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
1.1 INTRODUCTION.................................................................................................................................................1
1.2 SCOPE...........................................................................................................................................................................................................1
1.3 PURPOSE......................................................................................................................................................................................................1
1.4 ASSUMPTIONS AND DEPENDENCIES.........................................................................................................1
1.5 KEY OBJECTIVES............................................................................................................................................2
1.6 CONTRACT IDENTIFICATION......................................................................................................................2
1.7 REFERENCES....................................................................................................................................................2
1.8 CHANGE PROCEDURES.................................................................................................................................3
2.1 SYSTEM ARCHITECTURE...............................................................................................................................4
2.2 SYSTEM OVERVIEW.......................................................................................................................................4
2.2.1 Document Management Overview..............................................................................................................4
2.2.2 IEDB Curation Overview............................................................................................................................4
2.2.3 IEDB External Overview............................................................................................................................6
2.2.4 IEDB Analysis Resource Overview.............................................................................................................6
2.2.4.1 T Cell Epitope Prediction Tools..........................................................................................................................7
2.2.4.2 B Cell Epitope Prediction Tools..........................................................................................................................8
2.2.4.3 Analysis Tools.....................................................................................................................................................8
2.3 HARDWARE ARCHITECTURE......................................................................................................................8
2.4 SOFTWARE COMPONENTS.........................................................................................................................11
2.5 HARDWARE AND SOFTWARE RELATIONSHIPS....................................................................................13
3.1 DATABASE DESIGN AND DATA MODELS.................................................................................................14
3.2 OVERVIEW OF THE IEDB DATABASE ARCHITECTURE.............................................................................................................14
3.3 OVERVIEW OF IEDB DATABASE DESIGN.....................................................................................................................................14
3.4 OVERVIEW IEDB DATABASE CONTENT........................................................................................................................................14
3.5 IEDB REFERENCE DATA FLOW........................................................................................................................................................15
3.6 IEDB DATABASE BACKUP PROCEDURES......................................................................................................................................16
3.7 IEDB CURATION PHYSICAL DATA MODELS................................................................................................................................17
3.7.1 IEDB Reference and Base Data Model....................................................................................................17
3.7.2 IEDB TCell D2ata Model.........................................................................................................................18
3.7.3 IEDB BCell Data Model...........................................................................................................................19
3.7.4 IEDB MHC Binding Data Model..............................................................................................................20
3.7.5 IEDB MHC Ligand Elution Data Model..................................................................................................21
3.7.6 IEDB ChEBI Support Data Model..........................................................................................................221
3.7.7 IEDB User Data Model..........................................................................................................................232
3.7.8 IEDB Lookup Value Data Models..........................................................................................................243
3.8 IEDB EXTERNAL PHYSICAL DATA MODEL...............................................................................................................................254
3.9 IEDB ANALYSIS RESOURCE DATA MODEL...............................................................................................................................265

Immune Epitope Database and Analysis Resource Program i

 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
 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
System Architecture and Database Design Specification (v3.1)

1.1 Introduction
1.2 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.

1.3 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.

1.4 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.

Immune Epitope Database and Analysis Resource Program 1

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?

1.5 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.

1.6 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).

1.7 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
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/

1.8 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).
2.1 System Architecture
2.2 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.

2.2.1 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.

2.2.2 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.
 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

 Figure 2-2. Overview Document Classifier Process

2.2.3 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.

2.2.4 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.
2.2.4.1 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.
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.

2.2.4.2 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.

2.2.4.3 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.
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.
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

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)
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)
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

3.1 Database Design and Data Models
3.2 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.

3.3 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.

3.4 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.
 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)

3.5 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
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

ETL (PAN)

NEWDB_COPY IEDB_ANALYSIS
(Rollback Area) Rollback (Tools Database)

Re-curate
ETL (PAN)

Re-curate

ETL (PAN) IEDB_QUERY_YYYYMMDD

NEWDB NEWDB_PRODUCTION IEDB_PUBLIC

(Staging Area) (Production Items) ETL (PAN)
ETL (PAN)

Promote IEDB_PRIVATE

Figure 3-2. IEDB Reference Data Flow

3.6 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.
 3.7 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.

3.7.1 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.
ACTION_LOG
ACTION_LOG_ID NUMBER
SUBMISSION
REFERENCE_ID NUMBER
SUBMISSION_ID NUMBER
USER_ID NUMBER
REFERENCE_ID NUMBER
ACTION VARCHAR2(35)
SUBMITTER_NAME VARCHAR2(85)
ACTION_DATE DATE
SUBMISSION_DATE DATE
COMMENTS VARCHAR2(200)
SUBMITTER_USER_ID NUMBER
TIME NUMBER
NOTIFICATION_FLAG VARCHAR2(1)
LEVEL_OF_EFFORT VARCHAR2(10)
SUBMISSION_AUT HORS VARCHAR2(2000)
SUBMISSION_AFFILIATIONS VARCHAR2(2000) EPITOPE_COUNT NUMBER

COMMENTS PUBMED_ID
MEDLINE_DATE
ARTICLE_MESH_HEADINGS_LIST

ARTICLE_CHEMICAL_LIST
ARTICLE_ABSTRACT ARTICLE_AFFILIATIONS
ARTICLE_AUT HORS
ARTICLE_DATE ARTICLE_PAGES ARTICLE_TITLE
JOURNAL_VOLUME JOURNAL_ISSUE
ARTICLE_ID REFERENCE_ID JOURNAL_ID
SUBMISSION_TITLE VARCHAR2(400)
SUBMISSION_ABSTRACT VARCHAR2(4000)

MEDLINE_TA
JOURNAL_ISSN VARCHAR2(15)
JOURNAL_IDNUMBER JOURNAL_TITLE VARCHAR2(2000)
SUBMISSION_PDF_FLAG VARCHAR2(1)

RE
FE
SMILES_IMAGE_MAPPING

RE
SMILES_STRUCT URE VARCHAR2(3500) IMAGEBLOB

MAPPING_ID

NC
E

JOURNAL_ID = JOURNAL_ID

VARCHAR2(200)

JOURNAL
REFERENCE_ID NUMBER
REFERENCE_TYPE VARCHAR2(15)

ARTICLE
U
A_C_PATHOGEN_FLAG VARCHAR2(5)

T
H
SVM_CLASSIFIER_SCORE NUMBER

O
CURATION_STATUS VARCHAR2(100)

R CURRENT _USER_ID NUMBER

COMMON_NODES

NUMBER
FINDER_TYPE VARCHAR2(30)
NAME
TAX_ID

VARCHAR2(20)
VARCHAR2(2000)
VARCHAR2(10)
VARCHAR2(4000)
VARCHAR2(4000)
VARCHAR2(2000)
VARCHAR2(4000)
VARCHAR2(4000)
VARCHAR2(1000)
VARCHAR2(24)

VARCHAR2(35)
VARCHAR2(20)
VARCHAR2(15)
NUMBER
NUMBER
CURATION_KEYWORDS VARCHAR2(2000)

OBJEC
T_SUB
CURATEDBY VARCHAR2(85)

TYPE
AUTHOR_ID NUMBER
DIFFICULTY VARCHAR2(10)
REFERENCE_ID NUMBER
LAST_REVIEWER NUMBER REFERENCE_REFERENCE_ASSOC
FIRST_NAME VARCHAR2(100)

NUMBER
PRODUCT ION_FLAG VARCHAR2(1) REFERENCE_REFERENCE_ASSOC_ID NUMBER
MIDDLE_NAME VARCHAR2(100)
OBJECT_SUBTYPE_ID NUMBER RECOMMENDATION VARCHAR2(50) REFERENCE_ID NUMBER
LAST_NAME VARCHAR2(100) OBJECT_TYPE VARCHAR2(85) DATE_LAST_UPDATED DATE REF_REFERENCE_ID NUMBER
VARCHAR2(150)
NUMBER

FORE_NAME VARCHAR2(100) OBJECT_SUBTYPE VARCHAR2(85) EMAIL_NOTIFY_AUTHOR VARCHAR2(100) COMMENTS VARCHAR2(2000)

INITIALS VARCHAR2(35)
SORT _ORDER
SOURCE_ID = MOL2_SOURCE_ID

NUMBER
SOURCE_ID = MOL1_SOURCE_ID

EMAIL_NOTIFY_ADDRESS VARCHAR2(100)
SUFFIX VARCHAR2(35)

EPITOPE
ORGANISM_ID = ORGANISM_NCBI_TAX_ID

CHEM_TYPE_MAPPING EPITOPE_ID NUMBER

CHEM_TYPE_MAPPING_ID NUMBER REFERENCE_ID NUMBER
OBJECT_SUBTYPE = OBJECT_SUBTYPE
OBJECT_TYPE = OBJECT_TYPE

OBJECT_TYPE VARCHAR2(85) E_NAME VARCHAR2(85)

OBJECT_SUBTYPE VARCHAR2(85) E_LOCATION VARCHAR2(100)
CHEM_TYPE VARCHAR2(85) E_REGION_DOMAIN_FLAG VARCHAR2(200)
OBJECT_SUBTYPE = CHEM_SUBTYPE
OBJECT_TYPE = CHEM_TYPE

CHEM_SUBTYPE VARCHAR2(85) E_COMMENTS VARCHAR2(2000)

E_OBJECT_ID NUMBER
IMMUNOGEN_ID EPITOPE_ID

ANTIGEN_ID
MULT_CHAIN_MOL_NAME CARRIER_ID
SOURCE_MOLECULE_NAME
MOL2_CHEMICAL_TYPE

MOL2_ACCESSION
MOL2_NAME
MOL2_SOURCE_ID ORG_ORGANISM_ID
MOL2_MODIFICATION
MOL2_MODIFIED_SEQ

MOL1_ACCESSION
MOL1_NAME
MOL1_SOURCE_ID
MOL1_MODIFICATION
MOL1_MODIFIED_SEQ

MOL1_SEQ
TISSUE_TYPE ORIGIN

CELL_TYPE
ENDING_POSITION CELL_NAME
STARTING_POSITION
ORGANISM2_NAME REGION
ORGANISM_NAME ORGANISM2_ID
DERIVATIVE_TYPE ORGANISM_ID
OBJECT_DESCRIPTION
OBJECT_TYPE OBJECT_SUB_TYPE
OBJECT_ID REFERENCE_ID

