IEDB Inclusion Criteria
- 1 Inclusion/Exclusion Criteria
- 1.1 Relevant Experimental Data
- 1.1.1 Experimental Data
- 1.1.2 Scope and Exclusions
- 1.2 Epitopes Relevant to IEDB
- 1.1 Relevant Experimental Data
All articles and epitopes must meet inclusion criteria in order to be included in the database.
Relevant Experimental Data
The reference must report original and experimental epitope-related data.
- Computer derived predictions without functional experimental data will not be included in the database.
- Sequence analysis of defined epitopes will not be included in the database unless novel information is provided (e.g., identification of anchor residues).
- Reviews and meta analysis will not be included in the database.
- Data not shown is not curated.
- Personal communication is not sufficient for curation.
- When encountering data from previous publications which are included in figures or tables, the curator should determine if the previous record was curated and if it was not, the PMID should be sent to the Document Specialist to be included in the database.
Scope and Exclusions
The experimental data must fall within the scope of the database.
Relevant data includes:
- MHC binding data
- Epitope elution from MHC (Naturally processed MHC ligands)
- T cell responses to an epitope (including NK T cells)
- B cell/antibody responses to an epitope
Certain categories of experimental data will be specifically excluded from the database.
Exclusion: NK Epitopes
Epitopes that are recognized by Natural Killer cells (non-T cell) will be excluded from the database. Please note: NK T cell epitopes/ligands will be included (as noted in section (#Scope and Exclusions).
Exclusion: Non-Immunological Interpretation of "Epitope"
Experimental data describing "epitopes" in non-immunological contexts will not be included in the database. For example, the structures that are in contact in protein-protein interactions are sometimes referred to as an epitope. This interpretation of "epitope" will not be included in the database.
Exclusion: Epitope Tags
References discussing epitope tags utilized as a technical tool for immunoprecipitation, purification, and similar experiments will be excluded from the database.
References discussing superantigens in the context of peptide-MHC-super antigen complexes will be excluded from the database. However, B cell/antibody responses to superantigens (especially Staphylococcus enterotoxin B (SEB), a NIAID Category B priority pathogen) will be curated.
Important Note: In the event superantigen is used as part of an assay to stabilize the interaction of an epitope with MHC, the epitope studied is curatable and should be captured.
Exclusion: TCR Antagonism
Data related to TCR antagonism will not be curated. Author stated TCR antagonism will not be curated, however, TCR competition not specifically labeled as TCR antagonism by the authors will be curated. TCR antagonism used in an MHC binding inhibition assay will be captured as an MHC binding assay.
Exclusion: Antigen Processing
Data concerning the processing of antigens generated in order to study the effects of variables on processing rather than on the study of an epitope (i.e. the epitope is irrelevant) are not to be included in the database unless the identification of a novel epitope is demonstrated.
Exclusion: Adoptive Transfer
Assays involving adoptive transfer will not be curated at this time.
Epitopes Relevant to IEDB
|Epitope Class||Uncuratable||Epitopic Region (# residues)||Epitope|
|B-cell||> 5 kDa or 50 amino acids||12 - 50||1 ≤ x ≤ 11|
|Class I||> 5 kDa or 50 amino acids||12 - 50||7 ≤ x ≤ 11|
|Class II||> 5 kDa or 50 amino acids||16 - 50||7 ≤ x ≤ 15|
The database will only include epitopes of less than 50 residues in either a linear or conformational sequence. If the epitope is non-peptidergic, the mass restriction is to be less than 5000 Daltons to be included in the database.
Important Exception: Epitopes greater than 50 residues will be curated for certain pathogens including Botulinum toxin and anthrax epitopes.
