Contract No.

HHSN272001200010C

Immune Epitope Database and Analysis Program

System Architecture and Database Design Specification, v3.1

Curation v2.9.10 and External v3.6.0 releases

La Jolla Institute for Allergy and Immunology

9420 Athena Circle
La Jolla, CA 92037

858-752-6923
858-752-6987 (fax)
[email protected]

December 1, 2016
System Architecture and Database Design Specification (3.1)

Table of Contents

TABLE OF CONTENTS ............................................................................................................................................ I

1.0 INTRODUCTION ................................................................................................................................................1
1.1 SCOPE .................................................................................................................................................................1
1.2 PURPOSE .............................................................................................................................................................1
1.3 ASSUMPTIONS AND DEPENDENCIES ....................................................................................................................1
1.4 KEY OBJECTIVES ................................................................................................................................................2
1.5 CONTRACT IDENTIFICATION................................................................................................................................2
1.6 REFERENCES .......................................................................................................................................................2
1.7 CHANGE PROCEDURES ........................................................................................................................................3
2.0 SYSTEM ARCHITECTURE ..............................................................................................................................4
2.1 SYSTEM OVERVIEW ............................................................................................................................................4
2.1.1 Document Management Overview .............................................................................................................4
2.1.2 IEDB Curation Overview ...........................................................................................................................4
2.1.3 IEDB External Overview ............................................................................................................................6
2.1.4 IEDB Analysis Resource Overview ............................................................................................................6
2.1.4.1 T Cell Epitope Prediction Tools ........................................................................................................................... 7
2.1.4.2 B Cell Epitope Prediction Tools........................................................................................................................... 8
2.1.4.3 Analysis Tools...................................................................................................................................................... 8
2.2 HARDWARE ARCHITECTURE ...............................................................................................................................8
2.3 SOFTWARE COMPONENTS ................................................................................................................................. 11
2.4 HARDWARE AND SOFTWARE RELATIONSHIPS ................................................................................................... 13
3.0 DATABASE DESIGN AND DATA MODELS ................................................................................................ 14
3.1 OVERVIEW OF THE IEDB DATABASE ARCHITECTURE ...................................................................................... 14
3.2 OVERVIEW OF IEDB DATABASE DESIGN .......................................................................................................... 14
3.3 OVERVIEW IEDB DATABASE CONTENT............................................................................................................ 14
3.4 IEDB REFERENCE DATA FLOW ........................................................................................................................ 15
3.5 IEDB DATABASE BACKUP PROCEDURES .......................................................................................................... 16
3.6 IEDB CURATION PHYSICAL DATA MODELS ..................................................................................................... 17
3.6.1 IEDB Reference and Base Data Model. ................................................................................................... 17
3.6.2 IEDB TCell D2ata Model......................................................................................................................... 18
3.6.3 IEDB BCell Data Model .......................................................................................................................... 19
3.6.4 IEDB MHC Binding Data Model ............................................................................................................. 20
3.6.5 IEDB MHC Ligand Elution Data Model.................................................................................................. 21
3.6.6 IEDB ChEBI Support Data Model ......................................................................................................... 221
3.6.7 IEDB User Data Model .......................................................................................................................... 232
3.6.8 IEDB Lookup Value Data Models .......................................................................................................... 243
3.7 IEDB EXTERNAL PHYSICAL DATA MODEL..................................................................................................... 254
3.8 IEDB ANALYSIS RESOURCE DATA MODEL .................................................................................................... 265

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List of Tables
Table 1-1. IEDB Project, Technical and Scientific Resources ...................................................... 2
Table 2-1. IEDB Hardware Components ....................................................................................... 9
Table 2-2. IEDB Software Components ...................................................................................... 11
Table 2-3. Hardware and Software Relationships ....................................................................... 13
Table 3-1. IEDB Database Size ................................................................................................... 15

List of Figures

Figure 2-1. IEDB High Level Design Diagram ............................................................................. 5

Figure 2.2. Overview Document Classifier Process ...................................................................... 6
Figure 2-3. IEDB Production Environment ................................................................................. 10
Figure 3-1. IEDB Database Content ............................................................................................ 15
Figure 3.2. IEDB Reference Data Flow ....................................................................................... 16
Figure 3-3. IEDB Reference and Base Physical Data Model ...................................................... 17
Figure 3-4. IEDB TCell Assay Physical Data Model .................................................................. 18
Figure 3-5. IEDB BCell Assay Physical Data Model .................................................................. 19
Figure 3-6. IEDB MHC Binding Assay Physical Data Model .................................................... 20
Figure 3-7. IEDB MHC Ligand Elution Assay Physical Data Model ......................................... 21
Figure 3-8. IEDB ChEBI Support Physical Data Model ............................................................. 22
Figure 3-9. IEDB User Data Physical Data Model ...................................................................... 23
Figure 3-10. IEDB Lookup Value Physical Data Model ............................................................. 24
Figure 3-11. IEDB Public External Physical Data Model ........................................................... 25
Figure 3-12. IEDB Analysis Resource Physical Data Model ...................................................... 26

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IEDB System Architecture and Database Design Revision History

Revision Date Description
1.0 August 23, 2010 Initial Release
2.0 September 30, 2012 First post-renewal release
3.0 March 31, 2015 First release of IEDB 3.0
3.1 March 31, 2017 Update after adding the polling server

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1.0 Introduction
1.1 Scope
The scope of this document is to provide an architectural overview of the Immune Epitope
Database (IEDB) system hardware, database design and available applications. In doing so this
document will capture and convey the infrastructure and high-level database design which forms
the basis for the key IEDB system components, the Curation application and the External or
public facing application.

1.2 Purpose
The purpose of the IEDB system is to provide the scientific community a free public repository
of immune epitope data. The web-based IEDB system surpasses previously available immune
epitope databases by including detailed description of the experimental and immunological
context in which epitopes are recognized. The IEDB contains curated data relating to all
infectious diseases, including category A-C pathogens, emerging and re-emerging infections
diseases, allergens, diabetes, rheumatoid arthritis, multiple sclerosis and lupus as of December
2009. A team of highly trained curators continue to add more immune epitope data to the IEDB
on a weekly basis. The curators read scientific journal articles, identify immune epitope details
and associated data and enter data into the IEDB. A Data Submission Tool (DST) is also
integrated with the IEDB to facilitate external submission of data that supplement or is
independent of published journal articles.

The public facing IEDB application provides extensive query capabilities against the underlying
database. The IEDB Analysis Resource provides a collection of specialized tools for more
complex data analysis and prediction of epitopes. The target audience for the IEDB includes any
person capable of accessing the Internet; however the primary users are those within the
scientific community. The IEDB staff has worked diligently to successfully create a close
working relationship with the scientific community. User feedback and help requests are used to
continuously improve functionality and add new features to the IEDB system.

1.3 Assumptions and Dependencies

The following is a list of identified assumptions and dependencies for the IEDB project:

Assumptions:

• This system will be constructed as a web site.

• The features intended for the public will be accessible on the Internet.
• The system will be accessed using an Internet browser.
• The system will not be constructed to address classified data.
• System security will be based on permissions granted to authenticated users.

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Dependencies:

• The system will utilize taxonomy data from NCBI.

• The system will interact with PDB using web services.
• The system will interact with GenBank using web services.
• The system will interact with GenPept using web services.
• The system will retrieve citations from PubMed.
• The system will retrieve information from ChEBI web services.
• Add others?

1.4 Key Objectives

The key objective of the IEDB System Architecture and Database Design Document is to
provide a high-level overview of the system architecture and data models to support the database
design. This document will be revised to support new IEDB design features or any
modifications. Revisions to this document will follow the change procedure defined below in
section 1.7.

1.5 Contract Identification

La Jolla Institute for Allergy and Immunology (LJI) has developed, managed and maintained the
IEDB since December 2003 under contract number HHSN266200400006C and a seven-year
renewal contract number HHSN272001200010C. The following subcontractors assist LJI in the
ongoing development and maintenance of the project: Leidos and the Technical University of
Denmark (DTU).

1.6 References
Table 1-1. IEDB Project, Technical and Scientific Resources
IEDB Project Documents
RFP No. NIH-NIAID-DAIT-03-31
IEDB Curation Schema, Version 2.4
IEDB Curation Manual, September 02, 2009
IEDB User Documentation Version 2, January 21, 2009
IEDB Annual Compendium for2015, May 6, 2016
IEDB LinkOut procedure, July 22,2009
Field Guide for DST, Beta, April 15, 2009
The Ontology of Immune Epitopes (ONTIE) at http://ontology.immuneepitope.org/
Technical Materials
Designing Enterprise Applications with the J2EE Platform, 2nd Edition, Sun Microsystems, 2004

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Mastering BEA WebLogic Server: Best Practices for Building and Deploying J2EE Applications
by Gregory Nyberg, Robert Patrick et al. John Wiley & Sons, 2003
Struts: The Complete Reference by James Holmes, McGraw-Hill/Osborne, 2004
Mastering Jakarta Struts by James Goodwill, John Wiley & Sons, 2002
Professional Java Server Programming by Danny Ayers, Wrox Press Ltd., 1999
JUnit in Action by Vincent Massol, Manning Publications Co., 2004
Professional XML by Diedier Martin, Wrox Press Ltd., 1999
Instant UML by Pierre-Alain Muller, Wrox Press Ltd., 2000
Apache Lucene at http://lucene.apache.org/java/docs/index.html
PHP at www.php.net
Spring Framework at http://www.springsource.org/
Display Tag Library at http://displaytag.sourceforge.net/1.2/index.html
JSON at http://json.org/
Ajax: The Complete Reference, by Thomas Powell, McGraw-Hill Osborne Media 2008
MySQL database documentation at www.mysql.com/doc/refman/5.1/en/index.html
JavaScript: The Complete Reference, 2nd Edition, by Thomas Powell, McGraw-Hill Osborne
Media, 2004
Javascript, CSS, PHP reference material at www.w3schools.com
Apache Web Server documentation at httpd.apache.org/docs/2.2/
Dojo JavaScript library documentation at www.dojotoolkit.org/reference-guide/
Apache Tomcat documentation at tomcat.apache.org/tomcat-5.5-doc/index.html
Scientific Materials
Vita R, Overton JA, Greenbaum JA, Ponomarenko J, Clark JD, Cantrell JR, Wheeler DK,
Gabbard JL, Hix D, Sette A, Peters B. The immune epitope database (IEDB) 3.0. Nucleic Acids
Res. 2014 Oct 9. pii: gku938. [Epub ahead of print] PubMed PMID: 25300482.
The Ontology for Biomedical Investigations (OBI) at http://ontology.immuneepitope.org/

1.7 Change Procedures

This document is under change control and will continue to be updated as necessary. The
revision history of this document is tracked in the Revision History section at the beginning of
this document, page iii. Significant changes to the document will be represented by the new
version as being incremented by the next whole number (e.g. 2.0). Minor updates to this
document will be traced as minor releases (e.g.1.1).

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2.0 System Architecture

2.1 System Overview
The IEDB system is comprised of three main components: Curation (in which data is entered
into the database), External (which is accessed by external users to query the database), and
Document Management (which serves to identify relevant references and track their curation).
The IEDB also interfaces with different external resources to obtain data necessary for detailed
curation of a reference. Figure 2-1 below provides a high level representation of the IEDB
system design.

2.1.1 Document Management Overview

The Document Management component of the IEDB consists of the Curation Tracking System,
the Document Classifier and the Document Retriever. Document Management identifies what
journal articles should be curated, downloads a copy of the publication and tracks the status of
the article curation. The first step in curation is identifying relevant publications and is illustrated
in Figure 2-2. The Document Classifier uses queries of PubMed and the Protein Data Bank
(PDB), along with machine learning methods to identify all potential curation references. It is
implemented as a MySQL database and a set of Python scripts. Once a journal article has been
classified as a curation item, the Document Retriever fetches and downloads the associated PDF
file and makes it available for a curator to pick in the curation component of the system. The
Curation Tracking System (CTS) keeps track of each reference from when it is assigned to a
curator and all of the way through the curation process until it is approved and promoted to
production.

2.1.2 IEDB Curation Overview

The IEDB Curation toolset is only accessible by curation staff. This internal web-based
application includes a curation toolset that is used to perform all the "behind the scene" functions
such as curation, internal user administration, and system configuration. In addition, Curation
includes a Data Submission Tool (DST). The DST allows any user the ability to submit data
directly to the IEDB for curation. Submitted data are then transferred to the curation toolset,
where the submission is manually reviewed by curation staff. Once epitope data has been
entered, reviewed, and approved, it is released to IEDB External for public consumption. Section
3.6 contains the Curation data models.

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Document Management External Resources

Curation Tracking
System

Document Classifier NCBI SDSC PDB ChEBI

Document Retriever

Curation Staff IEDB Curation

Curator Toolset

Oracle

Data Submission
Tool (DST)

Public Access

IEDB External

Analysis Resource

Query Toolset
MYSQL

Solution Center

Figure 2-1. IEDB High Level Design Diagram

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Figure 2-2. Overview Document Classifier Process

2.1.3 IEDB External Overview

The primary Website that is accessible to the public is the IEDB External website
(http://www.iedb.org). The External application provides a query toolset which gives users the
ability to query and download epitope data. This public site is linked to the IEDB Analysis
Resource which contains tools for advanced analysis of epitope data including epitope prediction
tools. The External site also includes the Solutions Center which provides support mechanisms to
tutor, assist, and communicate with the user community. It also provides a portal for users to
submit help requests and feedback. Section 3.7 contains the External data model information.

2.1.4 IEDB Analysis Resource Overview

The Analysis Resource is a collection of T cell and antibody epitope prediction tools and
analysis tools. It resides on its own server, as described in Section 2.2. The IEDB website has
help information, examples, and references for all the tools in the Analysis Resource. All the
tools have been developed under the IEDB contract except for the tools developed by DTU. The
DTU prediction tools were developed under separate funding and were delivered as executables
for integration into the IEDB with the current IEDB contract funding. Source code for all tools
except those developed by DTU and executables for the DTU tools will be made available to the
follow-on entity during the transition period. Section 3.8 contains the Analysis Resource data
model information.

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2.1.4.1 T Cell Epitope Prediction Tools

The T cell epitope prediction tools fall into two categories – those that predict IC50 values for
peptides binding to specific MHC class I and II molecules and those that predict epitope
candidates based upon the processing of peptides in the cell.

For the MHC class I binding predictions, nine methods have been implemented, as listed below
with their aliases. The asterisk indicates tools developed by DTU:

• Consensus
• netMHCpan*
• Artificial neural network (ANN)
• Stabilized matrix method (SMM)
• SMM with a peptide:MHC binding energy covariance matrix (SMMPMBEC)
• Scoring matrices derived from combinatorial peptide libraries (Comblib_Sidney2008)
• PickPocket*
• netMHCcons*
• netMHCstabpan*

The MHC class II binding prediction offers the user six different methods:

• Consensus
• NetMHCIIpan*
• NN_align*
• Stabilized matrix method align (SMM_align)*
• Combinatorial library
• Sturniolo

There are two general categories of T cell epitope processing tools. The tool in the first category
combines predictors of proteasomal processing, TAP transport, and MHC binding to produce an
overall score for each peptide’s intrinsic potential of being a T cell epitope. The user can select
one of seven methods:

• netMHCpan*
• Artificial neural network (ANN)
• Stabilized matrix method (SMM)
• SMM with a peptide:MHC binding energy covariance matrix (SMMPMBEC)
• Scoring matrices derived from combinatorial peptide libraries (Comblib_Sidney2008)
• PickPocket*
• netMHCcons*

The second processing prediction category contains two neural network tools. NetChop is a
predictor of proteasomal cleavage sites and NetCTL predicts T cell epitopes along a protein
sequence. Both tools were developed by DTU.

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In addition, the Analysis Resource hosts MHC-NP, a tool that predicts peptides that are naturally
processed by MHC. This tool was developed by Sébastien Giguère Alexandre Drouin,
Alexandre Lacoste, Mario Marchand, Jacques Corbeil and François Laviolette.

2.1.4.2 B Cell Epitope Prediction Tools

There are three categories of antibody epitope prediction tools in the IEDB. The first is a
collection of six methods that predict continuous antibody epitopes. Five of them use amino acid
scales and the sixth, called BepiPred, predicts the location of linear epitopes using a combination
of a hidden Markov model and a propensity scale method. BepiPred was developed by DTU.
The second category contains DiscoTope, a tool developed by DTU that incorporates solvent-
accessible surface area calculations and contact distances into the prediction of antibody epitope
potential along the length of a protein sequence. This method can be used to predict
discontinuous epitopes. The third category includes ElliPro, which predicts epitopes based upon
solvent accessibility and flexibility. A fourth tool is available in this section of the website and
can be used for modeling antibody structures when a PDB structure is not available. Prediction
of ImmunoGlobulin Structure (PIGS) was developed by P. Marcatili and A. Tramontano.

2.1.4.3 Analysis Tools

The Analysis Resource has three tools that allow the user to further analyze a known epitope
sequence or group of sequences:

• Population Coverage - This tool calculates the fraction of individuals predicted to

respond to a given set of epitopes with known MHC restrictions. This calculation is
made on the basis of HLA genotypic frequencies assuming non-linkage disequilibrium
between HLA loci.

• Epitope Conservancy Analysis - This tool calculates the degree of conservancy of an

epitope within a given protein sequence set at different degrees of sequence identity. The
degree of conservation is defined as the fraction of protein sequences containing the
epitope at a given identity level.

• Epitope Cluster Analysis - This tool groups epitopes into clusters based on sequence
identity. A cluster is defined as a group of sequences that have a sequence similarity
greater than the minimum sequence identity threshold specified.

2.2 Hardware Architecture

The IEDB has three basic systems (curation, external, and tools) that reside in three different
locations. The curation system that is used for curating scientific literature and processing data
submissions from external researchers consists of three nearly identical hardware and software
environments. The three systems host a development system, a test system, and a curation
production system, which is the one actually used by the curators. Table 2-1 describes the
hardware components for the IEDB.

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Table 2-1. IEDB Hardware Components

Component Name Description
Protects servers from unauthorized access. Firewalls
exist at LJI and SDSC to support networks based in
Firewalls those locations.
Database servers support the database software.
There are twelve database servers used to support the
IEDB; two database servers running Oracle for
Curation (production and development), five database
servers running MySQL for External (two local
production, two remote production, and one local
development), and five database servers running
Oracle XE for the Finders, a search feature (two local
production, two remote production, and one
Database Servers development).
Servers that support the application software. There
are five application servers: two curation servers
(production and development) and three tools servers
(local production, remote production, and
Application Servers development).
The servers supporting the web software. There are
five web servers are used by External (local
Web Servers production, remote production, and development).
Virtual machine host servers are used to support the
Virtual Machine Host Servers External software (production and development).
All production and development machines are hosted
in a local Storage Area Network at their respective
SAN Storage geographical locations.