E_OBJECT_SUB_TYPE VARCHAR2(200)
PARENT_TAX_ID_STRING VARCHAR2(50)

DEPTH
ORGANISM_NAME RANK
NAME_EXTENSION
SCIENTIFIC_NAME PATH
ACTIVE_NODE
PARENT_TAX_ID
ORGANISM_ID TAX_ID

E_OBJECT_MOL_NAME VARCHAR2(535)
ORGANISM2_ID
ORGANISM_ID = ORGANISMO_IRDGANISM_ID =

E_OBJECT_ORGANISM_NAME VARCHAR2(250)
E_OBJECT_DESC VARCHAR2(535)
RELATED_OBJECT_ID NUMBER
REFERENCE_ID = REFERENCE_ID

REFERENCE_ID = REFERENCE_ID
RELATED_OBJECT_TYPE VARCHAR2(200)
RELATED_OBJECT_SUB_TYPE VARCHAR2(200)
RELATED_OBJECT_MOL_NAME VARCHAR2(535)
OBJECT
ORGANISM

RELATED_OBJECT_ORGANISM_NAME VARCHAR2(250)
ORGANISM_ID = TAX_ID

RELATED_OBJECT_DESC VARCHAR2(535)
E_EV VARCHAR2(100)
E_REF_START NUMBER
NUMBER
NUMBER
NUMBER
VARCHAR2(85)

VARCHAR2(535)
VARCHAR2(85)
VARCHAR2(15)
VARCHAR2(250)
NUMBER
NUMBER
VARCHAR2(85)
VARCHAR2(4000)
VARCHAR2(15)
VARCHAR2(250)
NUMBER
VARCHAR2(85)
VARCHAR2(4000)
VARCHAR2(2000)
VARCHAR2(85)

VARCHAR2(85)
VARCHAR2(85)
VARCHAR2(85)
NUMBER
NUMBER
VARCHAR2(1000)
VARCHAR2(250)
NUMBER
VARCHAR2(250)
NUMBER
VARCHAR2(500)

VARCHAR2(535)
VARCHAR2(200)
VARCHAR2(200)
NUMBER NUMBER
NUMBER
VARCHAR2(50)

VARCHAR2(150)
VARCHAR2(85)
VARCHAR2(500)
VARCHAR2(150)
NUMBER NUMBER
NUMBER

E_REF_END
OBJECT_SUB_TYPE

NUMBER
OBJECT_TYPE = OBJECT_TYPE REFERENCE_ID = REFERENCE_ID REFERENCE_ID = REFERENCE_ID OBJECT_SUBTYPE =

E_REF_REGION VARCHAR2(2000)
NUMBER

NUMBER

SOURCE : 1
SOURCE_ID NUMBER REFERENCE_ID = REFERENCE_ID
ACCESSION VARCHAR2(15)
DATABASE VARCHAR2(15)
NAME VARCHAR2(250) COMPLEX
ALIASES VARCHAR2(500) COMPLEX_ID NUMBER
ORGANISM_ID = ORGANISM_ID

CHEMICAL_TYPE VARCHAR2(85) REFERENCE_ID NUMBER

SOURCE_DATE DATE ATOM_PAIRS CLOB

SEQUENCE CLOB PDB_ID VARCHAR2(35)

OBJECT_ID = RELATED_OBJECT_ID

OBJECT_ID = E_OBJECT_ID

SMILES_STRUCT URE VARCHAR2(3500) PDB_CELL_CONTACT _AREA NUMBER

SYNONYMS CLOB E_CONTACT_AREA NUMBER

ORGANISM_ID NUMBER E_VIEWER_STATUS VARCHAR2(25)

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 MHC_C2_PDB_CHAIN VARCHAR2(10)

TCR_C1_PDB_CHAIN VARCHAR2(10)
PARENT_CHEBI_ACCESSION VARCHAR2(15)
TCR_C2_PDB_CHAIN VARCHAR2(10)
ANT_PDB_CHAIN VARCHAR2(10)
E_PDB_CHAIN VARCHAR2(10)
E_RESIDUES VARCHAR2(1000)
AB_ANT_RESIDUES VARCHAR2(1000)
E_MHC_RESIDUES VARCHAR2(1000)
E_TCR_RESIDUES VARCHAR2(1000)
ICD10_CODES
DESCRIPTION VARCHAR2(200)
CODE

IDCODE VARCHAR2(255)
PDB_ID_LIST

ALLERGEN_NODES MHC_E_RESIDUES VARCHAR2(1000)

MHC_TCR_RESIDUES VARCHAR2(1000)
TAX_ID NUMBER
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
COMMON_NAME VARCHAR2(150) CALC_E_CONTACT_AREA FLOAT(126)
RANK VARCHAR2(50) CALC_CELL_CONTACT _AREA FLOAT(126)
VARCHAR2(5)

NCBI_PATH VARCHAR2(500) CALC_E_RESIDUES VARCHAR2(1000)

RESOURCES_LINKS CALC_AB_ANT_RESIDUES VARCHAR2(1000)
ACTIVE_NODE NUMBER URL VARCHAR2(200) CALC_E_MHC_RESIDUES VARCHAR2(1000)
TITLE VARCHAR2(400) CALC_E_TCR_RESIDUES VARCHAR2(1000)
DESCRIPTION VARCHAR2(2000) CALC_MHC_E_RESIDUES VARCHAR2(1000)
STATUS VARCHAR2(15) CALC_MHC_TCR_RESIDUES VARCHAR2(1000)
CATEGORY VARCHAR2(200) CALC_TCR_E_RESIDUES VARCHAR2(1000)
DATE_ADDED DATE CALC_TCR_MHC_RESIDUES VARCHAR2(1000)
LAST_UPDATED DATE COMMENTS VARCHAR2(2000)
REFERENCE_ID = REFERENCE_ID

ATTEMPTS NUMBER COMPLEX_TYPE VARCHAR2(15)

TYPE_FLAG VARCHAR2(10)
C1_TYPE VARCHAR2(15)
REFERENCE_ID = REFERENCE_ID

C2_TYPE VARCHAR2(15)
REFERENCE_ID = REFERENCE_ID

REFERENCE_ID = REF_REFERENCE_ID
REFERENCE_ID = REFERENCE_ID

MHC_CHAIN1 VARCHAR2(15)
MHC_CHAIN2 VARCHAR2(15)
REFERENCE_ID = REFERENCE_ID

MHC_ALLELE_RESTRICTION
MHC_ALLELE_RESTRICTION_ID NUMBER
DISPLAYED_RESTRICTION VARCHAR2(85)
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)
INSTITUTIONVARCHAR2(200)
VARCHAR2(85)
CONT ACT_EMAIL VARCHAR2(85) PHONE_NUMBER
CONTACT_IDNUMBER CONTACT_NAME VARCHAR2(85)

LOCUS VARCHAR2(10) NAMES

REFERENCE_IDNUMBER
CONTACT_IDNUMBER
CONTACT_REFERENCE_ASSOC

ALIASES VARCHAR2(500)
SEROTYPE VARCHAR2(10)
SORT _ORDERNUMBER
CATEGORY_NAME VARCHAR2(80) PRIORITYNUMBER

REF_CATEGORY_ID
REFERENCE_CATEGORY

TAX_ID NUMBER CHEMICAL_TYPE VARCHAR2(85)

MOLECULE VARCHAR2(35) NAME_TXT VARCHAR2(150) SOURCE_DATE DATE
CONTACT_ID = CONTACT_ID

CHAIN_I_NAME VARCHAR2(10)
REF_CATEGORY_ID = REF_CATEGORY_ID

UNIQUE_NAME VARCHAR2(150) SEQUENCE CLOB

CHAIN_II_NAME VARCHAR2(10)
NAME_CLASS VARCHAR2(50)
NUMBER
REFERENCE_IDNUMBER REF_CATEGORY_ID

REFERENCE_CATEGORY_ASSOC

SMILES_STRUCT URE VARCHAR2(3500)

CHAIN_I_LOCUS VARCHAR2(10)
SYNONYMS CLOB
CONTACT

CHAIN_I_MUT ATION VARCHAR2(35)

ORGANISM_ID NUMBER
CHAIN_II_LOCUS VARCHAR2(10)
NUMBER

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

3.7.2 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)
AS_TYPE_ID NUMBER REFERENCE
EPITOPE
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_CONFORMAT ION 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
OBJECT_ID = ANT_CON_OBJECT_ID IV1_CON_OBJECT_ORGANISM_NAME VARCHAR2(250) CHAIN1_J_GENE_CALCULATED VARCHAR2(200)
OBJECT_TYPE VARCHAR2(200)
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)
OBJECT_ID = IV2_CON_OBJECT_ID IV2_IMM_OBJECT_ORGANISM_NAME VARCHAR2(250) CHAIN2_J_GENE_CURATED VARCHAR2(200)
ORIGIN VARCHAR2(85)
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)
OBJECT_ID = IVT_IMM_OBJECT_ID
MOL2_MODIFICATION VARCHAR2(85) IVT_RESPONDER_CELL_TYPE VARCHAR2(85)
MOL2_SOURCE_ID NUMBER
IVT_STIMULATOR_CELL_TYPE VARCHAR2(85)
ORG_ORGANISM_ID NUMBER RECEPTOR_ID = RECEPTOR_ID
OBJECT_ID = IV1_CON_OBJECT_ID IVT_IMM_TYPE VARCHAR2(50)
MOL2_NAME VARCHAR2(250) IVT_IMM_REF_NAME VARCHAR2(250)
MOL2_ACCESSION VARCHAR2(15) IVT_IMM_OBJECT_ID NUMBER
TCELL_ID = TCELL_ID
TCELL_RECEPTOR
MOL2_CHEMICAL_TYPE VARCHAR2(85)
IVT_IMM_OBJECT_SUB_TYPE VARCHAR2(200) 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)
OBJECT_ID = ADT_TCR_OBJECT_ID
ANTIGEN_ID NUMBER 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 DISPLAYED_RESTRICTION = LOCUS VARCHAR2(10)
ADT_IV_IMM_OBJECT_SUB_TYPE VARCHAR2(200) 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
ORGANISM_ID NUMBER
ADT_EFFECTOR_ORIGIN VARCHAR2(85)
TAX_ID NUMBER
ADT_COMMENTS VARCHAR2(2000)
ORGANISM_ID = APC_H_ORGANISM_ID PARENT_TAX_ID NUMBER
EFFECTOR_CELL_TYPE VARCHAR2(85)
ACTIVE_NODE NUMBER
EFFECTOR_TISSUE_TYPE VARCHAR2(85)
ORGANISM_ID = ADT_TCR_ORGANISM_ID
SCIENTIFIC_NAME VARCHAR2(150)
EFFECTOR_ORIGIN VARCHAR2(85)
PATH VARCHAR2(500)
MHC_ALLELE_NAME VARCHAR2(85)
NAME_EXTENSION VARCHAR2(85)
MHC_ALLELE_EV VARCHAR2(100)
COMPLEX ORGANISM_ID = ADT_H_ORGANISM_ID ORGANISM_NAME VARCHAR2(150)
MHC_AUTOLOGOUS VARCHAR2(1)
COMPLEX_ID NUMBER RANK VARCHAR2(50)
APC_CELL_TYPE VARCHAR2(85)
REFERENCE_ID NUMBER DEPTH NUMBER
APC_TISSUE_TYPE VARCHAR2(85) ORGANISM_ID = TCR_ORGANISM_ID
ATOM_PAIRS CLOB PARENT_TAX_ID_STRING VARCHAR2(50)
APC_ORIGIN VARCHAR2(85)
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) COMPLEX_ID = COMPLEX_ID ANT_CON_OBJECT_ID NUMBER SYNONYMS CLOB
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

