View source for Data Field Descriptions

==Introduction==

This document contains a listing of all of the fields in the IEDB with a brief description of how they are used by curators when entering the data. Please refer to the curation manual for more details on these fields or on curation rules. 
We welcome questions and/or feedback: help@iedb.org



==Epitope Fields==

This section captures the molecular structure of an epitope, which is defined as the structure interacting with receptors of the immune system (T cell, B cell/ antibody, MHC).

The fields utilized to capture epitope information are as follows:

'''Epitope location'''
This is a free text field used to identify where the exact sequence or structure of the epitope was provided, whether within the manuscript or if it was found outside of the primary reference. Tables, figures, text, or text sections, such as materials and methods, where the actual structure was provided should be entered. 

'''Epitope Name'''
This field should reflect how the author refers to the epitope being curated (p22, FLU 307-319, etc). If no name was provided by the author, the antigen name followed by the residues is acceptable (HA 307-319). 

'''Reference Starting Position and Reference Ending Position'''
The author specified positions are always recorded in the Reference Starting Position and Reference Ending Position fields exactly as the authors indicated them. Do not edit what the authors published. 

'''Reference Region'''
For conformational epitopes, the reference region field is to be filled with the conformational residues and positions exactly as stated by the authors.

'''Epitope Object'''
The epitope structure is entered via the Object Editor [[#Epitope Object]]


===='''Epitope Object'''====

The epitope structure is curated via the Object Editor. Assign the epitope’s source organism based on what the authors say. 
The object editor will allow an epitope to be of the following object types and subtypes:

*'''Sequence Molecule, no natural source'''
Subtypes: Peptide, no natural source, DNA, no natural source, and RNA, no natural source. This selection is used only for sequence molecules (peptides, RNA, DNA) that do not have a natural source. Epitopes of this type cannot have a natural source entered. They also cannot have source antigen and source organism as antigen or immunogen relations.

*'''Fragment of a natural sequence molecule'''
Subtype: Peptide from Protein. This selection is made for peptide sequences that are derived from natural proteins. The majority of epitopes will fall into this category. Epitopes of this type must have a natural source entered into the object editor.

*'''Discontinuous region on accession sequence molecule'''
Subtype: Discontinuous protein residues. This selection refers to discontinuous sequence epitopes. Epitopes of this type must have a natural source entered into the object editor.

*'''Region on Multi-Chain Molecule''' 
Subtype: Region on Multi-Chain Protein. This is the subtype to select for discontinuous epitopes that are made up of residues that reside on two chains of a multi-chain molecule. If the epitope is made up of residues that are only found on one chain of a multi-chain molecule, the single chain protein should be captured as the epitope source and the epitope object type and subtype will be Fragment of a natural sequence molecule-Peptide from Protein.

*'''Fragment of  a Natural Non-Sequence Molecule''' 
Subtypes: Peptidoglycan fragment, Glycolipid fragment, Carbohydrate fragment, Lipid fragment, Fatty acid fragment, Other fragment. This selection refers to natural non-sequence molecules that are derived from a larger natural molecule. Epitopes of this type must have a natural source which contains the epitope structure entered into the object editor. These epitope structures and their sources are selected from the Molecule Finder.

*'''Accession Non-sequence Molecule'''
Subtypes: Peptidoglycan, Glycolipid, Carbohydrate, Lipid, Fatty acid, Other. This selection refers to any non-sequence molecule that is not derived from a larger natural molecule. It may be natural or artificial. Epitopes of this type may have a source organism entered into the object editor, if needed. These epitope structures are selected from the Molecule Finder.

*'''Discontinuous Region on a Natural Non-Sequence Molecule''' 
Subtype: Polysaccharide repeating unit. This type is used for discontinuous non-sequence epitopes. Currently, only polysaccharide repeating units have been curated. These epitope structures and their sources are selected from the Molecule Finder.


====='''Object Editor'''=====

[[Image:objeditorpeptide.jpg]]

Once the object type and subtype have been selected, the object editor allows you to enter the peptide sequence of the epitope, select its source antigen from the molecule finder, and select its source organism from the organism finder.
 
First enter the peptide sequence and then click on the '''Molecule Finder''' button. The finder will search the previously used sources for ones that contain the peptide sequence that you entered and will only return hits that match and/or IEDB created source IDs (SRCs). When you see a molecule that contains the epitope sequence and its name matches the text of the reference, you then select it. The source organism will be auto-populated with the source organism of the molecule. You may need to alter the strain information to match your reference. Do not change the organism information across species.

The molecule finder will calculate the positions of the peptide within the source you selected and will auto-fill the starting and ending positions within the editor. These positions may or may not match the Reference Positions that you enter outside of the editor.

[[Image:objedisct.jpg]]

In order to enter discontinuous/conformational peptide epitopes, you follow the same steps, however, you enter '''Swiss-Prot/GenBank''' numbering along with the residues utilizing standard amino acid notation in the '''Discontinuous Residues''' field '''within''' the object editor.





[[Image:objeddisP.jpg]]

Non-sequence epitopes and their sources are selected from the '''Molecule Finder'''. If the non-sequence molecule that is needed is not already present within the Molecule Finder, see a senior curator to add this molecule along with its SMILES structure.

====Epitope Fields====

'''Epitope Evidence Code'''

This drop down menu is used to describe how certain the curator is of the source to which  he/she assigned the epitope. In some cases authors will provide exactly the accession ID for the epitope's source, while in other cases, the exact source organism may be vague.


*'''Author provided Identifier'''-Select this when the authors provide a Uniprot/Genbank ID & the epitope sequence is found within that source.


*'''Exact match to reference information'''-Use this selection when the source name and organism name exactly match the text and there is no doubt regarding the accession being the one intended by the authors.


*'''Representative selection''' (based on incomplete info)-Use this selection when there are several potential matches to the author provided source name and/or organism name and you must select among them.


*'''Imperfect match'''-Use this evidence code when the epitope sequence is found only within a source and/or organism strain that differs from exactly the source that the manuscript refers to. Do not assign sources across organism species. Because internal identifiers can be created, this is only to be used when the SRC would only be used  for this one case, and therefore will not be generated. An example is when a very specific lab strain was used.