All servers are virtual machines hosted in a VMWare ESX vSphere environment and utilize a
redundant SAN for storing the VMs. All local production virtual machines are replicated offsite
to the San Diego Supercomputer Center (SDSC) excluding the Curation servers.

At LJI the Curation database and application servers are hosted on dedicated ESX hosts on HP
BL460c G7 server blades. All other virtual machines are distributed amongst four ESX hosts on
HP BL465c G7 blades. All of the storage for IEDB VMs are located on a dedicated SAN storage
system.

The SDSC location currently utilizes SAN storage which is presented to a Supermicro Blade
System running VMWare vSphere. There are four Supermicro BHDGT host compute blades for
all VMs at SDSC.

The system that users see when they go to www.iedb.org is referred to as the external system.
Physical machines are located at LJI and are replicated offsite to an offsite facility at SDSC in La
Jolla, CA. The virtual servers in the production set are duplicated. One is used for staging the
weekly update while the other actually serves as the production machine visible to the public.
The staging and production environments are swapped weekly at the end of the update on the
staging machine.

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Figure 2-3 depicts the server configuration of the IEDB production environment. Section 2.3 lists
and describes the software used to develop and maintain the IEDB. The hardware and software
relationships are depicted in Section 2.4.

Figure 2-3. IEDB Production Environment

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2.3 Software Components

Table 2-2 Describes the software components for the IEDB application.

Table 2-2. IEDB Software Components

Component Name Description
Asynchronous JavaScript and XML techniques for faster, more dynamic user
AJAX interface. (External)
Apache Ant is a software tool for automating software build processes.
Ant (Curation and External)
An open source, XML based web services framework. Used by internal
Apache Axis curation system for retrieval of PubMed records. (Curation)
Apache Subversion SVN is an open source software versioning and revision control system.
(SVN) (Curation and External)
The Apache web server is responsible for handling HTTP requests, routing
Apache Web Server dynamic calls to either the Tomcat servlet container or PHP files. (External)
Open source jsp tag library specializing in tabular data presentation.
Display tag library (Curation)
Drools is a business logic management tool, used to enforce data validation
Drools (JBoss Drools) rules during the curation process. (Curation)
The Dojo Toolkit is an open source modular JavaScript library, used on
Dojo Javascript Toolkit forms, tree browsers and AJAX calls. (External)
Eclipse is an open source Integrated Development Environment. (Curation
Eclipse IDE and External)
High level abstraction of Java Servlets representing the 'View' layer of MVC
Java Server Pages architecture. (Curation and External)
MySQL / MariaDB Open source RDBMS used by the public facing query system as well as
Database analysis tools. MariaDB is a community-developed fork of MySQL (External)

Oracle Database 12c RDBMS used by internal curation system (Curation)

Lightweight server-side web development language, used within Apache
PHP Web Server. (External)
A general purpose high-level programming language used by the public
Python facing query system as well as analysis tools. (External)
An open source application framework for Java providing inversion of
Spring Framework control, data access and transaction management. (Curation)
Apache (formerly Jakarta project) Struts is an open source MVC framework
Struts for developing J2EE applications. (Curation and External)
Apache Tiles is a J2EE View framework, allowing JSP pages to be
Tiles developed modularly. (Curation and External)
Apache Tomcat is an open source servlet container. It is used for logic
Tomcat heavy operations on the Public facing site. (External)
WebLogic Application J2EE application server. Hosts web tier, application logic tier, and data
Server access tier for internal curation system. (Curation)

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Component Name Description

Web Ontology Used to represent taxonomies for use by the finder applications (Curation
Language (OWL) and External)
Extensible Markup Language is a set of rules for encoding documents in
machine readable form. It is used in the internal curation systems import
XML and export processes. (Curation)

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2.4 Hardware and Software Relationships

Each software component is used in conjunction with one or more hardware components. The
table below describes the hardware, operating systems and key software used with that hardware
component.

Table 2-3. Hardware and Software Relationships

Hardware Component Software Component
CentOS Enterprise Linux Server
Oracle Enterprise RDBMS
Application / Database Sun Java
Servers (Curation) WebLogic Server
CentOS Enterprise Linux Server
Sun Java
Apache Tomcat
Python
Apache HTTP Server
MariaDB
Application Servers (Tools) PHP
CentOS Enterprise Linux Server
Sun Java
Apache Tomcat
Python
Apache HTTP Server
Web / Database Servers MariaDB
(External) PHP

Virtual Machine Host Servers VMWare vSphere

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3.0 Database Design and Data Models

3.1 Overview of the IEDB Database Architecture
The main repository for immune epitope data is a relational database utilizing Oracle 12c as the
management system and hosted on a Linux virtual machine. jThis repository is where all
curation data is stored and maintained. There are three instances which exist to support the
development, test and production curation sites. The curation production instance supports the
curation staff and allows them to create and update curation data.

The curation database is normalized and converted to a MYSQL database which is hosted on a
Linux virtual machine. The External or public website uses this MYSQL database. The de-
normalization of the main curation database allows for faster query performance on the external
web site. A normalized version of the External MySQL database is also created and is available
for download on the Database Export page of the External site. The physical data model for this
database is represented in Figure 3-11.

3.2 Overview of IEDB Database Design

From a design standpoint, it is essential to first understand the domain and scope of the IEDB
system. The IEDB data structure has been refined many times since its initial creation. The
system will continue to change in response to other efforts including tool development, curation
of different types of epitopes, Epitope Discovery Group data submission, and community
feedback.

3.3 Overview IEDB Database Content

The scientific domain is critical to the design of the IEDB database. Within the IEDB data
architecture there are three major concepts; reference, epitope, and assay. The top level object
within our database is the reference. The origin of all data published in the database must be
cited. This information is captured as a reference. A reference can be a publication or a
submission and will contain one or more epitopes. Each epitope may have any number of assays
and corresponding immunizations. Each assay results in one data point or measurement. For
example, if four assays were performed to test the affinity of an epitope to a given MHC
molecule with different assay techniques, there would be four assay records, one for each
reading. Within the database each of these major concepts is represented by several tables.
Figure 3-1 depicts a high level overview of the IEDB data components and the associated
relationships.

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Figure 3-1. IEDB Database Content

Reference data are curated within an Oracle 12c database using the internal Curation IEDB site
(http://curation.iedb.org/home.do ). The Curation application is password protected and accessed
only by Curators. A weekly build process creates a read-only, de-normalized MYSQL database
from the curated references with have been promoted to production status. This MYSQL
database is used by the External IEDB site (www.iedb.org) which is open to the general public.
The sizes of the different databases are listed in Table 3-1 below.

Table 3-1. IEDB Database Size

Database Size
CURATION ORACLE 143GB (20GB compressed)
EXTERNAL MYSQL 36GB (6GB compressed)
MYSQL IEDB_PUBLIC 3GB (350MB compressed)
IEDB_ANALYSIS MYSQL 100MB (50MB compressed)

3.4 IEDB Reference Data Flow

The diagram below depicts how references flow between the internal and external application
databases. Using the internal Curation application, references are introduced from PubMed or via
submissions into the NEWDB “staging area” schema inside the Curation Oracle database. When
references are ready to be displayed on production, they are copied, or “promoted”, to the
NEWDB_PRODUCTION schema. A weekly build process recreates a set of de-normalized
tables inside the NEWDB_PRODUCTION schema representing the production curated
references. These tables are then transferred via the ETL utility PAN into the three MYSQL

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System Architecture and Database Design Specification (v3.1)

databases which are recreated during the weekly build. If a production reference needs to be
altered, the reference is copied from the NEWDB_PRODUCTION schema back into the
NEWDB schema for re-curation. At the same time, the reference is copied to the
NEWDB_COPY schema. This provides rollback capability so that any changes to the staging
area copy of the reference can be restored to the previous version from production. Data are
migrated between the three internal Oracle schemas via Oracle stored procedures. The
IEDB_ANALYSIS MYSQL database is used by the Epitope Prediction and Analysis Tools
website. The IEDB_QUERY_YYYYMMDD MYSQL database is used by the IEDB website.
The IEDB_PUBLIC MYSQL database is used for MYSQL database exports on the IEDB
website. The IEDB_PRIVATE are MySQL copies of the Oracle NEWDB and
NEWDB_PRODUCTION tables that can be used for internal development.

IEDB REFERENCE DATA FLOW

Internal Site External Site

ORACLE MYSQL

NEWDB_COPY IEDB_ANALYSIS
(Rollback Area) ETL (PAN) (Tools Database)

Rollback

Re-curate
ETL (PAN) IEDB_QUERY_YYYYMMDD

Re-curate

NEWDB NEWDB_PRODUCTION ETL (PAN) IEDB_PUBLIC

(Staging Area) (Production Items)

ETL (PAN)
ETL (PAN) IEDB_PRIVATE

Promote

Figure 3-2. IEDB Reference Data Flow

3.5 IEDB Database Backup Procedures

The Oracle 12c database used to store curation data is backed up using a variety of procedures. A
full set of “Hot” backups are performed daily for all the curated data in the NEWDB,
NEWDB_COPY and NEWDB_PRODUCTION schemas using Oracle’s export utility. Using a
defined process, these backups can be used to restore the curation database if needed or used to
refresh the test curation database to sync up test with production. Data files are also backed up as
part of the SAN storage system backup plan.

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3.6 IEDB Curation Physical Data Models

The following data models represent the key areas of the IEDB database. These tables represent
how the data is physically stored in the IEDB.

3.6.1 IEDB Reference and Base Data Model.

Figure 3-3 represents the Reference table and other related base tables of the curation
application. Note that for space considerations, assay tables and their relationships are not
displayed in this diagram. See the following individual assay diagrams for their direct
relationships to the base tables.
JOURNAL
ACTION_LOG
JOURNAL_ID NUMBER
SUBMISSION ACTION_LOG_ID NUMBER
JOURNAL_TITLE VARCHAR2(2000)
REFERENCE_ID NUMBER
JOURNAL_ISSN VARCHAR2(15) SUBMISSION_ID NUMBER
USER_ID NUMBER
MEDLINE_TA VARCHAR2(200) REFERENCE_ID NUMBER
ACTION VARCHAR2(35)
SUBMITTER_NAME VARCHAR2(85)
ACTION_DATE DATE
SUBMISSION_DATE DATE
COMMENTS VARCHAR2(200)
SUBMITTER_USER_ID NUMBER
JOURNAL_ID = JOURNAL_ID TIME NUMBER
NOTIFICATION_FLAG VARCHAR2(1)
LEVEL_OF_EFFORT VARCHAR2(10)
SUBMISSION_AUTHORS VARCHAR2(2000)
EPITOPE_COUNT NUMBER
ARTICLE SUBMISSION_AFFILIATIONS VARCHAR2(2000)
ARTICLE_ID NUMBER SUBMISSION_TITLE VARCHAR2(400)
REFERENCE_ID NUMBER SUBMISSION_ABSTRACT VARCHAR2(4000) REFERENCE_ID = REFERENCE_ID
SUBMISSION_PDF_FLAG VARCHAR2(1) REFERENCE_ID = REFERENCE_ID
JOURNAL_ID NUMBER
JOURNAL_VOLUME VARCHAR2(15) REFERENCE_CATEGORY
JOURNAL_ISSUE VARCHAR2(20) REF_CATEGORY_ID NUMBER
REFERENCE
ARTICLE_DATE VARCHAR2(35) CATEGORY_NAME VARCHAR2(80)
REFERENCE_ID = REFERENCE_ID REFERENCE_ID NUMBER
ARTICLE_PAGES VARCHAR2(24) PRIORITY NUMBER
ARTICLE_TITLE VARCHAR2(1000) REFERENCE_TYPE VARCHAR2(15)
SORT_ORDER NUMBER
ARTICLE_AUTHORS VARCHAR2(4000) A_C_PATHOGEN_FLAG VARCHAR2(5)
ARTICLE_ABSTRACT VARCHAR2(4000) SVM_CLASSIFIER_SCORE NUMBER
ARTICLE_AFFILIATIONS VARCHAR2(2000) CURATION_STATUS VARCHAR2(100)
ARTICLE_CHEMICAL_LIST VARCHAR2(4000) CURRENT_USER_ID NUMBER REF_CATEGORY_ID = REF_CATEGORY_ID
ARTICLE_MESH_HEADINGS_LIST VARCHAR2(4000) CURATION_KEYWORDS VARCHAR2(2000)
MEDLINE_DATE VARCHAR2(10) CURATEDBY VARCHAR2(85) REFERENCE_ID = REFERENCE_ID
COMMENTS VARCHAR2(2000) DIFFICULTY VARCHAR2(10) REFERENCE_CATEGORY_ASSOC
PUBMED_ID VARCHAR2(20) LAST_REVIEWER NUMBER REFERENCE_ID NUMBER
REFERENCE_ID = REFERENCE_ID PRODUCTION_FLAG VARCHAR2(1) REF_CATEGORY_ID NUMBER
RECOMMENDATION VARCHAR2(50)
OBJECT_SUBTYPE DATE_LAST_UPDATED DATE
OBJECT_SUBTYPE_ID NUMBER EMAIL_NOTIFY_AUTHOR VARCHAR2(100)
OBJECT_TYPE VARCHAR2(85) EMAIL_NOTIFY_ADDRESS VARCHAR2(100)
OBJECT_SUBTYPE VARCHAR2(85) EMAIL_NOTIFY_UNAVAILABLE_FLAG VARCHAR2(1) REFERENCE_ID = REF_REFERENCE_ID
AUTHOR SORT_ORDER NUMBER
AUTHOR_ID NUMBER REFERENCE_ID = REFERENCE_ID
REFERENCE_ID NUMBER
FIRST_NAME VARCHAR2(100)
MIDDLE_NAME VARCHAR2(100)
LAST_NAME VARCHAR2(100)
FORE_NAME VARCHAR2(100) OBJECT_TYPE = OBJECT_TYPE
INITIALS VARCHAR2(35) OBJECT_SUBTYPE = OBJECT_SUBTYPE
SUFFIX VARCHAR2(35) OBJECT_TYPE = OBJECT_TYPE REFERENCE_ID = REFERENCE_ID REFERENCE_ID = REFERENCE_ID REFERENCE_REFERENCE_ASSOC
OBJECT_SUBTYPE = OBJECT_SUB_TYPE
COLLECTIVE_NAME VARCHAR2(100) REFERENCE_REFERENCE_ASSOC_ID NUMBER
OBJECT_TYPE = CHEM_TYPE REFERENCE_ID NUMBER
OBJECT_SUBTYPE = CHEM_SUBTYPE REF_REFERENCE_ID NUMBER
COMMENTS VARCHAR2(2000)