3.7.3 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_COMMENT S 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_COMMENT S 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) PRODUCT ION_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_ROUT E 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_ROUT E 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)
IV2_CON_OBJECT_ID NUMBER CHAIN2_TYPE VARCHAR2(10)
MOL1_SEQ VARCHAR2(2000) OBJECT_ID = ADT_AB_OBJECT_ID
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_ROUT E 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 ADT _IV_CON_OBJECT_ORGANISM_NM VARCHAR2(250)
DISEASE_ID = ADT_IV_DISEASE_ID
PRODUCT ION_FLAG INTEGER ADT_IV_CON_OBJECT_DESC VARCHAR2(500)
ACCESSION VARCHAR2(15) ADT_AB_NAME VARCHAR2(200)
DISEASE_SOURCE VARCHAR2(15) DISEASE_ID = IV2_DISEASE_ID
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_COMMENT S 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_CONT ACT _AREA NUMBER SCIENTIFIC_NAME VARCHAR2(150)
ANT_OBJECT_MOL_NAME VARCHAR2(535)
ORGANISM_ID = ADT_H_ORGANISM_ID PATH VARCHAR2(500)
E_CONT ACT_AREA NUMBER 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) RANK VARCHAR2(50)
ANT_CON_OBJECT_ID NUMBER ORGANISM_ID = H_ORGANISM_ID
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) ANT _CON_OBJECT_DESC VARCHAR2(500)
COMPLEX_ID = COMPLEX_ID
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) ADT_AB_OBJECT_SUB_TYPE VARCHAR2(200) ASSAY_TYPE_ID NUMBER
CALC_ATOM_PAIRS CLOB ADT_AB_OBJECT_MOL_NAME VARCHAR2(535) CATEGORY VARCHAR2(50)
CALC_E_CONT ACT_AREA FLOAT(126) ADT_AB_OBJECT_ORGANISM_NAME VARCHAR2(250) ASSAY_TYPE VARCHAR2(50)
ASSAY_TYPE_ID = AS_TYPE_ID
CALC_CELL_CONT ACT _AREA FLOAT(126) AB_OBJECT_DESCRIPTION VARCHAR2(500) RESPONSE VARCHAR2(85)
CALC_E_RESIDUES VARCHAR2(1000) ADT_AB_OBJECT_DESCRIPTION VARCHAR2(500) UNITS VARCHAR2(30)
CALC_AB_ANT_RESIDUES VARCHAR2(1000) E_NAME VARCHAR2(85) OBI_ID VARCHAR2(100)
CALC_E_MHC_RESIDUES VARCHAR2(1000) E_OBJECT_DESC VARCHAR2(535) CLASS VARCHAR2(35)
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

 VARCHAR2(200)

VARCHAR2(150)

VARCHAR2(100)
VARCHAR2(85)

VARCHAR2(85)
VARCHAR2(35)

VARCHAR2(35)
VARCHAR2(10)
VARCHAR2(10)
VARCHAR2(10)
VARCHAR2(35)
VARCHAR2(10)
VARCHAR2(10)
VARCHAR2(10)
VARCHAR2(35)
VARCHAR2(10)
VARCHAR2(35)
NUMBER

NUMBER

NUMBER
NUMBER
MHC_ALLELE_RESTRICT ION
MHC_ALLELE_RESTRICT ION_ID
DISPLAYED_RESTRICTION

ORGANISM_NCBI_TAX_ID
Figure 3-6 represents MHC Binding assay data and its direct table relationships.

CHAIN_II_SOURCE_ID
RESTRICTION_LEVEL

CHAIN_I_SOURCE_ID
CHAIN_I_MUT ATION

CHAIN_II_MUTATION

REFERENCE
CHAIN_II_LOCUS
CHAIN_I_LOCUS
CHAIN_II_NAME
CHAIN_I_NAME

REFERENCE_ID REFERENCE_TYPE NUMBER

HAPLOTYPE
SYNONYMS

MOLECULE
SEROTYPE
ORGANISM

A_C_PATHOGEN_FLAG VARCHAR2(15)
INCLUDES

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

SVM_CLASSIFIER_SCORE CURATION_STATUS VARCHAR2(5)
LOCUS
CLASS

CURRENT _USER_ID CURATION_KEYWORDS NUMBER

IRI

CURATEDBY VARCHAR2(100)
DIFFICULTY LAST_REVIEWER NUMBER
PRODUCT ION_FLAG RECOMMENDATION VARCHAR2(2000)
DATE_LAST_UPDATED VARCHAR2(85)
EMAIL_NOTIFY_AUTHOR VARCHAR2(10)
EMAIL_NOTIFY_ADDRESS NUMBER
EMAIL_NOTIFY_UNAVAILABLE_FLAG VARCHAR2(1)
VARCHAR2(50) DATE
VARCHAR2(100)
VARCHAR2(100)
VARCHAR2(1)
DISPLAYED_RESTRICTION = MHC_ALLELE_NAME
REFERENCE_ID = REFERENCE_ID
COMPLEX
EPITOPE_ID = EPITOPE_ID
COMPLEX_ID REFERENCE_ID NUMBER NUMBER
MHC_BIND ATOM_PAIRS PDB_ID CLOB
PDB_CELL_CONT ACT _AREA VARCHAR2(35)
MHC_BIND_ID NUMBER NUMBER
E_CONT ACT_AREA NUMBER
REFERENCE_ID EPITOPE_ID NUMBER
E_VIEWER_STATUS NUMBER
AS_LOCATION AS_TYPE_ID VARCHAR2(100)
AB_C1_PDB_CHAIN VARCHAR2(25)
AS_CHAR_VALUE NUMBER
AB_C2_PDB_CHAIN VARCHAR2(10)
AS_NUM_VALUE VARCHAR2(50)
MHC_C1_PDB_CHAIN VARCHAR2(10)
AS_INEQUALITY NUMBER
3.7.4 IEDB MHC Binding Data Model

MHC_C2_PDB_CHAIN VARCHAR2(10)
AS_COMMENTS VARCHAR2(5)
ASSAY_TYPE TCR_C1_PDB_CHAIN VARCHAR2(10)
MHC_ALLELE_NAME VARCHAR2(2000)
TCR_C2_PDB_CHAIN VARCHAR2(10)
ASSAY_TYPE_ID NUMBER COMPLEX_ID VARCHAR2(85)
COMPLEX_ID = COMPLEX_ID ANT_PDB_CHAIN E_PDB_CHAIN VARCHAR2(10)
CATEGORY VARCHAR2(50) AS_TYPE NUMBER
VARCHAR2(50) E_RESIDUES AB_ANT_RESIDUES VARCHAR2(10)
ASSAY_TYPE ASSAY_TYPE_ID = AS_TYPE_ID AS_TYPE_RESPONSE VARCHAR2(50)
VARCHAR2(85) VARCHAR2(85) E_MHC_RESIDUES E_TCR_RESIDUES VARCHAR2(10)
RESPONSE AS_TYPE_UNITS E_NAME
VARCHAR2(30) MHC_E_RESIDUES VARCHAR2(1000)
UNITS OBI_ID CLASS E_OBJECT_DESC VARCHAR2(30)
VARCHAR2(100) MHC_ALLELE_CLASS VARCHAR2(85) MHC_TCR_RESIDUES VARCHAR2(1000)
VARCHAR2(35) VARCHAR2(535) TCR_E_RESIDUES VARCHAR2(1000)
VARCHAR2(35) TCR_MHC_RESIDUES VARCHAR2(1000)
CALC_ATOM_PAIRS CALC_E_CONT VARCHAR2(1000)
ACT_AREA CALC_CELL_CONT VARCHAR2(1000)
ACT_AREA CALC_E_RESIDUES VARCHAR2(1000)
CALC_AB_ANT_RESIDUES VARCHAR2(1000)
CALC_E_MHC_RESIDUES CLOB
CALC_E_TCR_RESIDUES FLOAT(126)
CALC_MHC_E_RESIDUES FLOAT(126)
CALC_MHC_TCR_RESIDUES VARCHAR2(1000)
CALC_TCR_E_RESIDUES VARCHAR2(1000)
CALC_TCR_MHC_RESIDUES VARCHAR2(1000)
COMMENTS VARCHAR2(1000)
COMPLEX_TYPE TYPE_FLAG VARCHAR2(1000)

VARCHAR2(2000)

VARCHAR2(2000)
VARCHAR2(100)
VARCHAR2(200)

VARCHAR2(200)
VARCHAR2(535)
VARCHAR2(250)
VARCHAR2(535)

VARCHAR2(200)
VARCHAR2(200)
VARCHAR2(535)
VARCHAR2(250)
VARCHAR2(535)
VARCHAR2(100)
VARCHAR2(85) C1_TYPE VARCHAR2(1000)
C2_TYPE VARCHAR2(1000)
NUMBER MHC_CHAIN1 MHC_CHAIN2 VARCHAR2(1000)
NUMBER