A region or fragment of >50aa from B. anthracis and C. botulinum will be curated as an epitopic region in the following cases:
To broaden the spectrum of information in the database, we currently exclude the repeated curation of epitopes once 10 key references have been included in the database. The original articles describing the epitope, MHC restriction data, antibody responses, and articles containing novel information regarding the epitope will be included in the approximately 10 references. A compiled list of "well-characterized" epitopes is listed in Table 2 and can also be found in the Curation Network folder (\\Curation\CurationNotes\blacklisted.xls).
|#||Common Name||Sequence||Positions||Source Species||Source Protein Name||Restriction Allele|
|1||TT Universal Helper epitope||QYIKANSKFIGITE||830-843||Clostridium tetani||Tetanus toxin||DRB1*1302|
|2||OVA 257-264||SIINFEKL||257-264||Gallus gallus (Chicken)||Ovalbumin||Kb|
|3||Ova 323-339||ISQAVHAAHAEINEAGR||323-339||Gallus gallus (Chicken)||Ovalbumin||H2-Ag7, RT1.B1|
|4||HEL 46-61||NTDGSTDYGILQINSR||46-61||Gallus gallus (Chicken)||Hen Egg white Lysozyme||H-2 IAk|
|5||HBV core 18-27||FLPSDFFPSV||18-27||Hepatitis B||Core Protein||A2|
|7||TAX 11-19||LLFGYPVYV||11-19||HTLV||Transcriptional activator (tax)||A*0201|
|8||SYFPEITHI||SYFPEITHI||367-375||Human||Tyrosine kinase JAK1||Kd|
|9||MART-1(27-35)||AAGIGILTV||27-35||Human||MART-1 (Tumor antigen)||A*0201|
|10||NY-ESO-1 epitope||SLLMWITQC||157-165||Human||Cancer/testis antigen NY-ESO-1||A*0201|
|11||Tyrosinase 370D||YMDGTMSQV||368-376||Human||Tyrosinase (Tumor antigen)||A*0201|
|12||gp100 210M||IMDQVPFSV||209-217||Human||Glycoprotein (melanocyte lineage-specific antigen)||A2|
|13||HER-2/neu 689-697||RLLQETELV||689-697||Human||HER-2/neu (Tumor antigen)||A*0201|
|14||HER-2/neu 369-377||KIFGSLAFL||369-377||Human||HER-2/neu (Tumor antigen)||A*0201|
|15||PLP 136-151||HSLGKWLGHPDKF||136-151||Human||Myelin proteolipid protein||H-2 IAs|
|16||MBP Ac1-11||Ac-ASQKRPSQRSK||1-11||Human||Myelin Basic protein||H-2 IAu|
|17||CMV pp65||NLVPMVATV||495-503||Human cytomegalovirus||Phosphoprotein 65 (pp65)||A*0201|
|19||Flu HA 307-319||PKYVKQNTLKLAT||307-319||Influenza||Haemagglutinin||DRB1*0101, DRB1*0401 (DR4Dw4), DRB1*0701, DRB1*1101, DRB5*0101(DR2a)|
|20||PA 224-233||SSLENFRAYV||224-233||Influenza||Acid Polymerase||H-2 Db|
|21||NP 366-374||ASNENMETM||366-374||Influenza||Nucleoprotein||H-2 Db|
|22||NP 147-155||TYQRTRALV||147-155||Influenza||Influenza Nucleoprotein||H-2 Kd|
|23||HA 110-120||SFERFEIFPKE||110-120||Influenza||Haemagglutinin||H-2 IEd|
|24||LCMV gp33||KAVYNFATC||33-41||LCMV||Glycoprotein||Kb, Db|
|25||LCMV gp 276||SGVENPGGYCL||276-286||LCMV||Glycoprotein||Db|
|26||LCMV np 396||FQPQNGQFI||396-404||LCMV||Nucleoprotein||Db|
|27||LCMV np 118-126||RPQASGYM||118-126||LCMV||Nucleoprotein||H-2 Ld|
|28||LLO 91-99||GYKDGNEYI||91-99||Listeria monocytogenes||Listeriolysin O||H-2 Kd|
|29||LLO 215-226||SQLIAKFGTAFK||215-226||Listeria monocytogenes||Listeriolysin O||H-2 IEk|
|30||LLO 190-201||NEKYAQAYPNVS||190-201||Listeria monocytogenes||Listeriolysin O||H-2 IAb|
|31||P60 449-457||IYVGNGQMI||449-457||Listeria monocytogenes||p60||H-2 Kd|
|32||P60 217-225||KYGVSVQDI||217-225||Listeria monocytogenes||p60||H-2 Kd|
|34||NANP||NANP||Plasmodium falciparum (malaria)||Circumsporozoite protein|
|35||MCC 88-103||SYIPSAEKI||252-260||Plasmodium berghei||Circumsporozoite protein||H-2 Kd|
|36||MCC 88-103||ANERADLIAYLKQATK||88-103||Macrobrachium malcolmsonii (moth)||Cytochrome c||H-2 IEk|
