The Human Glycome Atlas Project for cataloging all glycan-related omics data in human.

The Human Glycome Atlas (HGA) Project was launched in April 2023, spearheaded by three Japanese institutes: the Tokai National Higher Education and Research System, the National Institutes of Natural Sciences, and Soka University. This was the first time that a field in the life sciences was adopted by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) for a Large-scale Academic Frontiers Promotion Project. This project aims to construct a knowledgebase of human glycans and glycoproteins as a standard for the human glycome. A high-throughput pipeline for comprehensively analyzing 20,000 blood samples in its first five years is planned, at which time an access-controlled version of a human glycomics knowledgebase, called TOHSA, will be released. By the end of the final tenth year, TOHSA will provide a central resource linking human glycan data with other omics data including disease-related information.

Virus-CKB: an integrated bioinformatics platform and analysis resource for COVID-19 research.

Given the scale and rapid spread of the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there is an urgent need for medicines that can help before vaccines are available. In this study, we present a viral-associated disease-specific chemogenomics knowledgebase (Virus-CKB) and apply our computational systems pharmacology-target mapping to rapidly predict the FDA-approved drugs which can quickly progress into clinical trials to meet the urgent demand of the COVID-19 outbreak. Virus-CKB reuses the underlying platform of our DAKB-GPCRs but adds new features like multiple-compound support, multi-cavity protein support and customizable symbol display. Our one-stop computing platform describes the chemical molecules, genes and proteins involved in viral-associated diseases regulation. To date, Virus-CKB archived 65 antiviral drugs in the market, 107 viral-related targets with 189 available 3D crystal or cryo-EM structures and 2698 chemical agents reported for these target proteins. Moreover, Virus-CKB is implemented with web applications for the prediction of the relevant protein targets and analysis and visualization of the outputs, including HTDocking, TargetHunter, BBB predictor, NGL Viewer, Spider Plot, etc. The Virus-CKB server is accessible at https://www.cbligand.org/g/virus-ckb.

Tri©DB: an integrated platform of knowledgebase and reporting system for cancer precision medicine.

BACKGROUND: With the development of cancer precision medicine, a huge amount of high-dimensional cancer information has rapidly accumulated regarding gene alterations, diseases, therapeutic interventions and various annotations. The information is highly fragmented across multiple different sources, making it highly challenging to effectively utilize and exchange the information. Therefore, it is essential to create a resource platform containing well-aggregated, carefully mined, and easily accessible data for effective knowledge sharing. METHODS: In this study, we have developed "Consensus Cancer Core" (Tri©DB), a new integrative cancer precision medicine knowledgebase and reporting system by mining and harmonizing multifaceted cancer data sources, and presenting them in a centralized platform with enhanced functionalities for accessibility, annotation and analysis. RESULTS: The knowledgebase provides the currently most comprehensive information on cancer precision medicine covering more than 40 annotation entities, many of which are novel and have never been explored previously. Tri©DB offers several unique features: (i) harmonizing the cancer-related information from more than 30 data sources into one integrative platform for easy access; (ii) utilizing a variety of data analysis and graphical tools for enhanced user interaction with the high-dimensional data; (iii) containing a newly developed reporting system for automated annotation and therapy matching for external patient genomic data. Benchmark test indicated that Tri©DB is able to annotate 46% more treatments than two officially recognized resources, oncoKB and MCG. Tri©DB was further shown to have achieved 94.9% concordance with administered treatments in a real clinical trial. CONCLUSIONS: The novel features and rich functionalities of the new platform will facilitate full access to cancer precision medicine data in one single platform and accommodate the needs of a broad range of researchers not only in translational medicine, but also in basic biomedical research. We believe that it will help to promote knowledge sharing in cancer precision medicine. Tri©DB is freely available at www.biomeddb.org , and is hosted on a cutting-edge technology architecture supporting all major browsers and mobile handsets.

Creating an ignorance-base: Exploring known unknowns in the scientific literature.