NUMBER

NUMBER

NUMBER
NUMBER
VARCHAR2(2000)
VARCHAR2(15)
VARCHAR2(10)
VARCHAR2(15)
VARCHAR2(15)
VARCHAR2(15)

RELATED_OBJECT_ORGANISM_NAME
EPITOPE
VARCHAR2(15)

RELATED_OBJECT_MOL_NAME
RELATED_OBJECT_SUB_TYPE
E_OBJECT_ORGANISM_NAME
E_REGION_DOMAIN_FLAG

RELATED_OBJECT_DESC
RELATED_OBJECT_TYPE
E_OBJECT_MOL_NAME
E_OBJECT_SUB_TYPE

RELATED_OBJECT_ID
E_OBJECT_DESC
REFERENCE_ID

E_REF_REGION
E_COMMENT S

E_REF_START
E_OBJECT_ID
E_LOCATION

E_REF_END
EPITOPE_ID

E_NAME

E_EV
3.7.5 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 E_LOCATION VARCHAR2(100)
REFERENCE_ID NUMBER
EPITOPE_ID NUMBER E_REGION_DOMAIN_FLAG VARCHAR2(200)
REFERENCE_TYPE VARCHAR2(15)
AS_LOCATION VARCHAR2(100) E_COMMENTS VARCHAR2(2000)
A_C_PATHOGEN_FLAG VARCHAR2(5)
AS_TYPE_ID NUMBER E_OBJECT_ID NUMBER
SVM_CLASSIFIER_SCORE NUMBER
AS_CHAR_VALUE VARCHAR2(50) E_OBJECT_SUB_TYPE VARCHAR2(200)
CURATION_STATUS VARCHAR2(100)
AS_NUM_VALUE NUMBER E_OBJECT_MOL_NAME VARCHAR2(535)
CURRENT_USER_ID NUMBER
AS_INEQUALITY VARCHAR2(5) E_OBJECT_ORGANISM_NAME VARCHAR2(250)
CURATION_KEYWORDS VARCHAR2(2000)
AS_NUM_SUBJECTS NUMBER E_OBJECT_DESC VARCHAR2(535)
CURATEDBY VARCHAR2(85) REFERENCE_ID = REFERENCE_ID
AS_NUM_RESPONDED NUMBER EPITOPE_ID = EPITOPE_ID
RELATED_OBJECT_ID NUMBER
DIFFICULTY VARCHAR2(10)
AS_RESPONSE_FREQUENCY NUMBER RELATED_OBJECT_TYPE VARCHAR2(200)
LAST_REVIEWER NUMBER
AS_IMMUNIZATION_COMMENTS VARCHAR2(2000) RELATED_OBJECT_SUB_TYPE VARCHAR2(200)
PRODUCTION_FLAG VARCHAR2(1)
AS_COMMENTS VARCHAR2(2000) RELATED_OBJECT_MOL_NAME VARCHAR2(535)
RECOMMENDATION VARCHAR2(50)
H_ORGANISM_ID NUMBER RELATED_OBJECT_ORGANISM_NAME VARCHAR2(250)
DATE_LAST_UPDATED DATE
H_ORGANISM_NAME VARCHAR2(250) RELATED_OBJECT_DESC VARCHAR2(535)
EMAIL_NOTIFY_AUTHOR VARCHAR2(100)
H_SEX VARCHAR2(10) E_EV VARCHAR2(100)
EMAIL_NOTIFY_ADDRESS VARCHAR2(100)
H_AGE VARCHAR2(85) E_REF_START NUMBER
EMAIL_NOTIFY_UNAVAILABLE_FLAG VARCHAR2(1)
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)
HAPLOTYPE VARCHAR2(10) IV1_IMM_OBJECT_MOL_NAME VARCHAR2(535) ORGANISM_ID NUMBER
LOCUS VARCHAR2(10) IV1_IMM_OBJECT_ORGANISM_NAME VARCHAR2(135) ORGANISM_NAME VARCHAR2(250)
DISPLAYED_RESTRICTION = MHC_ALLELE_NAME
SEROTYPE VARCHAR2(10) IV1_IMM_OBJECT_DESC VARCHAR2(500) OBJECT_ID = ANT_OBJECT_ID ORGANISM2_ID NUMBER
MOLECULE VARCHAR2(35) IV1_IMM_EV VARCHAR2(100) ORGANISM2_NAME VARCHAR2(250)
CHAIN_I_NAME VARCHAR2(10) IV1_CON_OBJECT_ID NUMBER REGION VARCHAR2(1000)
CHAIN_II_NAME VARCHAR2(10) IV1_CON_OBJECT_SUB_TYPE VARCHAR2(200) STARTING_POSITION NUMBER
CHAIN_I_LOCUS VARCHAR2(10) IV1_CON_OBJECT_MOL_NAME VARCHAR2(535) OBJECT_ID = IV1_CON_OBJECT_ID ENDING_POSITION NUMBER
CHAIN_I_MUTATION VARCHAR2(35) IV1_CON_OBJECT_ORGANISM_NAME VARCHAR2(135) CELL_NAME VARCHAR2(85)
CHAIN_II_LOCUS VARCHAR2(10) IV1_CON_OBJECT_DESC VARCHAR2(500) CELL_TYPE VARCHAR2(85)
CHAIN_II_MUTATION VARCHAR2(35) IVT_PROCESS_TYPE VARCHAR2(85) TISSUE_TYPE VARCHAR2(85)
OBJECT_ID = IV1_IMM_OBJECT_ID
CHAIN_I_SOURCE_ID NUMBER IVT_IMM_TYPE VARCHAR2(50) ORIGIN VARCHAR2(85)
CHAIN_II_SOURCE_ID NUMBER IVT_IMM_REF_NAME VARCHAR2(250) MOL1_SEQ VARCHAR2(2000)
IRI VARCHAR2(100) IVT_IMM_OBJECT_SUB_TYPE VARCHAR2(200) MOL1_MODIFIED_SEQ VARCHAR2(4000)
IVT_IMM_OBJECT_MOL_NAME VARCHAR2(535) MOL1_MODIFICATION VARCHAR2(85)
IVT_IMM_OBJECT_ORGANISM_NAME VARCHAR2(135) OBJECT_ID = MOL1_SOURCE_ID NUMBER
IVT_IMM_OBJECT_DESC VARCHAR2(500) IVT_CON_OBJECT_ID 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)
ORGANISM_ID NUMBER
IVT_CON_OBJECT_MOL_NAME VARCHAR2(535) MOL2_SOURCE_ID NUMBER
TAX_ID NUMBER OBJECT_ID = IVT_IMM_OBJECT_ID
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) ANT_TYPE VARCHAR2(50) SOURCE_MOLECULE_NAME VARCHAR2(535)
ORGANISM_ID =
NAME_EXTENSION VARCHAR2(85) H_ORGANISM_ID 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 E_NAME VARCHAR2(85)
DISEASE_ID = IV1_DISEASE_ID 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
3.7.6 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 =
MAPPIN NUM
SEQUENCE CLOB SOURCE_ID
SMILES_STRUCT URE VARCHAR2(3500) G_ID BER
SYNONYMS CLOB SOURCE NUM
ORGANISM_ID NUMBER _ID BER
ORGANISM_NAME VARCHAR2(150) IMAGE BLOB
CHEBI_INCHI VARCHAR2(2000)
CHEBI_INFO_UPDATE DATE
CHEBI_INFO_UNAVAIL DATE
SOURCE_ID = SOURCE_ID

PARENT_CHEBI_ACCESSION VARCHAR2(15)

SOURCE_ID = SOURCE_ID

SOURCE_ID = SOURCE_ID CHEBI_CHILDREN

CHEBI_CH_ONTOLOGY_ID NUMBER
CHEBI_FORMULAE SOURCE_ID NUMBER
CHEBI_IUPAC
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

 Figure 3-9 represents the tables used for user authentication and authorization within the curation
INTERNAL_USER
USER_ID USER_NAME NUMBER
USER_FULL_NAME VARCHAR2(35)
ROLE USER_PASSWORD VARCHAR2(85)
ROLE_IDNUMBER PASSWORD_EXPIRE_DATE VARCHAR2(85)
EMAIL_ADDRESS DATE

Figure 3-9. IEDB User Data Physical Data Model

ROLE_NAMEVARCHAR2(35)
STATUS INSTITUTION COUNT RY VARCHAR2(80)
NUM_FAILED_LOGIN VARCHAR2(10)
VARCHAR2(200)
VARCHAR2(80)
NUMBER
ROLE_ID = ROLE_ID
USER_ID = INTERNAL_USER_ID
INTERNAL_USER_ROLE_ASSN USER_ID = USER_ID
INTERNAL_USER_IDNUMBER
ROLE_IDNUMBER
3.7.7 IEDB User Data Model

