nature bring excitement and expectation, as we wait to see where they will take us and how greatly they will impact the scholarly ecosystem. Perhaps most important is the need to accomplish this work in an open, collaborative manner, leveraging data standards along the way to enable interoperability and integration with existing architectures. <br><br

Enhancing SciENcv through semantic research profile integration with the VIVO-ISF ontology

SciENcv/VIVO-ISF alignment project poster presented at VIVO 2016

A comprehensive disease ontology for human disease curation

Presentation at the Biocuration 2018 conference: http://biocuration2018.cn/biocuration2018/<div><br></div><div>Abstract:</div><div><p>The Monarch Initiative is an international consortium that uses ontologies to integrate data from diverse sources in support of disease diagnostics and mechanism discovery. However, the lack of interoperability of ontologies across the basic–clinical divide is a challenge. </p><br><p>A large number of disease ontologies exist that represent different classification strategies or disease areas. The NCIt is a cancer ontology and used extensively in the clinical community, such as in the Genomic Data Commons, for drug applications, and for federal reporting. The NCIt is less well adopted in basic biomedical research in part due to its lack of interoperability with the OBO ontologies that are used more often by this community. </p><br><p>The Monarch Merged Disease Ontology (MONDO) integrates multiple disease vocabularies into a single coherent ontology. It was initialized via a semi-automatic method and has been iteratively enhanced with manual curation efforts. MONDO includes NCIt, the Online Mendelian Inheritance of Man (OMIM), which encompases Mendelian diseases, Orphanet, which focuses on rare diseases, the Experimental Factor Ontology (EFO) used for drug discovery, the Disease Ontology (DO), which broadly classifies human diseases, and a number of other disease resources.</p><br><p>MONDO IDs were assigned to integrated class cliques based upon historical cross-referencing within existing ontologies, using the kBOOM algorithm to determine equivalency, subclass relations, or other relationships. This new merged ontology will be maintained using this strategy, but is also being curated for completeness and clinical relevancy. For NCIt, we largely accepted axioms as-is, except we weakened the defining equivalent axioms to subClassOf and added defining axioms using intuitive design patterns. With this strategy, NCIt and MONDO are merged coherently with either IDs being available as clique leaders. Both of the MONDO and NCIt-OBO version ontologies are available to the community for biocuration of cancers and other human diseases on the OBO Foundry site. </p><div><br></div></div

The Ontology Development Group: A Visual Timeline

A poster presentation from the Oregon Health & Science University BICC 25 year anniversary celebration on October 28, 2016 describing the work of the Ontology Development Group in the OHSU Library.<div><br></div><div>The Ontology Development Group (ODG) strives to promote research innovations, service development, and education through semantically enabled technologies for the purposes of data management and publication, research reproducibility, and the building of novel tools for biomedical data exploration.</div

Who we are and what we contribute: The Open Research Information Framework as a means to understand scholarship

OpenRIF poster presented at VIVO 2016 and PNC/MLA 2016

OpenVIVO: A VIVO anyone can join

Poster presented June 14, 2016 at OR2016, Dublin I