*'''Internal Identifier-no external match available'''-This choice is to be made every time an internal IEDB source (SRC source) is selected.


'''Epitope Structure Defines'''


This is a drop down menu used to describe to what level the epitope structure was defined. Define the epitope as an exact epitope if the authors state that it is defined, optimal, or minimal. If the authors do not specify whether the epitope is minimal or not, then use the guidelines below. 

The choices are:

*'''exact epitope'''-For linear Antibody/B Cell and Class I epitopes, if the sequence is 11 residues or less in length (with a minimum of 7 aa for class I epitopes), the epitope should be designated as an Exact Epitope. For linear Class II epitopes, select Exact Epitope if the sequence is 15 residues or less in length.
*'''epitope containing region/antigenic site'''-For linear Antibody/B Cell and Class I epitopes, if the sequence is 12 residues or greater, Epitope Containing Region/Antigenic Site should be selected. For linear Class II epitopes, select Epitope Containing Region/Antigenic Site if the epitope sequence is 16 residues or greater in length.  
*'''partial epitope'''-For nonlinear/discontinuous epitopes and the curation of key residues, select Partial, Epitope Containing Region/Antigenic Site or Exact Epitope as applicable. 
*'''deduced epitope'''-Use this selection to describe epitope structures that were never actually tested in experimental assays, but were instead deduced via overlapping peptide scans, deletions, or mutations, etc. If an epitope is deduced and then tested in an assay, do not select this choice.See [[Curation Manual2.0#Deduced Epitopes]] for more information. 


'''Related Object Type'''
This is a drop down menu used to relate that the epitope has a relevant relationship with another molecule. The two choices are analog and mimotope. Select the appropriate choice and enter as much information as you can regarding the object. One may enter an organism name, an accession molecule, and/or a peptide sequence.
:'''The epitope is an analog of:'''-See the guidelines on [[Curation Manual2.0#Analogs]] before curating an epitope which is an analog. In most cases, analogs are not captured as epitopes. Analogs are artificial mutants of natural molecular structures with sequence homology to their biological counterparts.
:'''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.  Mimotopes should be captured as separate epitope records. See [[Curation Manual2.0#Mimotopes]] for more information.

'''Epitope Comments''' 
As with all comments fields, these fields should only be used when necessary. The comments should be a complete “stand alone” concept written in proper American English and must provide information of value that would otherwise be lost given the current IEDB fields. Any information derived from an assay belongs in the '''Comments on Assay''' field rather than the '''Epitope Comments''' field. Standardized comments may be utilized to provide examples of the type of information this field is meant to convey.

==MHC Binding Assay Fields==

Experimental data characterizing the interaction between an epitope and an MHC molecule is entered under the tab labeled MHC binding.

===MHC Fields===
The fields utilized to capture MHC binding contexts are as follows:

'''Location of Data'''
This field is used to identify where the MHC binding data appears. All tables, figures, or text where the actual binding data is provided should be entered. If bulking different figures or tables, enter all of them here. 

===='''Assay Information'''====

'''Assay'''

The '''Assay Finder''' is used to select the '''Assay Type''', '''Assay Type Group''', and '''Assay Type Units'''. 
The units available are EC50 nM, IC50 nM, t1/2 (min), Other (see comments)/None, KD nM, Koff (s^-1), Tm (degree C), and Angstroms. Be sure to utilize the correct units for the assay you are entering.

'''Qualitative Measurement'''
The <u>Qualitative Measurement</u> field is a '''''required field '''''. Select the appropriate response based upon the figures and text provided in the manuscript. All assay contexts in the database must be labeled as either positive or negative. 

It consist of a drop down menu of:
*Positive
*Positive-Low
*Positive-Intermediate
*Positive-High
*Negative

'''Measurement Inequality'''
These selections may be used in order to add additional information regarding the quantitative value. 

'''Quantitative Measurement'''
Whenever quantitative data are available, they must be captured.
Always capture quantitative values, when provided, for MHC binding assays. Be sure to select the appropriate units and check your math if conversions are required.


'''Assay Comments'''
This field is used to enter comments relevant to the binding assay such as comparisons made between the binding of an analog or mutant epitope to the binding of the native epitope. As with all comments fields, this field should only be used when necessary. The comments should be a complete “stand alone” concept written in proper English and must provide information of value that would otherwise be lost given the current IEDB fields.

===='''MHC Allele Name'''====
The Allele name is selected from the Allele Finder application. This table includes Allele Name, Class, Organism, Restriction level, Haplotype, Locus, Serotype, and Molecule. Each of the table headings can be used to order the table. The search window allows one to search by organism, class, and allele. Synonyms will also be found so if you enter an allele name into the finder and a different allele name is returned, be sure to note that they are synonyms.


==MHC Ligand Elution Fields==

The fields utilized to describe MHC Elution Assays are as follows:

'''Location of Data'''
This field is used to identify where the MHC elution data appears. All tables, figures, or text where the actual data is provided should be entered. If bulking different figures or tables, enter all of them here. 

'''Host Organism Name'''
Use the organism finder to select both the species and the strain of the host organism. Multiple hosts with the same MHC may be bulked. If so, then a comment must be made. See the section on [[Curation Manual2.0#Host Organism]] for more details.

'''Sex'''
Choices are M, F, or blank. Always capture the sex if possible.

'''Age'''
This is a free text field to enter the age(s) or range of the hosts. Always capture when provided.

'''MHC Types Present'''
In cases where the peptide is eluted from an indistict MHC group (HLA-DR), this field may be used to further describe the MHC present (HLA-DRB1).

====In vivo Process====

In order to capture an in vivo process, the organism from which the APC were derived must have been exposed to a relevant immunogen in vivo prior to harvesting the APC from the animal. If the APC were instead exposed to the immunogen in vitro, do not capture an in vivo process, but do select the in vivo process type of "No immunization". Describe the in vitro exposure of the APC to the immunogen in an in vitro process. If the organism is exposed in vivo and after harvest, the APC are also exposed in vitro, curate both in vivo and in vitro processes.

'''1st In Vivo Process Type'''

Select from the drop down menu the most applicable type. See the section on [[Curation Manual2.0#Process Types]] for further details.

