HIV molecular immunology database

 

Immunology API - API access for the LANL HIV Molecular Immunology Database

Immunology :: API.pod

CONTENTS

NAME

Immunology API - API access for the LANL HIV Molecular Immunology Database

VERSION

This documentation refers to API version v1.0.0.

SYNOPSIS

wget -O- 'https://www.hiv.lanl.gov/mojo/immunology/api/v1/epitope/ctl?id=42'

DESCRIPTION

The HIV Immunology API provides a public interface to retrieve data from the LANL HIV Molecular Immunology database. The returned data are formatted as JSON.

ENDPOINTS

All endpoints are relative to the server installation path. For example, if the API is installed at https://www.hiv.lanl.gov/mojo/immunology, then the full path of /api/v1/epitope/ctl would be https://www.hiv.lanl.gov/mojo/immunology/api/v1/epitope/ctl.

The following endpoints are available:

/api/v1/epitope/{table}

Search {table} in the immunology database and return the matching epitope records.

Search parameters

The {table} and at least one search parameter must be supplied; otherwise an error occurs. If multiple search parameters are supplied, then all of them must be satisfied.

/api/v1/list/binding_type/{table}

Retrieve the list of antibody binding types and IDs present in {table}. Antibody only.

/api/v1/list/country/{table}

Retrieve the list of country names and ISO country codes present in {table}.

/api/v1/list/hla/{table}

Retrieve the list of HLA/MHC types and IDs present in {table}. T cell only.

/api/v1/list/immunogen/{table}

Retrieve the list of immunogens and IDs present in {table}.

/api/v1/list/isotype/{table}

Retrieve the list of isotypes and IDs present in {table}. Antibody only.

/api/v1/list/keyword/{table}

Retrieve the list of keywords and IDs present in {table}.

/api/v1/list/outcome/{table}

Retrieve the list of outcomes (experimental methods and outcomes measured) and IDs present in {table}.

/api/v1/list/protein/{table}

Retrieve the list of proteins and IDs present in {table}.

/api/v1/list/species/{table}

Retrieve the list of species and IDs present in {table}.

/api/v1/list/subtype/{table}

Retrieve the list of subtypes and IDs present in {table}.

/api/v1/list/vaccine_adjuvant/{table}

Retrieve the list of vaccine adjuvants and IDs present in {table}.

/api/v1/list/vaccine_component/{table}

Retrieve the list of vaccine components and IDs present in {table}.

/api/v1/list/vaccine_strain/{table}

Retrieve the list of vaccine strains and IDs present in {table}.

/api/v1/list/vaccine_type/{table}

Retrieve the list of vaccine types and IDs present in {table}.

/api/vi/patient

Search the patient table in the immunology database and return the matching patient records.

/api/vi/patient_list/ethnicity

Retrieve the list of patient ethnicities.

/api/vi/patient_list/hla

Retrieve the list of patient HLA/MHC types and IDs.

/api/vi/patient_list/infection_country

Retrieve the list patient infection country names and codes.

/api/vi/patient_list/infection_year

Retrieve the list of patient infection years.

/api/vi/patient_list/progression

Retrieve the list patient HIV progression codes and names.

/api/vi/patient_list/risk_factor

Retrieve the list patient HIV risk factor codes and names.

/api/vi/patient_list/sex

Retrieve the list patient sexes.

/api/vi/patient_list/species

Retrieve the list patient species.

Search parameters

At least one search parameter must be supplied; otherwise an error occurs. If multiple search parameters are supplied, then all of them must be satisfied.

DATABASE ORGANIZATION

The information below explains what the database contains and the meaning of terms used in the search interfaces.

HIV T-Cell Epitopes

T-cell epitopes are categorized into cytotoxic T lymphocytes (CTL/CD8+) and helper T lymphocytes (T-helper/CD4+). The database organization for CTL/CD8+ and T-helper/CD4+ is identical, so they are described together.

T Cell Summary

The T cell databases include tables and associated references of HIV-specific T-cell epitopes arranged according to the location of the proteins in the HIV-1 genome. We attempted to make this section as comprehensive as possible, requiring that the epitope be contained within a defined region of a maximum of 30 amino acids, but not that the optimal boundaries be defined. Studies that were based on the analysis of whole proteins are described at the end of each protein section. The same epitope can have multiple entries, and each entry represents a single publication in this section of the database.

Recent studies utilize multiple functions attributed to T cells to define responses, and the simple distinctions of cytotoxic T cells and helper T cells have become blurred as more is learned about the range of responses triggered in CD4- and CD8-positive T cells responding to antigenic stimulus. When adding the most recent studies, we have tried to place T-cell responses in a reasonable manner into our traditional CTL and helper T-cell sections, and to specify the assay used to measure the response in each study.

T Cell Epitope Tables

Each T cell epitope has a multi-part basic entry:

HIV Antibody Binding Sites

Anibody Summary

The antibody database summarizes HIV-specific antibodies (Abs) arranged sequentially according to the location of their binding domain, organized by protein. We attempted to make this section as comprehensive as possible. For the monoclonal (MAbs) capable of binding to linear peptides, we require that the binding site be contained within a region of 30 or so amino acids to define the epitope, but not that the precise boundaries be defined. MAbs that do not bind to defined linear peptides are grouped by category at the end of each protein. Antibody categories, for example CD4 binding site (CD4BS) antibodies, are also noted in the index at the beginning of this section. Studies of polyclonal Ab responses are also included. Responses that are just characterized by binding to a protein, with no known specific binding site, are listed at the end of each protein.

Antibody Tables

Each MAb or polyclonal response has a multi-part basic entry:

Database Fields

This is a brief description of the database fields in the search and results pages. Please see above for more details.

API REFERENCE

The formal OpenAPI specification for this API is available via "api/v1", E.g., https://www.hiv.lanl.gov/mojo/immunology/api/v1. An HTML rendering is available via "api/v1.html", E.g., https://www.hiv.lanl.gov/mojo/immunology/api/v1.html.

BUGS AND LIMITATIONS

There are no known bugs in this app. Please report problems to the author at mailto:immuno@lanl.gov

SEE ALSO

HIV Molecular Immunology website https://www.hiv.lanl.gov/content/immunology

Immunology

OpenAPI/Swagger https://swagger.io

AUTHOR

LANL T-6 HIV Databases mailto:immuno@lanl.gov

LICENSE AND COPYRIGHT

Copyright © 2020–2021 Triad National Security, LLC. All rights reserved.

LA-UR-21-22506

Los Alamos National Laboratory, an affirmative action/equal opportunity employer, is operated by Triad National Security, LLC for the National Nuclear Security Administration of U.S. Department of Energy under contract 89233218CNA000001. Los Alamos National Laboratory strongly supports academic freedom and a researcher’s right to publish; as an institution, however, the Laboratory does not endorse the viewpoint of a publication or guarantee its technical correctness.

Questions or comments? Contact us at immuno@lanl.gov
 
Operated by Triad National Security, LLC, for the U.S. Department of Energy's National Nuclear Security Administration
Copyright © Triad National Security, LLC. All rights reserved | Disclaimer/Privacy

Dept of Health & Human Services Los Alamos National Institutes of Health