B Cell Discontinuous: Field-by-Field Guide

Epitope Name

(Optional)

This is a free-text field used to capture the name given to the epitope by the submitter (i.e. mAb 3F4 epitope). String must be restricted to 85 characters.

Reference Region

(Optional)

This is a free-text field used to capture the discontinuous amino acid residues comprising the epitope, based on their position(s) in the protein utilized by you in the study. PLEASE NOTE: If these positions match those in the "Discontinuous Residues" field (the next field), this field may be skipped. If there is a discrepancy between the positions in your protein and those in the protein you will cite in the "Epitope Source Protein GenBank ID" please complete this field.

The format must follow standard single-letter amino acid notation followed by the number indicating the position (i.e. E77, D78, P79, A80, D83, L84). Each amino acid/number combination must be separated by a comma and a space.

Discontinuous Residues

(Required)

This is a free-text field used to capture the discontinuous amino acid residues comprising the epitope, based on their position(s) in the "Epitope Source Protein GenBank ID" that is cited (please see the description for the next field). The format must follow standard single-letter amino acid notation followed by the number indicating the position (i.e. E77, D78, P79, A80, D83, L84). Each amino acid/number combination must be separated by a comma and a space.

Epitope Source Protein GenBank ID

(Required)

This field is used to provide the GenBank ID number of the protein from which the epitope is derived. A valid GenBank ID number must be provided, and the correctly positioned amino acids comprising the epitope must be contained within the sequence of the protein that is cited here. GenBank can be accessed at http://www.ncbi.nlm.nih.gov/Genbank/

Epitope Source Organism Taxonomy ID

(Optional)

This field is intended to capture the exact species and strain of the organism from which the epitope is derived. If this condition is satisfied by the "source organism" displayed in the GenBank record that is cited according to the guidelines above, then this field can be left empty and will be automatically populated by the source organism specified in the GenBank record. Otherwise, the source organism can be customized by inputting a taxonomy ID number corresponding to the desired source organism. The source organism that is cited must be of the same species as the organism in the cited GenBank record, but the strain can vary. Valid taxonomy ID numbers can be accessed at http://www.ncbi.nlm.nih.gov/Taxonomy/

Epitope Evidence Code

(Required)

This field is used to describe how certain the source protein and organism to which the epitope is assigned is known. The following selections are available:

• Author provided Identifier

  Use when an exact Genbank ID was used to generate the epitope sequence.

• Exact match to reference information

  Use when the protein source name in GenBank and organism strain name exactly match to only one possible protein in GenBank.

• Representative selection

  Use when there are several potential Genbank matches to the source protein name and/or organism name and you must select among them. For example, there are many Genbank records for the core protein of Hepatitis B.

• Imperfect match

  Use this evidence code when the exact protein or organism name cannot be found in Genbank records. For example, the epitope sequence was derived from a rare clinical isolate not present in NCBI so instead a generic organism name is used.

• Internal Identifier-no external match available

  This choice is to be used every time an internal IEDB source (SRC source) is used. This indicates that there were no Blast matches to a protein from the organism the epitope was derived from.

Epitope Related Object Type

(Optional)

This field is used to relate that the epitope has a relevant relationship with another molecule (for example, a peptide, protein, or an organism). The two choices are:

• The epitope is an analog of:

  Analogs are synthetic constructs of peptide sequences or chemical compounds that share some structural features in common with another sequence or compound.

• The epitope is a mimotope of:

  Mimotopes are functional mimics of natural molecular structures which bear little or no sequence homology to their biological counterparts.

In addition to the above, please select one of the following in order to define the related object (one of #1-3 below is required when related object type is chosen):

1. When the related object is a peptide, complete the following:

Related Peptide Linear Sequence: This is a free-text field used to capture the linear sequence of the peptide employing standard single-letter amino acid notation.