REFERENCE_ID = REFERENCE_ID
OBJECT
EPITOPE
CHEM_TYPE_MAPPING OBJECT_ID NUMBER
EPITOPE_ID NUMBER
REFERENCE_ID NUMBER CONTACT
CHEM_TYPE_MAPPING_ID NUMBER REFERENCE_ID NUMBER
OBJECT_TYPE VARCHAR2(200) CONTACT_ID NUMBER
OBJECT_TYPE VARCHAR2(85) E_NAME VARCHAR2(85)
OBJECT_SUB_TYPE VARCHAR2(200) CONTACT_NAME VARCHAR2(85)
OBJECT_SUBTYPE VARCHAR2(85) E_LOCATION VARCHAR2(100)
OBJECT_DESCRIPTION VARCHAR2(535) CONTACT_EMAIL VARCHAR2(85)
CHEM_TYPE VARCHAR2(85) E_REGION_DOMAIN_FLAG VARCHAR2(200)
DERIVATIVE_TYPE VARCHAR2(500) PHONE_NUMBER VARCHAR2(85)
CHEM_SUBTYPE VARCHAR2(85) E_COMMENTS VARCHAR2(2000) REFERENCE_ID = REFERENCE_ID
ORGANISM_ID NUMBER INSTITUTION VARCHAR2(200)
E_OBJECT_ID NUMBER
ORGANISM_NAME VARCHAR2(250)
E_OBJECT_SUB_TYPE VARCHAR2(200)
ORGANISM2_ID NUMBER
E_OBJECT_MOL_NAME VARCHAR2(535)
ORGANISM2_NAME VARCHAR2(250)
E_OBJECT_ORGANISM_NAME VARCHAR2(250)
REGION VARCHAR2(1000)
E_OBJECT_DESC VARCHAR2(535)
STARTING_POSITION NUMBER
SMILES_IMAGE_MAPPING RELATED_OBJECT_ID NUMBER CONTACT_ID = CONTACT_ID
ENDING_POSITION NUMBER
RELATED_OBJECT_TYPE VARCHAR2(200)
MAPPING_ID NUMBER CELL_NAME VARCHAR2(85)
RELATED_OBJECT_SUB_TYPE VARCHAR2(200)
SMILES_STRUCTURE VARCHAR2(3500) CELL_TYPE VARCHAR2(85)
RELATED_OBJECT_MOL_NAME VARCHAR2(535)
IMAGE BLOB TISSUE_TYPE VARCHAR2(85)
RELATED_OBJECT_ORGANISM_NAME VARCHAR2(250) CONTACT_REFERENCE_ASSOC
ORIGIN VARCHAR2(85)
RELATED_OBJECT_DESC VARCHAR2(535)
MOL1_SEQ VARCHAR2(2000) CONTACT_ID NUMBER
E_EV VARCHAR2(100)
MOL1_MODIFIED_SEQ VARCHAR2(4000) REFERENCE_ID NUMBER
E_REF_START NUMBER
MOL1_MODIFICATION VARCHAR2(85)
SOURCE_ID = MOL1_SOURCE_ID E_REF_END NUMBER
MOL1_SOURCE_ID NUMBER
E_REF_REGION VARCHAR2(2000)
MOL1_NAME VARCHAR2(250)
MOL1_ACCESSION VARCHAR2(15)
MOL2_MODIFIED_SEQ VARCHAR2(4000)
SOURCE : 1
MOL2_MODIFICATION VARCHAR2(85)
SOURCE_ID NUMBER MOL2_SOURCE_ID NUMBER OBJECT_ID = E_OBJECT_ID
ACCESSION VARCHAR2(15) ORG_ORGANISM_ID NUMBER OBJECT_ID = RELATED_OBJECT_ID
DATABASE VARCHAR2(15) MOL2_NAME VARCHAR2(250) COMPLEX
NAME VARCHAR2(250) MOL2_ACCESSION VARCHAR2(15)
ALIASES VARCHAR2(500) COMPLEX_ID NUMBER
MOL2_CHEMICAL_TYPE VARCHAR2(85) REFERENCE_ID NUMBER
CHEMICAL_TYPE VARCHAR2(85) SOURCE_MOLECULE_NAME VARCHAR2(535)
SOURCE_ID = MOL2_SOURCE_ID ATOM_PAIRS CLOB
SOURCE_DATE DATE MULT_CHAIN_MOL_NAME VARCHAR2(85)
SEQUENCE CLOB PDB_ID VARCHAR2(35)
CARRIER_ID NUMBER PDB_CELL_CONTACT_AREA NUMBER
SMILES_STRUCTURE VARCHAR2(3500) ANTIGEN_ID NUMBER
SYNONYMS CLOB E_CONTACT_AREA NUMBER
IMMUNOGEN_ID NUMBER E_VIEWER_STATUS VARCHAR2(25)
ORGANISM_ID NUMBER EPITOPE_ID NUMBER
ORGANISM_NAME VARCHAR2(150) AB_C1_PDB_CHAIN VARCHAR2(10)
CHEBI_INCHI VARCHAR2(2000) AB_C2_PDB_CHAIN VARCHAR2(10)
CHEBI_INFO_UPDATE DATE MHC_C1_PDB_CHAIN VARCHAR2(10)
CHEBI_INFO_UNAVAIL DATE PDB_ID_LIST MHC_C2_PDB_CHAIN VARCHAR2(10)
PARENT_CHEBI_ACCESSION VARCHAR2(15) IDCODE VARCHAR2(255) TCR_C1_PDB_CHAIN VARCHAR2(10)
TCR_C2_PDB_CHAIN VARCHAR2(10)
ANT_PDB_CHAIN VARCHAR2(10)
E_PDB_CHAIN VARCHAR2(10)
ORGANISM_ID = ORGANISM_ID
ORGANISM_ID = ORGANISM2_ID E_RESIDUES VARCHAR2(1000)
AB_ANT_RESIDUES VARCHAR2(1000)
E_MHC_RESIDUES VARCHAR2(1000)
ICD10_CODES E_TCR_RESIDUES VARCHAR2(1000)
ALLERGEN_NODES CODE VARCHAR2(5) MHC_E_RESIDUES VARCHAR2(1000)
TAX_ID NUMBER DESCRIPTION VARCHAR2(200) MHC_TCR_RESIDUES VARCHAR2(1000)
PARENT_TAX_ID NUMBER TCR_E_RESIDUES VARCHAR2(1000)
SCIENTIFIC_NAME VARCHAR2(150) TCR_MHC_RESIDUES VARCHAR2(1000)
PATH VARCHAR2(500) CALC_ATOM_PAIRS CLOB
ORGANISM
COMMON_NAME VARCHAR2(150) CALC_E_CONTACT_AREA FLOAT(126)
ORGANISM_ID NUMBER CALC_CELL_CONTACT_AREA FLOAT(126)
RANK VARCHAR2(50)
TAX_ID NUMBER CALC_E_RESIDUES VARCHAR2(1000)
NCBI_PATH VARCHAR2(500) RESOURCES_LINKS
PARENT_TAX_ID NUMBER CALC_AB_ANT_RESIDUES VARCHAR2(1000)
ACTIVE_NODE NUMBER
ACTIVE_NODE NUMBER URL VARCHAR2(200)
CALC_E_MHC_RESIDUES VARCHAR2(1000)
SCIENTIFIC_NAME VARCHAR2(150) TITLE VARCHAR2(400)
CALC_E_TCR_RESIDUES VARCHAR2(1000)
PATH VARCHAR2(500) DESCRIPTION VARCHAR2(2000)
CALC_MHC_E_RESIDUES VARCHAR2(1000)
NAME_EXTENSION VARCHAR2(85) STATUS VARCHAR2(15)
COMMON_NODES CALC_MHC_TCR_RESIDUES VARCHAR2(1000)
ORGANISM_NAME VARCHAR2(150) CATEGORY VARCHAR2(200)
CALC_TCR_E_RESIDUES VARCHAR2(1000)
TAX_ID NUMBER RANK VARCHAR2(50) DATE_ADDED DATE
CALC_TCR_MHC_RESIDUES VARCHAR2(1000)
NAME VARCHAR2(150) DEPTH NUMBER LAST_UPDATED DATE
COMMENTS VARCHAR2(2000)
FINDER_TYPE VARCHAR2(30) PARENT_TAX_ID_STRING VARCHAR2(50) ATTEMPTS NUMBER
COMPLEX_TYPE VARCHAR2(15)
TYPE_FLAG VARCHAR2(10)
C1_TYPE VARCHAR2(15)
C2_TYPE VARCHAR2(15)
ORGANISM_ID = ORGANISM_NCBI_TAX_ID MHC_CHAIN1 VARCHAR2(15)
MHC_CHAIN2 VARCHAR2(15)
MHC_ALLELE_RESTRICTION ORGANISM_ID = ORGANISM_ID

MHC_ALLELE_RESTRICTION_ID NUMBER
DISPLAYED_RESTRICTION VARCHAR2(85) ORGANISM_ID = TAX_ID
SYNONYMS VARCHAR2(200)
INCLUDES VARCHAR2(85)
RESTRICTION_LEVEL VARCHAR2(35) SOURCE : 2
ORGANISM VARCHAR2(150)
SOURCE_ID NUMBER
ORGANISM_NCBI_TAX_ID NUMBER
ACCESSION VARCHAR2(15)
CLASS VARCHAR2(35)
DATABASE VARCHAR2(15)
HAPLOTYPE VARCHAR2(10)
NAME VARCHAR2(250)
LOCUS VARCHAR2(10) NAMES
ALIASES VARCHAR2(500)
SEROTYPE VARCHAR2(10) TAX_ID NUMBER CHEMICAL_TYPE VARCHAR2(85)
MOLECULE VARCHAR2(35) NAME_TXT VARCHAR2(150) SOURCE_DATE DATE
CHAIN_I_NAME VARCHAR2(10) UNIQUE_NAME VARCHAR2(150) SEQUENCE CLOB
CHAIN_II_NAME VARCHAR2(10) NAME_CLASS VARCHAR2(50) SMILES_STRUCTURE VARCHAR2(3500)
CHAIN_I_LOCUS VARCHAR2(10)
SYNONYMS CLOB
CHAIN_I_MUTATION VARCHAR2(35)
ORGANISM_ID NUMBER
CHAIN_II_LOCUS VARCHAR2(10)
ORGANISM_NAME VARCHAR2(150)
CHAIN_II_MUTATION VARCHAR2(35)
CHEBI_INCHI VARCHAR2(2000)
CHAIN_I_SOURCE_ID NUMBER
CHEBI_INFO_UPDATE DATE
CHAIN_II_SOURCE_ID NUMBER
CHEBI_INFO_UNAVAIL DATE
IRI VARCHAR2(100)
PARENT_CHEBI_ACCESSION VARCHAR2(15)

Figure 3-3. IEDB Reference and Base Physical Data Model

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3.6.2 IEDB TCell Data Model

Figure 3-4 represents T cell assay data and its direct table relationships.
TCELL
TCELL_ID NUMBER
REFERENCE_ID NUMBER
EPITOPE_ID NUMBER
AS_LOCATION VARCHAR2(100)
EPITOPE AS_TYPE_ID NUMBER REFERENCE
AS_CHAR_VALUE VARCHAR2(50) REFERENCE_ID NUMBER
EPITOPE_ID NUMBER
AS_NUM_VALUE NUMBER REFERENCE_TYPE VARCHAR2(15)
REFERENCE_ID NUMBER
AS_INEQUALITY VARCHAR2(5) A_C_PATHOGEN_FLAG VARCHAR2(5)
E_NAME VARCHAR2(85)
AS_NUM_SUBJECTS NUMBER SVM_CLASSIFIER_SCORE NUMBER
E_LOCATION VARCHAR2(100)
AS_NUM_RESPONDED NUMBER CURATION_STATUS VARCHAR2(100)
E_REGION_DOMAIN_FLAG VARCHAR2(200)
AS_RESPONSE_FREQUENCY NUMBER REFERENCE_ID = REFERENCE_ID CURRENT_USER_ID NUMBER
E_COMMENTS VARCHAR2(2000)
EPITOPE_ID = EPITOPE_ID AS_IMMUNIZATION_COMMENTS VARCHAR2(2000) CURATION_KEYWORDS VARCHAR2(2000)
E_OBJECT_ID NUMBER
AS_COMMENTS VARCHAR2(2000) CURATEDBY VARCHAR2(85)
E_OBJECT_SUB_TYPE VARCHAR2(200)
AS_ANT_CONFORMATION VARCHAR2(20) DIFFICULTY VARCHAR2(10)
E_OBJECT_MOL_NAME VARCHAR2(535)
H_ORGANISM_ID NUMBER LAST_REVIEWER NUMBER
E_OBJECT_ORGANISM_NAME VARCHAR2(250)
H_ORGANISM_NAME VARCHAR2(250) PRODUCTION_FLAG VARCHAR2(1)
E_OBJECT_DESC VARCHAR2(535)
H_SEX VARCHAR2(10) RECOMMENDATION VARCHAR2(50)
RELATED_OBJECT_ID NUMBER
H_AGE VARCHAR2(85) DATE_LAST_UPDATED DATE
RELATED_OBJECT_TYPE VARCHAR2(200)
H_MHC_TYPES_PRESENT VARCHAR2(500) EMAIL_NOTIFY_AUTHOR VARCHAR2(100)
RELATED_OBJECT_SUB_TYPE VARCHAR2(200)
TCR_NAME VARCHAR2(85) EMAIL_NOTIFY_ADDRESS VARCHAR2(100)
RELATED_OBJECT_MOL_NAME VARCHAR2(535)
TCR_ORGANISM_ID NUMBER EMAIL_NOTIFY_UNAVAILABLE_FLAG VARCHAR2(1)
RELATED_OBJECT_ORGANISM_NAME VARCHAR2(250)
TCR_ORGANISM_NAME VARCHAR2(250)
RELATED_OBJECT_DESC VARCHAR2(535)
TCR_C1_TYPE VARCHAR2(85)
E_EV VARCHAR2(100)
TCR_C1_MOL_TYPE VARCHAR2(85)
E_REF_START NUMBER REFERENCE_ID = REFERENCE_ID
TCR_C2_TYPE VARCHAR2(85)
E_REF_END NUMBER
TCR_C2_MOL_TYPE VARCHAR2(85)
E_REF_REGION VARCHAR2(2000)
IV1_PROCESS_TYPE VARCHAR2(85) RECEPTOR
IV1_ADJUVANTS VARCHAR2(400) RECEPTOR_ID NUMBER
IV1_ROUTE VARCHAR2(35) REFERENCE_ID NUMBER
IV1_DOSE_SCHEDULE VARCHAR2(250) REF_NAME VARCHAR2(200)
IV1_ICD10 VARCHAR2(5) STABLE_ID NUMBER
IV1_DISEASE_NAME VARCHAR2(200) STABLE_NAME VARCHAR2(200)
IV1_DISEASE_STAGE VARCHAR2(85) SYNONYMS VARCHAR2(200)
IV1_IMM_TYPE VARCHAR2(50) RECEPTOR_ACCESSION VARCHAR2(200)
IV1_IMM_REF_NAME VARCHAR2(250) RECEPTOR_TYPE VARCHAR2(10)
IV1_IMM_OBJECT_ID NUMBER CHAIN1_TYPE VARCHAR2(10)
IV1_IMM_OBJECT_SUB_TYPE VARCHAR2(200) CHAIN1_SPECIES NUMBER
IV1_IMM_OBJECT_MOL_NAME VARCHAR2(535) CHAIN1_NUCLEOTIDE CLOB
IV1_IMM_OBJECT_ORGANISM_NAME VARCHAR2(250) CHAIN1_GENE_CALL_METHOD VARCHAR2(200)
IV1_IMM_OBJECT_DESC VARCHAR2(500) CHAIN_V_GENE_CURATED VARCHAR2(200)
IV1_IMM_EV VARCHAR2(100) CHAIN_V_GENE_CALCULATED VARCHAR2(200)
IV1_CON_OBJECT_ID NUMBER CHAIN1_D_GENE_CURATED VARCHAR2(200)
OBJECT
IV1_CON_OBJECT_SUB_TYPE VARCHAR2(200) CHAIN1_D_GENE_CALCULATED VARCHAR2(200)
OBJECT_ID NUMBER