'''Disease State'''
If the host organism has/had a disease that is/was the result of exposure to the immunogen being curated, use the Disease Finder to select the appropriate disease from those listed by ICD10 or generated by the IEDB. Be sure to follow the guidelines for Disease State for the in vivo Process type which was selected [[Curation Manual2.0#Process Types]]. Refer to the section on [[Curation Manual2.0#Disease State and Stage]] for further details.

'''Disease Stage'''
If disease state is filled, stage must also be filled and vice versa. The choices are:
*Acute
*Chronic
*Other
*Post
*Unknown
Refer to the section on [[Curation Manual2.0#Disease State and Stage]] for further details.

'''Immunogen Reference Name'''
This field is used to describe situations where the reference provides additional information regarding the immunogen such as life stage, fixation state, etc, than the object name as it appears in the object fields. 

'''Immunogen'''
The immunogen is entered via the object editor. First the relationship of the immunogen to the epitope must be selected. This drop down list is generated based upon the object type of the epitope to which the assay is associated. For example, if the epitope is of the object type Sequence molecule, no natural source, then the Immunogen Epitope Relation drop down list will not contain "Source Organism" as a choice because the epitope is not natural and therefore, it does not have a source organism. See the sections on [[Curation Manual2.0#Object Types and Subtypes]] and [[Curation Manual2.0#Epitope Relations]] for full explanations.

<u style="color:red">'''Important Note:'''</u> The immunogen is never the epitope. When curating MHC Ligand Elution contexts in which the organism is exposed to or the antigen presenting cells are incubated with the source organism of the epitope, the protein from which the epitope was derived, or a fragment of the source antigen, the immunogen should not be <epitope>, but rather the larger antigen from which the cells derived the epitope should be selected (source protein or source organism that was processed).

When the origin of the eluted peptide is not specifically known, the following guidelines apply:<br>
-epitope of viral origin is eluted, the antigen epitope relation is <source organism><br>
-epitope of known self origin is eluted, the antigen epitope relation is <source antigen><br>
-epitope of unknown origin is eluted, the antigen epitope relation is <other><br>


'''Immunogen Evidence Code'''

This drop down menu is used to describe how certain the curator is of the object he/she assigned as the immunogen. In some cases authors will provide exactly the accession ID for the immunogen, while in other cases, the exact immunogen may be vague.


*'''Author provided Identifier'''-Select this when the authors provide a Uniprot/Genbank ID or NCBI Taaxonomy ID for the immunogen.


*'''Exact match to reference information'''-Use this selection when the source name and organism name exactly match the text and there is no doubt regarding the immunogen object being the one intended by the authors.


*'''Representative selection''' (based on incomplete info)-Use this selection when there are several potential matches to the author provided source name and/or organism name and you must select among them.


*'''Imperfect match'''-Use this evidence code when the closest match to the immunogen name in the reference is a source and/or organism strain that differs from exactly what the manuscript refers to. Do not assign sources across organism species. Because internal identifiers can be created, this is only to be used when the SRC would only be used  for this one case, and therefore will not be generated. An example is when a very specific lab strain was used.


*'''Internal Identifier-no external match available'''-This choice is to be made every time an internal IEDB source (SRC source) is selected.


'''Immunogen Containing Object'''

The object editor is used to create the object that acts as a carrier, a delivery mechanism, or an expression mechanism for the immunogen. There is no need to repeat information regarding the immunogen unless it helps explain the carrier construct. For example, when the immunogen appears in the middle of a longer peptide construct, you may want to enter the entire peptide sequence. 

The possible object types for container objects are as follows:

*'''Recombinant Organism'''-Enter both the organism which is recombinant and the insert that has been engineered into it.
*'''Plasmid'''-Only enter information regarding the insert that is expressed by the plasmid.
*'''Infected Cell'''-Select the cell type which is infected. 
*'''Transfected Cell'''-Select the cell type and describe what is transfected into it.
*'''Pulsed Cell'''-Select the cell type and describe what is pulsed onto it.
*'''Display Library'''-Select from the subtypes of Phage display, Yeast display, Bacterial display, and Ribosomal display.
*'''Complexed Molecules'''-Select from a list of subtypes which allows the entry of peptide sequences, proteins, and all nonsequence molecule types. Peptide conjugate, Protein conjugate, and Multi-Antigenic Peptide (MAP) are commonly used subtypes.


'''Adjuvants'''
Select from an alphabetical drop down list that contains commonly used adjuvants. For rare adjuvants, select "Other" and use the Immunization Comments field to explain what was used.


'''Route'''
Select from an alphabetical list of commonly used routes. For rare routes, select "Other" and use the Immunization Comments field to explain how the immunization was performed.


'''Dose Schedule'''
This field should be filled with a very short description of dosage and number of doses. See standardized text for appropriate text, but be sure to remove the brackets that are contained in the standardized text.

====In vitro Process====

Use these fields to describe exposure of APC to an immunogen in vitro. 

'''In Vitro Administration Process Type'''

Currently the two choices are:

*'''Administration in vitro''' -select this choice when naive APC are exposed in vitro

'''Immunogen Reference Name'''
This field is used to describe situations where the reference provides additional information regarding the immunogen such as life stage, fixation state, etc, than the object name as it appears in the object fields. 

'''Immunogen'''
The immunogen is entered via the object editor. First the relationship of the immunogen to the epitope must be selected. This drop down list is generated based upon the object type of the epitope to which the assay is associated. For example, if the epitope is of the object type Sequence molecule, no natural source, then the Immunogen Epitope Relation drop down list will not contain "Source Organism" as a choice because the epitope is not natural and therefore, it does not have a source organism. See the sections on [[Curation Manual2.0#Object Types and Subtypes]] and [[Curation Manual2.0#Epitope Relations]] for full explanations.

<u style="color:red">'''Important Note:'''</u> The immunogen is never the epitope. When curating MHC Ligand Elution contexts in which the organism is exposed to or the antigen presenting cells are incubated with the source organism of the epitope, the protein from which the epitope was derived, or a fragment of the source antigen, the immunogen should not be <epitope>, but rather the larger antigen from which the cells derived the epitope should be selected (source antigen or source organism that was processed).