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

application.
3.7.8 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 COUNT RY
CELL_TYPEVARCHAR2(85) TCR_CHAIN VARCHA COUNTRYVARCHAR2(255)
CATEGORYVARCHAR2(35) _TYPE R2(35) SORT_ORDERNUMBER
SORT_ORDERNUMBER SORT_ORD NUMBER
ER
DISEASE_STAGE
DISEASE_STAGEVARCHAR2(85)
INVIVO_PROCESS_TYPE
INVIVO_PROCES VARCHAR SORT_ORDERNUMBER
INVITRO_PROCESS_TYPE
INVITRO_PROCESS_TYPE VARCHAR2(80 S_TYPE 2(80)
SORT_ORDER ) NUMBER SORT_ORDER NUMBER
CATEGORY VARCHAR2(25
TISSUE_TYPE )
RELATED_OBJECT_TYPE
TISSUEVARCHAR2(85) RELATED_OBJECT VARCHAR2 EVIDENCE_CODE
EVIDEN VARCH
CATEGORYVARCHAR2(35) _TYPE (255)
CE_CO AR2(10
SORT_ORDERNUMBER SORT_ORDER NUMBER
DE 0)
CATEG VARCH
QUALITATIVE_MEASUREMENT_TYPE ORY AR2(25
QUALITATIVE_MEASUREME VARCHAR2
SORT_ )
ADJUVANT
NT_TYPE SORT_ORDER (50) ADJUVA VARC
ORDER NUMB
ANTIBODY_TYPE NUMBER NT_NA HAR2(
STANDARDIZED_COMMENT ER
FORM VARCHAR2(10 ANTIBODY_TYPEVARCHAR2(255) ME 85)
CONFORMATIONAL_TYPE
STD_COMMEN 0) SORT_ORDERNUMBER SORT_O NUMB
CONFORMATIONAL_TYPEVARCHAR2(85)
RDER ER
T VARCHAR2(30
CHAIN_ISOTYPE
SORT_ORDER 0) NUMBER
ISOTYPE VARCHAR2(20)
CLASS VARCHAR2(20)
ISOTYPE_FLAG VARCHAR2(10) ADMINISTRATION_TYPE
SORT_ORDER NUMBER DERIVATIVE_TYPE
ADMINISTRATION_TYPEVARCHAR2(85) DERIVAT VARCH
IVE_TYP AR2(25
E 0)
SORT_O NUMB
ORIGIN RDER ER
IMMUNOGLOBULIN_DOMAIN
ORIGI VARCHAR2(8
THE_DOMAINVARCHAR2(35)
SORT_ORDERNUMBER
N 5) POST_TRANSLATION_MODIFICATI
POST_TRANS_MODIF
ON VARCHA
REGION_DOMAIN ICATION_TYPE R2(85)
ABBREVIATION VARCHA
REGION_DOMAINVARCHAR2(255)
SORT_ORDER R2(10)
SORT_ORDERNUMBER
NUMBE
IMMUNOGEN_FORM R
IMMUNOGE VARCHA
N_FORM R2(30)
ROUTE
ROUT VARCHAR2(3 IMMUNIZATION_DESCRIPTION
ESORT_ORDERNUMBER
5) ASSAY_ID NUMBER
IMMUNIZATION_DES VARCHAR2(
CRIPTION 1000)
MATERIALS_ASSAYED
MATERIALS_ASSAYED VARCHAR2(8
SORT_ORDER 5) NUMBER

Figure 3-10. IEDB Lookup Value Physical Data Model

 Figure 3-11 represents the key areas of the IEDB External database. The following data model
REFERENCE_CATEGORY REF_CATEGORY_ID ASSAY_TYPE : 3
NUMBER ASSAY_TYPE_ID NUMBER
SUBMISSION CATEGORY_NAME VARCHAR2(80) CATEGORY VARCHAR2(50) ASSAY_TYPE
SUBMISSION_IDNUMBER PRIORITYNUMBER
VARCHAR2(50) RESPONSE
REFERENCE_IDNUMBER SORT_ORDER NUMBER Physical Data Model Project : IEDB
VARCHAR2(85)
JOURNAL SUBMITTER_NAMEVARCHAR2(85) Model : IEDB_PUBLIC
UNITSVARCHAR2(30)
JOURNAL_ID NUMBER JOURNAL_TITLE SUBMISSION_DATEDATE SUBMISSION_AUT HORS OBI_IDVARCHAR2(100) Author : JRC Version 3.1 11/29/2016
VARCHAR2(2000) JOURNAL_ISSN VARCHAR2(2000) SUBMISSION_AFFILIATIONS ASSAY_TYPE_ID = CHILD_ASSAY_TYPE_ID CLASSVARCHAR2(35)
REFERENCE_LINKING ASSAY_TYPE_ID = CHILD_ASSAY_TYPE_ID
VARCHAR2(15) MEDLINE_TA VARCHAR2(200) VARCHAR2(2000) SUBMISSION_TITLEVARCHAR2(400)
SUBMISSION_ABSTRACT VARCHAR2(4000) REFERENCE_ID NUMBER REF_REFERENCE_ID ASSAY_TYPE_ID = ASSAY_TYPE_ID
REF_CATEGORY_ID = REF_CATEGORY_ID ASSAY_TYPE_ID = ASSAY_TYPE_ID
REFERENCE_CATEGORY_ASSOC NUMBER COMMENTS
REFERENCE_ID NUMBER VARCHAR2(2000)
JOURNAL_ID = JOURNAL_ID REF_CATEGORY_ID NUMBER TITLEVARCHAR2(1000) ASSAY_FINDER_TCELL_ANCESTRY ASSAY_TYPE_ID = ILD_ASSAY_TYPE_ID ASSAY_FINDER_BCELL_ANCESTRY

Figure 3-11. IEDB Public External Physical Data Model

NODE_IDNUMBER NODE_IDNUMBER
ARTICLE
COMPLEX : 2 ASSAY_TYPE_ID NUMBER ASSAY_TYPE_ID NUMBER
REFERENCE_ID = REFERENCE_ID
COMPLEX_IDNUMBER ARTICLE_ID REFERENCE_ID NUMBER NUMBER REFERENCE_ID = REFERENCE_ID
OBI_IDVARCHAR2(1000) CHILD_ASSAY_TYPE_ID OBI_IDVARCHAR2(1000) CHILD_ASSAY_TYPE_ID
REFERENCE_IDNUMBER JOURNAL_ID NUMBER REFERENCE_ID = REFERENCE_ID
NUMBER CHILD_OBI_IDVARCHAR2(1000)
REFERENCE_ID = REF_REFERENCE_ID
ASSAY_FINDER_ELUTION_ANCESTRY NUMBER CHILD_OBI_IDVARCHAR2(1000)
ATOM_PAIRSCLOB JOURNAL_VOLUME VARCHAR2(15) REFERENCE_ID = REFERENCE_ID
JOURNAL_ISSUE VARCHAR2(20) NODE_IDNUMBER
PDB_IDVARCHAR2(35)
ARTICLE_DATE VARCHAR2(35) ASSAY_TYPE_ID NUMBER
PDB_CELL_CONTACT_AREA NUMBER
E_CONTACT_AREA NUMBER ARTICLE_PAGES VARCHAR2(24) OBI_IDVARCHAR2(1000) CHILD_ASSAY_TYPE_ID
REFERENCE : 1
E_VIEWER_STATUS VARCHAR2(25) ARTICLE_TITLE ARTICLE_AUT VARCHAR2(1000) NUMBER CHILD_OBI_IDVARCHAR2(1000)
AB_C1_PDB_CHAIN VARCHAR2(10) REFERENCE_IDNUMBER
HORS VARCHAR2(4000)
AB_C2_PDB_CHAIN VARCHAR2(10) REFERENCE_TYPE VARCHAR2(15)
ARTICLE_ABSTRACT VARCHAR2(4000) GEOLOCATION : 2
MHC_C1_PDB_CHAIN VARCHAR2(10) CURATION_KEYWORDS VARCHAR2(2000)
ARTICLE_AFFILIATIONS VARCHAR2(2000) GAZ_IDVARCHAR2(200)
MHC_C2_PDB_CHAIN VARCHAR2(10) ARTICLE_CHEMICAL_LIST VARCHAR2(4000) DISPLAY_NAME VARCHAR2(500)
TCR_C1_PDB_CHAIN VARCHAR2(10) ARTICLE_MESH_HEADINGS_LIST VARCHAR2(4000) REFERENCE_ID = REFERENCE_ID
SECONDARY_NAMES VARCHAR2(500)
TCR_C2_PDB_CHAIN VARCHAR2(10) MEDLINE_DATEVARCHAR2(10)
ANT_PDB_CHAIN VARCHAR2(10) COMMENTSVARCHAR2(2000)
E_PDB_CHAIN E_RESIDUES VARCHAR2(10) PUBMED_IDVARCHAR2(20
AB_ANT_RESIDUES VARCHAR2(1000) GAZ_ID = H_GAZ_ID
E_MHC_RESIDUES VARCHAR2(1000)

represents a normalized version of the External MySQL database.

E_TCR_RESIDUES VARCHAR2(1000) REFERENCE_ID = REFERENCE_ID CURATED_EPITOPE : 2 CURATED_EPITOPE_ID NUMBER MHC_ELUTION
MHC_E_RESIDUES VARCHAR2(1000)
REFERENCE_IDNUMBER MHC_ELUTION_ID NUMBER NUMBER

