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Faria D, Eugénio P, Contreiras Silva M, Balbi L, Bedran G, Kallor AA, Nunes S, Palkowski A, Waleron M, Alfaro JA, Pesquita C. The Immunopeptidomics Ontology (ImPO). Database (Oxford) 2024; 2024:baae014. [PMID: 38857186 PMCID: PMC11164101 DOI: 10.1093/database/baae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 11/30/2023] [Accepted: 02/22/2024] [Indexed: 06/12/2024]
Abstract
The adaptive immune response plays a vital role in eliminating infected and aberrant cells from the body. This process hinges on the presentation of short peptides by major histocompatibility complex Class I molecules on the cell surface. Immunopeptidomics, the study of peptides displayed on cells, delves into the wide variety of these peptides. Understanding the mechanisms behind antigen processing and presentation is crucial for effectively evaluating cancer immunotherapies. As an emerging domain, immunopeptidomics currently lacks standardization-there is neither an established terminology nor formally defined semantics-a critical concern considering the complexity, heterogeneity, and growing volume of data involved in immunopeptidomics studies. Additionally, there is a disconnection between how the proteomics community delivers the information about antigen presentation and its uptake by the clinical genomics community. Considering the significant relevance of immunopeptidomics in cancer, this shortcoming must be addressed to bridge the gap between research and clinical practice. In this work, we detail the development of the ImmunoPeptidomics Ontology, ImPO, the first effort at standardizing the terminology and semantics in the domain. ImPO aims to encapsulate and systematize data generated by immunopeptidomics experimental processes and bioinformatics analysis. ImPO establishes cross-references to 24 relevant ontologies, including the National Cancer Institute Thesaurus, Mondo Disease Ontology, Logical Observation Identifier Names and Codes and Experimental Factor Ontology. Although ImPO was developed using expert knowledge to characterize a large and representative data collection, it may be readily used to encode other datasets within the domain. Ultimately, ImPO facilitates data integration and analysis, enabling querying, inference and knowledge generation and importantly bridging the gap between the clinical proteomics and genomics communities. As the field of immunogenomics uses protein-level immunopeptidomics data, we expect ImPO to play a key role in supporting a rich and standardized description of the large-scale data that emerging high-throughput technologies are expected to bring in the near future. Ontology URL: https://zenodo.org/record/10237571 Project GitHub: https://github.com/liseda-lab/ImPO/blob/main/ImPO.owl.
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Affiliation(s)
- Daniel Faria
- INESC-ID, Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol, 9, Lisboa 1000-029, Portugal
| | - Patrícia Eugénio
- LASIGE, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Marta Contreiras Silva
- LASIGE, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Laura Balbi
- LASIGE, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Georges Bedran
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, Gdańsk 80-822, Poland
| | - Ashwin Adrian Kallor
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, Gdańsk 80-822, Poland
| | - Susana Nunes
- LASIGE, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
| | - Aleksander Palkowski
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, Gdańsk 80-822, Poland
| | - Michal Waleron
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, Gdańsk 80-822, Poland
| | - Javier A Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, Gdańsk 80-822, Poland
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Rd, Victoria, British Columbia, BC V8P 5C2, Canada
- Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Old College, South Bridge, Edinburgh, EH8 9YL, UK
- The Canadian Association for Responsible AI in Medicine, Victoria, Canada
| | - Catia Pesquita
- LASIGE, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Lisboa 1749-016, Portugal
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Koşaloğlu-Yalçın Z, Blazeska N, Vita R, Carter H, Nielsen M, Schoenberger S, Sette A, Peters B. The Cancer Epitope Database and Analysis Resource (CEDAR). Nucleic Acids Res 2022; 51:D845-D852. [PMID: 36250634 PMCID: PMC9825495 DOI: 10.1093/nar/gkac902] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/26/2022] [Accepted: 10/07/2022] [Indexed: 01/30/2023] Open
Abstract
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. Detailed knowledge of the molecular characteristic of cancer epitopes and associated metadata is relevant to understanding and planning prophylactic and therapeutic applications and accurately characterizing naturally occurring immune responses and cancer immunopathology. CEDAR provides a freely accessible, comprehensive collection of cancer epitope and receptor data curated from the literature and serves as a companion site to the Immune Epitope Database (IEDB), which is focused on infectious, autoimmune, and allergic diseases. CEDAR is freely accessible at https://cedar.iedb.org/.