'''Immunogen Evidence Code'''

This drop down menu is used to describe how certain the curator is of the object he/she assigned as the immunogen. In some cases authors will provide exactly the accession ID for the immunogen, while in other cases, the exact immunogen may be vague.


*'''Author provided Identifier'''-Select this when the authors provide a Uniprot/Genbank ID or NCBI Taaxonomy ID for the immunogen.


*'''Exact match to reference information'''-Use this selection when the source name and organism name exactly match the text and there is no doubt regarding the immunogen object being the one intended by the authors.


*'''Representative selection''' (based on incomplete info)-Use this selection when there are several potential matches to the author provided source name and/or organism name and you must select among them.


*'''Imperfect match'''-Use this evidence code when the closest match to the immunogen name in the reference is a source and/or organism strain that differs from exactly what the manuscript refers to. Do not assign sources across organism species. Because internal identifiers can be created, this is only to be used when the SRC would only be used  for this one case, and therefore will not be generated. An example is when a very specific lab strain was used.


*'''Internal Identifier-no external match available'''-This choice is to be made every time an internal IEDB source (SRC source) is selected.


'''Immunogen Containing Object'''

The object editor is used to create the object that acts as a carrier, a delivery mechanism, or an expression mechanism for the immunogen. There is no need to repeat information regarding the immunogen unless it helps explain the carrier construct. For example, when the immunogen appears in the middle of a longer peptide construct, you may want to enter the entire peptide sequence. 

The possible object types for container objects are as follows:

*'''Recombinant Organism'''-Enter both the organism which is recombinant and the insert that has been engineered into it.
*'''Plasmid'''-Only enter information regarding the insert that is expressed by the plasmid.
*'''Infected Cell'''-Select the cell type which is infected. 
*'''Transfected Cell'''-Select the cell type and describe what is transfected into it.
*'''Pulsed Cell'''-Select the cell type and describe what is pulsed onto it.
*'''Display Library'''-Select from the subtypes of Phage display, Yeast display, Bacterial display, and Ribosomal display.
*'''Complexed Molecules'''-Select from a list of subtypes which allows the entry of peptide sequences, proteins, and all nonsequence molecule types. Peptide conjugate, Protein conjugate, and Multi-Antigenic Peptide (MAP) are commonly used subtypes.


'''Immunization Comments'''
Use this field to explain the host or host population and to explain to immunization procedures. If populations, routes, adjuvants, or disease stages were bulked, a comment is mandatory.

===='''Assay Information'''====


'''Assay'''


The '''Assay Finder''' is used to select the '''Assay Type''', '''Assay Type Group''', and '''Assay Type Units'''. 

'''Qualitative Measurement'''
The <u>Qualitative Measurement</u> field is a '''''required field '''''. Select the appropriate response based upon the figures and text provided in the manuscript. All assay contexts in the database must be labeled as either positive or negative. MHC Ligand elution assays are generally only curated when positive.

'''Measurement Inequality'''
These selections may be used in order to add additional information regarding the quantitative value. This field does not apply for Ligand Elution assays.

'''Quantitative Measurement'''
This field also does not apply as these assays do not have units.


====='''Antigen Presenting Cells'''=====
The APC that processed the immunogen and from which the MHC was derived are described here.

'''Cell Tissue Type'''
Select from the drop down menu of tissue types. Use "Other" if the appropriate tissue is not present, add a comment describing the tissue, and consult a senior curator about potentially adding to the list.  

'''Cell Type'''
Select from the drop down menu of cell types. Use "Other" if the appropriate cell type is not present, add a comment describing the tissue, and consult a senior curator about potentially adding to the list.  

'''Cell Culture Conditions'''
This field is used to describe the conditions of the APC at the time of assay. The potential choices are:

*'''Direct Ex Vivo'''
This is used to describe cells that were not exposed to any antigen in vitro prior to assay.

*'''Short Term Restimulated'''
This is used for cells stimulated with an antigen one or more times in vitro which is then washed out prior to the addition of the assay antigen. If cells are restimulated many rounds in vitro, select Cell Line/Clone instead.

*'''Cell Line / Clone'''
Use this selection for cell lines or clones that do not fall into the two following categories (B-LCL and hybridoma)

*'''Cell Line / Clone (EBV tranformed, B-LCL)'''
This is used to describe EBV transformed cell lines

*'''Cell Line / Clone (Hybridoma)'''
This is used to describe cell lines that are fused to create hybridomas

*'''Blast Activated'''
This is used to describe cells which are blast activated. Common examples are PHA and LPS stimulated cells.

*'''In Vivo'''
This selection is only used when the assay is performed in vivo

*'''Other / Unknown'''
Only chose this selection when the conditions of the cells is not described. In the event, the above categories do not apply, see a senior curator.



====='''MHC Allele'''=====

'''MHC Allele Name'''	
The Allele name is selected from the Allele Finder application. This table includes Allele Name, Class, Organism, Restriction level, Haplotype, Locus, Serotype, and Molecule. Each of the table headings can be used to order the table. The search window allows one to search by organism, class, and allele. Synonyms will also be found so if you enter an allele name into the finder and a different allele name is returned, be sure to note that they are synonyms.

'''MHC Evidence Code'''

MHC Ligand Elution evidence codes are as follows:

'''Single allele present:''' To be used when the antigen processing cells are engineered to express on one single MHC.


'''Antibody purification:''' To be used when authors utilize MHC specific antibody in order to isolate the MHC of interest. Please note full list of specific antibodies that may have been used (below). More recent curations will select from the full list of potential antibodies, while older curations will have "Antibody purification" as the evidence code. We are planning future recuration efforts to update these older records with the specific antibody used.


'''Inferred by motif or alleles present:''' To be used when the MHC types present upon the antigen processing cells or expressed in the organism the cells were taken from are used to infer the specific MHC that presented the epitope. MHC binding predictions will also use this evidence code. 