3.8 IEDB External Physical Data Model

MHC_TCR_RESIDUES VARCHAR2(1000)
E_NAMEVARCHAR2(150) CURATED_EPITOPE_ID = CURATED_EPITOPE_ID REFERENCE_ID NUMBER
TCR_E_RESIDUES VARCHAR2(1000)
E_LOCATIONVARCHAR2(100) CURATED_EPITOPE_ID VARCHAR2(100)
TCR_MHC_RESIDUES VARCHAR2(1000) REFERENCE_ID = REFERENCE_ID
REFERENCE_ID = REFERENCE_ID E_REGION_DOMAIN_FLAG VARCHAR2(200) AS_LOCATION NUMBER
CALC_ATOM_PAIRS VARCHAR2(1000)
E_COMMENTSVARCHAR2(2000) AS_TYPE_ID VARCHAR2(50)
CALC_E_CONTACT_AREA
CALC_CELL_CONTACT_AREA FLOAT(126)CLOB REFERENCE_ID = REFERENCE_ID E_OBJECT_IDNUMBER AS_CHAR_VALUE NUMBER
CALC_E_RESIDUESVARCHAR2(1000) FLOAT(126)
RELATED_OBJECT_ID NUMBER RELATED_OBJECT_TYPE AS_NUM_VALUE VARCHAR2(5)
CALC_AB_ANT_RESIDUES VARCHAR2(1000) TCELL : 1 VARCHAR2(200) AS_INEQUALITY NUMBER NUMBER
CALC_E_MHC_RESIDUES VARCHAR2(1000) CURATED_EPITOPE : 1 CURATED_EPITOPE_ID TCELL_ID REFERENCE_ID NUMBER NUMBER E_EV E_REF_START VARCHAR2(100) AS_NUM_SUBJECTS
CALC_E_TCR_RESIDUES VARCHAR2(1000) NUMBER CURATED_EPITOPE_ID NUMBER E_REF_END NUMBER NUMBER AS_NUM_RESPONDED
AS_RESPONSE_FREQUENCY NUMBER
CALC_MHC_E_RESIDUES VARCHAR2(1000) REFERENCE_ID NUMBER AS_LOCATION VARCHAR2(100) E_REF_REGION VARCHAR2(2000) AS_IMMUNIZATION_COMMENTS VARCHAR2(2000)
CALC_MHC_TCR_RESIDUES VARCHAR2(1000) E_NAME VARCHAR2(150) AS_TYPE_ID NUMBER
E_LOCATION VARCHAR2(100) AS_COMMENTS H_ORGANISM_ID H_GAZ_ID H_SEX VARCHAR2(4000)
CALC_TCR_E_RESIDUES VARCHAR2(1000) AS_CHAR_VALUE VARCHAR2(50) H_AGE NUMBER
E_REGION_DOMAIN_FLAG VARCHAR2(200) E_COMMENTSVARCHAR2(2000)
CALC_TCR_MHC_RESIDUES VARCHAR2(1000)
COMMENTSVARCHAR2(2000) AS_NUM_VALUE NUMBER H_MHC_TYPES_PRESENT IV1_PROCESS_TYPE VARCHAR2(255)
E_OBJECT_IDNUMBER CURATED_EPITOPE_ID = CURATED_EPITOPE_ID
RELATED_OBJECT_ID NUMBER AS_INEQUALITY VARCHAR2(5) IV1_ADJUVANTS IV1_ROUTE VARCHAR2(10)
CURATED_EPITOPE_ID = CURATED_EPITOPE_ID
RELATED_OBJECT_TYPE VARCHAR2(200) AS_NUM_SUBJECTS NUMBER COMPLEX : 1 ASSAY_TYPE_ID = AS_TYPE_ID IV1_DOSE_SCHEDULE VARCHAR2(85)
AS_NUM_RESPONDEDNUMBER AS_RESPONSE_FREQUENCY COMPLEX_ID NUMBER IV1_DISEASE_ID IV1_DISEASE_STAGE IV1_IMM_TYPE VARCHAR2(1000)
E_EV E_REF_START VARCHAR2(100) NUMBER AS_IMMUNIZATION_COMMENTS VARCHAR2(2000) IV1_IMM_REF_NAME IV1_IMM_OBJECT_ID IV1_IMM_EV VARCHAR2(85)
REFERENCE_ID NUMBER CLOB
E_REF_END NUMBER NUMBER VARCHAR2(35) IV1_CON_OBJECT_ID IVT_PROCESS_TYPE IVT_IMM_TYPE VARCHAR2(400)
COMPLEX_ID = COMPLEX_ID ATOM_PAIRS MHC_BIND ASSAY_TYPE : 2 ASSAY_TYPE_ID NUMBER
CURATED_EPITOPE_ID = CURATED_EPITOPE_ID E_REF_REGION VARCHAR2(2000) AS_COMMENTS VARCHAR2(4000) IVT_IMM_REF_NAME IVT_IMM_OBJECT_ID IVT_IMM_EV VARCHAR2(35)
PDB_ID MHC_BIND_ID NUMBER NUMBER
ASSAY_TYPE_ID = AS_TYPE_ID CATEGORY VARCHAR2(50)
H_ORGANISM_ID H_GAZ_ID NUMBER PDB_CELL_CONTACT_AREA NUMBER COMPLEX_ID = COMPLEX_ID
VARCHAR2(250)
REFERENCE_ID NUMBER ASSAY_TYPE VARCHAR2(50) RESPONSE
H_SEX VARCHAR2(255) E_CONTACT_AREA NUMBER NUMBER
OBJECT_ID = E_OBJECT_ID OBJECT_ID = RELATED_OBJECT_ID CURATED_EPITOPE_ID VARCHAR2(100) VARCHAR2(85)
H_AGE VARCHAR2(10) E_VIEWER_STATUS VARCHAR2(25) VARCHAR2(85)
AS_LOCATION NUMBER UNITSVARCHAR2(30)
BCELL H_MHC_TYPES_PRESENT VARCHAR2(85) AB_C1_PDB_CHAIN VARCHAR2(10) VARCHAR2(50)
OBJECT_ID = ANT_CON_OBJECT_ID AS_TYPE_ID VARCHAR2(50) OBI_IDVARCHAR2(100)
OBJECT : 1 VARCHAR2(1000) AB_C2_PDB_CHAIN VARCHAR2(10) VARCHAR2(250)
BCELL_ID REFERENCE_ID NUMBER NUMBER OBJECT_ID = IV1_CON_OBJECT_ID
TCR_NAME AS_CHAR_VALUE NUMBER CLASSVARCHAR2(35)
NUMBER OBJECT_IDNUMBER OBJECT_ID = ANT_OBJECT_ID TCR_C1_MOL_TYPE VARCHAR2(85) MHC_C1_PDB_CHAIN VARCHAR2(10) NUMBER
CURATED_EPITOPE_ID AS_LOCATION OBJECT_ID = AB_OBJECT_ID AS_NUM_VALUE VARCHAR2(5)
VARCHAR2(100) REFERENCE_IDNUMBER TCR_C2_MOL_TYPE VARCHAR2(85) MHC_C2_PDB_CHAIN VARCHAR2(10) VARCHAR2(100)
AS_TYPE_ID AS_CHAR_VALUE AS_INEQUALITY
OBJECT_TYPEVARCHAR2(200) VARCHAR2(85) TCR_C1_PDB_CHAIN VARCHAR2(10) AS_COMMENTS VARCHAR2(4000)
AS_NUM_VALUE AS_INEQUALITY NUMBER OBJECT_ID = ANT_CON_OBJECT_ID OBJECT_ID = ADT_IV_CON_OBJECT_ID IV1_PROCESS_TYPE ASSAY_TYPE_ID ASSAY_TYPE_ID = CH NUMBER
VARCHAR2(85) TCR_C2_PDB_CHAIN VARCHAR2(10) MHC_ALLELE_RESTRICTION_ID NUMBER
AS_NUM_SUBJECTS VARCHAR2(50) OBJECT_SUB_TYPE VARCHAR2(200) IV1_ADJUVANTS VARCHAR2(85)
OBJECT_ID = ADT_IV_IMM_OBJECT_ID IV1_ROUTE VARCHAR2(400) ANT_PDB_CHAIN VARCHAR2(10) MHC_ALLELE_NAME VARCHAR2(85)
AS_NUM_RESPONDED NUMBER OBJECT_ID = IV1_IMM_OBJECT_ID OBJECT_DESCRIPTION VARCHAR2(535) VARCHAR2(50)
IV1_DOSE_SCHEDULE VARCHAR2(35) E_PDB_CHAIN VARCHAR2(10) COMPLEX_ID NUMBER
AS_RESPONSE_FREQUENCY VARCHAR2(5) DERIVATIVE_TYPE VARCHAR2(500) MHC_ALLELE_RESTRICTION_ID = MHC_ALLELE_RESTRICTION_ID VARCHAR2(250)
NUMBER NUMBER OBJECT_ID = ANT_OBJECT_ID ORGANISM_IDNUMBER OBJECT_ID = IVT_CON_OBJECT_ID IV1_DISEASE_ID VARCHAR2(250) E_RESIDUES VARCHAR2(1000) IVT_CON_OBJECT_ID NUMBER
AS_IMMUNIZATION_COMMENTS
NUMBER ORGANISM2_IDNUMBER IV1_DISEASE_STAGE NUMBER AB_ANT_RESIDUES VARCHAR2(1000) MHC_ALLELE_RESTRICTION_ID NUMBER
VARCHAR2(100)
AS_COMMENTS
VARCHAR2(2000) OBJECT_ID = ADT_AB_OBJECT_ID REGIONVARCHAR2(1000) OBJECT_ID = IV2_CON_OBJECT_ID IV1_IMM_TYPE VARCHAR2(85) E_MHC_RESIDUES VARCHAR2(1000) OBJECT_ID = ANT_OBJECT_ID MHC_ALLELE_NAMEVARCHAR2(85)
AS_ANT_CONFORMATION OBJECT : 2
VARCHAR2(4000) STARTING_POSITION NUMBER OBJECT_ID = IV2_IMM_OBJECT_ID IV1_IMM_REF_NAME VARCHAR2(50) E_TCR_RESIDUES VARCHAR2(1000) OBJECT_ID = IV1_CON_OBJECT_ID MHC_ALLELE_EVVARCHAR2(100)
H_ORGANISM_ID H_GAZ_ID IV1_IMM_OBJECT_ID VARCHAR2(1000) MHC_ALLELE_RESTRICTION_ID = MHC_ALLELE_RESTRICTION_ID OBJECT_ID NUMBER NUMBER
VARCHAR2(20) OBJECT_ID = IV2_IMM_OBJECT_ID CELL_NAME
ENDING_POSITION VARCHAR2(85)
NUMBER VARCHAR2(250) MHC_E_RESIDUES VARCHAR2(1000) ANT_TYPEVARCHAR2(50)
H_SEX H_AGE IV1_IMM_EV VARCHAR2(1000) VARCHAR2(1000) REFERENCE_ID VARCHAR2(200)