Related Peptide Source Protein GenBank ID: This field is used to provide the GenBank ID number of the protein from which the peptide is derived. A valid GenBank ID number must be provided, and the complete and exact linear sequence of the peptide must be contained within the protein sequence of the protein that is cited here. GenBank can be accessed at http://www.ncbi.nlm.nih.gov/Genbank/

2. When the related object is a protein, complete the following:

Related Protein GenBank ID: This field is used to provide the GenBank ID number of the protein that is mimicked by the epitope. A valid GenBank ID number must be provided. GenBank can be accessed at http://www.ncbi.nlm.nih.gov/Genbank/

3. When the related object is a organism, complete the following:

Related Organism Taxonomy ID: This field is intended to capture the taxonomy ID of the exact species and strain of the organism that is mimicked by the epitope. Valid taxonomy ID numbers can be accessed at http://www.ncbi.nlm.nih.gov/Taxonomy/

Epitope Comments

(Optional)

This is an optional free-text field intended to provide database users with supplemental information about the epitope structure not otherwise provided by the other data fields. The comments must be limited to 2000 characters in length.

Host Organism Tax ID

(Required)

This field should indicate both the species and the strain (if applicable) of the host organism, and is restricted to a single species. Valid taxonomy ID numbers can be accessed at http://www.ncbi.nlm.nih.gov/Taxonomy/

NOTE: The NCBI taxonomy database contains the names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence. For organisms that are not represented in NCBI, such as inbred mouse strains, please use this link to obtain a valid host organism tax ID.

Host Organism Sex

(Optional)

This field captures the sex of the host organism. Valid options are:

• Use "M" for male
• Use "F" for female

Host Organism Age

(Optional)

This field captures the age of the host organism. It is a free-text field restricted to 35 characters.

1^st In Vivo Process Type

(Required)

This field is intended to capture how the host organism acquired the initial in vivo exposure or immunization. The valid selections are:

• Administration in vivo to cause disease

  To be used in cases of experimental induction of a disease by inoculation of an immunogen.

• Administration in vivo to prevent or reduce disease

  To be used when the intent of the immunization protocol is to prevent or reduce the establishment of a disease. To be used only for those assays that do not measure immune recognition directly, but that, instead, record the existence of disease.

• Administration in vivo

  To be used when there is an experimental inoculation of an immunogen and either it does not cause a disease or the outcome is unknown.

• Occurrence of infectious disease

  This is to be selected when an infectious disease is established as a result of a natural encounter with an immunogen. Infectious diseases include parasites. This process type is also to be used for elective (e.g. ingestion) and accidental exposures.

• Occurrence of allergy

  This process type is to be used when an allergic syndrome is established as the result of a natural encounter with an allergen. It will also be used for elective and accidental exposures.

• Occurrence of disease

  This process type is used for diseases that do not correspond to any of the above process types. Examples are toxic syndromes caused by toxins, prion-based diseases, and spontaneous diseases.

• Exposure with existing immune reactivity without evidence for disease

  This process type is to be used when the exposure is assumed because there is immunological recognition (antibody or T cell mediated recognition of the pathogen/allergen or parts of it), as when there is seropositivity for a pathogenic agent, but there is no explicit information regarding a disease outcome. The disease name and stage should be left blank.

• Documented exposure without evidence for disease

  This selection is used when there is a known event of exposure to a pathogenic agent, but there is no explicit information regarding a disease outcome of seropositivity. Examples include household contacts of diseased individuals or hospital staff without any information provided on seropositivity. The disease name and stage should be left blank.

• Environmental exposure to endemic/ubiquitous agent without evidence for disease

  This selection is to be used when there is inferred exposure to a pathogenic agent, by merit of its endemicity or ubiquity, but no information on the disease outcome, seropositivity, or actual events of exposure. For example, EBV exposure in healthy subjects and P.falciparum exposure in an endemic geographic area. The disease name and stage should be left blank.

• Exposure without evidence for disease

  This selection is to be used when there is the need to record an exposure and the above process types do not apply, and "No immunization" is inappropriate. The disease name and stage should be left blank.

• No immunization

  Use this process type when the host has no prior exposure to an immunizing agent relevant to the assay performed. Use this for naive hosts.

• Unknown

  Only use this selection when the route or mode of exposure is unknown.

Disease ID

(Required for select Process types - see chart below)

This field is used to capture the name of the disease afflicting the host organism. Valid selections must be made using the standard disease list available here.
The IEDB disease finder can also be used to search the diseases more efficiently. (PROVIDE LINK TO http://iedb.org/moleculeFinder.php?findertype=14).

NOTE: Submitter should input the complete alpha-numeric ID corresponding to the relevant disease, which will then be translated and displayed as a name in the IEDB. (i.e. inputting "DOID:14067" will lead to the display of "Plasmodium falciparum malaria" as the disease state and inputting "DTREE_00000146" will lead to the display of "severe and complicated malaria" as the disease state.).