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Affiliation(s)
| | - Nina Blazeska
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Randi Vita
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Hannah Carter
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Morten Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Argentina
| | - Stephen Schoenberger
- Laboratory of Cellular Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA,Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA,Department of Medicine, University of California San Diego, La Jolla, CA, USA
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Vita R, Mody A, Overton JA, Buus S, Haley ST, Sette A, Mallajosyula V, Davis MM, Long DL, Willis RA, Peters B, Altman JD. Minimal Information about MHC Multimers (MIAMM). JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:531-537. [PMID: 35042788 PMCID: PMC8830768 DOI: 10.4049/jimmunol.2100961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/09/2021] [Indexed: 02/03/2023]
Abstract
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/). Multimers are engineered reagents composed of a ligand and a MHC, which can be represented in a standardized format using ontology terminology. We provide an online Web site to host the details of the standard, as well as a validation tool to assist with the adoption of the standard. We hope that this publication will bring increased awareness of Minimal Information about MHC Multimers and drive acceptance, ultimately improving the quality and documentation of multimer data in the scientific literature.
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Affiliation(s)
- Randi Vita
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA;
| | - Apurva Mody
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
| | | | - Soren Buus
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA
| | - Mark M Davis
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA
| | - Dale L Long
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA; and
| | - Richard A Willis
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA; and
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA
| | - John D Altman
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA; and
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA
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Vita R, Mahajan S, Overton JA, Dhanda SK, Martini S, Cantrell JR, Wheeler DK, Sette A, Peters B. The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res 2020; 47:D339-D343. [PMID: 30357391 PMCID: PMC6324067 DOI: 10.1093/nar/gky1006] [Citation(s) in RCA: 1096] [Impact Index Per Article: 274.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/11/2018] [Indexed: 12/18/2022] Open
Abstract
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. Having been publicly accessible for >10 years, the recent focus of the IEDB has been improved query and reporting functionality to meet the needs of our users to access and summarize data that continues to grow in quantity and complexity. Here we present an update on our current efforts and future goals.
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Affiliation(s)
- Randi Vita
- La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery, La Jolla, CA 92037, USA
| | - Swapnil Mahajan
- La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery, La Jolla, CA 92037, USA
| | | | - Sandeep Kumar Dhanda
- La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery, La Jolla, CA 92037, USA
| | - Sheridan Martini
- La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery, La Jolla, CA 92037, USA
| | | | | | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery, La Jolla, CA 92037, USA.,University of California San Diego, Department of Medicine, La Jolla, CA 92093, USA
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery, La Jolla, CA 92037, USA.,University of California San Diego, Department of Medicine, La Jolla, CA 92093, USA
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Martini S, Nielsen M, Peters B, Sette A. The Immune Epitope Database and Analysis Resource Program 2003-2018: reflections and outlook. Immunogenetics 2019; 72:57-76. [PMID: 31761977 PMCID: PMC6970984 DOI: 10.1007/s00251-019-01137-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/12/2019] [Indexed: 12/12/2022]
Abstract
The Immune Epitope Database and Analysis Resource (IEDB) contains information related to antibodies and T cells across an expansive scope of research fields (infectious diseases, allergy, autoimmunity, and transplantation). Capture and representation of the data to reflect growing scientific standards and techniques have required continual refinement of our rigorous curation and query and reporting processes beginning with the automated classification of over 28 million PubMed abstracts, and resulting in easily searchable data from over 20,000 published manuscripts. Data related to MHC binding and elution, nonpeptidics, natural processing, receptors, and 3D structure is first captured through manual curation and subsequently maintained through recuration to reflect evolving scientific standards. Upon promotion to the free, public database, users can query and export records of specific relevance via the online web portal which undergoes iterative development to best enable efficient data access. In parallel, the companion Analysis Resource site hosts a variety of tools that assist in the bioinformatic analyses of epitopes and related structures, which can be applied to IEDB-derived and independent datasets alike. Available tools are classified into two categories: analysis and prediction. Analysis tools include epitope clustering, sequence conservancy, and more, while prediction tools cover T and B cell epitope binding, immunogenicity, and TCR/BCR structures. In addition to these tools, benchmarking servers which allow for unbiased performance comparison are also offered. In order to expand and support the user-base of both the database and Analysis Resource, the research team actively engages in community outreach through publication of ongoing work, conference attendance and presentations, hosting of user workshops, and the provision of online help. This review provides a description of the IEDB database infrastructure, curation and recuration processes, query and reporting capabilities, the Analysis Resource, and our Community Outreach efforts, including assessment of the impact of the IEDB across the research community.