|37||Hsp 234-252||LREAAEKAKIELSSSQSTS||234-252||Mycobacterium tuberculosis||Heat shock protein (HSP) 70||RT1.B|
|38||PCC 88-104||KAERADLIAYLKQATAK||88-104||Pigeon||Cytochrome c||H-2 IEk|
The above list plus any well characterized epitopes from additional sources encountered as the range of curated subjects is expanded are to be curated following the exceptions noted below. We avoid curating papers that focus on exploring strategies to enhance well characterized epitope's immunogenicity. These papers use well-characterized peptides to evaluate variables such as alternative immunogen constructs (MAPS/vectors) or adjuvants.
Important Note: When a well-characterized epitope is presented in the context of an epitopic region or domain, the longer peptide will be considered a well-characterized epitope.
- When well-characterized epitopes are studied in a novel host in terms of the MHC, TCR, antibody, or otherwise, the reference will be included in the database.
- When well-characterized epitopes are used as controls they will not be curated. However, when the well-characterized epitope is used as a reference for a novel epitope from the same source protein, the well-characterized epitope will also be captured.
- When a reference describes a well-characterized epitope in addition to other curatable epitopes, all of the epitopes from the reference will be captured.
- At the curators/EC discretion, papers describing new/additional original data relating to these epitopes can and will be curated. For example, if the paper make a novel discovery about the epitope.
References describing only epitopes derived from HIV/SIV will not be included in the database. However, when a manuscript describes epitopes from other relevant sources as well as HIV/SIV, all of the epitopes in the manuscript will be captured.
Epitope curation should be conducted in the following priority order:
A) NIAID Category A, B, and C priority pathogens and toxins:
The complete list of NIAID Category A, B, and C priority pathogens and toxins can be found at the following URL: http://www2.niaid.nih.gov/biodefense/bandc_priority.htm.
NIAID – Category A
Bacillus anthracis (anthrax)
Variola major (smallpox) and other pox viruses
Francisella tularensis (tularemia)
Viral hemorrhagic fevers
LCM, Junin virus, Machupo virus, Guanarito virus
Rift Valley Fever
NIAID – Category B
Coxiella burnetii (Q fever)
Brucella species (brucellosis)
Burkholderia mallei (glanders)
Ricin toxin (from Ricinus communis)
Epsilon toxin of Clostridium perfringens
Staphylococcus enterotoxin B
Typhus fever (Rickettsia prowazekii)
Food and Waterborne Pathogens
Viruses (Caliciviruses, Hepatitis A)
Additional viral encephalitides
West Nile Virus
Japanese Encephalitis Virus
Kyasanur Forest Virus
NIAID – Category C
Tickborne hemorrhagic fever viruses
Crimean-Congo Hemorrhagic fever virus
Tickborne encephalitis viruses
Multi-drug resistant TB
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV)
B) Emerging and Re-emerging pathogens:
Pathogens newly recognized in the past two decades
Australian bat lyssavirus
Hendra or equine morbilli virus
Human herpesvirus 8
Human herpesvirus 6
Coronaviruses/Severe Acute Respiratory Syndrome (SARS)
Streptococcus, group A
- Coccidioides immitis
C) Transplant rejection antigens and other alloantigens, Allergens, and Self antigens involved in autoimmunity
D) Infectious diseases not listed above under sections (#Curation Prioritization) A) and B)
E) Epitopes associated with cancer