Disease Stage

(Required when "Disease ID" is filled)

The Disease Stage field reflects the stage of the disease at the time the experimental data was generated. The Disease Stage may be described as:

• Acute/Recent onset

  A short-term infection or disease characterized by a dramatic onset and rapid recovery. Primary infections fall under this category.

• Chronic

  A long-term infection or illness and partial remission.

• Post

  Recovery from an illness, including latent (potentially existing but not presently evident or realized) and remission (a period during which symptoms of disease disappear [complete remission]). Note that partial remission will be recorded as "chronic."

• Other

  Any disease stage that cannot be classified under the selections above will be classified under "other." Household contacts will be recorded as "other."

• Unknown

  Used when the disease stage is not clearly specified or known.

Immunogen-Epitope Relation

(Required for select Process types - see chart below)

This field defines the relationship between the epitope and the biological agent responsible for the in vivo immunization of the host. The following selections are available:

• Source Antigen

  Select when the exact protein source of the epitope is the immunogen (i.e. protein immunization).

• Source Organism

  Select when the exact source organism of the epitope is the immunogen (i.e. natural or experimental infection).

The following table serves as a guideline for completing the 1^st In Vivo Process Type, Disease ID, and Immunogen-Epitope Relation fields.

1st In Vivo Process Types	Disease ID	Immunogen-Epitope Relation
Administration in vivo	None	Required
Administration in vivo to cause disease	Allowed	Required
Administration in vivo to prevent or reduce disease	None	Required
Occurrence of disease	Required	None
Occurrence of autoimmune disease	Required	None
Occurrence of infectious disease	Required	Required
Occurrence of allergy	Required	Required
Exposure with existing immune reactivity without evidence for disease	DTREE_00000014 or Blank	Required
Documented exposure without evidence for disease	DTREE_00000014 or Blank	Required
Environmental exposure to endemic/ubiquitous agent without evidence for disease	DTREE_00000014 or Blank	Required
Exposure without evidence for disease	DTREE_00000014 or Blank	Required
No immunization	DTREE_00000014 or Blank	None
Unknown	None	Allowed

In Vivo Immunogen Reference Name

(Optional)

This is a free-text field that can be utilized to provide a customized name for the immunogen that may provide more specific details to the user (i.e. Heat-killed Influenza A virus). The text should be limited to 250 characters.

Immunogen Evidence Code

(Required)

This field is used to describe how certain the entire object used as the immunogen is known. The following selections are available:

• Author provided Identifier

  Use when the object is a protein and the exact full protein sequence is provided by a Genbank ID.

• Exact match to reference information
  
  Use according to if the immunogen is a:
  Peptide: Use when the exact peptide sequence is known regardless of the peptide's source protein or organism.
  
  Organism: Use when the object is an organism and the exact species and strain are known.
  
  

• Representative selection
  
  Use according to if the immunogen is a:
  Peptide: Use when the object is a peptide and the exact peptide sequence is not known. This is common when the object is a large peptide construct, for example aa 1-400 of a protein, and the exact sequence of the entire peptide is not known.
  
  Protein: Use when the object is a protein and there are several potential matches in Genbank.
  
  Organism: Use if the object is an organism and the exact strain is unknown (as is common with humans exposed to a natural pathogen) or if several strains would be appropriate.
  
  

• Imperfect match

  Use if the object is an organism and the exact strain cannot be found in NCBI. This is common with rare isolates or species with complicated strain names.

• Internal Identifier-no external match available

  Use when the object is a protein and there is no protein in Genbank representative of the protein used. In this case an IEDB ID (SRC) will be created by the IEDB for your use.

Adjuvants

(Optional)

Please see this link for a complete list of valid selections:

Route

(Optional)

Please see this link for a complete list of valid selections:

Dose Schedule

(Optional)

Free-text field used to provide a description of dosage and number of doses. Text should be limited to 250 characters.

Immunization Comments

(Optional)

This is an optional free-text field intended to provide database users with supplemental information about the immunization protocol not otherwise provided by the other data fields. The comments must be limited to 2000 characters in length.