CELL_TYPEVARCHAR2(85) IV1_CON_OBJECT_ID NUMBER MHC_TCR_RESIDUES OBJECT_ID = IV1_IMM_OBJECT_ID ANT_REF_NAMEVARCHAR2(250)
H_MHC_TYPES_PRESENT NUMBER OBJECT_ID = TCR_OBJECT_ID
OBJECT_TYPE
TISSUE_TYPEVARCHAR2(85) IV2_PROCESS_TYPE VARCHAR2(100) TCR_E_RESIDUES ANT_OBJECT_IDNUMBER
IV1_PROCESS_TYPE IV1_ADJUVANTS VARCHAR2(255) OBJECT_ID = ADT_IV_IMM_OBJECT_ID CALC_ATOM_PAIRSCLOB CALC_E_CONTACT_AREA OBJECT_SUB_TYPE VARCHAR2(200)
ORIGINVARCHAR2(85) NUMBER TCR_MHC_RESIDUES OBJECT_ID = IVT_CON_OBJECT_ID APC_CELL_TYPEVARCHAR2(85)
IV1_ROUTE IV1_DOSE_SCHEDULE VARCHAR2(10) OBJECT_ID = IVT_IMM_OBJECT_ID IV2_ADJUVANTS FLOAT(126) CALC_CELL_CONTACT_AREA FLOAT(126) OBJECT_DESCRIPTION VARCHAR2(535)
MOL1_SEQVARCHAR2(4000) MOL1_MODIFIED_SEQ IV2_ROUTE VARCHAR2(85) OBJECT_ID = IVT_IMM_OBJECT_ID
APC_TISSUE_TYPEVARCHAR2(85)
IV1_DISEASE_ID IV1_DISEASE_STAGE VARCHAR2(85) OBJECT_ID = ADT_IV_CON_OBJECT_ID CALC_E_RESIDUESVARCHAR2(1000) MHC_ALLELE_RESTRICTION DERIVATIVE_TYPE VARCHAR2(500) APC_ORIGINVARCHAR2(85)
VARCHAR2(1000) VARCHAR2(4000) MOL1_MODIFICATION IV2_DOSE_SCHEDULE VARCHAR2(400) CALC_AB_ANT_RESIDUES VARCHAR2(1000) ORGANISM_IDNUMBER
IV1_IMM_TYPE IV1_IMM_REF_NAME MHC_ALLELE_RESTRICTION_ID NUMBER
VARCHAR2(85) MOL1_SOURCE_ID NUMBER OBJECT_ID = IV1_CON_OBJECT_ID IV2_DISEASE_ID VARCHAR2(35) ORGANISM2_IDNUMBER
IV1_IMM_OBJECT_ID IV1_IMM_EV VARCHAR2(85) CALC_E_MHC_RESIDUES VARCHAR2(1000) DISPLAYED_RESTRICTION VARCHAR2(85)
VARCHAR2(400)
OBJECT_ID = IV2_CON_OBJECT_ID MOL2_MODIFIED_SEQ VARCHAR2(4000) IV2_DISEASE_STAGE VARCHAR2(250) CALC_E_TCR_RESIDUES VARCHAR2(1000) REGIONVARCHAR2(1000)
IV1_CON_OBJECT_ID IV2_IMM_TYPE SYNONYMS VARCHAR2(200)
MOL2_MODIFICATION VARCHAR2(85) NUMBER STARTING_POSITION NUMBER
IV2_PROCESS_TYPE IV2_ADJUVANTS VARCHAR2(350) CALC_MHC_E_RESIDUES VARCHAR2(1000) INCLUDES VARCHAR2(85)
MOL2_SOURCE_ID NUMBER OBJECT_ID = IV1_IMM_OBJECT_ID VARCHAR2(85) ENDING_POSITION NUMBER DISEASE_ID = IV1_DISEASE_ID
IV2_ROUTE IV2_DOSE_SCHEDULE VARCHAR2(250) IV2_IMM_OBJECT_ID CALC_MHC_TCR_RESIDUES VARCHAR2(1000) RESTRICTION_LEVEL ORGANISM VARCHAR2(35)
MULT_CHAIN_MOL_NAME VARCHAR2(85) IV2_IMM_REF_NAME VARCHAR2(50) CELL_NAME VARCHAR2(85)
IV2_DISEASE_ID IV2_DISEASE_STAGE NUMBER CALC_TCR_E_RESIDUES VARCHAR2(1000) ORGANISM_NCBI_TAX_ID CLASS VARCHAR2(150)
VARCHAR2(250) CELL_TYPE VARCHAR2(85)
IV2_IMM_TYPE IV2_IMM_REF_NAME VARCHAR2(85) OBJECT_ID = ADT_TCR_OBJECT_ID CALC_TCR_MHC_RESIDUES VARCHAR2(1000) HAPLOTYPE LOCUS SEROTYPE MOLECULE NUMBER
SOURCE_ID = MOL2_SOURCE_ID NUMBER TISSUE_TYPE ORIGIN VARCHAR2(85)
IV2_IMM_OBJECT_ID IV2_IMM_EV VARCHAR2(50) IV2_IMM_EV IV2_CON_OBJECT_ID IVT_PROCESS_TYPE COMMENTS VARCHAR2(2000) VARCHAR2(35)
VARCHAR2(100) CHAIN_I_NAME CHAIN_II_NAME CHAIN_I_LOCUS MOL1_SEQ VARCHAR2(85)
REFERENCE : 2 IV2_CON_OBJECT_ID AB_NAME VARCHAR2(250) SOURCE_ID = MOL1_SOURCE_ID IVT_RESPONDER_CELL_TYPE VARCHAR2(85)
CHAIN_I_MUTATION CHAIN_II_LOCUS VARCHAR2(10) VARCHAR2(4000)
NUMBER NUMBER
IVT_STIMULATOR_CELL_TYPE VARCHAR2(85) MOL1_MODIFIED_SEQ VARCHAR2(4000) DISEASE : 2
REFERENCE_IDNUMBER AB_TYPE CHAIN_II_MUTATION CHAIN_I_SOURCE_ID VARCHAR2(10)
IVT_IMM_TYPE VARCHAR2(50)
VARCHAR2(85) MOL1_MODIFICATION VARCHAR2(85)
REFERENCE_TYPE VARCHAR2(15) CURATION_KEYWORDS AB_MATERIALS_ASSAYED VARCHAR2(100) SOURCE : 1 VARCHAR2(10) DISEASE_ID NUMBER DISEASE_NAME
IVT_IMM_REF_NAME VARCHAR2(250) CHAIN_II_SOURCE_ID
VARCHAR2(2000) AB_IMMUNOGLOBULIN_DOMAIN NUMBER SOURCE_ID NUMBER COMPLEX_ID = COMPLEX_ID VARCHAR2(50) MOL1_SOURCE_ID NUMBER MOL2_MODIFIED_SEQ VARCHAR2(200) SYNONYMS CLOB
IVT_IMM_OBJECT_ID NUMBER VARCHAR2(4000) MOL2_MODIFICATION
AB_C1_MOL_TYPE AB_C2_MOL_TYPE VARCHAR2(85) ACCESSION VARCHAR2(15) VARCHAR2(35) ACCESSION VARCHAR2(15)
IVT_IMM_EV VARCHAR2(100) VARCHAR2(85) MOL2_SOURCE_ID NUMBER
ADT_IV_PROCESS_TYPE VARCHAR2(400) DATABASE NAME VARCHAR2(15) VARCHAR2(35) DISEASE_SOURCE VARCHAR2(15)
IVT_CON_OBJECT_ID NUMBER MHC_ALLELE_RESTRICTION_ID = MHC_ALLELE_RESTRICTION_ID
MULT_CHAIN_MOL_NAME VARCHAR2(85) ORGANISM_ID = H_ORGANISM_ID
ADT_IV_ADJUVANTS VARCHAR2(35) ALIASES VARCHAR2(535) VARCHAR2(10)
ADT_IV_PROCESS_TYPE VARCHAR2(85)
REFERENCE_ID = REFERENCE_ID ADT_IV_ROUTE VARCHAR2(250) CHEMICAL_TYPE VARCHAR2(500) ORGANISM_ID = ORGANISM_ID ORGANISM_ID = ORGANISM2_ID VARCHAR2(35)
ADT_IV_ADJUVANTS VARCHAR2(400)
ADT_IV_DOSE_SCHEDULE NUMBER SOURCE_DATE VARCHAR2(85) VARCHAR2(10)
ADT_IV_ROUTE VARCHAR2(35)
ADT_IV_DISEASE_ID VARCHAR2(85) SEQUENCE DATE VARCHAR2(35)
ADT_IV_DOSE_SCHEDULE VARCHAR2(250) DISEASE_ID = DISEASE_ID DISEASE_ID = CHILD_DISEASE_ID
RECEPTOR ADT_IV_DISEASE_STAGE VARCHAR2(50) CLOB NUMBER NUMBER
SMILES_STRUCT URE VARCHAR2(3500) ADT_IV_DISEASE_ID NUMBER
RECEPTOR_ID REFERENCE_ID NUMBER NUMBER ADT_IV_IMM_TYPE VARCHAR2(250)
SYNONYMSCLOB ADT_IV_DISEASE_STAGE VARCHAR2(85)
REF_NAME VARCHAR2(200) ADT_IV_IMM_REF_NAME NUMBER
ORGANISM_IDNUMBER ADT_IV_IMM_TYPE VARCHAR2(50) MHC_ALLELE_RESTRICT ON_ID = IEDB_MHC_ID MHC_ALLELE_RESTRICTION_ID = CHILD_IEDB_MHC_ID DISEASE_ANCESTRY
STABLE_ID NUMBER ADT_IV_IMM_OBJECT_ID VARCHAR2(3500)
ORGANISM_NAME VARCHAR2(150) ADT_IV_IMM_REF_NAME VARCHAR2(250)
STABLE_NAME SYNONYMS VARCHAR2(200) ADT_IV_IMM_EV NUMBER DISEASE_IDNUMBER
SMILES_IMAGE BLOB ADT_IV_IMM_OBJECT_ID NUMBER
RECEPTOR_ACCESSION VARCHAR2(200) ADT_IV_CON_OBJECT_ID VARCHAR2(200) ALLELE_FINDER_ANCESTRY CHILD_DISEASE_IDNUMBER
ORGANISM_ID = ORGANISM_ID ADT_IV_IMM_EV VARCHAR2(100)
RECEPTOR_TYPE VARCHAR2(200) ADT_AB_NAME VARCHAR2(35) NODE_ID IEDB_MHC_ID NUMBER NUMBER
ADT_IV_CON_OBJECT_ID NUMBER OBJECT_ID = OBJECT_ID
CHAIN1_TYPE VARCHAR2(10) ADT_AB_TYPE VARCHAR2(600) OBI_ID VARCHAR2(1000)
VARCHAR2(85) ORGANISM : 2 ADT_TCR_NAME VARCHAR2(85)
CHAIN1_SPECIES VARCHAR2(10) ADT_AB_MATERIALS_ASSAYED VARCHAR2(85)
VARCHAR2(85) ORGANISM_ID = ADT_H_ORGANISM_ID ORGANISM_ID = H_ORGANISM_ID CHILD_IEDB_MHC_ID NUMBER
