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F1000Research 2021Bioinformatics is becoming an essential tool for the majority of biological and biomedical researchers. Although bioinformatics data is exploited by academic and...
Bioinformatics is becoming an essential tool for the majority of biological and biomedical researchers. Although bioinformatics data is exploited by academic and industrial researchers, limited focus is on teaching this area to undergraduates, postgraduates and senior scientists. Many scientists are developing their own expertise without formal training and often without appreciating the source of the data they are reliant upon. Some universities do provide courses on a variety of bioinformatics resources and tools, a few also provide biocuration projects, during which students submit data to annotation resources. To assess the usefulness and enjoyability of annotation projects a survey was sent to University College London (UCL) students who have undertaken Gene Ontology biocuration projects. Analysis of survey responses suggest that these projects provide students with an opportunity not only to learn about bioinformatics resources but also to improve their literature analysis, presentation and writing skills. Biocuration student projects provide valuable annotations as well as enabling students to develop a variety of skills relevant to their future careers. It is also hoped that, as future scientists, these students will critically assess their own manuscripts and ensure that these are written with the biocurators of the future in mind.
Topics: Computational Biology; Gene Ontology; Humans; Students; Universities
PubMed: 35211294
DOI: 10.12688/f1000research.72808.2 -
Applied Clinical Informatics 2014To assses the relationship between methods of documenting visit notes and note quality for primary care providers (PCPs) and specialists, and to determine the factors...
OBJECTIVE
To assses the relationship between methods of documenting visit notes and note quality for primary care providers (PCPs) and specialists, and to determine the factors that contribute to higher quality notes for two chronic diseases.
METHODS
Retrospective chart review of visit notes at two academic medical centers. Two physicians rated the subjective quality of content areas of the note (vital signs, medications, lifestyle, labs, symptoms, assessment & plan), overall quality, and completed the 9 item Physician Documentation Quality Instrument (PDQI-9). We evaluated quality ratings in relation to the primary method of documentation (templates, free-form or dictation) for both PCPs and specialists. A one factor analysis of variance test was used to examine differences in mean quality scores among the methods.
RESULTS
A total of 112 physicians, 71 primary care physicians (PCP) and 41 specialists, wrote 240 notes. For specialists, templated notes had the highest overall quality scores (p≤0.001) while for PCPs, there was no statistically significant difference in overall quality score. For PCPs, free form received higher quality ratings on vital signs (p = 0.01), labs (p = 0.002), and lifestyle (p = 0.002) than other methods; templated notes had a higher rating on medications (p≤0.001). For specialists, templated notes received higher ratings on vital signs, labs, lifestyle and medications (p = 0.001).
DISCUSSION
There was no significant difference in subjective quality of visit notes written using free-form documentation, dictation or templates for PCPs. The subjective quality rating of templated notes was higher than that of dictated notes for specialists.
CONCLUSION
As there is wide variation in physician documentation methods, and no significant difference in note quality between methods, recommending one approach for all physicians may not deliver optimal results.
Topics: Academic Medical Centers; Chronic Disease; Coronary Artery Disease; Diabetes Mellitus; Documentation; Electronic Health Records; Humans; Patient Care; Physicians, Primary Care; Quality of Health Care; Retrospective Studies
PubMed: 25024762
DOI: 10.4338/ACI-2014-01-RA-0007 -
Cellenium-a scalable and interactive visual analytics app for exploring multimodal single-cell data.Bioinformatics (Oxford, England) Jun 2023Multimodal single-cell sequencing data provide detailed views into the molecular biology of cells. To allow for interactive analyses of such rich data and to readily...
SUMMARY
Multimodal single-cell sequencing data provide detailed views into the molecular biology of cells. To allow for interactive analyses of such rich data and to readily derive insights from it, new analysis solutions are required. In this work, we present Cellenium, our new scalable visual analytics web application that enables users to semantically integrate and organize all their single-cell RNA-, ATAC-, and CITE-sequencing studies. Users can then find relevant studies and analyze single-cell data within and across studies. An interactive cell annotation feature allows for adding user-defined cell types.
AVAILABILITY AND IMPLEMENTATION
Source code and documentation are freely available under an MIT license and are available on GitHub (https://github.com/Bayer-Group/cellenium). The server backend is implemented in PostgreSQL, Python 3, and GraphQL, the frontend is written in ReactJS, TypeScript, and Mantine css, and plots are generated using plotlyjs, seaborn, vega-lite, and nivo.rocks. The application is dockerized and can be deployed and orchestrated on a standard workstation via docker-compose.