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Affiliation(s)
- Sheridan Martini
- Division of Vaccine Discovery, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
| | - Morten Nielsen
- Department Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark.,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.,Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.,Department of Medicine, University of California San Diego, La Jolla, CA, USA
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Aguilar-Lazcano CA, Rechy-Ramirez EJ, Hu H, Rios-Figueroa HV, Marin-Hernandez A. Interaction Modalities Used on Serious Games for Upper Limb Rehabilitation: A Systematic Review. Games Health J 2019; 8:313-325. [PMID: 31287734 DOI: 10.1089/g4h.2018.0129] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
This systematic review aims to analyze the state-of-the-art regarding interaction modalities used on serious games for upper limb rehabilitation. A systematic search was performed in IEEE Xplore and Web of Science databases. PRISMA and QualSyst protocols were used to filter and assess the articles. Articles must meet the following inclusion criteria: they must be written in English; be at least four pages in length; use or develop serious games; focus on upper limb rehabilitation; and be published between 2007 and 2017. Of 121 articles initially retrieved, 33 articles met the inclusion criteria. Three interaction modalities were found: vision systems (42.4%), complementary vision systems (30.3%), and no-vision systems (27.2%). Vision systems and no-vision systems obtained a similar mean QualSyst (86%) followed by complementary vision systems (85.7%). Almost half of the studies used vision systems as the interaction modality (42.4%) and used the Kinect sensor to collect the body movements (48.48%). The shoulder was the most treated body part in the studies (19%). A key limitation of vision systems and complementary vision systems is that their device performances might be affected by lighting conditions. A main limitation of the no-vision systems is that the range-of-motion in angles of the body movement might not be measured accurately. Due to a limited number of studies, fruitful areas for further research could be the following: serious games focused on finger rehabilitation and trauma injuries, game difficulty adaptation based on user's muscle strength and posture, and multisensor data fusion on interaction modalities.
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Affiliation(s)
| | | | - Huosheng Hu
- School of Computer Science and Electronic Engineering, University of Essex, Colchester, United Kingdom
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Mahajan S, Vita R, Shackelford D, Lane J, Schulten V, Zarebski L, Jespersen MC, Marcatili P, Nielsen M, Sette A, Peters B. Epitope Specific Antibodies and T Cell Receptors in the Immune Epitope Database. Front Immunol 2018; 9:2688. [PMID: 30515166 PMCID: PMC6255941 DOI: 10.3389/fimmu.2018.02688] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/31/2018] [Indexed: 11/13/2022] Open
Abstract
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. For previously captured full length receptor sequencing data, we have calculated the corresponding CDR sequences and gene usage information using IMGT numbering and VDJ gene nomenclature format. To integrate information from receptors defined at different levels of resolution, we grouped receptors based on their host species, receptor type and CDR3 sequence. As of August 2018, we have cataloged sequence information for more than 22,510 receptors in 18,292 receptor groups, shown to bind to more than 2,241 distinct epitopes. These data are accessible as full exports and through a new dedicated query interface. The later combines the new ability to search by receptor characteristics with previously existing capability to search by epitope characteristics such as the infectious agent the epitope is derived from, or the kind of immune response involved in its recognition. We expect that this comprehensive capture of epitope specific immune receptor information will provide new insights into receptor-epitope interactions, and facilitate the development of novel tools that help in the analysis of receptor repertoire data.
