BackgroundPatients 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.ObjectiveThe aim of this review was to identify to what extent CDS is adopted in multimorbidity.MethodsThis 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.ResultsA 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.ConclusionsThis 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.

BackgroundAutomatic identification of term variants or acceptable alternative free-text terms for gene and protein names from the millions of biomedical publications is a challenging task. Ontologies, such as the Cardiovascular Disease Ontology (CVDO), capture domain knowledge in a computational form and can provide context for gene/protein names as written in the literature. This study investigates: 1) if word embeddings from Deep Learning algorithms can provide a list of term variants for a given gene/protein of interest; and 2) if biological knowledge from the CVDO can improve such a list without modifying the word embeddings created.MethodsWe have manually annotated 105 gene/protein names from 25 PubMed titles/abstracts and mapped them to 79 unique UniProtKB entries corresponding to gene and protein classes from the CVDO. Using more than 14 M PubMed articles (titles and available abstracts), word embeddings were generated with CBOW and Skip-gram. We setup two experiments for a synonym detection task, each with four raters, and 3672 pairs of terms (target term and candidate term) from the word embeddings created. For Experiment I, the target terms for 64 UniProtKB entries were those that appear in the titles/abstracts; Experiment II involves 63 UniProtKB entries and the target terms are a combination of terms from PubMed titles/abstracts with terms (i.e. increased context) from the CVDO protein class expressions and labels.ResultsIn Experiment I, Skip-gram finds term variants (full and/or partial) for 89% of the 64 UniProtKB entries, while CBOW finds term variants for 67%. In Experiment II (with the aid of the CVDO), Skip-gram finds term variants for 95% of the 63 UniProtKB entries, while CBOW finds term variants for 78%. Combining the results of both experiments, Skip-gram finds term variants for 97% of the 79 UniProtKB entries, while CBOW finds term variants for 81%.ConclusionsThis study shows performance improvements for both CBOW and Skip-gram on a gene/protein synonym detection task by adding knowledge formalised in the CVDO and without modifying the word embeddings created. Hence, the CVDO supplies context that is effective in inducing term variability for both CBOW and Skip-gram while reducing ambiguity. Skip-gram outperforms CBOW and finds more pertinent term variants for gene/protein names annotated from the scientific literature.Electronic supplementary materialThe online version of this article (10.1186/s13326-018-0181-1) contains supplementary material, which is available to authorized users.

Extracting information from peptidomics data is a major current challenge, as endogenous peptides can result from the activity of multiple enzymes. Proteolytic enzymes can display overlapping or complementary specificity. The activity spectrum of human endogenous peptide-generating proteases is not fully known. Hence, the indirect study of proteolytic enzymes through the analysis of its substrates is largely hampered. Antimicrobial peptides (AMPs) represent a primordial set of immune defense molecules generated by proteolytic cleavage of precursor proteins. These peptides can be modulated by host and microorganismal stimuli, which both dictate proteolytic enzymes' expression and activity. Peptidomics is an attractive approach to identify peptides with a biological role and to assess proteolytic activity. However, bioinformatics tools to deal with peptidomics data are lacking. PROTEASIX is an excellent choice for the prediction of AMPsgenerating proteases based on the reconstitution of a substrate's cleavage sites and the crossing of such information with known proteases' specificity retrieved by several publicly available databases. Therefore, the focus of the present tutorial is to explore the potential of PROTEASIX when gather information concerning proteases involved in the generation of human AMPs and to teach the user how to make the most out of peptidomics results using PROTEASIX.

No abstract

No abstract