IV1_CON_OBJECT_MOL_NAME VARCHAR2(535) CHAIN1_J_GENE_CURATED VARCHAR2(200)
REFERENCE_ID NUMBER
IV1_CON_OBJECT_ORGANISM_NAME VARCHAR2(250) CHAIN1_J_GENE_CALCULATED VARCHAR2(200)
OBJECT_TYPE VARCHAR2(200) OBJECT_ID = ANT_CON_OBJECT_ID
IV1_CON_OBJECT_DESC VARCHAR2(500) CHAIN1_FULL_SEQ CLOB
OBJECT_SUB_TYPE VARCHAR2(200)
IV2_PROCESS_TYPE VARCHAR2(85) CHAIN1_ACCESSION VARCHAR2(200)
OBJECT_DESCRIPTION VARCHAR2(535) OBJECT_ID = ANT_OBJECT_ID IV2_ADJUVANTS VARCHAR2(400) CHAIN1_CDR3_SEQ_CURATED CLOB
DERIVATIVE_TYPE VARCHAR2(500)
IV2_ROUTE VARCHAR2(35) CHAIN1_CDR3_SEQ_CALCULATED CLOB
ORGANISM_ID NUMBER
IV2_DOSE_SCHEDULE VARCHAR2(250) CHAIN1_CDR3_CALL_METHOD VARCHAR2(200)
ORGANISM_NAME VARCHAR2(250) OBJECT_ID = ADT_IV_CON_OBJECT_ID IV2_ICD10 VARCHAR2(5) CHAIN2_TYPE VARCHAR2(10)
ORGANISM2_ID NUMBER
IV2_DISEASE_NAME VARCHAR2(200) CHAIN2_SPECIES NUMBER
ORGANISM2_NAME VARCHAR2(250)
OBJECT_ID = ADT_IV_IMM_OBJECT_ID IV2_DISEASE_STAGE VARCHAR2(85) CHAIN2_NUCLEOTIDE CLOB
REGION VARCHAR2(1000)
IV2_IMM_TYPE VARCHAR2(50) CHAIN2_GENE_CALL_METHOD VARCHAR2(200)
STARTING_POSITION NUMBER
IV2_IMM_REF_NAME VARCHAR2(250) CHAIN2_V_GENE_CURATED VARCHAR2(200)
ENDING_POSITION NUMBER
IV2_IMM_OBJECT_ID NUMBER CHAIN2_V_GENE_CALCULATED VARCHAR2(200)
CELL_NAME VARCHAR2(85) OBJECT_ID = IVT_CON_OBJECT_ID IV2_IMM_OBJECT_SUB_TYPE VARCHAR2(200) CHAIN2_D_GENE_CURATED VARCHAR2(200)
CELL_TYPE VARCHAR2(85)
IV2_IMM_OBJECT_MOL_NAME VARCHAR2(535) CHAIN2_D_GENE_CALCULATED VARCHAR2(200)
TISSUE_TYPE VARCHAR2(85)
IV2_IMM_OBJECT_ORGANISM_NAME VARCHAR2(250) CHAIN2_J_GENE_CURATED VARCHAR2(200)
ORIGIN VARCHAR2(85) OBJECT_ID = IV2_CON_OBJECT_ID
IV2_IMM_OBJECT_DESC VARCHAR2(500) CHAIN2_J_GENE_CALCULATED VARCHAR2(200)
MOL1_SEQ VARCHAR2(2000)
IV2_IMM_EV VARCHAR2(100) CHAIN2_FULL_SEQ CLOB
MOL1_MODIFIED_SEQ VARCHAR2(4000) OBJECT_ID = IV2_IMM_OBJECT_ID IV2_CON_OBJECT_ID NUMBER CHAIN2_ACCESSION VARCHAR2(200)
MOL1_MODIFICATION VARCHAR2(85)
IV2_CON_OBJECT_SUB_TYPE VARCHAR2(200) CHAIN2_CDR3_SEQ_CURATED CLOB
MOL1_SOURCE_ID NUMBER
IV2_CON_OBJECT_MOL_NAME VARCHAR2(535) CHAIN2_CDR3_SEQ_CALCULATED CLOB
MOL1_NAME VARCHAR2(250) OBJECT_ID = TCR_OBJECT_ID IV2_CON_OBJECT_ORGANISM_NAME VARCHAR2(250) CHAIN2_CDR3_CALL_METHOD VARCHAR2(200)
MOL1_ACCESSION VARCHAR2(15)
IV2_CON_OBJECT_DESC VARCHAR2(500)
MOL2_MODIFIED_SEQ VARCHAR2(4000)
IVT_PROCESS_TYPE VARCHAR2(85)
MOL2_MODIFICATION VARCHAR2(85) OBJECT_ID = IVT_IMM_OBJECT_ID IVT_RESPONDER_CELL_TYPE VARCHAR2(85)
MOL2_SOURCE_ID NUMBER
IVT_STIMULATOR_CELL_TYPE VARCHAR2(85)
ORG_ORGANISM_ID NUMBER RECEPTOR_ID = RECEPTOR_ID
IVT_IMM_TYPE VARCHAR2(50)
MOL2_NAME VARCHAR2(250) OBJECT_ID = IV1_CON_OBJECT_ID
IVT_IMM_REF_NAME VARCHAR2(250)
MOL2_ACCESSION VARCHAR2(15)
IVT_IMM_OBJECT_ID NUMBER TCELL_RECEPTOR
MOL2_CHEMICAL_TYPE VARCHAR2(85)
IVT_IMM_OBJECT_SUB_TYPE VARCHAR2(200) TCELL_ID = TCELL_ID
TCELL_ID NUMBER
SOURCE_MOLECULE_NAME VARCHAR2(535)
OBJECT_ID = IV1_IMM_OBJECT_ID IVT_IMM_OBJECT_MOL_NAME VARCHAR2(535) RECEPTOR_ID NUMBER
MULT_CHAIN_MOL_NAME VARCHAR2(85)
IVT_IMM_OBJECT_ORGANISM_NAME VARCHAR2(250)
CARRIER_ID NUMBER
IVT_IMM_OBJECT_DESC VARCHAR2(500)
ANTIGEN_ID NUMBER OBJECT_ID = ADT_TCR_OBJECT_ID
IVT_IMM_EV VARCHAR2(100)
IMMUNOGEN_ID NUMBER
IVT_CON_OBJECT_ID NUMBER
EPITOPE_ID NUMBER
IVT_CON_OBJECT_SUB_TYPE VARCHAR2(200)
IVT_CON_OBJECT_MOL_NAME VARCHAR2(535)
IVT_CON_OBJECT_ORGANISM_NAME VARCHAR2(250)
IVT_CON_OBJECT_DESC VARCHAR2(500) MHC_ALLELE_RESTRICTION
ADT_IV_PROCESS_TYPE VARCHAR2(85) MHC_ALLELE_RESTRICTION_ID NUMBER
ADT_IV_ADJUVANTS VARCHAR2(400) DISPLAYED_RESTRICTION VARCHAR2(85)
ADT_IV_ROUTE VARCHAR2(35) SYNONYMS VARCHAR2(200)
ADT_IV_DOSE_SCHEDULE VARCHAR2(250) INCLUDES VARCHAR2(85)
ADT_IV_ICD10 VARCHAR2(5) RESTRICTION_LEVEL VARCHAR2(35)
ADT_IV_DISEASE_NAME VARCHAR2(200) ORGANISM VARCHAR2(150)
ADT_IV_DISEASE_STAGE VARCHAR2(85) ORGANISM_NCBI_TAX_ID NUMBER
ADT_IV_IMM_TYPE VARCHAR2(50) CLASS VARCHAR2(35)
ADT_IV_IMM_REF_NAME VARCHAR2(250) HAPLOTYPE VARCHAR2(10)
ADT_IV_IMM_OBJECT_ID NUMBER LOCUS VARCHAR2(10)
ADT_IV_IMM_OBJECT_SUB_TYPE VARCHAR2(200) DISPLAYED_RESTRICTION = MHC_ALLELE_NAME SEROTYPE VARCHAR2(10)
ADT_IV_IMM_OBJECT_MOL_NAME VARCHAR2(535) MOLECULE VARCHAR2(35)
ADT_IV_IMM_OBJECT_ORGANISM_NM VARCHAR2(250) CHAIN_I_NAME VARCHAR2(10)
ADT_IV_IMM_OBJECT_DESC VARCHAR2(500) CHAIN_II_NAME VARCHAR2(10)
ADT_IV_IMM_EV VARCHAR2(100) CHAIN_I_LOCUS VARCHAR2(10)
ADT_IV_CON_OBJECT_ID NUMBER CHAIN_I_MUTATION VARCHAR2(35)
ADT_IV_CON_OBJECT_SUB_TYPE VARCHAR2(200) CHAIN_II_LOCUS VARCHAR2(10)
ADT_IV_CON_OBJECT_MOL_NAME VARCHAR2(535) CHAIN_II_MUTATION VARCHAR2(35)
ADT_IV_CON_OBJECT_ORGANISM_NM VARCHAR2(250) CHAIN_I_SOURCE_ID NUMBER
ADT_IV_CON_OBJECT_DESC VARCHAR2(500) CHAIN_II_SOURCE_ID NUMBER
ADT_TCR_NAME VARCHAR2(85) IRI VARCHAR2(100)
ADT_TCR_ORGANISM_ID NUMBER
ADT_TCR_ORGANISM_NAME VARCHAR2(250)
ADT_TCR_C1_MOL_TYPE VARCHAR2(85)
ADT_TCR_C2_MOL_TYPE VARCHAR2(85)
ADT_H_ORGANISM_ID NUMBER
ADT_H_ORGANISM_NAME VARCHAR2(250)
ADT_H_AGE VARCHAR2(85)
ADT_H_SEX VARCHAR2(10)
ADT_H_MHC_TYPES_PRESENT VARCHAR2(500)
ADT_EFFECTOR_CELL_TYPE VARCHAR2(85)
ORGANISM
ADT_EFFECTOR_TISSUE_TYPE VARCHAR2(85) ORGANISM_ID = H_ORGANISM_ID
ADT_EFFECTOR_ORIGIN VARCHAR2(85) ORGANISM_ID NUMBER
ADT_COMMENTS VARCHAR2(2000) TAX_ID NUMBER
ORGANISM_ID = APC_H_ORGANISM_ID PARENT_TAX_ID NUMBER
EFFECTOR_CELL_TYPE VARCHAR2(85)
EFFECTOR_TISSUE_TYPE VARCHAR2(85) ACTIVE_NODE NUMBER
EFFECTOR_ORIGIN VARCHAR2(85) ORGANISM_ID = ADT_TCR_ORGANISM_ID SCIENTIFIC_NAME VARCHAR2(150)
MHC_ALLELE_NAME VARCHAR2(85) PATH VARCHAR2(500)
MHC_ALLELE_EV VARCHAR2(100) NAME_EXTENSION VARCHAR2(85)
ORGANISM_ID = ADT_H_ORGANISM_ID ORGANISM_NAME VARCHAR2(150)
COMPLEX MHC_AUTOLOGOUS VARCHAR2(1)
COMPLEX_ID NUMBER APC_CELL_TYPE VARCHAR2(85) RANK VARCHAR2(50)
REFERENCE_ID NUMBER APC_TISSUE_TYPE VARCHAR2(85) DEPTH NUMBER
ORGANISM_ID = TCR_ORGANISM_ID
ATOM_PAIRS CLOB APC_ORIGIN VARCHAR2(85) PARENT_TAX_ID_STRING VARCHAR2(50)
PDB_ID VARCHAR2(35) APC_H_ORGANISM_ID NUMBER
PDB_CELL_CONTACT_AREA NUMBER APC_H_ORGANISM_NAME VARCHAR2(250)
E_CONTACT_AREA NUMBER APC_H_AGE VARCHAR2(85)
E_VIEWER_STATUS VARCHAR2(25) APC_H_SEX VARCHAR2(10)
AB_C1_PDB_CHAIN VARCHAR2(10) APC_H_MHC_TYPES_PRESENT VARCHAR2(500)
AB_C2_PDB_CHAIN VARCHAR2(10) ANT_TYPE VARCHAR2(50)
MHC_C1_PDB_CHAIN VARCHAR2(10) ANT_REF_NAME VARCHAR2(250)
MHC_C2_PDB_CHAIN VARCHAR2(10) ANT_OBJECT_ID NUMBER
TCR_C1_PDB_CHAIN VARCHAR2(10) ANT_OBJECT_SUB_TYPE VARCHAR2(200)
TCR_C2_PDB_CHAIN VARCHAR2(10) ANT_OBJECT_MOL_NAME VARCHAR2(535)
ANT_PDB_CHAIN VARCHAR2(10) ANT_OBJECT_ORGANISM_NAME VARCHAR2(250) DISEASE
E_PDB_CHAIN VARCHAR2(10) ANT_OBJECT_DESC VARCHAR2(500) DISEASE_ID = IV1_DISEASE_ID
DISEASE_ID NUMBER
E_RESIDUES VARCHAR2(1000) ANT_EV VARCHAR2(100) DISEASE_NAME VARCHAR(100)
AB_ANT_RESIDUES VARCHAR2(1000) ANT_CON_OBJECT_ID NUMBER SYNONYMS CLOB
COMPLEX_ID = COMPLEX_ID
E_MHC_RESIDUES VARCHAR2(1000) ANT_CON_OBJECT_SUB_TYPE VARCHAR2(200) DISEASE_ID = IV2_DISEASE_ID CURATION_FLAG INTEGER
E_TCR_RESIDUES VARCHAR2(1000) ANT_CON_OBJECT_MOL_NAME VARCHAR2(535) PRODUCTION_FLAG INTEGER
MHC_E_RESIDUES VARCHAR2(1000) ANT_CON_OBJECT_ORGANISM_NAME VARCHAR2(135) ACCESSION VARCHAR2(15)
MHC_TCR_RESIDUES VARCHAR2(1000) ANT_CON_OBJECT_DESC VARCHAR2(500) DISEASE_SOURCE VARCHAR2(15)
DISEASE_ID = ADT_IV_DISEASE_ID
TCR_E_RESIDUES VARCHAR2(1000) COMPLEX_ID NUMBER SORT_ORDER INTEGER
TCR_MHC_RESIDUES VARCHAR2(1000) AS_TYPE VARCHAR2(50)
CALC_ATOM_PAIRS CLOB AS_TYPE_RESPONSE VARCHAR2(85)
CALC_E_CONTACT_AREA FLOAT(126) AS_TYPE_UNITS VARCHAR2(30)
CALC_CELL_CONTACT_AREA FLOAT(126) TCR_OBJECT_ID NUMBER
CALC_E_RESIDUES VARCHAR2(1000) TCR_OBJECT_SUB_TYPE VARCHAR2(200)
CALC_AB_ANT_RESIDUES VARCHAR2(1000) TCR_OBJECT_MOL_NAME VARCHAR2(535)
CALC_E_MHC_RESIDUES VARCHAR2(1000) TCR_OBJECT_ORGANISM_NAME VARCHAR2(250)
CALC_E_TCR_RESIDUES VARCHAR2(1000) ADT_TCR_OBJECT_ID NUMBER
CALC_MHC_E_RESIDUES VARCHAR2(1000) ADT_TCR_OBJECT_SUB_TYPE VARCHAR2(200)
CALC_MHC_TCR_RESIDUES VARCHAR2(1000) ADT_TCR_OBJECT_MOL_NAME VARCHAR2(535)
ASSAY_TYPE
CALC_TCR_E_RESIDUES VARCHAR2(1000) ADT_TCR_OBJECT_ORGANISM_NAME VARCHAR2(250)
ASSAY_TYPE_ID NUMBER
CALC_TCR_MHC_RESIDUES VARCHAR2(1000) TCR_OBJECT_DESCRIPTION VARCHAR2(500)
CATEGORY VARCHAR2(50)
COMMENTS VARCHAR2(2000) ADT_TCR_OBJECT_DESCRIPTION VARCHAR2(500)
ASSAY_TYPE VARCHAR2(50)
COMPLEX_TYPE VARCHAR2(15) E_NAME VARCHAR2(85) ASSAY_TYPE_ID = AS_TYPE_ID RESPONSE VARCHAR2(85)
TYPE_FLAG VARCHAR2(10) E_OBJECT_DESC VARCHAR2(535)
UNITS VARCHAR2(30)
C1_TYPE VARCHAR2(15) MHC_ALLELE_CLASS VARCHAR2(35)
OBI_ID VARCHAR2(100)
C2_TYPE VARCHAR2(15) IV1_DISEASE_ID NUMBER
CLASS VARCHAR2(35)
MHC_CHAIN1 VARCHAR2(15) IV2_DISEASE_ID NUMBER
MHC_CHAIN2 VARCHAR2(15) ADT_IV_DISEASE_ID NUMBER
H_GAZ_ID VARCHAR2(255)
H_GAZ_NAME VARCHAR2(255)
ADT_H_GAZ_ID VARCHAR2(255)
ADT_H_GAZ_NAME VARCHAR2(255)
RECEPTOR_ID NUMBER