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Affiliation(s)
- Swapnil Mahajan
- Center for Infectious Disease, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Randi Vita
- Center for Infectious Disease, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Deborah Shackelford
- Center for Infectious Disease, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Jerome Lane
- Center for Infectious Disease, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Veronique Schulten
- Center for Infectious Disease, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Laura Zarebski
- Center for Infectious Disease, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Martin Closter Jespersen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Paolo Marcatili
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Morten Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark.,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Alessandro Sette
- Center for Infectious Disease, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,University of California San Diego, La Jolla, CA, United States
| | - Bjoern Peters
- Center for Infectious Disease, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,University of California San Diego, La Jolla, CA, United States
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Vita R, Overton JA, Mungall CJ, Sette A, Peters B. FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:4877121. [PMID: 29688354 PMCID: PMC5819722 DOI: 10.1093/database/bax105] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/21/2017] [Indexed: 12/13/2022]
Abstract
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. By presenting curated data in a searchable database, we have liberated it from the tables and figures of journal articles, making it more accessible and usable by immunologists. Recently, the principles of Findability, Accessibility, Interoperability and Reusability have been formulated as goals that data repositories should meet to enhance the usefulness of their data holdings. We here examine how the IEDB complies with these principles and identify broad areas of success, but also areas for improvement. We describe short-term improvements to the IEDB that are being implemented now, as well as a long-term vision of true 'machine-actionable interoperability', which we believe will require community agreement on standardization of knowledge representation that can be built on top of the shared use of ontologies.
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Affiliation(s)
- Randi Vita
- La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery and Center for Emerging Diseases and Biodefense, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - James A Overton
- La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery and Center for Emerging Diseases and Biodefense, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Christopher J Mungall
- Lawrence Berkeley National Laboratory, Division of Environmental Genomics and Systems Biology, 1 Cyclotron Rd Berkeley, CA 94720, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery and Center for Emerging Diseases and Biodefense, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery and Center for Emerging Diseases and Biodefense, 9420 Athena Circle, La Jolla, CA 92037, USA
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MIRO: guidelines for minimum information for the reporting of an ontology. J Biomed Semantics 2018; 9:6. [PMID: 29347969 PMCID: PMC5774126 DOI: 10.1186/s13326-017-0172-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 12/22/2017] [Indexed: 01/07/2023] Open
Abstract
Background Creation and use of ontologies has become a mainstream activity in many disciplines, in particular, the biomedical domain. Ontology developers often disseminate information about these ontologies in peer-reviewed ontology description reports. There appears to be, however, a high degree of variability in the content of these reports. Often, important details are omitted such that it is difficult to gain a sufficient understanding of the ontology, its content and method of creation. Results We propose the Minimum Information for Reporting an Ontology (MIRO) guidelines as a means to facilitate a higher degree of completeness and consistency between ontology documentation, including published papers, and ultimately a higher standard of report quality. A draft of the MIRO guidelines was circulated for public comment in the form of a questionnaire, and we subsequently collected 110 responses from ontology authors, developers, users and reviewers. We report on the feedback of this consultation, including comments on each guideline, and present our analysis on the relative importance of each MIRO information item. These results were used to update the MIRO guidelines, mainly by providing more detailed operational definitions of the individual items and assigning degrees of importance. Based on our revised version of MIRO, we conducted a review of 15 recently published ontology description reports from three important journals in the Semantic Web and Biomedical domain and analysed them for compliance with the MIRO guidelines. We found that only 41.38% of the information items were covered by the majority of the papers (and deemed important by the survey respondents) and a large number of important items are not covered at all, like those related to testing and versioning policies. Conclusions We believe that the community-reviewed MIRO guidelines can contribute to improving significantly the quality of ontology description reports and other documentation, in particular by increasing consistent reporting of important ontology features that are otherwise often neglected.
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Vita R, Overton JA, Peters B. Identification of errors in the IEDB using ontologies. Database (Oxford) 2018; 2018:4904119. [PMID: 29688357 PMCID: PMC5824775 DOI: 10.1093/database/bay005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/11/2017] [Accepted: 01/04/2018] [Indexed: 12/02/2022]
Abstract
The Immune Epitope Database (IEDB) is a free online resource that has manually curated over 18 500 references from the scientific literature. Our database presents experimental data relating to the recognition of immune epitopes by the adaptive immune system in a structured, searchable manner. In order to be consistent and accurate in our data representation across many different journals, authors and curators, we have implemented several quality control measures, such as curation rules, controlled vocabularies and links to external ontologies and other resources. Ontologies and other resources have greatly benefited the IEDB through improved search interfaces, easier curation practices, interoperability between the IEDB and other databases and the identification of errors within our dataset. Here, we will elaborate on how ontology mapping and usage can be used to find and correct errors in a manually curated database.Database URL: www.iedb.org.
