SciBite Curation Jamboree for World Menopause Day

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To mark World Menopause Day, staff from across SciBite tried their hand at literature curation with a menopause theme. The goal was to find words or phrases related to menopause that are missing from the SciBite vocabularies. Our vocabularies are the basis of our software solutions and cover many different topics in the healthcare and pharmaceutical domains, such as drugs, anatomy and diseases. They are mainly based on public standards and are used in a variety of ways to help our customers standardise their data and efficiently find relevant literature and documentation around their subject of interest, for use in drug discovery, manufacturing and more.

Curation of SciBite vocabularies is performed by the SciBite Ontology Team and is largely a manual process, so we thought it would be interesting to give staff from our other teams a taste of what curation involves whilst contributing to this most important subject. We had project managers, software developers, product managers, data scientists and technical consultants join the curation team for the session.

During the jamboree, we used TERMite, our Named Entity Recognition engine, to view documents, articles and webpages on the subject of menopause and identify terms that were not recognised by any of our vocabularies (see screenshot below). If the word or phrase is not present in our vocabularies, it means that insightful information or data is invisible to our customers. By adding these entities, we increase the likelihood that the information is easily found and used for improving the understanding and management of menopause.

Overall, more than 200 menopause-related words and phrases were identified during the session and will now be reviewed by curators and added to the relevant vocabularies. In addition, we will suggest any missing concepts be added to the relevant public ontologies to contribute to the improvement of those valuable public resources.
We hope to organise future curation jamborees focused on specific healthcare or disease recognition days throughout the year.

The screenshot shows some menopause-specific entities in SciBite’s Named Entity Recognition engine, TERMite. Entities are separated by pipes. Though basic concepts like “menopause” and “hormone therapy”, or “hormone” and “implant”, are found in our vocabularies, the more specific entities such as “menopause hormone therapy” and “hormone pellet (subcutaneous implant)” are not. This project will ensure these are added to the SciBite vocabularies and made available for our customers.

Rachael Huntley

Lead Scientific Curator, SciBite

Rachael Huntley is Lead Scientific Curator at SciBite with over 20 years biocuration experience. Dr. Huntley received her PhD in plant biochemistry from the University of Cambridge and completed post-doctoral research in both Cambridge, UK and Stanford, USA.

During her time at EMBL-EBI and University College London she contributed to functional annotation of human proteins and microRNAs involved in human health and disease. Throughout her biocuration career, she has worked closely with the Gene Ontology Consortium and major pharmaceutical companies and has contributed to the development of ontologies, biocuration standards and curation tools.

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