'''Note:''' These are the full list of subtypes for '''Antibody purification:'''

Antibody purification - 10.3.6

Antibody purification - 14.4.4

Antibody purification - 28-14-8S

Antibody purification - 34-5-8S

Antibody purification - B123.2

Antibody purification - B22-249.R1

Antibody purification - B7/21

Antibody purification - B8-24-3

Antibody purification - BB7.2

Antibody purification - HB180

Antibody purification - IVD12

Antibody purification - L243

Antibody purification - LB3.1

Antibody purification - M1/42

Antibody purification - ME1

Antibody purification - MKD6

Antibody purification - SF1-1.1.1

Antibody purification - SPVL3

Antibody purification - Tu39

Antibody purification - W6/32

Antibody purification - Y-3

Antibody purification - Y3JP

====='''Antigen'''=====

'''Antigen Reference Name'''
This field is used to describe situations where the reference provides additional information regarding the antigen.

'''Antigen'''
The antigen is entered via the object editor. First the relationship of the immunogen to the epitope must be selected. The antigen in these assay is always the epitope. "Epitope" is the only available choice.


'''Assay Comments'''
This field is used to enter comments relevant to the elution assay such as conditions that altered processing of the epitope. As with all comments fields, this field should only be used when necessary. The comments should be a complete “stand alone” concept written in proper English and must provide information of value that would otherwise be lost given the current IEDB fields.

==T Cell Assay Fields==

The fields utilized to describe T Cell Assays are as follows:

'''Location of Data'''
This field is used to identify where the T cell data being described by this context appears in the manuscript. All tables, figures, or text where the actual data is provided should be entered. If bulking different figures or tables, enter all of them here. 

'''Host Organism Name'''
Use the organism finder to select both the species and the strain of the host organism. Multiple hosts with the same MHC may be bulked. If so, then a comment must be made. See the section on [[Curation Manual2.0#Host Organism]] for more details.

'''Sex'''
Choices are M, F, or blank. Always capture the sex if possible.

'''Age'''
This is a free text field to enter the age(s) or range of the hosts. Always capture when provided.

'''MHC Types Present'''
In cases where the peptide is recognized in the context of an indistict MHC group (HLA-DR), this field may be used to further describe the MHC present (HLA-DRB1). Additionally, when restriction is not known, the MHC Types present field should be used to describe the alleles present among the responding hosts.

====In vivo Process====

In order to capture an in vivo process, the organism from which the effector cells were derived must have been exposed to a relevant immunogen in vivo prior to harvesting the effector cells from the animal. If the effectors were instead exposed to the immunogen in vitro, do not capture an in vivo process, but do select the in vivo process type of "No immunization". If the organism is exposed in vivo and after harvest, the effectors are also exposed in vitro, curate both in vivo and in vitro processes.

=====1st In Vivo Process Type=====
Select from the drop down menu the most applicable type. See the section on [[Curation Manual2.0#Process Types]] for further details.

'''Disease State'''
If the host organism has/had a disease that is/was the result of exposure to the immunogen being curated, use the Disease Finder to select the appropriate disease from those listed by ICD10 or generated by the IEDB. Be sure to follow the guidelines for Disease State for the in vivo Process type which was selected [[Curation Manual2.0#Process Types]]. Refer to the section on [[Curation Manual2.0#Disease State and Stage]] for further details.

'''Disease Stage'''
If disease state is filled, stage must also be filled and vice versa. The choices are:
*Acute
*Chronic
*Other
*Post
*Unknown
Refer to the section on [[Curation Manual2.0#Disease State and Stage]] for further details.

'''Immunogen Reference Name'''
This field is used to describe situations where the reference provides additional information regarding the immunogen such as life stage, fixation state, etc, than the object name as it appears in the object fields. 

'''Immunogen'''
The immunogen is entered via the object editor. First the relationship of the immunogen to the epitope must be selected. This drop down list is generated based upon the object type of the epitope to which the assay is associated. For example, if the epitope is of the object type Sequence molecule, no natural source, then the Immunogen Epitope Relation drop down list will not contain "Source Organism" as a choice because the epitope is not natural and therefore, it does not have a source organism. See the sections on [[Curation Manual2.0#Object Types and Subtypes]] and [[Curation Manual2.0#Epitope Relations]] for full explanations.

'''Immunogen Evidence Code'''

This drop down menu is used to describe how certain the curator is of the object he/she assigned as the immunogen. In some cases authors will provide exactly the accession ID for the immunogen, while in other cases, the exact immunogen may be vague.


*'''Author provided Identifier'''-Select this when the authors provide a Uniprot/Genbank ID or NCBI Taaxonomy ID for the immunogen.


*'''Exact match to reference information'''-Use this selection when the source name and organism name exactly match the text and there is no doubt regarding the immunogen object being the one intended by the authors.


*'''Representative selection''' (based on incomplete info)-Use this selection when there are several potential matches to the author provided source name and/or organism name and you must select among them.


*'''Imperfect match'''-Use this evidence code when the closest match to the immunogen name in the reference is a source and/or organism strain that differs from exactly what the manuscript refers to. Do not assign sources across organism species. Because internal identifiers can be created, this is only to be used when the SRC would only be used  for this one case, and therefore will not be generated. An example is when a very specific lab strain was used.


*'''Internal Identifier-no external match available'''-This choice is to be made every time an internal IEDB source (SRC source) is selected.


'''Immunogen Containing Object'''

The object editor is used to create the object that acts as a carrier, a delivery mechanism, or an expression mechanism for the immunogen. There is no need to repeat information regarding the immunogen unless it helps explain the carrier construct. For example, when the immunogen appears in the middle of a longer peptide construct, you may want to enter the entire peptide sequence. 

The possible object types for container objects are as follows:

*'''Recombinant Organism'''-Enter both the organism which is recombinant and the insert that has been engineered into it.
*'''Plasmid'''-Only enter information regarding the insert that is expressed by the plasmid.
*'''Infected Cell'''-Select the cell type which is infected. 
*'''Transfected Cell'''-Select the cell type and describe what is transfected into it.
*'''Pulsed Cell'''-Select the cell type and describe what is pulsed onto it.
*'''Display Library'''-Select from the subtypes of Phage display, Yeast display, Bacterial display, and Ribosomal display.
*'''Complexed Molecules'''-Select from a list of subtypes which allows the entry of peptide sequences, proteins, and all nonsequence molecule types. Peptide conjugate, Protein conjugate, and Multi-Antigenic Peptide (MAP) are commonly used subtypes.