Topics: Mobile Applications; Software; Documentation
PubMed: 37261846
DOI: 10.1093/bioinformatics/btad349 -
Journal of Biomedical Semantics Apr 2021Iranian traditional medicine, also known as Persian Medicine, is a holistic school of medicine with a long prolific history. It describes numerous concepts and the...
BACKGROUND
Iranian traditional medicine, also known as Persian Medicine, is a holistic school of medicine with a long prolific history. It describes numerous concepts and the relationships between them. However, no unified language system has been proposed for the concepts of this medicine up to the present time. Considering the extensive terminology in the numerous textbooks written by the scholars over centuries, comprehending the totality of concepts is obviously a very challenging task. To resolve this issue, overcome the obstacles, and code the concepts in a reusable manner, constructing an ontology of the concepts of Iranian traditional medicine seems a necessity.
CONSTRUCTION AND CONTENT
Makhzan al-Advieh, an encyclopedia of materia medica compiled by Mohammad Hossein Aghili Khorasani, was selected as the resource to create an ontology of the concepts used to describe medicinal substances. The steps followed to accomplish this task included (1) compiling the list of classes via examination of textbooks, and text mining the resource followed by manual review to ensure comprehensiveness of extracted terms; (2) arranging the classes in a taxonomy; (3) determining object and data properties; (4) specifying annotation properties including ID, labels (English and Persian), alternative terms, and definitions (English and Persian); (5) ontology evaluation. The ontology was created using Protégé with adherence to the principles of ontology development provided by the Open Biological and Biomedical Ontology (OBO) foundry.
UTILITY AND DISCUSSION
The ontology was finalized with inclusion of 3521 classes, 15 properties, and 20,903 axioms in the Iranian traditional medicine General Ontology (IrGO) database, freely available at http://ir-go.net/ . An indented list and an interactive graph view using WebVOWL were used to visualize the ontology. All classes were linked to their instances in UNaProd database to create a knowledge base of ITM materia medica.
CONCLUSION
We constructed an ontology-based knowledge base of ITM concepts in the domain of materia medica to help offer a shared and common understanding of this concept, enable reuse of the knowledge, and make the assumptions explicit. This ontology will aid Persian medicine practitioners in clinical decision-making to select drugs. Extending IrGO will bridge the gap between traditional and conventional schools of medicine, helping guide future research in the process of drug discovery.
Topics: Biological Ontologies; Data Mining; Iran; Language; Medicine, Traditional
PubMed: 33863373
DOI: 10.1186/s13326-021-00237-1 -
Database : the Journal of Biological... Jan 2019This study proposes a text similarity model to help biocuration efforts of the Conserved Domain Database (CDD). CDD is a curated resource that catalogs annotated...
This study proposes a text similarity model to help biocuration efforts of the Conserved Domain Database (CDD). CDD is a curated resource that catalogs annotated multiple sequence alignment models for ancient domains and full-length proteins. These models allow for fast searching and quick identification of conserved motifs in protein sequences via Reverse PSI-BLAST. In addition, CDD curators prepare summaries detailing the function of these conserved domains and specific protein families, based on published peer-reviewed articles. To facilitate information access for database users, it is desirable to specifically identify the referenced articles that support the assertions of curator-composed sentences. Moreover, CDD curators desire an alert system that scans the newly published literature and proposes related articles of relevance to the existing CDD records. Our approach to address these needs is a text similarity method that automatically maps a curator-written statement to candidate sentences extracted from the list of referenced articles, as well as the articles in the PubMed Central database. To evaluate this proposal, we paired CDD description sentences with the top 10 matching sentences from the literature, which were given to curators for review. Through this exercise, we discovered that we were able to map the articles in the reference list to the CDD description statements with an accuracy of 77%. In the dataset that was reviewed by curators, we were able to successfully provide references for 86% of the curator statements. In addition, we suggested new articles for curator review, which were accepted by curators to be added into the reference list at an acceptance rate of 50%. Through this process, we developed a substantial corpus of similar sentences from biomedical articles on protein sequence, structure and function research, which constitute the CDD text similarity corpus. This corpus contains 5159 sentence pairs judged for their similarity on a scale from 1 (low) to 5 (high) doubly annotated by four CDD curators. Curator-assigned similarity scores have a Pearson correlation coefficient of 0.70 and an inter-annotator agreement of 85%. To date, this is the largest biomedical text similarity resource that has been manually judged, evaluated and made publicly available to the community to foster research and development of text similarity algorithms.
