Standardizing Free-Text Data Exemplified by Age and Data-Location Fields in the Immune Epitope Database.

Background: While unstructured data, such as free text, constitutes a large amount of publicly available biomedical data, it is underutilized in automated analyses due to the difficulty of extracting meaning from it. Normalizing free-text data, , removing inessential variance, enables the use of structured vocabularies like ontologies to represent the data and allow for harmonized queries over it. This paper presents an adaptable tool for free-text normalization and an evaluation of the application of this tool to two different sets of unstructured biomedical data curated from the literature in the Immune Epitope Database (IEDB): age and data-location.

The Immune Epitope Database (IEDB): 2024 update.

Over the past 20 years, the Immune Epitope Database (IEDB, iedb.org) has established itself as the foremost resource for immune epitope data. The IEDB catalogs published epitopes and their contextual experimental data in a freely searchable public resource.

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.

PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins.

Background: Numerous tools exist for biological sequence comparisons and search. One case of particular interest for immunologists is finding matches for linear peptide T cell epitopes, typically between 8 and 15 residues in length, in a large set of protein sequences. Both to find exact matches or matches that account for residue substitutions.

IEDB and CEDAR: Two Sibling Databases to Serve the Global Scientific Community.

Various methodologies have been utilized to analyze epitope-specific responses in the context of non-self-antigens, such as those associated with infectious diseases and allergies, and in the context of self-antigens, such as those associated with transplantation, autoimmunity, and cancer. Further to this, epitope-specific data, and its associated immunological context, are crucial to training and developing predictive algorithms and pipelines for the development of specific vaccines and diagnostics. In this chapter, we describe the methodology utilized to derive two sibling resources, the Immune Epitope Database (IEDB) and Cancer Epitope Database and Analysis Resource (CEDAR), to specifically host this data, and make them freely available to the scientific community.

Coronavirus Immunotherapeutic Consortium Database.

The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has seen multiple anti-SARS-CoV-2 antibodies being generated globally. It is difficult, however, to assemble a useful compendium of these biological properties if they are derived from experimental measurements performed at different sites under different experimental conditions. The Coronavirus Immunotherapeutic Consortium (COVIC) circumvents these issues by experimentally testing blinded antibodies side by side for several functional activities.

A curated collection of human vaccination response signatures.

Recent advances in high-throughput experiments and systems biology approaches have resulted in hundreds of publications identifying "immune signatures". Unfortunately, these are often described within text, figures, or tables in a format not amenable to computational processing, thus severely hampering our ability to fully exploit this information. Here we present a data model to represent immune signatures, along with the Human Immunology Project Consortium (HIPC) Dashboard ( www.

The Cancer Epitope Database and Analysis Resource (CEDAR).

We established The Cancer Epitope Database and Analysis Resource (CEDAR) to catalog all epitope data in the context of cancer. The specific molecular targets of adaptive T cell and B cell immune responses are referred to as epitopes. Epitopes derived from cancer antigens are of high relevance as they are recognized by anti-cancer immune cells.

Minimal Information about MHC Multimers (MIAMM).

With the goal of improving the reproducibility and annotatability of MHC multimer reagent data, we present the establishment of a new data standard: Minimal Information about MHC Multimers (https://miamm.lji.org/).

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.

Biological ontologies are used to organize, curate and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies (OBO) Foundry was created to address this by facilitating the development, harmonization, application and sharing of ontologies, guided by a set of overarching principles.

Standardization of assay representation in the Ontology for Biomedical Investigations.

The Ontology for Biomedical Investigations (OBI) underwent a focused review of assay term annotations, logic and hierarchy with a goal to improve and standardize these terms. As a result, inconsistencies in W3C Web Ontology Language (OWL) expressions were identified and corrected, and additionally, standardized design patterns and a formalized template to maintain them were developed. We describe here this informative and productive process to describe the specific benefits and obstacles for OBI and the universal lessons for similar projects.

SARS-CoV-2 human T cell epitopes: Adaptive immune response against COVID-19.

Over the past year, numerous studies in the peer reviewed and preprint literature have reported on the virological, epidemiological and clinical characteristics of the coronavirus, SARS-CoV-2. To date, 25 studies have investigated and identified SARS-CoV-2-derived T cell epitopes in humans. Here, we review these recent studies, how they were performed, and their findings.

TCRMatch: Predicting T-Cell Receptor Specificity Based on Sequence Similarity to Previously Characterized Receptors.

The adaptive immune system in vertebrates has evolved to recognize non-self antigens, such as proteins expressed by infectious agents and mutated cancer cells. T cells play an important role in antigen recognition by expressing a diverse repertoire of antigen-specific receptors, which bind epitopes to mount targeted immune responses. Recent advances in high-throughput sequencing have enabled the routine generation of T-cell receptor (TCR) repertoire data.

An immunologically friendly classification of non-peptidic ligands.

The Immune Epitope Database (IEDB) freely provides experimental data regarding immune epitopes to the scientific public. The main users of the IEDB are immunologists who can easily use our web interface to search for peptidic epitopes via their simple single-letter codes. For example, 'A' stands for 'alanine'.

A behind-the-scenes tour of the IEDB curation process: an optimized process empirically integrating automation and human curation efforts.

The Immune Epitope Database and Analysis Resource (IEDB) provides the scientific community with open access to epitope data, as well as epitope prediction and analysis tools. The IEDB houses the most extensive collection of experimentally validated B-cell and T-cell epitope data, sourced primarily from published literature by expert curation. The data procurement requires systematic identification, categorization, curation and quality-checking processes.

A structured model for immune exposures.

An Immune Exposure is the process by which components of the immune system first encounter a potential trigger. The ability to describe consistently the details of the Immune Exposure process was needed for data resources responsible for housing scientific data related to the immune response. This need was met through the development of a structured model for Immune Exposures.

Reporting and connecting cell type names and gating definitions through ontologies.

Background: Human immunology studies often rely on the isolation and quantification of cell populations from an input sample based on flow cytometry and related techniques. Such techniques classify cells into populations based on the detection of a pattern of markers. The description of the cell populations targeted in such experiments typically have two complementary components: the description of the cell type targeted (e.

Epitope Specific Antibodies and T Cell Receptors in the Immune Epitope Database.

The Immune Epitope Database (IEDB) is a free public resource which catalogs experiments characterizing immune epitopes. To accommodate data from next generation repertoire sequencing experiments, we recently updated how we capture and query epitope specific antibodies and T cell receptors. Specifically, we are now storing partial receptor sequences sufficient to determine CDRs and VDJ gene usage which are commonly identified by repertoire sequencing.

The Immune Epitope Database (IEDB): 2018 update.

The Immune Epitope Database (IEDB, iedb.org) captures experimental data confined in figures, text and tables of the scientific literature, making it freely available and easily searchable to the public. The scope of the IEDB extends across immune epitope data related to all species studied and includes antibody, T cell, and MHC binding contexts associated with infectious, allergic, autoimmune, and transplant related diseases.

ImmunomeBrowser: a tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins.

Motivation: Datasets that are derived from different studies (e.g. MHC ligand elution, MHC binding, B/T cell epitope screening etc.

FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability.

The Immune Epitope Database (IEDB), at www.iedb.org, has the mission to make published experimental data relating to the recognition of immune epitopes easily available to the scientific public.