'''Adjuvants'''
Select from an alphabetical drop down list that contains commonly used adjuvants. For rare adjuvants, select "Other" and use the Immunization Comments field to explain what was used.


'''Route'''
Select from an alphabetical list of commonly used routes. For rare routes, select "Other" and use the Immunization Comments field to explain how the immunization was performed.


'''Dose Schedule'''
This field should be filled with a very short description of dosage and number of doses. See standardized text for appropriate text, but be sure to remove the brackets that are contained in the standardized text.


=====2nd In Vivo Process Type=====
In cases where the organism was immunized with a second, different, but relevant immunogen in vivo prior to assay, utilize the second in vivo process fields. These fields are identical to the fields for 1st in vivo process.
See the section on [[Curation Manual2.0#Process Types]] for further details.


====In vitro Process====

Use these fields to describe exposure of effector cells to an immunogen in vitro. 

'''In Vitro Administration Process Type'''

The choices are:

*'''Primary induction in vitro''' -select this choice when naive effector cells are exposed in vitro

*'''Restimulation in vitro''' -select this choice when the organism which was the source of the effector cells was previously exposed to an immunogen in vivo prior to the harvest of the effectors and the effectors were also exposed to an immunogen in vitro.


'''Responder Cell Type'''
This field describes the cell population which is exposed in vitro prior to the assay and from which the effector cells will eventually be generated. For example, if PBMC are incubated with an immunogen and then CD8+ cells are subsequently isolated for an assay, this field should reflect "PBMC".
 
'''Stimulator Cell Type'''
This field describes the cells which present the in vito immunogen to the responder population prior to assay. These are APC.


'''Immunogen Reference Name'''
This field is used to describe situations where the reference provides additional information regarding the immunogen such as life stage, fixation state, etc, than the object name as it appears in the object fields. 

'''Immunogen'''
The immunogen is entered via the object editor. First the relationship of the immunogen to the epitope must be selected. This drop down list is generated based upon the object type of the epitope to which the assay is associated. For example, if the epitope is of the object type Sequence molecule, no natural source, then the Immunogen Epitope Relation drop down list will not contain "Source Organism" as a choice because the epitope is not natural and therefore, it does not have a source organism. See the sections on [[Curation Manual2.0#Object Types and Subtypes]] and [[Curation Manual2.0#Epitope Relations]] for full explanations.


'''Immunogen Evidence Code'''

This drop down menu is used to describe how certain the curator is of the object he/she assigned as the immunogen. In some cases authors will provide exactly the accession ID for the immunogen, while in other cases, the exact immunogen may be vague.


*'''Author provided Identifier'''-Select this when the authors provide a Uniprot/Genbank ID or NCBI Taaxonomy ID for the immunogen.


*'''Exact match to reference information'''-Use this selection when the source name and organism name exactly match the text and there is no doubt regarding the immunogen object being the one intended by the authors.


*'''Representative selection''' (based on incomplete info)-Use this selection when there are several potential matches to the author provided source name and/or organism name and you must select among them.


*'''Imperfect match'''-Use this evidence code when the closest match to the immunogen name in the reference is a source and/or organism strain that differs from exactly what the manuscript refers to. Do not assign sources across organism species. Because internal identifiers can be created, this is only to be used when the SRC would only be used  for this one case, and therefore will not be generated. An example is when a very specific lab strain was used.


*'''Internal Identifier-no external match available'''-This choice is to be made every time an internal IEDB source (SRC source) is selected.


'''Immunogen Containing Object'''

The object editor is used to create the object that acts as a carrier, a delivery mechanism, or an expression mechanism for the immunogen. There is no need to repeat information regarding the immunogen unless it helps explain the carrier construct. For example, when the immunogen appears in the middle of a longer peptide construct, you may want to enter the entire peptide sequence. 

The possible object types for container objects are as follows:

*'''Recombinant Organism'''-Enter both the organism which is recombinant and the insert that has been engineered into it.
*'''Plasmid'''-Only enter information regarding the insert that is expressed by the plasmid.
*'''Infected Cell'''-Select the cell type which is infected. 
*'''Transfected Cell'''-Select the cell type and describe what is transfected into it.
*'''Pulsed Cell'''-Select the cell type and describe what is pulsed onto it.
*'''Display Library'''-Select from the subtypes of Phage display, Yeast display, Bacterial display, and Ribosomal display.
*'''Complexed Molecules'''-Select from a list of subtypes which allows the entry of peptide sequences, proteins, and all nonsequence molecule types. Peptide conjugate, Protein conjugate, and Multi-Antigenic Peptide (MAP) are commonly used subtypes.


'''Immunization Comments'''
Use this field to explain the host or host population and to explain to immunization procedures. If populations, routes, adjuvants, or disease stages were bulked, a comment is mandatory.

===='''Adoptive Transfer'''====

==Guidelines on T Cell Assays==

The adoptive transfer fields are used to curate assays performed on epitope specific effector material derived from an animal which received an adoptive transfer of immune material.

In cases where adoptive transfer was performed in a curatable in vivo assay, select the appropriate in vivo assay type of the subtype "after adoptive transfer" and use the adoptive transfer comments field to capture the details of what material was transferred and any procedures performed on the recipient animal.

*In order to be curated, this assay must be epitope relevant, that is, the transferred material must be epitope specific.


'''Adoptive Transfer Comments'''

Explain the adoptive transfer procedure in complete concise sentences.


If the assay is in vitro:

try to bulk the assay under another similar assay without an AT step using the assay comments.

if there is no other assay to bulk it under, select the correct in vitro assay type and be sure to explain the AT steps in the AT comments field.

===='''Assay Information'''====

'''Assay'''

The '''Assay Finder''' is used to select the '''Assay Type''', '''Assay Type Group''', and '''Assay Type Units'''. 
Be sure to utilize the correct units for the assay you are entering.