Topics: Algorithms; Data Curation; Databases, Protein; Protein Domains; Proteins; PubMed; Sequence Alignment
PubMed: 31267135
DOI: 10.1093/database/baz064 -
Journal of Medical Systems Jul 2022The major impact on healthcare through the ongoing digital transformation and new technologies results in opportunities for improving quality of care. Electronic patient...
The major impact on healthcare through the ongoing digital transformation and new technologies results in opportunities for improving quality of care. Electronic patient records (EPR) are a substantial part in this transformation, even though their influence on documentation remains often unclear. This review aims to answer the question of which effect the introduction of the EPR has on the documentation proper in hospitals. To do this, studies are reviewed that analyze the documentation itself, rather than merely conducting interviews or surveys about it. Several databases were searched in this systematic review (PubMed including PubMed, PubMed Central and Medline; PDQ Evidence; Web of Science Core Collection; CINHAL). To be included, studies needed to analyze written documentation and empirical data, be in either German or English language, published between 2010 and 2020, conducted in a hospital setting, focused on transition from paper-based to electronic patient records, and peer reviewed. Quantitative, qualitative and mixed methods studies were included. Studies were independently screened for inclusion by two researchers in three stages (title, abstract, full text) and, in case of disagreement, discussed with a third person from the research team until consensus was reached. The main outcome assessed was whether the studies indicated a negative or positive effect on documentation (e.g. changing the completeness of documentation) by introducing an EPR. Mixed Methods Appraisal Tool was used to assess the individual risk of bias in the included studies. Overall, 264 studies were found. Of these, 17 met the inclusion criteria and were included in this review. Of all included studies, 11 of 17 proved a positive effect of the introduction of the EPR on documentation such as an improved completeness or guideline adherence of the documentation. Six of 17 showed a mixed effect with positive and negative or no changes. No study showed an exclusively negative effect. Most studies found a positive effect of EPR introduction on documentation. However, it is difficult to draw specific conclusions about how the EPR affects or does not affect documentation since the included studies examined a variety of outcomes. As a result, various scenarios are conceivable with higher or reduced burden for practitioners. Additionally, the impact on treatment remains unclear.
Topics: Documentation; Electronic Health Records; Hospitals; Humans
PubMed: 35781136
DOI: 10.1007/s10916-022-01840-0 -
Surgery Research and Practice 2015Introduction. The Royal College of Surgeons in England published guidelines in 2008 outlining the information that should be documented at each surgery. St. James's...
Introduction. The Royal College of Surgeons in England published guidelines in 2008 outlining the information that should be documented at each surgery. St. James's Hospital uses a standard operation sheet for all surgical procedures and these were examined to assess documentation standards. Objectives. To retrospectively audit the hand written orthopaedic operative notes according to established guidelines. Methods. A total of 63 operation notes over seven months were audited in terms of date and time of surgery, surgeon, procedure, elective or emergency indication, operative diagnosis, incision details, signature, closure details, tourniquet time, postop instructions, complications, prosthesis, and serial numbers. Results. A consultant performed 71.4% of procedures; however, 85.7% of the operative notes were written by the registrar. The date and time of surgery, name of surgeon, procedure name, and signature were documented in all cases. The operative diagnosis and postoperative instructions were frequently not documented in the designated location. Incision details were included in 81.7% and prosthesis details in only 30% while the tourniquet time was not documented in any. Conclusion. Completion and documentation of operative procedures were excellent in some areas; improvement is needed in documenting tourniquet time, prosthesis and incision details, and the location of operative diagnosis and postoperative instructions.
PubMed: 26357669
DOI: 10.1155/2015/782720 -
European Journal of Cancer (Oxford,... Oct 2018Currently, there are between 300,000 and 500,000 childhood cancer survivors (CCSs) in Europe. A significant proportion is at high risk, and at least 60% of them develop...
BACKGROUND
Currently, there are between 300,000 and 500,000 childhood cancer survivors (CCSs) in Europe. A significant proportion is at high risk, and at least 60% of them develop adverse health-related outcomes that can appear several years after treatment completion. Many survivors are unaware of their personal risk, and there seems to be a general lack of information among healthcare providers about pathophysiology and natural history of treatment-related complications. This can generate incorrect or delayed diagnosis and treatments.