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Affiliation(s)
- Randi Vita
- Center for Infectious Disease, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - James A Overton
- Center for Infectious Disease, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Bjoern Peters
- Center for Infectious Disease, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
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Vita R, Overton JA, Sette A, Peters B. Better living through ontologies at the Immune Epitope Database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:3074785. [PMID: 28365732 PMCID: PMC5467561 DOI: 10.1093/database/bax014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 02/06/2017] [Indexed: 12/27/2022]
Abstract
The Immune Epitope Database (IEDB) project incorporates independently developed ontologies and controlled vocabularies into its curation and search interface. This simplifies curation practices, improves the user query experience and facilitates interoperability between the IEDB and other resources. While the use of independently developed ontologies has long been recommended as a best practice, there continues to be a significant number of projects that develop their own vocabularies instead, or that do not fully utilize the power of ontologies that they are using. We describe how we use ontologies in the IEDB, providing a concrete example of the benefits of ontologies in practice. Database URL:www.iedb.org
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Affiliation(s)
- Randi Vita
- La Jolla Institute for Allergy & Immunology, Center for Infectious Disease, La Jolla, CA 92037, USA
| | - James A Overton
- La Jolla Institute for Allergy & Immunology, Center for Infectious Disease, La Jolla, CA 92037, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy & Immunology, Center for Infectious Disease, La Jolla, CA 92037, USA
| | - Bjoern Peters
- La Jolla Institute for Allergy & Immunology, Center for Infectious Disease, La Jolla, CA 92037, USA
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El Bissati K, Zhou Y, Paulillo SM, Raman SK, Karch CP, Roberts CW, Lanar DE, Reed S, Fox C, Carter D, Alexander J, Sette A, Sidney J, Lorenzi H, Begeman IJ, Burkhard P, McLeod R. Protein nanovaccine confers robust immunity against Toxoplasma. NPJ Vaccines 2017; 2:24. [PMID: 29263879 PMCID: PMC5627305 DOI: 10.1038/s41541-017-0024-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 11/08/2022] Open
Abstract
We designed and produced a self-assembling protein nanoparticle. This self-assembling protein nanoparticle contains five CD8+ HLA-A03-11 supertypes-restricted epitopes from antigens expressed during Toxoplasma gondii's lifecycle, the universal CD4+ T cell epitope PADRE, and flagellin as a scaffold and TLR5 agonist. These CD8+ T cell epitopes were separated by N/KAAA spacers and optimized for proteasomal cleavage. Self-assembling protein nanoparticle adjuvanted with TLR4 ligand-emulsion GLA-SE were evaluated for their efficacy in inducing IFN-γ responses and protection of HLA-A*1101 transgenic mice against T. gondii. Immunization, using self-assembling protein nanoparticle-GLA-SE, activated CD8+ T cells to produce IFN-γ. Self-assembling protein nanoparticle-GLA-SE also protected HLA-A*1101 transgenic mice against subsequent challenge with Type II parasites. Hence, combining CD8+ T cell-eliciting peptides and PADRE into a multi-epitope protein that forms a nanoparticle, administered with GLA-SE, leads to efficient presentation by major histocompatibility complex Class I and II molecules. Furthermore, these results suggest that activation of TLR4 and TLR5 could be useful for development of vaccines that elicit T cells to prevent toxoplasmosis in humans.