Figure 3-4. IEDB TCell Assay Physical Data Model

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3.6.3 IEDB BCell Data Model

Figure 3-5 represents B cell assay data and its direct table relationships.
BCELL
BCELL_ID NUMBER
EPITOPE REFERENCE_ID NUMBER
EPITOPE_ID NUMBER EPITOPE_ID NUMBER REFERENCE
REFERENCE_ID NUMBER AS_LOCATION VARCHAR2(100) REFERENCE_ID NUMBER
E_NAME VARCHAR2(85) AS_TYPE_ID NUMBER REFERENCE_TYPE VARCHAR2(15)
E_LOCATION VARCHAR2(100) AS_CHAR_VALUE VARCHAR2(50) A_C_PATHOGEN_FLAG VARCHAR2(5)
E_REGION_DOMAIN_FLAG VARCHAR2(200) AS_NUM_VALUE NUMBER SVM_CLASSIFIER_SCORE NUMBER
E_COMMENTS VARCHAR2(2000) AS_INEQUALITY VARCHAR2(5) CURATION_STATUS VARCHAR2(100)
E_OBJECT_ID NUMBER AS_NUM_SUBJECTS NUMBER CURRENT_USER_ID NUMBER
E_OBJECT_SUB_TYPE VARCHAR2(200) AS_NUM_RESPONDED NUMBER CURATION_KEYWORDS VARCHAR2(2000)
E_OBJECT_MOL_NAME VARCHAR2(535) AS_RESPONSE_FREQUENCY NUMBER CURATEDBY VARCHAR2(85)
REFERENCE_ID = REFERENCE_ID
E_OBJECT_ORGANISM_NAME VARCHAR2(250) EPITOPE_ID = EPITOPE_ID AS_IMMUNIZATION_COMMENTS VARCHAR2(2000) DIFFICULTY VARCHAR2(10)
E_OBJECT_DESC VARCHAR2(535) AS_COMMENTS VARCHAR2(2000) LAST_REVIEWER NUMBER
RELATED_OBJECT_ID NUMBER AS_ANT_CONFORMATION VARCHAR2(20) PRODUCTION_FLAG VARCHAR2(1)
RELATED_OBJECT_TYPE VARCHAR2(200) H_ORGANISM_NAME VARCHAR2(250) RECOMMENDATION VARCHAR2(50)
RELATED_OBJECT_SUB_TYPE VARCHAR2(200) H_ORGANISM_ID NUMBER DATE_LAST_UPDATED DATE
RELATED_OBJECT_MOL_NAME VARCHAR2(535) H_SEX VARCHAR2(10) EMAIL_NOTIFY_AUTHOR VARCHAR2(100)
RELATED_OBJECT_ORGANISM_NAME VARCHAR2(250) H_AGE VARCHAR2(85) EMAIL_NOTIFY_ADDRESS VARCHAR2(100)
RELATED_OBJECT_DESC VARCHAR2(535) H_MHC_TYPES_PRESENT VARCHAR2(500) EMAIL_NOTIFY_UNAVAILABLE_FLAG VARCHAR2(1)
E_EV VARCHAR2(100) IV1_PROCESS_TYPE VARCHAR2(85)
E_REF_START NUMBER IV1_ADJUVANTS VARCHAR2(400)
E_REF_END NUMBER IV1_ROUTE VARCHAR2(350)
E_REF_REGION VARCHAR2(2000) IV1_DOSE_SCHEDULE VARCHAR2(250)
IV1_ICD10 VARCHAR2(5)
IV1_DISEASE_NAME VARCHAR2(200)
IV1_DISEASE_STAGE VARCHAR2(85) REFERENCE_ID = REFERENCE_ID
IV1_IMM_TYPE VARCHAR2(50)
IV1_IMM_REF_NAME VARCHAR2(250)
IV1_IMM_OBJECT_ID NUMBER
IV1_IMM_OBJECT_SUB_TYPE VARCHAR2(200)
IV1_IMM_OBJECT_MOL_NAME VARCHAR2(535) RECEPTOR
IV1_IMM_OBJECT_ORGANISM_NAME VARCHAR2(250) RECEPTOR_ID NUMBER
IV1_IMM_OBJECT_DESC VARCHAR2(500) REFERENCE_ID NUMBER
IV1_IMM_EV VARCHAR2(100) REF_NAME VARCHAR2(200)
IV1_CON_OBJECT_ID NUMBER STABLE_ID NUMBER
IV1_CON_OBJECT_SUB_TYPE VARCHAR2(200) STABLE_NAME VARCHAR2(200)
OBJECT IV1_CON_OBJECT_MOL_NAME VARCHAR2(535) SYNONYMS VARCHAR2(200)
IV1_CON_OBJECT_ORGANISM_NAME VARCHAR2(250) RECEPTOR_ACCESSION VARCHAR2(200)
OBJECT_ID NUMBER
IV1_CON_OBJECT_DESC VARCHAR2(500) RECEPTOR_TYPE VARCHAR2(10)
REFERENCE_ID NUMBER
OBJECT_ID = IV1_CON_OBJECT_ID IV2_PROCESS_TYPE VARCHAR2(85) CHAIN1_TYPE VARCHAR2(10)
OBJECT_TYPE VARCHAR2(200)
IV2_ADJUVANTS VARCHAR2(400) CHAIN1_SPECIES NUMBER
OBJECT_SUB_TYPE VARCHAR2(200)
IV2_ROUTE VARCHAR2(35) CHAIN1_NUCLEOTIDE CLOB
OBJECT_DESCRIPTION VARCHAR2(535) OBJECT_ID = AB_OBJECT_ID
IV2_DOSE_SCHEDULE VARCHAR2(250) CHAIN1_GENE_CALL_METHOD VARCHAR2(200)
DERIVATIVE_TYPE VARCHAR2(500)
IV2_ICD10 VARCHAR2(5) CHAIN_V_GENE_CURATED VARCHAR2(200)
ORGANISM_ID NUMBER
IV2_DISEASE_NAME VARCHAR2(200) CHAIN_V_GENE_CALCULATED VARCHAR2(200)
ORGANISM_NAME VARCHAR2(250) OBJECT_ID = ANT_CON_OBJECT_ID
IV2_DISEASE_STAGE VARCHAR2(85) CHAIN1_D_GENE_CURATED VARCHAR2(200)
ORGANISM2_ID NUMBER
IV2_IMM_TYPE VARCHAR2(50) CHAIN1_D_GENE_CALCULATED VARCHAR2(200)
ORGANISM2_NAME VARCHAR2(250)
IV2_IMM_REF_NAME VARCHAR2(250) CHAIN1_J_GENE_CURATED VARCHAR2(200)
REGION VARCHAR2(1000) OBJECT_ID = IV1_IMM_OBJECT_ID IV2_IMM_OBJECT_ID NUMBER CHAIN1_J_GENE_CALCULATED VARCHAR2(200)
STARTING_POSITION NUMBER
IV2_IMM_OBJECT_SUB_TYPE VARCHAR2(200) CHAIN1_FULL_SEQ CLOB
ENDING_POSITION NUMBER
IV2_IMM_OBJECT_MOL_NAME VARCHAR2(535) CHAIN1_ACCESSION VARCHAR2(200)
CELL_NAME VARCHAR2(85)
OBJECT_ID = ANT_OBJECT_ID IV2_IMM_OBJECT_ORGANISM_NAME VARCHAR2(250) CHAIN1_CDR3_SEQ_CURATED CLOB
CELL_TYPE VARCHAR2(85)
IV2_IMM_OBJECT_DESC VARCHAR2(500) CHAIN1_CDR3_SEQ_CALCULATED CLOB
TISSUE_TYPE VARCHAR2(85)
IV2_IMM_EV VARCHAR2(3500) CHAIN1_CDR3_CALL_METHOD VARCHAR2(200)
ORIGIN VARCHAR2(85)
OBJECT_ID = ADT_AB_OBJECT_ID
IV2_CON_OBJECT_ID NUMBER CHAIN2_TYPE VARCHAR2(10)
MOL1_SEQ VARCHAR2(2000)
IV2_CON_OBJECT_SUB_TYPE VARCHAR2(200) CHAIN2_SPECIES NUMBER
MOL1_MODIFIED_SEQ VARCHAR2(4000)
IV2_CON_OBJECT_MOL_NAME VARCHAR2(535) CHAIN2_NUCLEOTIDE CLOB
MOL1_MODIFICATION VARCHAR2(85)
IV2_CON_OBJECT_ORGANISM_NAME VARCHAR2(250) CHAIN2_GENE_CALL_METHOD VARCHAR2(200)
MOL1_SOURCE_ID NUMBER
OBJECT_ID = IV2_IMM_OBJECT_ID IV2_CON_OBJECT_DESC VARCHAR2(500) CHAIN2_V_GENE_CURATED VARCHAR2(200)
MOL1_NAME VARCHAR2(250)
AB_NAME VARCHAR2(200) CHAIN2_V_GENE_CALCULATED VARCHAR2(200)
MOL1_ACCESSION VARCHAR2(15)
AB_ORGANISM_ID NUMBER CHAIN2_D_GENE_CURATED VARCHAR2(200)
MOL2_MODIFIED_SEQ VARCHAR2(4000)
AB_ORGANISM_NAME VARCHAR2(250) CHAIN2_D_GENE_CALCULATED VARCHAR2(200)
MOL2_MODIFICATION VARCHAR2(85)
AB_TYPE VARCHAR2(35) CHAIN2_J_GENE_CURATED VARCHAR2(200)
MOL2_SOURCE_ID NUMBER OBJECT_ID = ADT_IV_IMM_OBJECT_ID
AB_MATERIALS_ASSAYED VARCHAR2(600) CHAIN2_J_GENE_CALCULATED VARCHAR2(200)
ORG_ORGANISM_ID NUMBER
AB_IMMUNOGLOBULIN_DOMAIN VARCHAR2(85) CHAIN2_FULL_SEQ CLOB
MOL2_NAME VARCHAR2(250)
AB_C1_MOL_TYPE VARCHAR2(85) CHAIN2_ACCESSION VARCHAR2(200)
MOL2_ACCESSION VARCHAR2(15)
OBJECT_ID = ADT_IV_CON_OBJECT_ID AB_C1_ISOTYPE VARCHAR2(20) CHAIN2_CDR3_SEQ_CURATED CLOB
MOL2_CHEMICAL_TYPE VARCHAR2(85)
AB_C2_MOL_TYPE VARCHAR2(85) CHAIN2_CDR3_SEQ_CALCULATED CLOB
SOURCE_MOLECULE_NAME VARCHAR2(535)
AB_C2_ISOTYPE VARCHAR2(20) CHAIN2_CDR3_CALL_METHOD VARCHAR2(200)
MULT_CHAIN_MOL_NAME VARCHAR2(85)
ADT_IV_PROCESS_TYPE VARCHAR2(85)
CARRIER_ID NUMBER OBJECT_ID = IV2_CON_OBJECT_ID ADT_IV_ADJUVANTS VARCHAR2(400)
ANTIGEN_ID NUMBER
ADT_IV_ROUTE VARCHAR2(35)
IMMUNOGEN_ID NUMBER
ADT_IV_DOSE_SCHEDULE VARCHAR2(250)
EPITOPE_ID NUMBER
ADT_IV_ICD10 VARCHAR2(5)
ADT_IV_DISEASE_NAME VARCHAR2(200)
ADT_IV_DISEASE_STAGE VARCHAR2(85)
ADT_IV_IMM_TYPE VARCHAR2(50) RECEPTOR_ID = RECEPTOR_ID
ADT_IV_IMM_REF_NAME VARCHAR2(250)
ADT_IV_IMM_OBJECT_ID NUMBER
ADT_IV_IMM_OBJECT_SUB_TYPE VARCHAR2(200)
ADT_IV_IMM_OBJECT_MOL_NAME VARCHAR2(535)
ADT_IV_IMM_OBJECT_ORGANISM_NM VARCHAR2(250)
ADT_IV_IMM_OBJECT_DESC VARCHAR2(500)
DISEASE BCELL_RECEPTOR
ADT_IV_IMM_EV VARCHAR2(100) BCELL_ID = BCELL_ID
DISEASE_ID NUMBER ADT_IV_CON_OBJECT_ID NUMBER BCELL_ID NUMBER
DISEASE_NAME VARCHAR(100) DISEASE_ID = IV1_DISEASE_ID
ADT_IV_CON_OBJECT_SUB_TYPE VARCHAR2(200) RECEPTOR_ID NUMBER
SYNONYMS CLOB ADT_IV_CON_OBJECT_MOL_NAME VARCHAR2(535)
CURATION_FLAG INTEGER DISEASE_ID = ADT_IV_DISEASE_ID ADT_IV_CON_OBJECT_ORGANISM_NM VARCHAR2(250)
PRODUCTION_FLAG INTEGER ADT_IV_CON_OBJECT_DESC VARCHAR2(500)
ACCESSION VARCHAR2(15) ADT_AB_NAME VARCHAR2(200)
DISEASE_ID = IV2_DISEASE_ID
DISEASE_SOURCE VARCHAR2(15) ADT_AB_TYPE VARCHAR2(35)
SORT_ORDER INTEGER ADT_AB_MATERIALS_ASSAYED VARCHAR2(600)
ADT_AB_IMMUNOGLOBULIN_DOMAIN VARCHAR2(85)
ADT_AB_C1_MOL_TYPE VARCHAR2(85)
ADT_AB_C2_MOL_TYPE VARCHAR2(85)
ADT_H_ORGANISM_NAME VARCHAR2(250)
ADT_H_ORGANISM_ID NUMBER
ADT_H_AGE VARCHAR2(85)
ADT_H_SEX VARCHAR2(10)
ADT_H_MHC_TYPES_PRESENT VARCHAR2(500)
COMPLEX ORGANISM
ADT_COMMENTS VARCHAR2(2000)
COMPLEX_ID NUMBER ORGANISM_ID NUMBER
ANT_TYPE VARCHAR2(50)
REFERENCE_ID NUMBER ORGANISM_ID = AB_ORGANISM_ID TAX_ID NUMBER
ANT_REF_NAME VARCHAR2(250)
ATOM_PAIRS CLOB PARENT_TAX_ID NUMBER
ANT_OBJECT_ID NUMBER
PDB_ID VARCHAR2(35) ACTIVE_NODE NUMBER
ANT_OBJECT_SUB_TYPE VARCHAR2(200)
PDB_CELL_CONTACT_AREA NUMBER SCIENTIFIC_NAME VARCHAR2(150)
ANT_OBJECT_MOL_NAME VARCHAR2(535) ORGANISM_ID = ADT_H_ORGANISM_ID
E_CONTACT_AREA NUMBER PATH VARCHAR2(500)
ANT_OBJECT_ORGANISM_NAME VARCHAR2(250)
E_VIEWER_STATUS VARCHAR2(25) NAME_EXTENSION VARCHAR2(85)
ANT_OBJECT_DESC VARCHAR2(500)
AB_C1_PDB_CHAIN VARCHAR2(10) ORGANISM_NAME VARCHAR2(150)
ANT_EV VARCHAR2(100)
AB_C2_PDB_CHAIN VARCHAR2(10) ORGANISM_ID = H_ORGANISM_ID RANK VARCHAR2(50)
ANT_CON_OBJECT_ID NUMBER
MHC_C1_PDB_CHAIN VARCHAR2(10) DEPTH NUMBER
ANT_CON_OBJECT_SUB_TYPE VARCHAR2(200)
MHC_C2_PDB_CHAIN VARCHAR2(10) PARENT_TAX_ID_STRING VARCHAR2(50)
ANT_CON_OBJECT_MOL_NAME VARCHAR2(535)
TCR_C1_PDB_CHAIN VARCHAR2(10)
ANT_CON_OBJECT_ORGANISM_NAME VARCHAR2(250)
TCR_C2_PDB_CHAIN VARCHAR2(10) COMPLEX_ID = COMPLEX_ID ANT_CON_OBJECT_DESC VARCHAR2(500)
ANT_PDB_CHAIN VARCHAR2(10)
COMPLEX_ID NUMBER
E_PDB_CHAIN VARCHAR2(10)
AS_TYPE VARCHAR2(50)
E_RESIDUES VARCHAR2(1000)
AS_TYPE_RESPONSE VARCHAR2(85)
AB_ANT_RESIDUES VARCHAR2(1000)
AS_TYPE_UNITS VARCHAR2(30)
E_MHC_RESIDUES VARCHAR2(1000)
AB_OBJECT_ID NUMBER
E_TCR_RESIDUES VARCHAR2(1000)
AB_OBJECT_SUB_TYPE VARCHAR2(200)
MHC_E_RESIDUES VARCHAR2(1000)
AB_OBJECT_MOL_NAME VARCHAR2(535)
MHC_TCR_RESIDUES VARCHAR2(1000)
AB_OBJECT_ORGANISM_NAME VARCHAR2(250)
TCR_E_RESIDUES VARCHAR2(1000) ASSAY_TYPE
ADT_AB_OBJECT_ID NUMBER
TCR_MHC_RESIDUES VARCHAR2(1000) ASSAY_TYPE_ID NUMBER
ADT_AB_OBJECT_SUB_TYPE VARCHAR2(200)
CALC_ATOM_PAIRS CLOB CATEGORY VARCHAR2(50)
ADT_AB_OBJECT_MOL_NAME VARCHAR2(535)
CALC_E_CONTACT_AREA FLOAT(126) ASSAY_TYPE VARCHAR2(50)
ADT_AB_OBJECT_ORGANISM_NAME VARCHAR2(250) ASSAY_TYPE_ID = AS_TYPE_ID
CALC_CELL_CONTACT_AREA FLOAT(126) RESPONSE VARCHAR2(85)
AB_OBJECT_DESCRIPTION VARCHAR2(500)
CALC_E_RESIDUES VARCHAR2(1000) UNITS VARCHAR2(30)
ADT_AB_OBJECT_DESCRIPTION VARCHAR2(500)
CALC_AB_ANT_RESIDUES VARCHAR2(1000) OBI_ID VARCHAR2(100)
E_NAME VARCHAR2(85)
CALC_E_MHC_RESIDUES VARCHAR2(1000) CLASS VARCHAR2(35)
E_OBJECT_DESC VARCHAR2(535)
CALC_E_TCR_RESIDUES VARCHAR2(1000)
IV1_DISEASE_ID NUMBER
CALC_MHC_E_RESIDUES VARCHAR2(1000)
IV2_DISEASE_ID NUMBER
CALC_MHC_TCR_RESIDUES VARCHAR2(1000)
ADT_IV_DISEASE_ID NUMBER
H_GAZ_ID VARCHAR2(255)
H_GAZ_NAME VARCHAR2(255)
ADT_H_GAZ_ID VARCHAR2(255)
ADT_H_GAZ_NAME VARCHAR2(255)
RECEPTOR_ID NUMBER

Figure 3-5. IEDB BCell Assay Physical Data Model

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3.6.4 IEDB MHC Binding Data Model

Figure 3-6 represents MHC Binding assay data and its direct table relationships.
MHC_ALLELE_RESTRICTION
MHC_ALLELE_RESTRICTION_ID NUMBER
DISPLAYED_RESTRICTION VARCHAR2(85)
REFERENCE SYNONYMS VARCHAR2(200)
EPITOPE REFERENCE_ID NUMBER INCLUDES VARCHAR2(85)
EPITOPE_ID NUMBER REFERENCE_TYPE VARCHAR2(15) RESTRICTION_LEVEL VARCHAR2(35)
REFERENCE_ID NUMBER A_C_PATHOGEN_FLAG VARCHAR2(5) ORGANISM VARCHAR2(150)
E_NAME VARCHAR2(85) SVM_CLASSIFIER_SCORE NUMBER ORGANISM_NCBI_TAX_ID NUMBER
E_LOCATION VARCHAR2(100) CURATION_STATUS VARCHAR2(100) CLASS VARCHAR2(35)
E_REGION_DOMAIN_FLAG VARCHAR2(200) CURRENT_USER_ID NUMBER HAPLOTYPE VARCHAR2(10)
E_COMMENTS VARCHAR2(2000) CURATION_KEYWORDS VARCHAR2(2000) LOCUS VARCHAR2(10)
E_OBJECT_ID NUMBER CURATEDBY VARCHAR2(85) SEROTYPE VARCHAR2(10)
E_OBJECT_SUB_TYPE VARCHAR2(200) DIFFICULTY VARCHAR2(10) MOLECULE VARCHAR2(35)
E_OBJECT_MOL_NAME VARCHAR2(535) LAST_REVIEWER NUMBER CHAIN_I_NAME VARCHAR2(10)
E_OBJECT_ORGANISM_NAME VARCHAR2(250) PRODUCTION_FLAG VARCHAR2(1) CHAIN_II_NAME VARCHAR2(10)
E_OBJECT_DESC VARCHAR2(535) RECOMMENDATION VARCHAR2(50) CHAIN_I_LOCUS VARCHAR2(10)
RELATED_OBJECT_ID NUMBER DATE_LAST_UPDATED DATE CHAIN_I_MUTATION VARCHAR2(35)
RELATED_OBJECT_TYPE VARCHAR2(200) EMAIL_NOTIFY_AUTHOR VARCHAR2(100) CHAIN_II_LOCUS VARCHAR2(10)
RELATED_OBJECT_SUB_TYPE VARCHAR2(200) EMAIL_NOTIFY_ADDRESS VARCHAR2(100) CHAIN_II_MUTATION VARCHAR2(35)
RELATED_OBJECT_MOL_NAME VARCHAR2(535) EMAIL_NOTIFY_UNAVAILABLE_FLAG VARCHAR2(1) CHAIN_I_SOURCE_ID NUMBER
RELATED_OBJECT_ORGANISM_NAME VARCHAR2(250) CHAIN_II_SOURCE_ID NUMBER
RELATED_OBJECT_DESC VARCHAR2(535) IRI VARCHAR2(100)
E_EV VARCHAR2(100)
DISPLAYED_RESTRICTION = MHC_ALLELE_NAME
E_REF_START NUMBER
E_REF_END NUMBER REFERENCE_ID = REFERENCE_ID
E_REF_REGION VARCHAR2(2000) COMPLEX
EPITOPE_ID = EPITOPE_ID
COMPLEX_ID NUMBER
REFERENCE_ID NUMBER
MHC_BIND
ATOM_PAIRS CLOB
MHC_BIND_ID NUMBER PDB_ID VARCHAR2(35)
REFERENCE_ID NUMBER PDB_CELL_CONTACT_AREA NUMBER
EPITOPE_ID NUMBER E_CONTACT_AREA NUMBER
AS_LOCATION VARCHAR2(100) E_VIEWER_STATUS VARCHAR2(25)
AS_TYPE_ID NUMBER AB_C1_PDB_CHAIN VARCHAR2(10)
AS_CHAR_VALUE VARCHAR2(50) AB_C2_PDB_CHAIN VARCHAR2(10)
AS_NUM_VALUE NUMBER MHC_C1_PDB_CHAIN VARCHAR2(10)
AS_INEQUALITY VARCHAR2(5) MHC_C2_PDB_CHAIN VARCHAR2(10)
ASSAY_TYPE AS_COMMENTS VARCHAR2(2000) TCR_C1_PDB_CHAIN VARCHAR2(10)
ASSAY_TYPE_ID NUMBER MHC_ALLELE_NAME VARCHAR2(85) TCR_C2_PDB_CHAIN VARCHAR2(10)
CATEGORY VARCHAR2(50) COMPLEX_ID NUMBER COMPLEX_ID = COMPLEX_ID
ANT_PDB_CHAIN VARCHAR2(10)
ASSAY_TYPE VARCHAR2(50) ASSAY_TYPE_ID = AS_TYPE_ID AS_TYPE VARCHAR2(50) E_PDB_CHAIN VARCHAR2(10)
RESPONSE VARCHAR2(85) AS_TYPE_RESPONSE VARCHAR2(85) E_RESIDUES VARCHAR2(1000)
UNITS VARCHAR2(30) AS_TYPE_UNITS VARCHAR2(30) AB_ANT_RESIDUES VARCHAR2(1000)
OBI_ID VARCHAR2(100) E_NAME VARCHAR2(85) E_MHC_RESIDUES VARCHAR2(1000)
CLASS VARCHAR2(35) E_OBJECT_DESC VARCHAR2(535) E_TCR_RESIDUES VARCHAR2(1000)
MHC_ALLELE_CLASS VARCHAR2(35) MHC_E_RESIDUES VARCHAR2(1000)
MHC_TCR_RESIDUES VARCHAR2(1000)
TCR_E_RESIDUES VARCHAR2(1000)
TCR_MHC_RESIDUES VARCHAR2(1000)
CALC_ATOM_PAIRS CLOB
CALC_E_CONTACT_AREA FLOAT(126)
CALC_CELL_CONTACT_AREA FLOAT(126)
CALC_E_RESIDUES VARCHAR2(1000)
CALC_AB_ANT_RESIDUES VARCHAR2(1000)
CALC_E_MHC_RESIDUES VARCHAR2(1000)
CALC_E_TCR_RESIDUES VARCHAR2(1000)
CALC_MHC_E_RESIDUES VARCHAR2(1000)
CALC_MHC_TCR_RESIDUES VARCHAR2(1000)
CALC_TCR_E_RESIDUES VARCHAR2(1000)
CALC_TCR_MHC_RESIDUES VARCHAR2(1000)
COMMENTS VARCHAR2(2000)
COMPLEX_TYPE VARCHAR2(15)
TYPE_FLAG VARCHAR2(10)
C1_TYPE VARCHAR2(15)
C2_TYPE VARCHAR2(15)
MHC_CHAIN1 VARCHAR2(15)
MHC_CHAIN2 VARCHAR2(15)

Figure 3-6. IEDB MHC Binding Assay Physical Data Model

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3.6.5 IEDB MHC Ligand Elution Data Model