ADT_TCR_ORGANISM_ID NUMBER
CHAIN1_NUCLEOTIDE NUMBER VARCHAR2(85) ORGANISM_ID NUMBER NUMBER NUMBER CHILD_OBI_ID VARCHAR2(1000)
VARCHAR2(400) VARCHAR2(35) ORGANISM_ID = APC_H_ORGANISM_ID ADT_TCR_C1_MOL_TYPE VARCHAR2(85)
CLOB VARCHAR2(250) ORGANISM_ID = H_ORGANISM_ID PARENT_TAX_ID VARCHAR2(500) VARCHAR2(50)
ADT_H_GAZ_ID
ADT_TCR_C2_MOL_TYPE VARCHAR2(85)
CHAIN1_GENE_CALL_METHOD VARCHAR2(200) NUMBER VARCHAR2(85) VARCHAR2(50) VARCHAR2(250) ACTIVE_NODE PATH ORGANISM_ID = ADT_TCR_ORGANISM_ID ADT_H_AGE ORGANISM : 1
ADT_H_ORGANISM_ID NUMBER
CHAIN1_V_GENE_CURATED VARCHAR2(200) RANK
NUMBER VARCHAR2(100) NUMBER VARCHAR2(200) ORGANISM_ID = ADT_H_ORGANISM_ID ADT_H_SEXVARCHAR2(10) ADT_H_MHC_TYPES_PRESENT
VARCHAR2(255) ORGANISM_IDNUMBER
CHAIN1_V_GENE_CALCULATED VARCHAR2(200) VARCHAR2(35) VARCHAR2(600) VARCHAR2(1000) ADT_EFFECTOR_CELL_TYPE VARCHAR2(85)
VARCHAR2(85) ORGANISM_ID = SOURCE_ORGANISM_ORG_ID PARENT_TAX_IDNUMBER
CHAIN1_D_GENE_CURATED VARCHAR2(200) ADT_EFFECTOR_TISSUE_TYPE VARCHAR2(85) ACTIVE_NODE NUMBER
CHAIN1_D_GENE_CALCULATED VARCHAR2(200) EPITOPE_OBJECT PATH VARCHAR2(500)
ORGANISM_ID = ORGANISM_ID
CHAIN1_J_GENE_CURATED VARCHAR2(200) ADT_EFFECTOR_ORIGIN VARCHAR2(85) EPITOPE RANK VARCHAR2(50)
EPITOPE_ID NUMBER
CHAIN1_J_GENE_CALCULATED VARCHAR2(200) ORGANISM_NAMES ADT_COMMENTS VARCHAR2(2000) EPITOPE_ID DESCRIPTION NUMBER
OBJECT_ID NUMBER
CHAIN1_FULL_SEQCLOB EFFECTOR_CELL_TYPE VARCHAR2(85) LINEAR_PEPTIDE_SEQ VARCHAR2(535) SOURCE_ANTIGEN_ACCESSION VARCHAR2(50)
ORGANISM_ID NUMBER
CHAIN1_ACCESSIONVARCHAR2(200) EFFECTOR_TISSUE_TYPE VARCHAR2(85) VARCHAR2(4000) SOURCE_ORGANISM_ORG_ID NUMBER
NAME_TXT VARCHAR2(150)
CHAIN1_CDR3_SEQ_CURATED CLOB EFFECTOR_ORIGIN VARCHAR2(85) SOURCE : 2 LINEAR_PEPTIDE_MODIFIED_SEQ VARCHAR2(4000)
NAME_CLASS VARCHAR2(50) MHC_ALLELE_RESTRICTION_ID NUMBER
CHAIN1_CDR3_SEQ_CALCULATED CLOB LINEAR_PEPTIDE_MODIFICATION VARCHAR2(85)
ADT_AB_IMMUNOGLOBULIN_DOMAIN VARCHAR2(85) MHC_ALLELE_NAME VARCHAR2(85) SOURCE_IDNUMBER
CHAIN1_CDR3_CALL_METHOD VARCHAR2(200) NON_AA_SOURCE_IDNUMBER EPITOPE_ID = EPITOPE_ID
ADT_AB_C1_MOL_TYPE VARCHAR2(85) MHC_ALLELE_EV VARCHAR2(100) ACCESSIONVARCHAR2(15)
CHAIN2_TYPEVARCHAR2(10) DISC_SOURCE_IDNUMBER
ADT_AB_C2_MOL_TYPE VARCHAR2(85) MHC_AUTOLOGOUS VARCHAR2(1) DATABASEVARCHAR2(15)
CHAIN2_SPECIESNUMBER ASSAY_TYPE : 1 ASSAY_TYPE_ID NUMBER DISC_REGIONVARCHAR2(4000)
ADT_H_ORGANISM_ID NUMBER APC_CELL_TYPE VARCHAR2(85) NAMEVARCHAR2(535)
CATEGORY VARCHAR2(50) DISC_MODIFICATIONVARCHAR2(85)
CHAIN2_NUCLEOTIDECLOB CHAIN2_GENE_CALL_METHOD ADT_H_GAZ_ID VARCHAR2(255) ALIASESVARCHAR2(500)
ORGANISM_ID = ORG_ID
CHAIN2_V_GENE_CURATED VARCHAR2(200) ASSAY_TYPE VARCHAR2(50) RESPONSE ASSAY_TYPE_ID = AS_TYPE_ID APC_TISSUE_TYPE VARCHAR2(85) MC_REGIONVARCHAR2(4000)
VARCHAR2(200) ORGANISM_ID = CHILD_ORG_ID ORGANISM_ID = ORG_ID ORGANISM_ID = CHILD_ORG_ID
CHAIN2_V_GENE_CALCULATED VARCHAR2(200) ADT_H_AGE ADT_H_SEX VARCHAR2(85) APC_ORIGIN VARCHAR2(85) CHEMICAL_TYPE VARCHAR2(85) SOURCE_ID = NON_AA_SOURCE_ID
ASSAY_TYPE_ID = AS_TYPE_ID VARCHAR2(85) MC_MOL1_SOURCE_IDNUMBER
CHAIN2_D_GENE_CURATED VARCHAR2(200) ADT_H_MHC_TYPES_PRESENT VARCHAR2(10) UNITSVARCHAR2(30) APC_H_ORGANISM_ID NUMBER SOURCE_DATE DATE MC_MOL1_MODIFICATIONVARCHAR2(85)
CHAIN2_D_GENE_CALCULATED VARCHAR2(200) ADT_COMMENTS VARCHAR2(1000) OBI_IDVARCHAR2(100) APC_H_AGE APC_H_SEX VARCHAR2(85) SEQUENCECLOB MC_MOL2_SOURCE_IDNUMBER
CHAIN2_J_GENE_CURATED VARCHAR2(200) ANT_TYPE VARCHAR2(2000) VARCHAR2(10) SMILES_STRUCT URE VARCHAR2(3500)
SYNONYMS CLOB NUMBER
CLASSVARCHAR2(35) APC_H_MHC_TYPES_PRESENT VARCHAR2(1000) MC_MOL2_MODIFICATIONVARCHAR2(85)
CHAIN2_J_GENE_CALCULATED VARCHAR2(200) ANT_REF_NAME ANT_OBJECT_ID VARCHAR2(50) ANT_TYPE VARCHAR2(50) ORGANISM_ID VARCHAR2(150)
CHAIN2_FULL_SEQCLOB ANT_EV VARCHAR2(250) ANT_REF_NAME VARCHAR2(250) ORGANISM_NAME BLOB
DISEASE_ID = IV1_DISEASE_ID
CHAIN2_ACCESSIONVARCHAR2(200) ANT_CON_OBJECT_ID COMPLEX_ID NUMBER ANT_OBJECT_ID ANT_EV NUMBER SMILES_IMAGE
AB_OBJECT_ID VARCHAR2(100) DISEASE : 1
CHAIN2_CDR3_SEQ_CURATED CLOB DISEASE_ID = IV2_DISEASE_ID DISEASE_ID = IV1_DISEASE_ID DISEASE_ID = ANT_CON_OBJECT_ID VARCHAR2(100)
CHAIN2_CDR3_SEQ_CALCULATED CLOB NUMBER NUMBER DISEASE_ID NUMBER DISEASE_NAME ORGANISM_FINDER_SRC_ANCESTRY
COMPLEX_ID NUMBER NUMBER ORGANISM_FINDER_HOST_ANCESTRY
CHAIN2_CDR3_CALL_METHOD VARCHAR2(200) NUMBER VARCHAR2(200) SYNONYMS CLOB IV 2_DISEASE_ID TCR_OBJECT_ID NODE_IDNUMBER
ADT_AB_OBJECT_IDNUMBER DISEASE_ID = ADT_IV_DISEASE_ID NUMBER NUMBER NODE_IDNUMBER
ACCESSION VARCHAR2(15) OBI_IDVARCHAR2(1000)
DISEASE_ID = ADT_IV_DISEASE_ID ADT_TCR_OBJECT_ID ORG_IDNUMBER
DISEASE_SOURCE VARCHAR2(15) SOURCE_ID = SOURCE_ID CHILD_ORG_IDVARCHAR2(500)
OBI_IDVARCHAR2(1000)
TCELL : 2 SOURCE_ID = CHILD_SOURCE_ID SOURCE_ID = SOURCE_ID ORG_IDNUMBER
GAZ_ID = H_GAZ_ID
SOURCE_ID = CHILD_SOURCE_ID CHILD_ORG_ID VARCHAR2(500)
GAZ_ID = ADT_H_GAZ_ID CHILD_OBI_IDVARCHAR2(1000)
TCELL_ID NUMBER RECEPTOR_ID = RECEPTOR_ID
CHILD_OBI_IDVARCHAR2(1000)
REFERENCE_IDNUMBER BCELL_ID = BCELL_ID CHILD_OBI_SPECIES_OBI VARCHAR2(500)
GAZ_ID = H_GAZ_ID GAZ_ID = ADT_H_GAZ_ID
GEOLOCATION : 1
RECEPTOR_ID = RECEPTOR_ID
GAZ_IDVARCHAR2(200)
MOLECULE_FINDER_PROT_ANCESTRY MOLECULE_FINDER_NONP_ANCESTRY
BCELL_RECEPTOR DISPLAY_NAME VARCHAR2(500)
NODE_IDNUMBER NODE_IDNUMBER
TCELL_ID = TCELL_ID BCELL_ID NUMBER RECEPTOR_ID SECONDARY_NAMES VARCHAR2(500)
SOURCE_IDNUMBER SOURCE_IDNUMBER
NUMBER
OBI_IDVARCHAR2(1000) OBI_IDVARCHAR2(1000)
CHILD_SOURCE_ID NUMBER CHILD_SOURCE_ID NUMBER
GAZ_ID = OBI_ID GAZ_ID = CH ILD_OBI_ID
CHILD_OBI_IDVARCHAR2(1000) CHILD_OBI_IDVARCHAR2(1000)
TCELL_RECEPTOR
RECEPTOR_ID NUMBER TCELL_ID GEOLOC_FINDER_ANCESTRY
NUMBER NODE_IDNUMBER
OBI_IDVARCHAR2(200)
CHILD_OBI_IDVARCHAR2(200)
3.9 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