'''Qualitative Measurement'''
The <u>Qualitative Measurement</u> field is a '''''required field '''''. Select the appropriate response based upon the figures and text provided in the manuscript. All assay contexts in the database must be labeled as either positive or negative. At times, this can be controversial. The overriding rule is to follow what the author states, however, data may be present without comment from the authors regarding the result. For truly confusing data, the author may be contacted for clarification. For data that can be reasonably considered negative or positive based upon other information provided in the manuscript, the curator may make a judgment. 

It consist of a drop down menu of:
*Positive
*Positive-Low
*Positive-Intermediate
*Positive-High
*Negative


'''Measurement Inequality'''
These selections may be used in order to add additional information regarding the quantitative value. 

'''Quantitative Measurement'''
T cell assays do not usually have quantitative values. Quantitative values in FACs assays may be misleading due to gating of specific populations. Be sure to select the appropriate units and check your math if conversions are required.

'''Number of Subjects Tested'''
Use this field to enter the number of subjects that were tested or the number of distinct subjects that effector cells were assayed from.	

'''Number of Subjects Responded'''	
Of the number tested, enter the number that responded by recognition of the assay antigen.

'''Response Frequency (%)'''
This field will be calculated for you if you enter the above two values. If the percentage of subjects that responded is known, but the number tested and number responded is not known, enter the response frequency here.

====='''Effector Cells'''=====

Effector cell assignment is made following these guidelines:

*Phenotype identification- Direct demonstration of the effector cell phenotype will be used to assign effector cell type. For example, CD8+ staining of the population producing IFNg. 

*Cell Isolation –Isolation or purification procedures will be used to identify the cell type of the effector cells present in the assay. For example, the use of a cell population after CD8 depletion would be identified as CD4+ T cells. 

*Biological process measured-The response measured by the assay type will '''NOT''' be used to identify the cell type of the effector cells. For example, measurement of proliferation may be an indicator of CD4+ T cells, however, if splenocytes were used in the assay, the effector cell type should be entered as splenocytes. 

*MHC Restriction –MHC restriction of the epitope will '''NOT''' be used to assign the cell type of the effector cells used in the assay. That is, if PBMC are used in an assay utilizing a Class II epitope, PBMC will be entered into the effector cell field. However, assignment of specific MHC restriction or restriction to the level of Class I or Class II should be performed whenever possible and may be attributed to the assay type when the authors state or imply such.


The effector cells that recognized the assay antigen are described via the following fields:

'''Effector Cell Tissue Type'''	
Select from the drop down menu of tissue types. Use "Other" if the appropriate tissue is not present, add a comment describing the tissue, and consult a senior curator about potentially adding to the list.  

'''Effector Cell Type'''
Select from the drop down menu of cell types. Use "Other" if the appropriate cell type is not present, add a comment describing the tissue, and consult a senior curator about potentially adding to the list.  
When different effector cells are used in the same assay type, they may be bulked. For multiple effector cell types, different T cell lines and clones may be bulked as well as PBMC and select T cell populations (CD4+, for example). When bulking effector cell types, be sure to capture the most relevant data and never bulk different immunogens or different immunized host species.

'''Effector Cell Culture Conditions'''
This field is used to describe the conditions of the effector cells at the time of assay. The potential choices are:

*'''Direct Ex Vivo'''
This is used to describe cells that were not exposed to any antigen in vitro prior to assay.

*'''Short Term Restimulated'''
This is used for cells stimulated with an antigen one or more times in vitro which is then washed out prior to the addition of the assay antigen. If cells are restimulated many rounds in vitro, select Cell Line/Clone instead.

*'''Cell Line / Clone'''
Use this selection for cell lines or clones that do not fall into the two following categories (B-LCL and hybridoma)

*'''Cell Line / Clone (EBV tranformed, B-LCL)'''
This is used to describe EBV transformed cell lines

*'''Cell Line / Clone (Hybridoma)'''
This is used to describe cell lines that are fused to create hybridomas

*'''Blast Activated'''
This is used to describe cells which are blast activated. Common examples are PHA and LPS stimulated cells.

*'''In Vivo'''
This selection is only used when the assay is performed in vivo

*'''Other / Unknown'''
Only chose this selection when the conditions of the cells is not described. In the event, the above categories do not apply, see a senior curator.


======'''Assayed TCR Molecule'''======

The TCR of the effector cells may be described in detail. This is only done when the TCR is chimeric, the author has provided an external identifier (Uni-prot or GenBank ID), or there is additional pertinent information to capture.

'''Assayed TCR Molecule Name'''
This is a free text field to capture the name of the TCR. The name of T cell clones, when specified by the authors, is entered only when there is a clear reason to do so. For example, the authors describe recognition or lack thereof by certain clones and specifically discuss the unusual reactivity of the clones.  Differing fine specificity of clones does not warrant entering the clone names. All clones generated through immunization with the same immunogen may be bulked, regardless of the restimulating antigen, carriers, or adjuvants.

'''Assayed TCR Molecule Chain 1 Type'''	
This is a drop down menu of chain types.

'''Assayed TCR Molecule Chain 2 Type'''	
This is a drop down menu of chain types.

'''Assayed TCR Molecule'''
The TCR molecule is entered via the object editor application. Complete the relevant information for a multi-chain molecule in order to describe the TCR molecule studied in the assay.

====='''Antigen Presenting Cells'''=====

When different APC are used in the same assay type, they may be bulked. Curate the APC giving the best response or the APC type that was used most often in the reference. 
The APC that presented the antigen to the effector cells are described in the same manner as the effector cells above utilizing the following fields:

'''Cell Tissue Type'''

'''Cell Type'''

'''Cell Culture Conditions'''


'''Autologous or Syngeneic'''

The relationship of the source organism of the APC to the source organism of the epitope is described in this field.
The choices are:
*Yes   
*No   
*None 

The default value is set on None so be sure to select Yes or No when entering APC.
Autologous is when the APC are derived from the same organism from whom the effector cells were derived. Syngeneic means genetically identical members of the same species.  