Figure 3-7 represents MHC Ligand Elution assay data and its direct table relationships.
EPITOPE
EPITOPE_ID NUMBER
MHC_ELUTION
REFERENCE_ID NUMBER
REFERENCE MHC_ELUTION_ID NUMBER
E_NAME VARCHAR2(85)
REFERENCE_ID NUMBER
REFERENCE_ID NUMBER E_LOCATION VARCHAR2(100)
EPITOPE_ID NUMBER
REFERENCE_TYPE VARCHAR2(15) E_REGION_DOMAIN_FLAG VARCHAR2(200)
AS_LOCATION VARCHAR2(100)
A_C_PATHOGEN_FLAG VARCHAR2(5) E_COMMENTS VARCHAR2(2000)
AS_TYPE_ID NUMBER
SVM_CLASSIFIER_SCORE NUMBER E_OBJECT_ID NUMBER
AS_CHAR_VALUE VARCHAR2(50)
CURATION_STATUS VARCHAR2(100) E_OBJECT_SUB_TYPE VARCHAR2(200)
AS_NUM_VALUE NUMBER
CURRENT_USER_ID NUMBER E_OBJECT_MOL_NAME VARCHAR2(535)
AS_INEQUALITY VARCHAR2(5)
CURATION_KEYWORDS VARCHAR2(2000) E_OBJECT_ORGANISM_NAME VARCHAR2(250)
AS_NUM_SUBJECTS NUMBER
CURATEDBY VARCHAR2(85) REFERENCE_ID = REFERENCE_ID E_OBJECT_DESC VARCHAR2(535)
AS_NUM_RESPONDED NUMBER EPITOPE_ID = EPITOPE_ID
DIFFICULTY VARCHAR2(10) RELATED_OBJECT_ID NUMBER
AS_RESPONSE_FREQUENCY NUMBER
LAST_REVIEWER NUMBER RELATED_OBJECT_TYPE VARCHAR2(200)
AS_IMMUNIZATION_COMMENTS VARCHAR2(2000)
PRODUCTION_FLAG VARCHAR2(1) RELATED_OBJECT_SUB_TYPE VARCHAR2(200)
AS_COMMENTS VARCHAR2(2000)
RECOMMENDATION VARCHAR2(50) RELATED_OBJECT_MOL_NAME VARCHAR2(535)
H_ORGANISM_ID NUMBER
DATE_LAST_UPDATED DATE RELATED_OBJECT_ORGANISM_NAME VARCHAR2(250)
H_ORGANISM_NAME VARCHAR2(250)
EMAIL_NOTIFY_AUTHOR VARCHAR2(100) RELATED_OBJECT_DESC VARCHAR2(535)
H_SEX VARCHAR2(10)
EMAIL_NOTIFY_ADDRESS VARCHAR2(100) E_EV VARCHAR2(100)
H_AGE VARCHAR2(85)
EMAIL_NOTIFY_UNAVAILABLE_FLAG VARCHAR2(1) E_REF_START NUMBER
H_MHC_TYPES_PRESENT VARCHAR2(500)
E_REF_END NUMBER
IV1_PROCESS_TYPE VARCHAR2(85)
E_REF_REGION VARCHAR2(2000)
IV1_ADJUVANTS VARCHAR2(400)
IV1_ROUTE VARCHAR2(35)
MHC_ALLELE_RESTRICTION IV1_DOSE_SCHEDULE VARCHAR2(250)
MHC_ALLELE_RESTRICTION_ID NUMBER IV1_ICD10 VARCHAR2(5)
IV1_DISEASE_NAME VARCHAR2(200) OBJECT
DISPLAYED_RESTRICTION VARCHAR2(85)
IV1_DISEASE_STAGE VARCHAR2(85) OBJECT_ID NUMBER
SYNONYMS VARCHAR2(200)
IV1_IMM_TYPE VARCHAR2(50) REFERENCE_ID NUMBER
INCLUDES VARCHAR2(85)
IV1_IMM_REF_NAME VARCHAR2(250) OBJECT_TYPE VARCHAR2(200)
RESTRICTION_LEVEL VARCHAR2(35)
IVT_IMM_OBJECT_ID NUMBER OBJECT_SUB_TYPE VARCHAR2(200)
ORGANISM VARCHAR2(150)
IV1_IMM_OBJECT_ID NUMBER OBJECT_DESCRIPTION VARCHAR2(535)
ORGANISM_NCBI_TAX_ID NUMBER
IV1_IMM_OBJECT_SUB_TYPE VARCHAR2(200) DERIVATIVE_TYPE VARCHAR2(500)
CLASS VARCHAR2(35)
IV1_IMM_OBJECT_MOL_NAME VARCHAR2(535) ORGANISM_ID NUMBER
HAPLOTYPE VARCHAR2(10)
IV1_IMM_OBJECT_ORGANISM_NAME VARCHAR2(135) ORGANISM_NAME VARCHAR2(250)
LOCUS VARCHAR2(10) DISPLAYED_RESTRICTION = MHC_ALLELE_NAME
IV1_IMM_OBJECT_DESC VARCHAR2(500) OBJECT_ID = ANT_OBJECT_ID ORGANISM2_ID NUMBER
SEROTYPE VARCHAR2(10)
IV1_IMM_EV VARCHAR2(100) ORGANISM2_NAME VARCHAR2(250)
MOLECULE VARCHAR2(35)
IV1_CON_OBJECT_ID NUMBER REGION VARCHAR2(1000)
CHAIN_I_NAME VARCHAR2(10)
IV1_CON_OBJECT_SUB_TYPE VARCHAR2(200) STARTING_POSITION NUMBER
CHAIN_II_NAME VARCHAR2(10) OBJECT_ID = IV1_CON_OBJECT_ID
IV1_CON_OBJECT_MOL_NAME VARCHAR2(535) ENDING_POSITION NUMBER
CHAIN_I_LOCUS VARCHAR2(10)
IV1_CON_OBJECT_ORGANISM_NAME VARCHAR2(135) CELL_NAME VARCHAR2(85)
CHAIN_I_MUTATION VARCHAR2(35)
IV1_CON_OBJECT_DESC VARCHAR2(500) CELL_TYPE VARCHAR2(85)
CHAIN_II_LOCUS VARCHAR2(10)
IVT_PROCESS_TYPE VARCHAR2(85) TISSUE_TYPE VARCHAR2(85)
CHAIN_II_MUTATION VARCHAR2(35) OBJECT_ID = IV1_IMM_OBJECT_ID
IVT_IMM_TYPE VARCHAR2(50) ORIGIN VARCHAR2(85)
CHAIN_I_SOURCE_ID NUMBER
IVT_IMM_REF_NAME VARCHAR2(250) MOL1_SEQ VARCHAR2(2000)
CHAIN_II_SOURCE_ID NUMBER
IVT_IMM_OBJECT_SUB_TYPE VARCHAR2(200) MOL1_MODIFIED_SEQ VARCHAR2(4000)
IRI VARCHAR2(100)
IVT_IMM_OBJECT_MOL_NAME VARCHAR2(535) MOL1_MODIFICATION VARCHAR2(85)
IVT_IMM_OBJECT_ORGANISM_NAME VARCHAR2(135) OBJECT_ID = IVT_CON_OBJECT_ID MOL1_SOURCE_ID NUMBER
IVT_IMM_OBJECT_DESC VARCHAR2(500) MOL1_NAME VARCHAR2(250)
IVT_IMM_EV VARCHAR2(100) MOL1_ACCESSION VARCHAR2(15)
IVT_CON_OBJECT_ID NUMBER MOL2_MODIFIED_SEQ VARCHAR2(4000)
ORGANISM IVT_CON_OBJECT_SUB_TYPE VARCHAR2(200) MOL2_MODIFICATION VARCHAR2(85)
OBJECT_ID = IVT_IMM_OBJECT_ID
ORGANISM_ID NUMBER IVT_CON_OBJECT_MOL_NAME VARCHAR2(535) MOL2_SOURCE_ID NUMBER
TAX_ID NUMBER IVT_CON_OBJECT_ORGANISM_NAME VARCHAR2(135) ORG_ORGANISM_ID NUMBER
PARENT_TAX_ID NUMBER IVT_CON_OBJECT_DESC VARCHAR2(500) MOL2_NAME VARCHAR2(250)
ACTIVE_NODE NUMBER MHC_ALLELE_NAME VARCHAR2(85) MOL2_ACCESSION VARCHAR2(15)
SCIENTIFIC_NAME VARCHAR2(150) MHC_ALLELE_EV VARCHAR2(100) MOL2_CHEMICAL_TYPE VARCHAR2(85)
PATH VARCHAR2(500) ORGANISM_ID = H_ORGANISM_ID ANT_TYPE VARCHAR2(50) SOURCE_MOLECULE_NAME VARCHAR2(535)
NAME_EXTENSION VARCHAR2(85) ANT_REF_NAME VARCHAR2(250) MULT_CHAIN_MOL_NAME VARCHAR2(85)
ORGANISM_NAME VARCHAR2(150) ANT_OBJECT_ID NUMBER CARRIER_ID NUMBER
RANK VARCHAR2(50) ANT_OBJECT_SUB_TYPE VARCHAR2(200) ANTIGEN_ID NUMBER
DEPTH NUMBER ANT_OBJECT_MOL_NAME VARCHAR2(535) IMMUNOGEN_ID NUMBER
PARENT_TAX_ID_STRING VARCHAR2(50) ANT_OBJECT_ORGANISM_NAME VARCHAR2(135) EPITOPE_ID NUMBER
ANT_OBJECT_DESC VARCHAR2(500)
AS_TYPE VARCHAR2(50)
AS_TYPE_RESPONSE VARCHAR2(85)
AS_TYPE_UNITS VARCHAR2(30)
DISEASE
APC_CELL_TYPE VARCHAR2(85) ASSAY_TYPE
DISEASE_ID NUMBER
APC_TISSUE_TYPE VARCHAR2(85) ASSAY_TYPE_ID NUMBER
DISEASE_NAME VARCHAR(100)
APC_ORIGIN VARCHAR2(85) ASSAY_TYPE_ID = AS_TYPE_ID CATEGORY VARCHAR2(50)
SYNONYMS CLOB DISEASE_ID = IV1_DISEASE_ID
E_NAME VARCHAR2(85) ASSAY_TYPE VARCHAR2(50)
CURATION_FLAG INTEGER
E_OBJECT_DESC VARCHAR2(535) RESPONSE VARCHAR2(85)
PRODUCTION_FLAG INTEGER
MHC_ALLELE_CLASS VARCHAR2(35) UNITS VARCHAR2(30)
ACCESSION VARCHAR2(15)
IV1_DISEASE_ID NUMBER OBI_ID VARCHAR2(100)
DISEASE_SOURCE VARCHAR2(15)
H_GAZ_ID VARCHAR2(255) CLASS VARCHAR2(35)
SORT_ORDER INTEGER
H_GAZ_NAME VARCHAR2(255)

Figure 3-7. IEDB MHC Ligand Elution Assay Physical Data Model

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3.6.6 IEDB ChEBI Support Data Model

Figure 3-8 represents ChEBI molecule data which is downloaded locally for use within the
curation application.
SOURCE
SOURCE_ID NUMBER
ACCESSION VARCHAR2(15)
DATABASE VARCHAR2(15)
NAME VARCHAR2(250)
ALIASES VARCHAR2(500)
CHEMICAL_TYPE VARCHAR2(85) CHEBI_IMAGE_MAPPING
SOURCE_DATE DATE SOURCE_ID = SOURCE_ID
MAPPING_ID NUMBER
SEQUENCE CLOB SOURCE_ID NUMBER
SMILES_STRUCTURE VARCHAR2(3500) IMAGE BLOB
SYNONYMS CLOB
ORGANISM_ID NUMBER
ORGANISM_NAME VARCHAR2(150)
CHEBI_INCHI VARCHAR2(2000)
CHEBI_INFO_UPDATE DATE
CHEBI_INFO_UNAVAIL DATE
PARENT_CHEBI_ACCESSION VARCHAR2(15) SOURCE_ID = SOURCE_ID

SOURCE_ID = SOURCE_ID

SOURCE_ID = SOURCE_ID CHEBI_CHILDREN

CHEBI_CH_ONTOLOGY_ID NUMBER
CHEBI_FORMULAE
CHEBI_IUPAC SOURCE_ID NUMBER
CHEBI_FORMULAE_ID NUMBER CHILD_CHEBI_ID VARCHAR2(50)
CHEBI_IUPAC_ID NUMBER
SOURCE_ID NUMBER CHILD_CHEBI_NAME VARCHAR2(2000)
SOURCE_ID NUMBER
FORMULA_DATA VARCHAR2(2000) CHILD_STATUS VARCHAR2(2000)
IUPAC_DATA VARCHAR2(2000)
FORMULA_SOURCE VARCHAR2(2000) SOURCE_ID = SOURCE_ID CHILD_TYPE VARCHAR2(2000)
IUPAC_SOURCE VARCHAR2(2000)
FORMULA_TYPE VARCHAR2(2000) CHILD_CYCLIC_REL VARCHAR2(20)
IUPAC_TYPE VARCHAR2(2000)
DATE_SAVED DATE DATE_SAVED DATE
DATE_SAVED DATE

CHEBI_PARENTS
CHEBI_P_ONTOLOGY_ID NUMBER
SOURCE_ID NUMBER
PARENT_CHEBI_ID VARCHAR2(50)
PARENT_CHEBI_NAME VARCHAR2(2000)
PARENT_STATUS VARCHAR2(2000)
PARENT_TYPE VARCHAR2(2000)
PARENT_CYCLIC_REL VARCHAR2(20)
DATE_SAVED DATE

CHEBI_IUPAC_ID = CHEBI_IUPAC_ID

CHEBI_FORMULAE_ID = CHEBI_FORMULAE_ID
CHEBI_CH_ONTOLOGY_ID = CHEBI_CH_ONTOLOGY_ID

CHEBI_P_ONTOLOGY_ID = CHEBI_P_ONTOLOGY_ID

CHEBI_COMMENTS
CHEBI_COMMENTS_ID NUMBER
CHEBI_FORMULAE_ID NUMBER
CHEBI_IUPAC_ID NUMBER
CHEBI_P_ONTOLOGY_ID NUMBER
CHEBI_CH_ONTOLOGY_ID NUMBER
CHEBI_COMMENTS_DATE VARCHAR2(2000)
CHEBI_COMMENTS_TEXT VARCHAR2(2000)
DATE_SAVED DATE

Figure 3-8. IEDB ChEBI Support Physical Data Model

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3.6.7 IEDB User Data Model

Figure 3-9 represents the tables used for user authentication and authorization within the curation
application.

INTERNAL_USER
USER_ID NUMBER
USER_NAME VARCHAR2(35)
USER_FULL_NAME VARCHAR2(85)
ROLE
USER_PASSWORD VARCHAR2(85)
ROLE_ID NUMBER PASSWORD_EXPIRE_DATE DATE
ROLE_NAME VARCHAR2(35) EMAIL_ADDRESS VARCHAR2(80)
STATUS VARCHAR2(10)
INSTITUTION VARCHAR2(200)
COUNTRY VARCHAR2(80)
NUM_FAILED_LOGIN NUMBER

ROLE_ID = ROLE_ID

USER_ID = INTERNAL_USER_ID

USER_ID = USER_ID
INTERNAL_USER_ROLE_ASSN
INTERNAL_USER_ID NUMBER
ROLE_ID NUMBER

PREVIOUS_PASSWORD
PREVIOUS_PASSWORD_ID NUMBER
USER_ID NUMBER
PASSWORD VARCHAR2(85)
PASSWORD_EXPIRE_DATE DATE

Figure 3-9. IEDB User Data Physical Data Model

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System Architecture and Database Design Specification (v3.1)

3.6.8 IEDB Lookup Value Data Models

Figure 3-10 represents tables used to manage “list of values”. These are used within list boxes on
input forms within the curation application.

CELL_TYPE TCR_CHAIN_TYPE COUNTRY

CELL_TYPE VARCHAR2(85) TCR_CHAIN_TYPE VARCHAR2(35) COUNTRY VARCHAR2(255)
CATEGORY VARCHAR2(35) SORT_ORDER NUMBER SORT_ORDER NUMBER
SORT_ORDER NUMBER

INVIVO_PROCESS_TYPE DISEASE_STAGE
INVITRO_PROCESS_TYPE INVIVO_PROCESS_TYPE VARCHAR2(80) DISEASE_STAGE VARCHAR2(85)
INVITRO_PROCESS_TYPE VARCHAR2(80) SORT_ORDER NUMBER SORT_ORDER NUMBER
SORT_ORDER NUMBER
CATEGORY VARCHAR2(25)
RELATED_OBJECT_TYPE EVIDENCE_CODE
RELATED_OBJECT_TYPE VARCHAR2(255) EVIDENCE_CODE VARCHAR2(100)
TISSUE_TYPE
SORT_ORDER NUMBER CATEGORY VARCHAR2(25)
TISSUE VARCHAR2(85) SORT_ORDER NUMBER
CATEGORY VARCHAR2(35)
SORT_ORDER NUMBER QUALITATIVE_MEASUREMENT_TYPE
ADJUVANT
QUALITATIVE_MEASUREMENT_TYPE VARCHAR2(50)
ADJUVANT_NAME VARCHAR2(85)
SORT_ORDER NUMBER
STANDARDIZED_COMMENT SORT_ORDER NUMBER
FORM VARCHAR2(100)
STD_COMMENT VARCHAR2(300) ANTIBODY_TYPE
SORT_ORDER NUMBER ANTIBODY_TYPE VARCHAR2(255)
CONFORMATIONAL_TYPE
SORT_ORDER NUMBER
CONFORMATIONAL_TYPE VARCHAR2(85)
CHAIN_ISOTYPE
ISOTYPE VARCHAR2(20)
CLASS VARCHAR2(20)
ISOTYPE_FLAG VARCHAR2(10) ADMINISTRATION_TYPE DERIVATIVE_TYPE
SORT_ORDER NUMBER ADMINISTRATION_TYPE VARCHAR2(85) DERIVATIVE_TYPE VARCHAR2(250)
SORT_ORDER NUMBER

ORIGIN
ORIGIN VARCHAR2(85) IMMUNOGLOBULIN_DOMAIN
SORT_ORDER NUMBER THE_DOMAIN VARCHAR2(35) POST_TRANSLATION_MODIFICATION
POST_TRANS_MODIFICATION_TYPE VARCHAR2(85)
ABBREVIATION VARCHAR2(10)
REGION_DOMAIN SORT_ORDER NUMBER
REGION_DOMAIN VARCHAR2(255) IMMUNOGEN_FORM
SORT_ORDER NUMBER IMMUNOGEN_FORM VARCHAR2(30)

ROUTE
ROUTE VARCHAR2(35) IMMUNIZATION_DESCRIPTION
SORT_ORDER NUMBER ASSAY_ID NUMBER
IMMUNIZATION_DESCRIPTION VARCHAR2(1000)

MATERIALS_ASSAYED
MATERIALS_ASSAYED VARCHAR2(85)
SORT_ORDER NUMBER

Figure 3-10. IEDB Lookup Value Physical Data Model

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3.7 IEDB External Physical Data Model

Figure 3-11 represents the key areas of the IEDB External database. The following data model
represents a normalized version of the External MySQL database.