Assayed Antibody Source Material

(Required)

This field captures the source of the assayed antibodies. Please see this link for a complete list of valid selections:

Assayed Antibody Immunoglobulin Domain

(Required)

This field captures the immunoglobulin domain of the assayed antibodies. Please see this link for a complete list of valid selections:

Assayed Antibody Purification Status

(Required)

This field captures the purification status of the assayed antibodies. Please see this link for a complete list of valid selections:

Assayed Antibody Name

(Optional - required only for monoclonal antibodies)

This field captures the name of the assayed antibodies.

Assayed Antibody Heavy Chain Type

(Optional)

This field captures the heavy chain type of the assayed antibodies. Please see this link for a complete list of valid selections:

Assayed Antibody Light Chain Type

(Optional)

This field captures the light chain type of the assayed antibodies. Please see this link for a complete list of valid selections:

Antigen-Epitope Relation

(Required)

This field defines the relationship between the epitope and the biological agent responsible for eliciting the response from the effector cells in the assay. The following selections are available:

• Source Antigen

  Select when the exact protein source of the epitope is the restimulating agent (i.e. protein restimulation).

• Source Organism

  Select when the exact source organism of the epitope is the restimulating agent.

Antigen Reference Name

(Optional)

This is a free-text field that can be utilized to provide a customized name for the antigen that may provide more specific details to the user. The text should be limited to 250 characters.

Antigen Conformation

(Required)

This field describes the conformational type of the antigen used in a B cell assay as either native or non-native.

• Native

  To be used when no alteration to the tertiary structure of the tested antigen has been made. Native conformation is commonly accepted as the biologically active form of the protein (or other chemical type). This also includes synthetic or recombinant peptides identified by the authors as having native conformation.

• Non-Native/Unknown

  To be used when the tested antigen is not in its native conformation. This would include short synthetic peptides and proteins that are deliberately denatured or denatured in their preparation.

Antigen Evidence Code

(Required)

This field is used to describe how certain the entire object used as the antigen is known. The following selections are available:

• Author provided Identifier

  Use when the object is a protein and the exact full protein sequence is provided by a Genbank ID.

• Exact match to reference information
  
  Use according to if the antigen is a:
  Peptide: Use when the exact peptide sequence is known regardless of the peptide's source protein or organism.
  
  Organism: Use when the object is an organism and the exact species and strain are known.
  
  

• Representative selection
  
  Use according to if the antigen is a:
  Peptide: Use when the object is a peptide and the exact peptide sequence is not known. This is common when the object is a large peptide construct, for example aa 1-400 of a protein, and the exact sequence of the entire peptide is not known.
  
  Protein: Use when the object is a protein and there are several potential matches in Genbank.
  
  Organism: Use if the object is an organism and the exact strain is unknown (as is common with humans exposed to a natural pathogen) or if several strains would be appropriate.
  
  

• Imperfect match

  Use if the object is an organism and the exact strain cannot be found in NCBI. This is common with rare isolates or species with complicated strain names.

• Internal Identifier-no external match available

  Use when the object is a protein and there is no protein in Genbank representative of the protein used. In this case an IEDB ID (SRC) will be created by the IEDB for your use.

Assay Type

(Required)

The Assay Type, Assay Response, and Assay Units fields together display the appropriate assay information. Please note that the three individual fields can only be used in the combinations provided in the list of valid selections. Please see this link for a complete list of valid selections.

Assay Response

(Required)

The Assay Type, Assay Response, and Assay Units fields together display the appropriate assay information. Please note that the three individual fields can only be used in the combinations provided in the list of valid selections. Please see this link for a complete list of valid selections.

Assay Units

(Required)

The Assay Type, Assay Response, and Assay Units fields together display the appropriate assay information. Please note that the three individual fields can only be used in the combinations provided in the list of valid selections. Please see this link for a complete list of valid selections.

Qualitative Measurement

(Required)

Qualitative assessment of the value measured in the assay. Valid selections are:

• Positive
• Positive-Low
• Positive-Intermediate
• Positive-High
• Negative

Quantitative Measurement

(Optional)

Actual numerical value measured in the assay. Valid data must be a number equal or greater than 0.

Number of Subjects Tested

(Optional)

This field captures the number of subjects tested in the assay, and must be a number.

Number of Subjects Responded

(Optional)

This field captures the number of subjects that responded positively in the assay, and must be a number.

Assay Comments

(Optional)

This is an optional free-text field intended to provide database users with supplemental information about the assay not otherwise provided by the other data fields. The comments must be limited to 2000 characters in length.