BACKGROUND: Scientific discovery progresses by exploring new and uncharted territory. More specifically, it advances by a process of transforming unknown unknowns first into known unknowns, and then into knowns. Over the last few decades, researchers have developed many knowledge bases to capture and connect the knowns, which has enabled topic exploration and contextualization of experimental results. But recognizing the unknowns is also critical for finding the most pertinent questions and their answers. Prior work on known unknowns has sought to understand them, annotate them, and automate their identification. However, no knowledge-bases yet exist to capture these unknowns, and little work has focused on how scientists might use them to trace a given topic or experimental result in search of open questions and new avenues for exploration. We show here that a knowledge base of unknowns can be connected to ontologically grounded biomedical knowledge to accelerate research in the field of prenatal nutrition. RESULTS: We present the first ignorance-base, a knowledge-base created by combining classifiers to recognize ignorance statements (statements of missing or incomplete knowledge that imply a goal for knowledge) and biomedical concepts over the prenatal nutrition literature. This knowledge-base places biomedical concepts mentioned in the literature in context with the ignorance statements authors have made about them. Using our system, researchers interested in the topic of vitamin D and prenatal health were able to uncover three new avenues for exploration (immune system, respiratory system, and brain development) by searching for concepts enriched in ignorance statements. These were buried among the many standard enriched concepts. Additionally, we used the ignorance-base to enrich concepts connected to a gene list associated with vitamin D and spontaneous preterm birth and found an emerging topic of study (brain development) in an implied field (neuroscience). The researchers could look to the field of neuroscience for potential answers to the ignorance statements. CONCLUSION: Our goal is to help students, researchers, funders, and publishers better understand the state of our collective scientific ignorance (known unknowns) in order to help accelerate research through the continued illumination of and focus on the known unknowns and their respective goals for scientific knowledge.

"KRiShI": a manually curated knowledgebase on rice sheath blight disease.

Knowledgebase for rice sheath blight information (KRiShI) is a manually curated user-friendly knowledgebase for rice sheath blight (SB) disease that allows users to efficiently mine, visualize, search, benchmark, download, and update meaningful data and information related to SB using its easy and interactive interface. KRiShI collects and integrates widely scattered and unstructured information from various scientific literatures, stores it under a single window, and makes it available to the community in a user-friendly manner. From basic information, best management practices, host resistance, differentially expressed genes, proteins, metabolites, resistance genes, pathways, and OMICS scale experiments, KRiShI presents these in the form of easy and comprehensive tables, diagrams, and pictures. The "Search" tab allows users to verify if their input rice gene id(s) are Rhizoctonia solani (R. solani) responsive and/or resistant. KRiShI will serve as a valuable resource for easy and quick access to data and information related to rice SB disease for both the researchers and the farmers. To encourage community curation a submission facility is made available. KRiShI can be found at http://www.tezu.ernet.in/krishi .

Towards more personalized digital health interventions: a clustering method of action and coping plans to promote physical activity.

BACKGROUND: Despite effectiveness of action and coping planning in digital health interventions to promote physical activity (PA), attrition rates remain high. Indeed, support to make plans is often abstract and similar for each individual. Nevertheless, people are different, and context varies. Tailored support at the content level, involving suggestions of specific plans that are personalized to the individual, may reduce attrition and improve outcomes in digital health interventions. The aim of this study was to investigate whether user information relates toward specific action and coping plans using a clustering method. In doing so, we demonstrate how knowledge can be acquired in order to develop a knowledge-base, which might provide personalized suggestions in a later phase. METHODS: To establish proof-of-concept for this approach, data of 65 healthy adults, including 222 action plans and 204 coping plans, were used and were collected as part of the digital health intervention MyPlan 2.0 to promote PA. As a first step, clusters of action plans, clusters of coping plans and clusters of combinations of action plans and barriers of coping plans were identified using hierarchical clustering. As a second step, relations with user information (i.e. gender, motivational stage, ...) were examined using anova's and chi2-tests. RESULTS: First, three clusters of action plans, eight clusters of coping plans and eight clusters of the combination of action and coping plans were identified. Second, relating these clusters to user information was possible for action plans: 1) Users with a higher BMI related more to outdoor leisure activities (F = 13.40, P < .001), 2) Women, users that didn't perform PA regularly yet, or users with a job related more to household activities (X2 = 16.92, P < .001; X2 = 20.34, P < .001; X2 = 10.79, P = .004; respectively), 3) Younger users related more to active transport and different sports activities (F = 14.40, P < .001). However, relating clusters to user information proved difficult for the coping plans and combination of action and coping plans. CONCLUSIONS: The approach used in this study might be a feasible approach to acquire input for a knowledge-base, however more data (i.e. contextual and dynamic user information) from possible end users should be acquired in future research. This might result in a first type of context-aware personalized suggestions on the content level. TRIAL REGISTRATION: The digital health intervention MyPlan 2.0 was preregistered as a clinical trial (ID:NCT03274271). Release date: 6-September-2017.

LinkedImm: a linked data graph database for integrating immunological data.