REFERENCE_CATEGORY
ASSAY_TYPE : 3
REF_CATEGORY_ID NUMBER
CATEGORY_NAME VARCHAR2(80) ASSAY_TYPE_ID NUMBER
SUBMISSION CATEGORY VARCHAR2(50)
PRIORITY NUMBER
SUBMISSION_ID NUMBER SORT_ORDER NUMBER ASSAY_TYPE VARCHAR2(50)
Physical Data Model
REFERENCE_ID NUMBER RESPONSE VARCHAR2(85)
Project : IEDB
JOURNAL SUBMITTER_NAME VARCHAR2(85) UNITS VARCHAR2(30)
SUBMISSION_DATE DATE OBI_ID VARCHAR2(100) Model : IEDB_PUBLIC
JOURNAL_ID NUMBER
SUBMISSION_AUTHORS VARCHAR2(2000) REF_CATEGORY_ID = REF_CATEGORY_ID CLASS VARCHAR2(35) Author : JRC Version 3.1 11/29/2016
JOURNAL_TITLE VARCHAR2(2000) ASSAY_TYPE_ID = CHILD_ASSAY_TYPE_ID
SUBMISSION_AFFILIATIONS VARCHAR2(2000) REFERENCE_LINKING ASSAY_TYPE_ID = CHILD_ASSAY_TYPE_ID
JOURNAL_ISSN VARCHAR2(15)
SUBMISSION_TITLE VARCHAR2(400) REFERENCE_ID NUMBER
MEDLINE_TA VARCHAR2(200) ASSAY_TYPE_ID = ASSAY_TYPE_ID
SUBMISSION_ABSTRACT VARCHAR2(4000) REFERENCE_CATEGORY_ASSOC REF_REFERENCE_ID NUMBER ASSAY_TYPE_ID = ASSAY_TYPE_ID
REFERENCE_ID NUMBER COMMENTS VARCHAR2(2000)
REF_CATEGORY_ID NUMBER TITLE VARCHAR2(1000)
JOURNAL_ID = JOURNAL_ID ASSAY_FINDER_TCELL_ANCESTRY ASSAY_TYPE_ID = ASSAY_TYPE_ID ASSAY_TYPE_ID = CHILD_ASSAY_TYPE_ID ASSAY_FINDER_BCELL_ANCESTRY
NODE_ID NUMBER NODE_ID NUMBER
COMPLEX : 2 ARTICLE ASSAY_TYPE_ID NUMBER ASSAY_TYPE_ID NUMBER
ARTICLE_ID NUMBER REFERENCE_ID = REFERENCE_ID OBI_ID VARCHAR2(1000)
COMPLEX_ID NUMBER REFERENCE_ID = REFERENCE_ID OBI_ID VARCHAR2(1000)
REFERENCE_ID NUMBER REFERENCE_ID NUMBER REFERENCE_ID = REFERENCE_ID CHILD_ASSAY_TYPE_ID NUMBER
REFERENCE_ID = REF_REFERENCE_ID CHILD_ASSAY_TYPE_ID NUMBER
ATOM_PAIRS CLOB JOURNAL_ID NUMBER CHILD_OBI_ID VARCHAR2(1000) ASSAY_FINDER_ELUTION_ANCESTRY
REFERENCE_ID = REFERENCE_ID CHILD_OBI_ID VARCHAR2(1000)
PDB_ID VARCHAR2(35) JOURNAL_VOLUME VARCHAR2(15) NODE_ID NUMBER
PDB_CELL_CONTACT_AREA NUMBER JOURNAL_ISSUE VARCHAR2(20) ASSAY_TYPE_ID NUMBER
E_CONTACT_AREA NUMBER ARTICLE_DATE VARCHAR2(35) OBI_ID VARCHAR2(1000)
E_VIEWER_STATUS VARCHAR2(25) ARTICLE_PAGES VARCHAR2(24) REFERENCE : 1 CHILD_ASSAY_TYPE_ID NUMBER
AB_C1_PDB_CHAIN VARCHAR2(10) ARTICLE_TITLE VARCHAR2(1000) REFERENCE_ID NUMBER CHILD_OBI_ID VARCHAR2(1000)
AB_C2_PDB_CHAIN VARCHAR2(10) ARTICLE_AUTHORS VARCHAR2(4000) REFERENCE_TYPE VARCHAR2(15)
ARTICLE_ABSTRACT VARCHAR2(4000) CURATION_KEYWORDS VARCHAR2(2000) GEOLOCATION : 2
MHC_C1_PDB_CHAIN VARCHAR2(10)
MHC_C2_PDB_CHAIN VARCHAR2(10) ARTICLE_AFFILIATIONS VARCHAR2(2000) GAZ_ID VARCHAR2(200)
TCR_C1_PDB_CHAIN VARCHAR2(10) ARTICLE_CHEMICAL_LIST VARCHAR2(4000) DISPLAY_NAME VARCHAR2(500)
TCR_C2_PDB_CHAIN VARCHAR2(10) ARTICLE_MESH_HEADINGS_LIST VARCHAR2(4000) REFERENCE_ID = REFERENCE_ID SECONDARY_NAMES VARCHAR2(500)
ANT_PDB_CHAIN VARCHAR2(10) MEDLINE_DATE VARCHAR2(10)
E_PDB_CHAIN VARCHAR2(10) COMMENTS VARCHAR2(2000)
E_RESIDUES VARCHAR2(1000) PUBMED_ID VARCHAR2(20
AB_ANT_RESIDUES VARCHAR2(1000) GAZ_ID = H_GAZ_ID
E_MHC_RESIDUES VARCHAR2(1000)
E_TCR_RESIDUES VARCHAR2(1000)
REFERENCE_ID = REFERENCE_ID CURATED_EPITOPE : 2 MHC_ELUTION
MHC_E_RESIDUES VARCHAR2(1000)
MHC_TCR_RESIDUES VARCHAR2(1000) CURATED_EPITOPE_ID NUMBER MHC_ELUTION_ID NUMBER
TCR_E_RESIDUES VARCHAR2(1000) REFERENCE_ID NUMBER REFERENCE_ID NUMBER
CURATED_EPITOPE_ID = CURATED_EPITOPE_ID
TCR_MHC_RESIDUES VARCHAR2(1000) E_NAME VARCHAR2(150) CURATED_EPITOPE_ID NUMBER
CALC_ATOM_PAIRS CLOB REFERENCE_ID = REFERENCE_ID E_LOCATION VARCHAR2(100) AS_LOCATION VARCHAR2(100)
REFERENCE_ID = REFERENCE_ID E_REGION_DOMAIN_FLAG VARCHAR2(200)
CALC_E_CONTACT_AREA FLOAT(126) AS_TYPE_ID NUMBER
CALC_CELL_CONTACT_AREA FLOAT(126) E_COMMENTS VARCHAR2(2000) AS_CHAR_VALUE VARCHAR2(50)
REFERENCE_ID = REFERENCE_ID
CALC_E_RESIDUES VARCHAR2(1000) E_OBJECT_ID NUMBER AS_NUM_VALUE NUMBER
CALC_AB_ANT_RESIDUES VARCHAR2(1000) RELATED_OBJECT_ID NUMBER AS_INEQUALITY VARCHAR2(5)
TCELL : 1 RELATED_OBJECT_TYPE VARCHAR2(200)
CALC_E_MHC_RESIDUES VARCHAR2(1000) CURATED_EPITOPE : 1 AS_NUM_SUBJECTS NUMBER
TCELL_ID NUMBER E_EV VARCHAR2(100)
CALC_E_TCR_RESIDUES VARCHAR2(1000) AS_NUM_RESPONDED NUMBER
CURATED_EPITOPE_ID NUMBER REFERENCE_ID NUMBER E_REF_START NUMBER
CALC_MHC_E_RESIDUES VARCHAR2(1000) AS_RESPONSE_FREQUENCY NUMBER
REFERENCE_ID NUMBER CURATED_EPITOPE_ID NUMBER E_REF_END NUMBER
CALC_MHC_TCR_RESIDUES VARCHAR2(1000) AS_IMMUNIZATION_COMMENTS VARCHAR2(2000)
E_NAME VARCHAR2(150) AS_LOCATION VARCHAR2(100) E_REF_REGION VARCHAR2(2000)
CALC_TCR_E_RESIDUES VARCHAR2(1000) AS_COMMENTS VARCHAR2(4000)
E_LOCATION VARCHAR2(100) AS_TYPE_ID NUMBER
CALC_TCR_MHC_RESIDUES VARCHAR2(1000) H_ORGANISM_ID NUMBER
E_REGION_DOMAIN_FLAG VARCHAR2(200) AS_CHAR_VALUE VARCHAR2(50)
COMMENTS VARCHAR2(2000) H_GAZ_ID VARCHAR2(255)
E_COMMENTS VARCHAR2(2000) AS_NUM_VALUE NUMBER
H_SEX VARCHAR2(10)
E_OBJECT_ID NUMBER AS_INEQUALITY VARCHAR2(5)
CURATED_EPITOPE_ID = CURATED_EPITOPE_ID CURATED_EPITOPE_ID = CURATED_EPITOPE_ID H_AGE VARCHAR2(85)
RELATED_OBJECT_ID NUMBER AS_NUM_SUBJECTS NUMBER COMPLEX : 1
H_MHC_TYPES_PRESENT VARCHAR2(1000)
RELATED_OBJECT_TYPE VARCHAR2(200) AS_NUM_RESPONDED NUMBER COMPLEX_ID NUMBER IV1_PROCESS_TYPE VARCHAR2(85)
E_EV VARCHAR2(100) AS_RESPONSE_FREQUENCY NUMBER REFERENCE_ID NUMBER IV1_ADJUVANTS VARCHAR2(400)
E_REF_START NUMBER AS_IMMUNIZATION_COMMENTS VARCHAR2(2000) ATOM_PAIRS CLOB ASSAY_TYPE : 2
COMPLEX_ID = COMPLEX_ID MHC_BIND IV1_ROUTE VARCHAR2(35)
E_REF_END NUMBER AS_COMMENTS VARCHAR2(4000) PDB_ID VARCHAR2(35)
CURATED_EPITOPE_ID = CURATED_EPITOPE_ID ASSAY_TYPE_ID NUMBER ASSAY_TYPE_ID = AS_TYPE_ID IV1_DOSE_SCHEDULE VARCHAR2(250)
E_REF_REGION VARCHAR2(2000) MHC_BIND_ID NUMBER ASSAY_TYPE_ID = AS_TYPE_ID
H_ORGANISM_ID NUMBER PDB_CELL_CONTACT_AREA NUMBER COMPLEX_ID = COMPLEX_ID CATEGORY VARCHAR2(50)
REFERENCE_ID NUMBER IV1_DISEASE_ID NUMBER
H_GAZ_ID VARCHAR2(255) E_CONTACT_AREA NUMBER ASSAY_TYPE VARCHAR2(50)
CURATED_EPITOPE_ID NUMBER IV1_DISEASE_STAGE VARCHAR2(85)
OBJECT_ID = E_OBJECT_ID OBJECT_ID = RELATED_OBJECT_ID H_SEX VARCHAR2(10) E_VIEWER_STATUS VARCHAR2(25)
AS_LOCATION VARCHAR2(100) RESPONSE VARCHAR2(85) IV1_IMM_TYPE VARCHAR2(50)
H_AGE VARCHAR2(85) AB_C1_PDB_CHAIN VARCHAR2(10) UNITS VARCHAR2(30)
BCELL AS_TYPE_ID NUMBER IV1_IMM_REF_NAME VARCHAR2(250)
H_MHC_TYPES_PRESENT VARCHAR2(1000) AB_C2_PDB_CHAIN VARCHAR2(10) OBI_ID VARCHAR2(100)
OBJECT : 1 OBJECT_ID = ANT_CON_OBJECT_ID AS_CHAR_VALUE VARCHAR2(50) IV1_IMM_OBJECT_ID NUMBER
BCELL_ID NUMBER OBJECT_ID = IV1_CON_OBJECT_ID TCR_NAME VARCHAR2(85) MHC_C1_PDB_CHAIN VARCHAR2(10)
OBJECT_ID NUMBER OBJECT_ID = ANT_OBJECT_ID AS_NUM_VALUE NUMBER CLASS VARCHAR2(35) IV1_IMM_EV VARCHAR2(100)
REFERENCE_ID NUMBER TCR_C1_MOL_TYPE VARCHAR2(85) MHC_C2_PDB_CHAIN VARCHAR2(10)
OBJECT_ID = AB_OBJECT_ID REFERENCE_ID NUMBER AS_INEQUALITY VARCHAR2(5) IV1_CON_OBJECT_ID NUMBER
CURATED_EPITOPE_ID NUMBER TCR_C2_MOL_TYPE VARCHAR2(85) TCR_C1_PDB_CHAIN VARCHAR2(10)
OBJECT_TYPE VARCHAR2(200) OBJECT_ID = ADT_IV_CON_OBJECT_ID AS_COMMENTS VARCHAR2(4000) IVT_PROCESS_TYPE VARCHAR2(85)
AS_LOCATION VARCHAR2(100) IV1_PROCESS_TYPE VARCHAR2(85) TCR_C2_PDB_CHAIN VARCHAR2(10)
OBJECT_ID = ANT_CON_OBJECT_ID OBJECT_SUB_TYPE VARCHAR2(200) MHC_ALLELE_RESTRICTION_ID NUMBER IVT_IMM_TYPE VARCHAR2(50)
AS_TYPE_ID NUMBER IV1_ADJUVANTS VARCHAR2(400) ANT_PDB_CHAIN VARCHAR2(10)
OBJECT_DESCRIPTION VARCHAR2(535) OBJECT_ID = ADT_IV_IMM_OBJECT_ID MHC_ALLELE_NAME VARCHAR2(85) IVT_IMM_REF_NAME VARCHAR2(250)
AS_CHAR_VALUE VARCHAR2(50) IV1_ROUTE VARCHAR2(35) E_PDB_CHAIN VARCHAR2(10)
OBJECT_ID = IV1_IMM_OBJECT_ID DERIVATIVE_TYPE VARCHAR2(500) COMPLEX_ID NUMBER IVT_IMM_OBJECT_ID NUMBER
AS_NUM_VALUE NUMBER IV1_DOSE_SCHEDULE VARCHAR2(250) E_RESIDUES VARCHAR2(1000)
ORGANISM_ID NUMBER OBJECT_ID = IVT_CON_OBJECT_ID MHC_ALLELE_RESTRICTION_ID = MHC_ALLELE_RESTRICTION_ID IVT_IMM_EV VARCHAR2(100)
AS_INEQUALITY VARCHAR2(5) IV1_DISEASE_ID NUMBER AB_ANT_RESIDUES VARCHAR2(1000)
OBJECT_ID = ANT_OBJECT_ID ORGANISM2_ID NUMBER IVT_CON_OBJECT_ID NUMBER
AS_NUM_SUBJECTS NUMBER IV1_DISEASE_STAGE VARCHAR2(85) E_MHC_RESIDUES VARCHAR2(1000)
REGION VARCHAR2(1000) MHC_ALLELE_RESTRICTION_ID NUMBER
AS_NUM_RESPONDED NUMBER OBJECT_ID = IV2_CON_OBJECT_ID IV1_IMM_TYPE VARCHAR2(50) E_TCR_RESIDUES VARCHAR2(1000) OBJECT_ID = ANT_OBJECT_ID MHC_ALLELE_NAME VARCHAR2(85)
AS_RESPONSE_FREQUENCY NUMBER OBJECT_ID = ADT_AB_OBJECT_ID STARTING_POSITION NUMBER IV1_IMM_REF_NAME VARCHAR2(250) MHC_E_RESIDUES VARCHAR2(1000) OBJECT : 2
ENDING_POSITION NUMBER OBJECT_ID = IV1_CON_OBJECT_ID MHC_ALLELE_EV VARCHAR2(100)
AS_IMMUNIZATION_COMMENTS VARCHAR2(2000) OBJECT_ID = IV2_IMM_OBJECT_ID IV1_IMM_OBJECT_ID NUMBER MHC_TCR_RESIDUES VARCHAR2(1000) MHC_ALLELE_RESTRICTION_ID = MHC_ALLELE_RESTRICTION_ID OBJECT_ID NUMBER
CELL_NAME VARCHAR2(85) ANT_TYPE VARCHAR2(50)
AS_COMMENTS VARCHAR2(4000) OBJECT_ID = IV2_IMM_OBJECT_ID IV1_IMM_EV VARCHAR2(100) TCR_E_RESIDUES VARCHAR2(1000) REFERENCE_ID NUMBER OBJECT_ID = IV1_IMM_OBJECT_ID ANT_REF_NAME VARCHAR2(250)
AS_ANT_CONFORMATION VARCHAR2(20) CELL_TYPE VARCHAR2(85) IV1_CON_OBJECT_ID NUMBER
OBJECT_ID = TCR_OBJECT_ID TCR_MHC_RESIDUES VARCHAR2(1000) OBJECT_TYPE VARCHAR2(200) ANT_OBJECT_ID NUMBER
H_ORGANISM_ID NUMBER TISSUE_TYPE VARCHAR2(85) IV2_PROCESS_TYPE VARCHAR2(85)
OBJECT_ID = ADT_IV_IMM_OBJECT_ID CALC_ATOM_PAIRS CLOB OBJECT_SUB_TYPE VARCHAR2(200) OBJECT_ID = IVT_CON_OBJECT_ID
APC_CELL_TYPE VARCHAR2(85)
H_GAZ_ID VARCHAR2(255) ORIGIN VARCHAR2(85) IV2_ADJUVANTS VARCHAR2(400)
OBJECT_ID = IVT_IMM_OBJECT_ID CALC_E_CONTACT_AREA FLOAT(126) OBJECT_DESCRIPTION VARCHAR2(535) APC_TISSUE_TYPE VARCHAR2(85)
H_SEX VARCHAR2(10) MOL1_SEQ VARCHAR2(4000) IV2_ROUTE VARCHAR2(35) CALC_CELL_CONTACT_AREA FLOAT(126) DERIVATIVE_TYPE VARCHAR2(500) OBJECT_ID = IVT_IMM_OBJECT_ID
MOL1_MODIFIED_SEQ VARCHAR2(4000) MHC_ALLELE_RESTRICTION APC_ORIGIN VARCHAR2(85)
H_AGE VARCHAR2(85) OBJECT_ID = ADT_IV_CON_OBJECT_ID IV2_DOSE_SCHEDULE VARCHAR2(250) CALC_E_RESIDUES VARCHAR2(1000) ORGANISM_ID NUMBER
H_MHC_TYPES_PRESENT VARCHAR2(1000) MOL1_MODIFICATION VARCHAR2(85) OBJECT_ID = IV1_CON_OBJECT_ID IV2_DISEASE_ID NUMBER
MHC_ALLELE_RESTRICTION_ID NUMBER
CALC_AB_ANT_RESIDUES VARCHAR2(1000) ORGANISM2_ID NUMBER
IV1_PROCESS_TYPE VARCHAR2(85) MOL1_SOURCE_ID NUMBER IV2_DISEASE_STAGE VARCHAR2(85)
DISPLAYED_RESTRICTION VARCHAR2(85)
OBJECT_ID = IV2_CON_OBJECT_ID CALC_E_MHC_RESIDUES VARCHAR2(1000) REGION VARCHAR2(1000)
IV1_ADJUVANTS VARCHAR2(400) MOL2_MODIFIED_SEQ VARCHAR2(4000) IV2_IMM_TYPE VARCHAR2(50)
SYNONYMS VARCHAR2(200)
OBJECT_ID = IV1_IMM_OBJECT_ID CALC_E_TCR_RESIDUES VARCHAR2(1000) STARTING_POSITION NUMBER