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Affiliation(s)
- Kamal El Bissati
- Departments of OVS, The University of Chicago, 5841S Maryland Ave, Chicago, IL 60637 USA
| | - Ying Zhou
- Departments of OVS, The University of Chicago, 5841S Maryland Ave, Chicago, IL 60637 USA
| | | | | | - Christopher P. Karch
- Institute of Materials Science and Department of Molecular and Cell Biology, University of Connecticut, 97 North Eagleville Road, Storrs, CT 06269 USA
| | - Craig W. Roberts
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE UK
| | - David E. Lanar
- Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD 20910 USA
| | - Steve Reed
- Infectious Diseases Research Institute, 1616 Eastlake Ave E #400, Seattle, WA 98102 USA
| | - Chris Fox
- Infectious Diseases Research Institute, 1616 Eastlake Ave E #400, Seattle, WA 98102 USA
| | - Darrick Carter
- Infectious Diseases Research Institute, 1616 Eastlake Ave E #400, Seattle, WA 98102 USA
| | - Jeff Alexander
- PaxVax, 3985-A Sorrento Valley Blvd, San Diego, CA 92121 USA
| | - Alessandro Sette
- La Jolla Institute of Allergy and Immunology, 9420 Athena Cir, La Jolla, CA 92037 USA
| | - John Sidney
- La Jolla Institute of Allergy and Immunology, 9420 Athena Cir, La Jolla, CA 92037 USA
| | - Hernan Lorenzi
- J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD 20850 USA
| | - Ian J. Begeman
- Departments of OVS, The University of Chicago, 5841S Maryland Ave, Chicago, IL 60637 USA
| | - Peter Burkhard
- Alpha-O Peptides AG, Lörracherstrasse 50, 4125 Riehen, Switzerland
- Institute of Materials Science and Department of Molecular and Cell Biology, University of Connecticut, 97 North Eagleville Road, Storrs, CT 06269 USA
| | - Rima McLeod
- Departments of OVS, The University of Chicago, 5841S Maryland Ave, Chicago, IL 60637 USA
- Pediatrics (Infectious Diseases), The University of Chicago, 5841S Maryland Ave, Chicago, IL 60637 USA
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13
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Tso GJ, Tu SW, Musen MA, Goldstein MK. High-Risk Drug-Drug Interactions Between Clinical Practice Guidelines for Management of Chronic Conditions. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2017; 2017:531-539. [PMID: 28815153 PMCID: PMC5543385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Clinicians and clinical decision-support systems often follow pharmacotherapy recommendations for patients based on clinical practice guidelines (CPGs). In multimorbid patients, these recommendations can potentially have clinically significant drug-drug interactions (DDIs). In this study, we describe and validate a method for programmatically detecting DDIs among CPG recommendations. The system extracts pharmacotherapy intervention recommendations from narrative CPGs, normalizes the terms, creates a mapping of drugs and drug classes, and then identifies occurrences of DDIs between CPG pairs. We used this system to analyze 75 CPGs written by authoring entities in the United States that discuss outpatient management of common chronic diseases. Using a reference list of high-risk DDIs, we identified 2198 of these DDIs in 638 CPG pairs (46 unique CPGs). Only 9 high-risk DDIs were discussed by both CPGs in a pairing. In 69 of the pairings, neither CPG had a pharmacologic reference or a warning of the possibility of a DDI.
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Affiliation(s)
- Geoffrey J. Tso
- VA Palo Alto Health Care System, Palo Alto, CA;,Stanford University, Stanford, CA
| | | | | | - Mary K. Goldstein
- VA Palo Alto Health Care System, Palo Alto, CA;,Stanford University, Stanford, CA
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Abstract
Easy access to a vast collection of experimental data on immune epitopes can greatly facilitate the development of therapeutics and vaccines. The Immune Epitope Database and Analysis Resource (IEDB) was developed to provide such a resource as a free service to the biomedical research community. The IEDB contains epitope and assay information related to infectious diseases, autoimmune diseases, allergic diseases, and transplant/alloantigens for humans, nonhuman primates, mice, and any other species studied. It contains T cell, B cell, MHC binding, and MHC ligand elution experiments. Its data are curated primarily from the published literature and also include direct submissions from researchers involved in epitope discovery. This article describes the process of capturing data from these sources and how the information is organized in the IEDB data. Different approaches for querying the data are then presented, using the home page search interface and the various specialized search interfaces. Specific examples covering diverse applications of interest are given to highlight the power and functionality of the IEDB.
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15
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Verspoor K, Oellrich A, Collier N, Groza T, Rocca-Serra P, Soldatova L, Dumontier M, Shah N. Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop. J Biomed Semantics 2016; 7:66. [PMID: 27955708 PMCID: PMC5154111 DOI: 10.1186/s13326-016-0108-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 11/18/2016] [Indexed: 12/04/2022] Open
Abstract
This special issue covers selected papers from the 18th Bio-Ontologies Special Interest Group meeting and Phenotype Day, which took place at the Intelligent Systems for Molecular Biology (ISMB) conference in Dublin in 2015. The papers presented in this collection range from descriptions of software tools supporting ontology development and annotation of objects with ontology terms, to applications of text mining for structured relation extraction involving diseases and phenotypes, to detailed proposals for new ontologies and mapping of existing ontologies. Together, the papers consider a range of representational issues in bio-ontology development, and demonstrate the applicability of bio-ontologies to support biological and clinical knowledge-based decision making and analysis. The full set of papers in the Thematic Issue is available at http://www.biomedcentral.com/collections/sig.
