A case study on sepsis using PubMed and Deep Learning for ontology learning

We investigate the application of distributional semantics models for facilitating unsupervised extraction of biomedical terms from unannotated corpora.Term extraction is used as the first step of an ontology learning process that aims to (semi-)automatic annotation of biomedical concepts and relations from more than 300K PubMed titles and abstracts. We experimented with both traditional distributional semantics methods such as Latent Semantic Analysis (LSA) and Latent Dirichlet Allocation (LDA) as well as the neural language models CBOW and Skip-gram from Deep Learning. The evaluation conducted concentrates on sepsis, a major life-threatening condition, and shows that Deep Learning models outperform LSA and LDA with much higher precision

MetaMap versus BERT models with explainable active learning: ontology-based experiments with prior knowledge for COVID-19

Emergence of the Coronavirus 2019 Disease has highlighted further the need for timely support for clinicians as they manage severely ill patients. We combine Semantic Web technologies with Deep Learning for Natural Language Processing with the aim of converting human-readable best evi-dence/practice for COVID-19 into that which is computer-interpretable. We present the results of experiments with 1212 clinical ideas (medical terms and expressions) from two UK national healthcare services specialty guides for COVID-19 and three versions of two BMJ Best Practice documents for COVID-19. The paper seeks to recognise and categorise clinical ideas, performing a Named Entity Recognition (NER) task, with an ontology providing extra terms as context and describing the intended meaning of categories understandable by clinicians. The paper investigates: 1) the performance of classical NER using MetaMap versus NER with fine-tuned BERT models; 2) the integration of both NER approaches using a lightweight ontology developed in close collaboration with senior doctors; and 3) the easy interpretation by junior doctors of the main classes from the ontology once populated with NER results. We report the NER performance and the observed agreement for human audits

MetaMap versus BERT models with explainable active learning: ontology-based experiments with prior knowledge for COVID-19

Emergence of the Coronavirus 2019 Disease has highlighted further the need for timely support for clinicians as they manage severely ill patients. We combine Semantic Web technologies with Deep Learning for Natural Language Processing with the aim of converting human-readable best evi-dence/practice for COVID-19 into that which is computer-interpretable. We present the results of experiments with 1212 clinical ideas (medical terms and expressions) from two UK national healthcare services specialty guides for COVID-19 and three versions of two BMJ Best Practice documents for COVID-19. The paper seeks to recognise and categorise clinical ideas, performing a Named Entity Recognition (NER) task, with an ontology providing extra terms as context and describing the intended meaning of categories understandable by clinicians. The paper investigates: 1) the performance of classical NER using MetaMap versus NER with fine-tuned BERT models; 2) the integration of both NER approaches using a lightweight ontology developed in close collaboration with senior doctors; and 3) the easy interpretation by junior doctors of the main classes from the ontology once populated with NER results. We report the NER performance and the observed agreement for human audits

Adoption of clinical decision support in multimorbidity: a systematic review.

BACKGROUND: Patients with multiple conditions have complex needs and are increasing in number as populations age. This multimorbidity is one of the greatest challenges facing health care. Having more than 1 condition generates (1) interactions between pathologies, (2) duplication of tests, (3) difficulties in adhering to often conflicting clinical practice guidelines, (4) obstacles in the continuity of care, (5) confusing self-management information, and (6) medication errors. In this context, clinical decision support (CDS) systems need to be able to handle realistic complexity and minimize iatrogenic risks. OBJECTIVE: The aim of this review was to identify to what extent CDS is adopted in multimorbidity. METHODS: This review followed PRISMA guidance and adopted a multidisciplinary approach. Scopus and PubMed searches were performed by combining terms from 3 different thesauri containing synonyms for (1) multimorbidity and comorbidity, (2) polypharmacy, and (3) CDS. The relevant articles were identified by examining the titles and abstracts. The full text of selected/relevant articles was analyzed in-depth. For articles appropriate for this review, data were collected on clinical tasks, diseases, decision maker, methods, data input context, user interface considerations, and evaluation of effectiveness. RESULTS: A total of 50 articles were selected for the full in-depth analysis and 20 studies were included in the final review. Medication (n=10) and clinical guidance (n=8) were the predominant clinical tasks. Four studies focused on merging concurrent clinical practice guidelines. A total of 17 articles reported their CDS systems were knowledge-based. Most articles reviewed considered patients’ clinical records (n=19), clinical practice guidelines (n=12), and clinicians’ knowledge (n=10) as contextual input data. The most frequent diseases mentioned were cardiovascular (n=9) and diabetes mellitus (n=5). In all, 12 articles mentioned generalist doctor(s) as the decision maker(s). For articles reviewed, there were no studies referring to the active involvement of the patient in the decision-making process or to patient self-management. None of the articles reviewed adopted mobile technologies. There were no rigorous evaluations of usability or effectiveness of the CDS systems reported. CONCLUSIONS: This review shows that multimorbidity is underinvestigated in the informatics of supporting clinical decisions. CDS interventions that systematize clinical practice guidelines without considering the interactions of different conditions and care processes may lead to unhelpful or harmful clinical actions. To improve patient safety in multimorbidity, there is a need for more evidence about how both conditions and care processes interact. The data needed to build this evidence base exist in many electronic health record systems and are underused

Additional file 1 of The Proteasix Ontology

PxO Metazoa ontology: Ontology metrics; ELK reasoner times; and SPARQL queries execution times. (PDF 141 kb

The Proteasix Ontology

Abstract Background The Proteasix Ontology (PxO) is an ontology that supports the Proteasix tool; an open-source peptide-centric tool that can be used to predict automatically and in a large-scale fashion in silico the proteases involved in the generation of proteolytic cleavage fragments (peptides) Methods The PxO re-uses parts of the Protein Ontology, the three Gene Ontology sub-ontologies, the Chemical Entities of Biological Interest Ontology, the Sequence Ontology and bespoke extensions to the PxO in support of a series of roles: 1. To describe the known proteases and their target cleaveage sites. 2. To enable the description of proteolytic cleaveage fragments as the outputs of observed and predicted proteolysis. 3. To use knowledge about the function, species and cellular location of a protease and protein substrate to support the prioritisation of proteases in observed and predicted proteolysis. Results The PxO is designed to describe the biological underpinnings of the generation of peptides. The peptide-centric PxO seeks to support the Proteasix tool by separating domain knowledge from the operational knowledge used in protease prediction by Proteasix and to support the confirmation of its analyses and results. Availability The Proteasix Ontology may be found at: http://bioportal.bioontology.org/ontologies/PXO . This ontology is free and open for use by everyone