Dataset Information

KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response.

ABSTRACT: Integrated, up-to-date data about SARS-CoV-2 and coronavirus disease 2019 (COVID-19) is crucial for the ongoing response to the COVID-19 pandemic by the biomedical research community. While rich biological knowledge exists for SARS-CoV-2 and related viruses (SARS-CoV, MERS-CoV), integrating this knowledge is difficult and time consuming, since much of it is in siloed databases or in textual format. Furthermore, the data required by the research community varies drastically for different tasks - the optimal data for a machine learning task, for example, is much different from the data used to populate a browsable user interface for clinicians. To address these challenges, we created KG-COVID-19, a flexible framework that ingests and integrates biomedical data to produce knowledge graphs (KGs) for COVID-19 response. This KG framework can also be applied to other problems in which siloed biomedical data must be quickly integrated for different research applications, including future pandemics. An effective response to the COVID-19 pandemic relies on integration of many different types of data available about SARS-CoV-2 and related viruses. KG-COVID-19 is a framework for producing knowledge graphs that can be customized for downstream applications including machine learning tasks, hypothesis-based querying, and browsable user interface to enable researchers to explore COVID-19 data and discover relationships.

SUBMITTER: Reese J

PROVIDER: S-EPMC7444288 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response.

Reese Justin J Unni Deepak D Callahan Tiffany J TJ Cappelletti Luca L Ravanmehr Vida V Carbon Seth S Fontana Tommaso T Blau Hannah H Matentzoglu Nicolas N Harris Nomi L NL Munoz-Torres Monica C MC Robinson Peter N PN Joachimiak Marcin P MP Mungall Christopher J CJ

bioRxiv : the preprint server for biology 20200818

Integrated, up-to-date data about SARS-CoV-2 and coronavirus disease 2019 (COVID-19) is crucial for the ongoing response to the COVID-19 pandemic by the biomedical research community. While rich biological knowledge exists for SARS-CoV-2 and related viruses (SARS-CoV, MERS-CoV), integrating this knowledge is difficult and time consuming, since much of it is in siloed databases or in textual format. Furthermore, the data required by the research community varies drastically for different tasks - ...[more]

PMID: 32839776

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Project description:Knowledge graphs (KGs) are an important tool for representing complex relationships between entities in the biomedical domain. Several methods have been proposed for learning embeddings that can be used to predict new links in such graphs. Some methods ignore valuable attribute data associated with entities in biomedical KGs, such as protein sequences, or molecular graphs. Other works incorporate such data, but assume that entities can be represented with the same data modality. This is not always the case for biomedical KGs, where entities exhibit heterogeneous modalities that are central to their representation in the subject domain. We aim to understand how to incorporate multimodal data into biomedical KG embeddings, and analyze the resulting performance in comparison with traditional methods. We propose a modular framework for learning embeddings in KGs with entity attributes, that allows encoding attribute data of different modalities while also supporting entities with missing attributes. We additionally propose an efficient pretraining strategy for reducing the required training runtime. We train models using a biomedical KG containing approximately 2 million triples, and evaluate the performance of the resulting entity embeddings on the tasks of link prediction, and drug-protein interaction prediction, comparing against methods that do not take attribute data into account. In the standard link prediction evaluation, the proposed method results in competitive, yet lower performance than baselines that do not use attribute data. When evaluated in the task of drug-protein interaction prediction, the method compares favorably with the baselines. Further analyses show that incorporating attribute data does outperform baselines over entities below a certain node degree, comprising approximately 75% of the diseases in the graph. We also observe that optimizing attribute encoders is a challenging task that increases optimization costs. Our proposed pretraining strategy yields significantly higher performance while reducing the required training runtime. BioBLP allows to investigate different ways of incorporating multimodal biomedical data for learning representations in KGs. With a particular implementation, we find that incorporating attribute data does not consistently outperform baselines, but improvements are obtained on a comparatively large subset of entities below a specific node-degree. Our results indicate a potential for improved performance in scientific discovery tasks where understudied areas of the KG would benefit from link prediction methods.

Dataset Information

KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response.

Publications

KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response.

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