IV1_ROUTE VARCHAR2(350) MOL2_MODIFICATION VARCHAR2(85) IV2_IMM_REF_NAME VARCHAR2(250)
INCLUDES VARCHAR2(85)
CALC_MHC_E_RESIDUES VARCHAR2(1000) ENDING_POSITION NUMBER DISEASE_ID = IV1_DISEASE_ID
IV1_DOSE_SCHEDULE VARCHAR2(250) MOL2_SOURCE_ID NUMBER IV2_IMM_OBJECT_ID NUMBER
RESTRICTION_LEVEL VARCHAR2(35)
OBJECT_ID = ADT_TCR_OBJECT_ID CALC_MHC_TCR_RESIDUES VARCHAR2(1000) CELL_NAME VARCHAR2(85)
IV1_DISEASE_ID NUMBER MULT_CHAIN_MOL_NAME VARCHAR2(85) IV2_IMM_EV VARCHAR2(100)
ORGANISM VARCHAR2(150)
CALC_TCR_E_RESIDUES VARCHAR2(1000) CELL_TYPE VARCHAR2(85)
IV1_DISEASE_STAGE VARCHAR2(85) ORGANISM_NCBI_TAX_ID NUMBER
IV2_CON_OBJECT_ID NUMBER CALC_TCR_MHC_RESIDUES VARCHAR2(1000) TISSUE_TYPE VARCHAR2(85)
IV1_IMM_TYPE VARCHAR2(50) CLASS VARCHAR2(35)
SOURCE_ID = MOL2_SOURCE_ID IVT_PROCESS_TYPE VARCHAR2(85) COMMENTS VARCHAR2(2000) ORIGIN VARCHAR2(85)
IV1_IMM_REF_NAME VARCHAR2(250) HAPLOTYPE VARCHAR2(10)
SOURCE_ID = MOL1_SOURCE_ID IVT_RESPONDER_CELL_TYPE VARCHAR2(85) MOL1_SEQ VARCHAR2(4000)
REFERENCE : 2 IV1_IMM_OBJECT_ID NUMBER LOCUS VARCHAR2(10)
IVT_STIMULATOR_CELL_TYPE VARCHAR2(85) MOL1_MODIFIED_SEQ VARCHAR2(4000) DISEASE : 2
REFERENCE_ID NUMBER IV1_IMM_EV VARCHAR2(100) SEROTYPE VARCHAR2(10)
IVT_IMM_TYPE VARCHAR2(50) MOL1_MODIFICATION VARCHAR2(85) DISEASE_ID NUMBER
REFERENCE_TYPE VARCHAR2(15) IV1_CON_OBJECT_ID NUMBER SOURCE : 1 MOLECULE VARCHAR2(50)
IVT_IMM_REF_NAME VARCHAR2(250) MOL1_SOURCE_ID NUMBER DISEASE_NAME VARCHAR2(200)
CURATION_KEYWORDS VARCHAR2(2000) IV2_PROCESS_TYPE VARCHAR2(85) SOURCE_ID NUMBER CHAIN_I_NAME VARCHAR2(35)
IVT_IMM_OBJECT_ID NUMBER COMPLEX_ID = COMPLEX_ID MOL2_MODIFIED_SEQ VARCHAR2(4000) SYNONYMS CLOB
IV2_ADJUVANTS VARCHAR2(400) ACCESSION VARCHAR2(15) CHAIN_II_NAME VARCHAR2(35)
IVT_IMM_EV VARCHAR2(100) MOL2_MODIFICATION VARCHAR2(85) ACCESSION VARCHAR2(15)
IV2_ROUTE VARCHAR2(35) DATABASE VARCHAR2(15) CHAIN_I_LOCUS VARCHAR2(10)
IVT_CON_OBJECT_ID NUMBER MOL2_SOURCE_ID NUMBER DISEASE_SOURCE VARCHAR2(15)
IV2_DOSE_SCHEDULE VARCHAR2(250) NAME VARCHAR2(535) MHC_ALLELE_RESTRICTION_ID = MHC_ALLELE_RESTRICTION_ID CHAIN_I_MUTATION VARCHAR2(35) ORGANISM_ID = H_ORGANISM_ID
ADT_IV_PROCESS_TYPE VARCHAR2(85) MULT_CHAIN_MOL_NAME VARCHAR2(85)
IV2_DISEASE_ID NUMBER ALIASES VARCHAR2(500) CHAIN_II_LOCUS VARCHAR2(10)
REFERENCE_ID = REFERENCE_ID ORGANISM_ID = ORGANISM_ID ORGANISM_ID = ORGANISM2_ID ADT_IV_ADJUVANTS VARCHAR2(400)
IV2_DISEASE_STAGE VARCHAR2(85) CHEMICAL_TYPE VARCHAR2(85) CHAIN_II_MUTATION VARCHAR2(35)
ADT_IV_ROUTE VARCHAR2(35)
IV2_IMM_TYPE VARCHAR2(50) SOURCE_DATE DATE CHAIN_I_SOURCE_ID NUMBER
ADT_IV_DOSE_SCHEDULE VARCHAR2(250)
IV2_IMM_REF_NAME VARCHAR2(250) SEQUENCE CLOB CHAIN_II_SOURCE_ID NUMBER
ADT_IV_DISEASE_ID NUMBER DISEASE_ID = DISEASE_ID DISEASE_ID = CHILD_DISEASE_ID
RECEPTOR
IV2_IMM_OBJECT_ID NUMBER SMILES_STRUCTURE VARCHAR2(3500) ADT_IV_DISEASE_STAGE VARCHAR2(85)
RECEPTOR_ID NUMBER IV2_IMM_EV VARCHAR2(3500) SYNONYMS CLOB ADT_IV_IMM_TYPE VARCHAR2(50)
REFERENCE_ID NUMBER IV2_CON_OBJECT_ID NUMBER ORGANISM_ID NUMBER ADT_IV_IMM_REF_NAME VARCHAR2(250)
REF_NAME VARCHAR2(200) MHC_ALLELE_RESTRICTION_ID = IEDB_MHC_ID MHC_ALLELE_RESTRICTION_ID = CHILD_IEDB_MHC_ID DISEASE_ANCESTRY
AB_NAME VARCHAR2(200) ORGANISM_NAME VARCHAR2(150) ADT_IV_IMM_OBJECT_ID NUMBER
STABLE_ID NUMBER AB_TYPE VARCHAR2(35) SMILES_IMAGE BLOB DISEASE_ID NUMBER
ADT_IV_IMM_EV VARCHAR2(100)
STABLE_NAME VARCHAR2(200) AB_MATERIALS_ASSAYED VARCHAR2(600) ALLELE_FINDER_ANCESTRY CHILD_DISEASE_ID NUMBER
ADT_IV_CON_OBJECT_ID NUMBER
SYNONYMS VARCHAR2(200) AB_IMMUNOGLOBULIN_DOMAIN VARCHAR2(85) ORGANISM_ID = ORGANISM_ID NODE_ID NUMBER
ADT_TCR_NAME VARCHAR2(85)
RECEPTOR_ACCESSION VARCHAR2(200) AB_C1_MOL_TYPE VARCHAR2(85) IEDB_MHC_ID NUMBER OBJECT_ID = OBJECT_ID
ADT_TCR_ORGANISM_ID NUMBER
RECEPTOR_TYPE VARCHAR2(10) AB_C2_MOL_TYPE VARCHAR2(85) OBI_ID VARCHAR2(1000)
ORGANISM_ID = ADT_H_ORGANISM_ID ORGANISM : 2 ADT_TCR_C1_MOL_TYPE VARCHAR2(85)
CHAIN1_TYPE VARCHAR2(10) ORGANISM_ID = H_ORGANISM_ID
ADT_IV_PROCESS_TYPE VARCHAR2(85) ORGANISM_ID NUMBER ADT_TCR_C2_MOL_TYPE VARCHAR2(85) CHILD_IEDB_MHC_ID NUMBER
CHAIN1_SPECIES NUMBER ADT_IV_ADJUVANTS VARCHAR2(400) CHILD_OBI_ID VARCHAR2(1000)
PARENT_TAX_ID NUMBER ORGANISM_ID = APC_H_ORGANISM_ID ADT_H_ORGANISM_ID NUMBER
CHAIN1_NUCLEOTIDE CLOB ADT_IV_ROUTE VARCHAR2(35)
ORGANISM_ID = H_ORGANISM_ID ACTIVE_NODE NUMBER ADT_H_GAZ_ID VARCHAR2(255)
CHAIN1_GENE_CALL_METHOD VARCHAR2(200) ADT_IV_DOSE_SCHEDULE VARCHAR2(250) ORGANISM_ID = ADT_TCR_ORGANISM_ID ORGANISM : 1
PATH VARCHAR2(500) ADT_H_AGE VARCHAR2(85)
CHAIN1_V_GENE_CURATED VARCHAR2(200) ADT_IV_DISEASE_ID NUMBER ORGANISM_ID NUMBER
RANK VARCHAR2(50) ADT_H_SEX VARCHAR2(10)
CHAIN1_V_GENE_CALCULATED VARCHAR2(200) ORGANISM_ID = ADT_H_ORGANISM_ID
ADT_IV_DISEASE_STAGE VARCHAR2(85) ADT_H_MHC_TYPES_PRESENT VARCHAR2(1000) ORGANISM_ID = SOURCE_ORGANISM_ORG_ID PARENT_TAX_ID NUMBER
CHAIN1_D_GENE_CURATED VARCHAR2(200) ADT_IV_IMM_TYPE VARCHAR2(50) ACTIVE_NODE NUMBER
ADT_EFFECTOR_CELL_TYPE VARCHAR2(85)
CHAIN1_D_GENE_CALCULATED VARCHAR2(200) ADT_IV_IMM_REF_NAME VARCHAR2(250) PATH VARCHAR2(500)
ADT_EFFECTOR_TISSUE_TYPE VARCHAR2(85) EPITOPE_OBJECT
CHAIN1_J_GENE_CURATED VARCHAR2(200) ADT_IV_IMM_OBJECT_ID NUMBER ORGANISM_ID = ORGANISM_ID RANK VARCHAR2(50)
ADT_EFFECTOR_ORIGIN VARCHAR2(85) EPITOPE
CHAIN1_J_GENE_CALCULATED VARCHAR2(200) ADT_IV_IMM_EV VARCHAR2(100) EPITOPE_ID NUMBER
ADT_COMMENTS VARCHAR2(2000) EPITOPE_ID NUMBER
CHAIN1_FULL_SEQ CLOB ORGANISM_NAMES OBJECT_ID NUMBER
ADT_IV_CON_OBJECT_ID NUMBER EFFECTOR_CELL_TYPE VARCHAR2(85) DESCRIPTION VARCHAR2(535)
CHAIN1_ACCESSION VARCHAR2(200) ADT_AB_NAME VARCHAR2(200) ORGANISM_ID NUMBER SOURCE_ANTIGEN_ACCESSION VARCHAR2(50)
EFFECTOR_TISSUE_TYPE VARCHAR2(85) LINEAR_PEPTIDE_SEQ VARCHAR2(4000)
CHAIN1_CDR3_SEQ_CURATED CLOB ADT_AB_TYPE VARCHAR2(35) NAME_TXT VARCHAR2(150) SOURCE_ORGANISM_ORG_ID NUMBER
EFFECTOR_ORIGIN VARCHAR2(85) LINEAR_PEPTIDE_MODIFIED_SEQ VARCHAR2(4000)
CHAIN1_CDR3_SEQ_CALCULATED CLOB ADT_AB_MATERIALS_ASSAYED VARCHAR2(600) NAME_CLASS VARCHAR2(50) SOURCE : 2
MHC_ALLELE_RESTRICTION_ID NUMBER LINEAR_PEPTIDE_MODIFICATION VARCHAR2(85)
CHAIN1_CDR3_CALL_METHOD VARCHAR2(200) ADT_AB_IMMUNOGLOBULIN_DOMAIN VARCHAR2(85) SOURCE_ID NUMBER
MHC_ALLELE_NAME VARCHAR2(85) NON_AA_SOURCE_ID NUMBER
CHAIN2_TYPE VARCHAR2(10) ADT_AB_C1_MOL_TYPE VARCHAR2(85) ACCESSION VARCHAR2(15) EPITOPE_ID = EPITOPE_ID
MHC_ALLELE_EV VARCHAR2(100) DISC_SOURCE_ID NUMBER
CHAIN2_SPECIES NUMBER ADT_AB_C2_MOL_TYPE VARCHAR2(85) DATABASE VARCHAR2(15)
ASSAY_TYPE : 1 MHC_AUTOLOGOUS VARCHAR2(1) DISC_REGION VARCHAR2(4000)
CHAIN2_NUCLEOTIDE CLOB ADT_H_ORGANISM_ID NUMBER NAME VARCHAR2(535)
APC_CELL_TYPE VARCHAR2(85) DISC_MODIFICATION VARCHAR2(85)
CHAIN2_GENE_CALL_METHOD VARCHAR2(200) ASSAY_TYPE_ID NUMBER
ADT_H_GAZ_ID VARCHAR2(255) APC_TISSUE_TYPE VARCHAR2(85) ALIASES VARCHAR2(500) ORGANISM_ID = ORG_ID
CHAIN2_V_GENE_CURATED VARCHAR2(200) CATEGORY VARCHAR2(50) SOURCE_ID = NON_AA_SOURCE_ID MC_REGION VARCHAR2(4000)
ADT_H_AGE VARCHAR2(85) ASSAY_TYPE_ID = AS_TYPE_ID APC_ORIGIN VARCHAR2(85) CHEMICAL_TYPE VARCHAR2(85)
MC_MOL1_SOURCE_ID NUMBER ORGANISM_ID = CHILD_ORG_ID ORGANISM_ID = ORG_ID ORGANISM_ID = CHILD_ORG_ID
CHAIN2_V_GENE_CALCULATED VARCHAR2(200) ASSAY_TYPE VARCHAR2(50)
ADT_H_SEX VARCHAR2(10) ASSAY_TYPE_ID = AS_TYPE_ID APC_H_ORGANISM_ID NUMBER SOURCE_DATE DATE
MC_MOL1_MODIFICATION VARCHAR2(85)
CHAIN2_D_GENE_CURATED VARCHAR2(200) RESPONSE VARCHAR2(85)
ADT_H_MHC_TYPES_PRESENT VARCHAR2(1000) APC_H_AGE VARCHAR2(85) SEQUENCE CLOB
MC_MOL2_SOURCE_ID NUMBER
CHAIN2_D_GENE_CALCULATED VARCHAR2(200) UNITS VARCHAR2(30)
ADT_COMMENTS VARCHAR2(2000) APC_H_SEX VARCHAR2(10) SMILES_STRUCTURE VARCHAR2(3500)
MC_MOL2_MODIFICATION VARCHAR2(85)
CHAIN2_J_GENE_CURATED VARCHAR2(200) OBI_ID VARCHAR2(100)
ANT_TYPE VARCHAR2(50) APC_H_MHC_TYPES_PRESENT VARCHAR2(1000) SYNONYMS CLOB
CHAIN2_J_GENE_CALCULATED VARCHAR2(200) CLASS VARCHAR2(35)
ANT_REF_NAME VARCHAR2(250) ANT_TYPE VARCHAR2(50) ORGANISM_ID NUMBER
CHAIN2_FULL_SEQ CLOB ANT_OBJECT_ID NUMBER ORGANISM_NAME VARCHAR2(150)
ANT_REF_NAME VARCHAR2(250)
CHAIN2_ACCESSION VARCHAR2(200) ANT_EV VARCHAR2(100) DISEASE_ID = IV1_DISEASE_ID SMILES_IMAGE BLOB
ANT_OBJECT_ID NUMBER
CHAIN2_CDR3_SEQ_CURATED CLOB DISEASE : 1 DISEASE_ID = IV1_DISEASE_ID
ANT_CON_OBJECT_ID NUMBER ANT_EV VARCHAR2(100)
CHAIN2_CDR3_SEQ_CALCULATED CLOB COMPLEX_ID NUMBER DISEASE_ID = IV2_DISEASE_ID DISEASE_ID NUMBER
DISEASE_ID = IV2_DISEASE_ID ANT_CON_OBJECT_ID NUMBER ORGANISM_FINDER_SRC_ANCESTRY
CHAIN2_CDR3_CALL_METHOD VARCHAR2(200) AB_OBJECT_ID NUMBER DISEASE_NAME VARCHAR2(200) ORGANISM_FINDER_HOST_ANCESTRY
COMPLEX_ID NUMBER NODE_ID NUMBER
ADT_AB_OBJECT_ID NUMBER DISEASE_ID = ADT_IV_DISEASE_ID SYNONYMS CLOB TCR_OBJECT_ID NUMBER NODE_ID NUMBER
DISEASE_ID = ADT_IV_DISEASE_ID OBI_ID VARCHAR2(1000)
ACCESSION VARCHAR2(15) ADT_TCR_OBJECT_ID NUMBER ORG_ID NUMBER
SOURCE_ID = SOURCE_ID CHILD_ORG_ID VARCHAR2(500)
DISEASE_SOURCE VARCHAR2(15) OBI_ID VARCHAR2(1000)
ORG_ID NUMBER
TCELL : 2 SOURCE_ID = CHILD_SOURCE_ID SOURCE_ID = SOURCE_ID SOURCE_ID = CHILD_SOURCE_ID
CHILD_ORG_ID VARCHAR2(500)
GAZ_ID = H_GAZ_ID CHILD_OBI_ID VARCHAR2(1000)
TCELL_ID NUMBER GAZ_ID = ADT_H_GAZ_ID CHILD_OBI_ID VARCHAR2(1000)
RECEPTOR_ID = RECEPTOR_ID CHILD_OBI_SPECIES_OBI VARCHAR2(500)
REFERENCE_ID NUMBER BCELL_ID = BCELL_ID
GAZ_ID = H_GAZ_ID GAZ_ID = ADT_H_GAZ_ID
GEOLOCATION : 1
RECEPTOR_ID = RECEPTOR_ID
GAZ_ID VARCHAR2(200)
DISPLAY_NAME VARCHAR2(500) MOLECULE_FINDER_PROT_ANCESTRY
BCELL_RECEPTOR MOLECULE_FINDER_NONP_ANCESTRY
SECONDARY_NAMES VARCHAR2(500) NODE_ID NUMBER
TCELL_ID = TCELL_ID BCELL_ID NUMBER NODE_ID NUMBER
SOURCE_ID NUMBER
RECEPTOR_ID NUMBER SOURCE_ID NUMBER
OBI_ID VARCHAR2(1000)
OBI_ID VARCHAR2(1000)
CHILD_SOURCE_ID NUMBER
CHILD_SOURCE_ID NUMBER
GAZ_ID = OBI_ID GAZ_ID = CHILD_OBI_ID CHILD_OBI_ID VARCHAR2(1000)
CHILD_OBI_ID VARCHAR2(1000)
TCELL_RECEPTOR
RECEPTOR_ID NUMBER GEOLOC_FINDER_ANCESTRY
TCELL_ID NUMBER NODE_ID NUMBER
OBI_ID VARCHAR2(200)
CHILD_OBI_ID VARCHAR2(200)

Figure 3-11. IEDB Public External Physical Data Model

Immune Epitope Database and Analysis Resource Program 25

System Architecture and Database Design Specification (v3.1)

3.8 IEDB Analysis Resource Data Model

Figure 3-12 represents the data which is generated for use within the Analysis Resource tools.

Figure 3-12. IEDB Analysis Resource Physical Data Model

Immune Epitope Database and Analysis Resource Program 26