METHOD
The Survivorship Passport (SurPass) consists of electronic documents, which summarise the clinical history of the childhood or adolescent cancer survivor. It was developed by paediatric oncologists of the PanCare and SIOPE networks and IT experts of Cineca, together with parents, patients, and survivors' organisations within the European Union-funded European Network for Cancer research in Children and Adolescents. It consists of a template of a web-based, simply written document, translatable in all European languages, to be given to each CCS. The SurPass provides a summary of each survivor's clinical history, with detailed information about the original cancer and of treatments received, together with personalised follow-up and screening recommendations based on guidelines published by the International Guidelines Harmonization Group and PanCareSurFup.
RESULTS
The SurPass data schema contains a maximum of 168 variables and uses internationally approved nomenclature, except for radiotherapy fields, where a new classification was defined by radiotherapy experts. The survivor-specific screening recommendations are mainly based on treatment received and are automatically suggested, thanks to built-in algorithms. These may be adapted and further individualised by the treating physician in case of special disease and survivor circumstances. The SurPass was tested at the Istituto Giannina Gaslini, Italy, and received positive feedback. It is now being integrated at the institutional, regional and national level.
CONCLUSIONS
The SurPass is potentially an essential tool for improved and more harmonised follow-up of CCS. It also has the potential to be a useful tool for empowering CCSs to be responsible for their own well-being and preventing adverse events whenever possible. With sufficient commitment on the European level, this solution should increase the capacity to respond more effectively to the needs of European CCS.
Topics: Age of Onset; Antineoplastic Agents; Cancer Survivors; Continuity of Patient Care; Documentation; Electronic Health Records; Europe; Forms and Records Control; Humans; Neoplasms; Radiotherapy; Risk Assessment; Risk Factors; Stem Cell Transplantation; Time Factors; Translating; Treatment Outcome
PubMed: 30138773
DOI: 10.1016/j.ejca.2018.07.006 -
Database : the Journal of Biological... Oct 2022The coronavirus disease 2019 (COVID-19) pandemic has compelled biomedical researchers to communicate data in real time to establish more effective medical treatments and...
The coronavirus disease 2019 (COVID-19) pandemic has compelled biomedical researchers to communicate data in real time to establish more effective medical treatments and public health policies. Nontraditional sources such as preprint publications, i.e. articles not yet validated by peer review, have become crucial hubs for the dissemination of scientific results. Natural language processing (NLP) systems have been recently developed to extract and organize COVID-19 data in reasoning systems. Given this scenario, the BioCreative COVID-19 text mining tool interactive demonstration track was created to assess the landscape of the available tools and to gauge user interest, thereby providing a two-way communication channel between NLP system developers and potential end users. The goal was to inform system designers about the performance and usability of their products and to suggest new additional features. Considering the exploratory nature of this track, the call for participation solicited teams to apply for the track, based on their system's ability to perform COVID-19-related tasks and interest in receiving user feedback. We also recruited volunteer users to test systems. Seven teams registered systems for the track, and >30 individuals volunteered as test users; these volunteer users covered a broad range of specialties, including bench scientists, bioinformaticians and biocurators. The users, who had the option to participate anonymously, were provided with written and video documentation to familiarize themselves with the NLP tools and completed a survey to record their evaluation. Additional feedback was also provided by NLP system developers. The track was well received as shown by the overall positive feedback from the participating teams and the users. Database URL: https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vii/track-4/.
Topics: COVID-19; Data Mining; Databases, Factual; Documentation; Humans; Natural Language Processing
PubMed: 36197453
DOI: 10.1093/database/baac084 -
Ugeskrift For Laeger May 2019In this review, a guide on how to write a scientific abstract is given. When junior researchers submit an abstract for a conference or a manuscript for a journal, a... (Review)
Review
In this review, a guide on how to write a scientific abstract is given. When junior researchers submit an abstract for a conference or a manuscript for a journal, a well-written abstract is the key to acceptance and publication. Being able to catch the interest of the reader, while keeping the length to a minimum, is an art, which can be learned by practice.
Topics: Abstracting and Indexing; Learning; Publishing; Writing
PubMed: 31124438
DOI: No ID Found