Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features.

Background: TogoID ( https://togoid.dbcls.jp/ ) is an identifier (ID) conversion service designed to link IDs across diverse categories of life science databases.

Predicting the effects of drugs and unveiling their mechanisms of action using an interpretable pharmacodynamic mechanism knowledge graph (IPM-KG).

Background: Multiple studies have aimed to consolidate drug-related data and predict drug effects. However, most of these studies have focused on integrating diverse data through correlation rather than representing them based on the pharmacodynamic mechanism of action (MOA). It is thus crucial to obtain interpretability to validate prediction results.

Examining HPO by organ and system to facilitate practical use by clinicians.

The Human Phenotype Ontology (HPO) is widely used for annotating clinical text data, and sufficient annotation is crucial for the effective utilization of clinical texts. It was known that the use of LLMs can successfully extract symptoms and findings, but cannot annotate them with the HPO. We hypothesized that one of the potential issue for this is the lack of appropriate terms in the HPO.

jPOST environment accelerates the reuse and reanalysis of public proteome mass spectrometry data.

jPOST (https://jpostdb.org/) comprises jPOSTrepo (https://repository.jpostdb.

The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF.

Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that are used for further downstream analysis of new spectra. There are many different formats used for encoding spectral libraries, but none have undergone a standardization process to ensure broad applicability to many applications. As part of the Human Proteome Organization Proteomics Standards Initiative (PSI), we have developed a standardized format for encoding spectral libraries, called mzSpecLib (https://psidev.

Customizing GPT for natural language dialogue interface in database access.

The paper presents Anatomy3DExplorer, a customized ChatGPT designed as a natural language dialogue interface for exploring 3D models of anatomical structures. It illustrates the significant potential of large language models (LLMs) as user-friendly interfaces for database access. Furthermore, it showcases the seamless integration of LLMs and database APIs, within the GPTS framework, offering a promising and straightforward approach.

Recording provenance of workflow runs with RO-Crate.

Recording the provenance of scientific computation results is key to the support of traceability, reproducibility and quality assessment of data products. Several data models have been explored to address this need, providing representations of workflow plans and their executions as well as means of packaging the resulting information for archiving and sharing. However, existing approaches tend to lack interoperable adoption across workflow management systems.

Enteropathway: the metabolic pathway database for the human gut microbiota.

The human gut microbiota produces diverse, extensive metabolites that have the potential to affect host physiology. Despite significant efforts to identify metabolic pathways for producing these microbial metabolites, a comprehensive metabolic pathway database for the human gut microbiota is still lacking. Here, we present Enteropathway, a metabolic pathway database that integrates 3269 compounds, 3677 reactions, and 876 modules that were obtained from 1012 manually curated scientific literature.

A systematic exploration of unexploited genes for oxidative stress in Parkinson's disease.

Human disease-associated gene data are accessible through databases, including the Open Targets Platform, DisGeNET, miRTex, RNADisease, and PubChem. However, missing data entries in such databases are anticipated because of curational errors, biases, and text-mining failures. Additionally, the extensive research on human diseases has led to challenges in registering comprehensive data.

Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy.

Dynamic changes in protein glycosylation impact human health and disease progression. However, current resources that capture disease and phenotype information focus primarily on the macromolecules within the central dogma of molecular biology (DNA, RNA, proteins). To gain a better understanding of organisms, there is a need to capture the functional impact of glycans and glycosylation on biological processes.

High expression of serine protease, Brachyurin in the posterior midgut of black soldier fly (Hermetia illucens) during horse dropping processing.

Objective: Livestock droppings cause some environmental problems, but they have the potential to be used as effective biomass resources. The black soldier fly (BSF), Hermetia illucens (Diptera: Stratiomyidae), is suitable for efficiently processing such resources. By using BSF larvae for the disposal of livestock droppings, we can obtain two valuable products: protein resources and organic fertilizer.

Time-course transcriptome data of silk glands in day 0-7 last-instar larvae of Bombyx mori (w1 pnd strain).

Time-course transcriptome expression data were constructed for four parts of the silk gland (anterior, middle, and posterior parts of the middle silk gland, along with the posterior silk gland) in the domestic silkworm, Bombyx mori, from days 0 to 7 of the last-instar larvae. For sample preparation, silk glands were extracted from one female and one male larva every 24 hours accurately after the fourth ecdysis. The reliability of these transcriptome data was confirmed by comparing the transcripts per million (TPM) values of the silk gene and quantitative reverse transcription PCR results.

ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data.

ChIP-Atlas (https://chip-atlas.org/) presents a suite of data-mining tools for analyzing epigenomic landscapes, powered by the comprehensive integration of over 376 000 public ChIP-seq, ATAC-seq, DNase-seq and Bisulfite-seq experiments from six representative model organisms. To unravel the intricacies of chromatin architecture that mediates the regulome-initiated generation of transcriptional and phenotypic diversity within cells, we report ChIP-Atlas 3.

rs10924104 in the expression enhancer motif of CD58 confers susceptibility to human autoimmune diseases.

CD58 plays roles in cell adhesion and co-stimulation with antigen presentation from major histocompatibility complex class II on antigen-presenting cells to T-cell antigen receptors on naïve T cells. CD58 reportedly contributes to the development of various human autoimmune diseases. Recently, genome-wide association studies (GWASs) identified CD58 as a susceptibility locus for autoimmune diseases such as systemic lupus erythematosus (SLE), multiple sclerosis (MS), and primary biliary cholangitis (PBC).

The Human Phenotype Ontology in 2024: phenotypes around the world.

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English.

SARS-CoV-2 HaploGraph: visualization of SARS-CoV-2 haplotype spread in Japan.

Since the early phase of the coronavirus disease 2019 (COVID-19) pandemic, a number of research institutes have been sequencing and sharing high-quality severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes to trace the route of infection in Japan. To provide insight into the spread of COVID-19, we developed a web platform named SARS-CoV-2 HaploGraph to visualize the emergence timing and geographical transmission of SARS-CoV-2 haplotypes. Using data from the GISAID EpiCoV database as of June 4, 2022, we created a haplotype naming system by determining the ancestral haplotype for each epidemic wave and showed prefecture- or region-specific haplotypes in each of four waves in Japan.

Development of an integrated and inferenceable RDF database of glycan, pathogen and disease resources.

Glycans are known to play extremely important roles in infections by viruses and pathogens. In fact, the SARS-CoV-2 virus has been shown to have evolved due to a single change in glycosylation. However, data resources on glycans, pathogens and diseases are not well organized.

A workflow reproducibility scale for automatic validation of biological interpretation results.

Background: Reproducibility of data analysis workflow is a key issue in the field of bioinformatics. Recent computing technologies, such as virtualization, have made it possible to reproduce workflow execution with ease. However, the reproducibility of results is not well discussed; that is, there is no standard way to verify whether the biological interpretation of reproduced results is the same.

CIRO: COVID-19 infection risk ontology.

Public health authorities perform contact tracing for highly contagious agents to identify close contacts with the infected cases. However, during the pandemic caused by coronavirus disease 2019 (COVID-19), this operation was not employed in countries with high patient volumes. Meanwhile, the Japanese government conducted this operation, thereby contributing to the control of infections, at the cost of arduous manual labor by public health officials.

Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows.

Background: Many open-source workflow systems have made bioinformatics data analysis procedures portable. Sharing these workflows provides researchers easy access to high-quality analysis methods without the requirement of computational expertise. However, published workflows are not always guaranteed to be reliably reusable.