BACKGROUND: Many systems biology studies leverage the integration of multiple data types (across different data sources) to offer a more comprehensive view of the biological system being studied. While SQL (Structured Query Language) databases are popular in the biomedical domain, NoSQL database technologies have been used as a more relationship-based, flexible and scalable method of data integration. RESULTS: We have created a graph database integrating data from multiple sources. In addition to using a graph-based query language (Cypher) for data retrieval, we have developed a web-based dashboard that allows users to easily browse and plot data without the need to learn Cypher. We have also implemented a visual graph query interface for users to browse graph data. Finally, we have built a prototype to allow the user to query the graph database in natural language. CONCLUSION: We have demonstrated the feasibility and flexibility of using a graph database for storing and querying immunological data with complex biological relationships. Querying a graph database through such relationships has the potential to discover novel relationships among heterogeneous biological data and metadata.

An Update on MRMAssayDB: A Comprehensive Resource for Targeted Proteomics Assays in the Community.

Precise multiplexed quantification of proteins in biological samples can be achieved by targeted proteomics using multiple or parallel reaction monitoring (MRM/PRM). Combined with internal standards, the method achieves very good repeatability and reproducibility enabling excellent protein quantification and allowing longitudinal and cohort studies. A laborious part of performing such experiments lies in the preparation steps dedicated to the development and validation of individual protein assays. Several public repositories host information on targeted proteomics assays, including NCI's Clinical Proteomic Tumor Analysis Consortium assay portals, PeptideAtlas SRM Experiment Library, SRMAtlas, PanoramaWeb, and PeptideTracker, with all offering varying levels of details. We introduced MRMAssayDB in 2018 as an integrated resource for targeted proteomics assays. The Web-based application maps and links the assays from the repositories, includes comprehensive up-to-date protein and sequence annotations, and provides multiple visualization options on the peptide and protein level. We have extended MRMAssayDB with more assays and extensive annotations. Currently it contains >828 000 assays covering >51 000 proteins from 94 organisms, of which >17 000 proteins are present in >2400 biological pathways, and >48 000 mapping to >21 000 Gene Ontology terms. This is an increase of about four times the number of assays since introduction. We have expanded annotations of interaction, biological pathways, and disease associations. A newly added visualization module for coupled molecular structural annotation browsing allows the user to interactively examine peptide sequence and any known PTMs and disease mutations, and map all to available protein 3D structures. Because of its integrative approach, MRMAssayDB enables a holistic view of suitable proteotypic peptides and commonly used transitions in empirical data. Availability: http://mrmassaydb.proteincentre.com.

An Efficient 3D Human Pose Retrieval and Reconstruction from 2D Image-Based Landmarks.

We propose an efficient and novel architecture for 3D articulated human pose retrieval and reconstruction from 2D landmarks extracted from a 2D synthetic image, an annotated 2D image, an in-the-wild real RGB image or even a hand-drawn sketch. Given 2D joint positions in a single image, we devise a data-driven framework to infer the corresponding 3D human pose. To this end, we first normalize 3D human poses from Motion Capture (MoCap) dataset by eliminating translation, orientation, and the skeleton size discrepancies from the poses and then build a knowledge-base by projecting a subset of joints of the normalized 3D poses onto 2D image-planes by fully exploiting a variety of virtual cameras. With this approach, we not only transform 3D pose space to the normalized 2D pose space but also resolve the 2D-3D cross-domain retrieval task efficiently. The proposed architecture searches for poses from a MoCap dataset that are near to a given 2D query pose in a definite feature space made up of specific joint sets. These retrieved poses are then used to construct a weak perspective camera and a final 3D posture under the camera model that minimizes the reconstruction error. To estimate unknown camera parameters, we introduce a nonlinear, two-fold method. We exploit the retrieved similar poses and the viewing directions at which the MoCap dataset was sampled to minimize the projection error. Finally, we evaluate our approach thoroughly on a large number of heterogeneous 2D examples generated synthetically, 2D images with ground-truth, a variety of real in-the-wild internet images, and a proof of concept using 2D hand-drawn sketches of human poses. We conduct a pool of experiments to perform a quantitative study on PARSE dataset. We also show that the proposed system yields competitive, convincing results in comparison to other state-of-the-art methods.

The Role of Knowledge Availability in Forming Inferences with Rural Middle Grade English Learners.

We investigated differences in knowledge-based inferencing between rural, middle grade monolingual English-speaking students and English learners. Students were introduced to facts about an imaginary planet Gan followed by a multi-episode story about Gan. Participants were tested on the accuracy of fact recall and inferences using this knowledge at three time points (i.e., immediate, one-week, and one-month follow-up). Results show that monolingual English-speaking students significantly outperformed English learners on the inference task. Both subgroups made elaborative inferences more accurately than coherence. Students' ability to recall knowledge base facts was the strongest predictor of their ability to accurately make inferences using this knowledge at each time point.