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Affiliation(s)
- Karin Verspoor
- Department of Computing and Information Systems, The University of Melbourne, Melbourne, VIC, Australia.
| | - Anika Oellrich
- MRC Social, Genetic & Developmental Psychiatry Centre (SGDP), King's College London, London, SE5 8AF, UK
| | - Nigel Collier
- The Language Technology Lab, Department of Theoretical and Applied Linguistics, University of Cambridge, Cambridge, UK
| | - Tudor Groza
- Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
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Kinjo AR, Bekker GJ, Suzuki H, Tsuchiya Y, Kawabata T, Ikegawa Y, Nakamura H. Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. Nucleic Acids Res 2016; 45:D282-D288. [PMID: 27789697 PMCID: PMC5210648 DOI: 10.1093/nar/gkw962] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/06/2016] [Accepted: 10/11/2016] [Indexed: 11/14/2022] Open
Abstract
The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described.
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Affiliation(s)
- Akira R Kinjo
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Gert-Jan Bekker
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hirofumi Suzuki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuko Tsuchiya
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Kawabata
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yasuyo Ikegawa
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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Berges I, Antón D, Bermúdez J, Goñi A, Illarramendi A. TrhOnt: building an ontology to assist rehabilitation processes. J Biomed Semantics 2016; 7:60. [PMID: 27716359 PMCID: PMC5050577 DOI: 10.1186/s13326-016-0104-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/20/2016] [Indexed: 11/21/2022] Open
Abstract
Background One of the current research efforts in the area of biomedicine is the representation of knowledge in a structured way so that reasoning can be performed on it. More precisely, in the field of physiotherapy, information such as the physiotherapy record of a patient or treatment protocols for specific disorders must be adequately modeled, because they play a relevant role in the management of the evolutionary recovery process of a patient. In this scenario, we introduce TrhOnt, an application ontology that can assist physiotherapists in the management of the patients’ evolution via reasoning supported by semantic technology. Methods The ontology was developed following the NeOn Methodology. It integrates knowledge from ontological (e.g. FMA ontology) and non-ontological resources (e.g. a database of movements, exercises and treatment protocols) as well as additional physiotherapy-related knowledge. Results We demonstrate how the ontology fulfills the purpose of providing a reference model for the representation of the physiotherapy-related information that is needed for the whole physiotherapy treatment of patients, since they step for the first time into the physiotherapist’s office, until they are discharged. More specifically, we present the results for each of the intended uses of the ontology listed in the document that specifies its requirements, and show how TrhOnt can answer the competency questions defined within that document. Moreover, we detail the main steps of the process followed to build the TrhOnt ontology in order to facilitate its reproducibility in a similar context. Finally, we show an evaluation of the ontology from different perspectives. Conclusions TrhOnt has achieved the purpose of allowing for a reasoning process that changes over time according to the patient’s state and performance.
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Affiliation(s)
- Idoia Berges
- University of the Basque Country, UPV/EHU, Paseo Manuel de Lardizabal, 1, Donostia-San Sebastián, 20018, Spain.
| | - David Antón
- University of the Basque Country, UPV/EHU, Paseo Manuel de Lardizabal, 1, Donostia-San Sebastián, 20018, Spain
| | - Jesús Bermúdez
- University of the Basque Country, UPV/EHU, Paseo Manuel de Lardizabal, 1, Donostia-San Sebastián, 20018, Spain
| | - Alfredo Goñi
- University of the Basque Country, UPV/EHU, Paseo Manuel de Lardizabal, 1, Donostia-San Sebastián, 20018, Spain
| | - Arantza Illarramendi
- University of the Basque Country, UPV/EHU, Paseo Manuel de Lardizabal, 1, Donostia-San Sebastián, 20018, Spain
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Ontology in Immunology. Transplantation 2016; 100:2014-5. [PMID: 27547864 DOI: 10.1097/tp.0000000000001445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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