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Helen Parkinson

Publications and source records attributed to Helen Parkinson.

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Expanding the Human Ancestry Ontology to include under-represented populations and ethnicities for broader utility in annotations

Successful discovery, integration and reuse of data relies on the availability of rich, well-structured and machine-readable metadata to describe every aspect of the data, from sample sources to collection processes to experimental protocols. The use of standardised terminologies to express concepts in a harmonised fashion lies at the core of high-quality data annotation, increasing the FAIRness of the data, facilitating data integration and promoting reproducibility. Here, we describe the Human Ancestry Ontology (HANCESTRO), originally developed to improve standardised reporting of genetic ancestry genomic resources such as the NHGRI-EBI GWAS Catalog and the Human Cell Atlas through high-level population descriptors, and more recently expanded to include diverse and previously under-represented populations in genomics and genetics research. HANCESTRO provides a framework for population descriptors that includes both ancestry based on the analysis of genetic information and self-reported ethnicity, which is based on social and cultural factors that don't necessarily align with genetic populations. By enabling the accurate and interoperable representation of population-related data, it promotes inclusive, representative and reproducible science.

q-bio.OT

OxO2 -- A SSSOM mapping browser for logically sound crosswalks

EMBL-EBI created OxO to enable users to map between datasets that are annotated with different ontologies. Mappings identified by the first version of OxO were not necessarily logically sound, lacked important provenance information such as author and reviewer, and could timeout or crash for certain requests. In this paper we introduce OxO2 to address these concerns. Provenance is addressed by implementing SSSOM, a mapping standard that defines provenance for mappings. SSSOM defines the conditions under which logical sound mappings can be derived and is implemented in OxO2 using Nemo, a Datalog rule engine. To ensure reasoning is performant and memory efficient, Nemo implements a number of strategies that ensures OxO2 will be stable for all requests. Due to these changes, OxO2 users will be able to integrate between disparate datasets with greater confidence.

cs.DB

OLS4: A new Ontology Lookup Service for a growing interdisciplinary knowledge ecosystem

The Ontology Lookup Service (OLS) is an open source search engine for ontologies which is used extensively in the bioinformatics and chemistry communities to annotate biological and biomedical data with ontology terms. Recently there has been a significant increase in the size and complexity of ontologies due to new scales of biological knowledge, such as spatial transcriptomics, new ontology development methodologies, and curation on an increased scale. Existing Web-based tools for ontology browsing such as BioPortal and OntoBee do not support the full range of definitions used by today's ontologies. In order to support the community going forward, we have developed OLS4, implementing the complete OWL2 specification, internationalization support for multiple languages, and a new user interface with UX enhancements such as links out to external databases. OLS4 has replaced OLS3 in production at EMBL-EBI and has a backwards compatible API supporting users of OLS3 to transition.

cs.IR

A framework for developing a knowledge management platform

Knowledge management (KM) involves collecting, organizing, storing, and disseminating information to improve decision-making, innovation, and performance. Implementing KM at scale has become essential for organizations to effectively leverage vast accessible data. This paper is a compilation of concepts that emerged from KM workshops hosted by EMBL-EBI, attended by SMEs and industry. We provide guidance on envisioning, executing, evaluating, and evolving knowledge management platforms. We emphasize essential considerations such as setting knowledge domain boundaries and measuring success, as well as the importance of making knowledge accessible for downstream applications and non-computational users and highlights necessary personal and organizational skills for success. We stress the importance of collaboration and the need for convergence on shared principles and commitment to provide or seek resources to advance KM. The community is invited to join the journey of KM and contribute to the advancement of the field by applying and improving on the guidelines described.

cs.DB