When the APC are not autologous or syngeneic, further describe their source with the following fields:

'''Cell Source Organism'''	

'''Sex	'''

'''Age'''



===='''MHC Allele'''====

'''MHC Allele Name'''	

When restriction of the epitope is known or demonstrated, always capture it here. 
*Different APC with the same MHC should be bulked. 
*Assays performed to demonstrate restriction should be bulked. 
*Positive responses with APC of different MHC should never be bulked. All assays for an epitope with more than one restriction should be duplicated for each positive allele.
*If restriction is demonstrated only to a class level(Class I or Class II), be sure to capture that here. In such a case, you may also use MHC Types present to further describe the alleles present.

The Allele name is selected from the Allele Finder application. This table includes Allele Name, Class, Organism, Restriction level, Haplotype, Locus, Serotype, and Molecule. Each of the table headings can be used to order the table. The search window allows one to search by organism, class, and allele. Synonyms will also be found so if you enter an allele name into the finder and a different allele name is returned, be sure to note that they are synonyms.


'''MHC Evidence Code'''

Further explain how the restriction was demonstrated via the evidence codes. Only one evidence code may be selected at a time, therefore the code referring to the assay type which most narrowly defined the restriction of the epitope should be used. Select the highest one available in each reference and apply it to all assays for that epitope. Bulk restriction determining assays under other assay by the use of the evidence code. The evidence code is meant to replace the need for comments.

The choices are:

*Cited reference
Use this one when the authors state that the restriction of the epitope was already known prior to their publication.

*MHC binding assay
Use this one when authors perform MHC binding assays in the same reference to demonstrate restriction.

*T cell assay -Single MHC type present
This code is to be used when the APC (or tetramer/multimer) utilized in a T cell assay expresses only a single allele and the assay is positive, thus demonstrating the restriction.

*T cell assay -MHC subset identification
Select this code when authors isolate certain subsets of MHC bearing APC (as with an antibody) to demonstrate restriction.

*T cell assay -Mismatched MHC molecules
This code is used when a T cell assay is performed utilizing different APC with different alleles are used to show restriction.

*T cell assay -T cell subset identification
This code refers to the isolation of T cell subsets to show restriction. Blocking antibodies or purification of subsets (CD4/CD8) are commonly used.

*T cell assay -Biological process measured
Use this code when the authors consider the type of response they measured to be indicative of a certain T cell subset, such as CTL assays being Class I restricted.

*MHC binding prediction
This code is to be used when predictive analysis of the epitope-MHC interaction, based upon the sequence or structure of the epitope without experimental assay, is used to infer a restriction.

*Statistical association
This is the lowest evidence code and refers to the association of a positive response with the presence of certain alleles within the responding population.

===='''Antigen'''====

'''Antigen Reference Name'''
This field is used to describe situations where the reference provides additional information regarding the antigen such as life stage, fixation state, etc, other than the object name as it appears in the object fields.

'''Antigen'''
The antigen is entered via the object editor. 
First the relationship of the antigen to the epitope must be selected. This drop down list is generated based upon the object type of the epitope to which the assay is associated. For example, if the epitope is of the object type Sequence molecule, no natural source, then the Antigen Epitope Relation drop down list will not contain "Source Organism" as a choice because the epitope is not natural and therefore, it does not have a source organism. See the sections on [[Curation Manual2.0#Object Types and Subtypes]] and [[Curation Manual2.0#Epitope Relations]] for full explanations.


'''Antigen Evidence Code'''

This drop down menu is used to describe how certain the curator is of the object he/she assigned as the antigen. In some cases authors will provide exactly the accession ID for the antigen, while in other cases, the exact antigen may be vague.


*'''Author provided Identifier'''-Select this when the authors provide a Uniprot/Genbank ID or NCBI Taaxonomy ID for the antigen.


*'''Exact match to reference information'''-Use this selection when the source name and organism name exactly match the text and there is no doubt regarding the antigen object being the one intended by the authors.


*'''Representative selection''' (based on incomplete info)-Use this selection when there are several potential matches to the author provided source name and/or organism name and you must select among them.


*'''Imperfect match'''-Use this evidence code when the closest match to the antigen name in the reference is a source and/or organism strain that differs from exactly what the manuscript refers to. Do not assign sources across organism species. Because internal identifiers can be created, this is only to be used when the SRC would only be used  for this one case, and therefore will not be generated. An example is when a very specific lab strain was used.


*'''Internal Identifier-no external match available'''-This choice is to be made every time an internal IEDB source (SRC source) is selected.


'''Antigen Containing Object'''

The object editor is used to create the object that acts as a carrier, a delivery mechanism, or an expression mechanism for the antigen. There is no need to repeat information regarding the antigen unless it helps explain the carrier construct. For example, when the antigen appears in the middle of a longer peptide construct, you may want to enter the entire peptide sequence. 

The possible object types for container objects are as follows:

*'''Recombinant Organism'''-Enter both the organism which is recombinant and the insert that has been engineered into it.
*'''Plasmid'''-Only enter information regarding the insert that is expressed by the plasmid.
*'''Infected Cell'''-Select the cell type which is infected. 
*'''Transfected Cell'''-Select the cell type and describe what is transfected into it.
*'''Pulsed Cell'''-Select the cell type and describe what is pulsed onto it.
*'''Display Library'''-Select from the subtypes of Phage display, Yeast display, Bacterial display, and Ribosomal display.
*'''Complexed Molecules'''-Select from a list of subtypes which allows the entry of peptide sequences, proteins, and all nonsequence molecule types. Peptide conjugate, Protein conjugate, and Multi-Antigenic Peptide (MAP) are commonly used subtypes.

===='''Assay Comments'''====
This field is used to enter comments relevant to the T cell assay. If bulking different assays, there should be a comment. If neither the immunogen nor the antigen are the epitope, there should be a comment. As with all comments fields, this field should only be used when necessary. The comments should be a complete “stand alone” concept written in proper English and must provide information of value that would otherwise be lost given the current IEDB fields.

==B Cell Assay Fields==

The fields utilized to describe T Cell Assays are as follows:

'''Location of Data'''
This field is used to identify where the T cell data being described by this context appears in the manuscript. All tables, figures, or text where the actual data is provided should be entered. If bulking different figures or tables, enter all of them here. 

'''Host Organism Name'''
Use the organism finder to select both the species and the strain of the host organism. Multiple hosts with the same MHC may be bulked. If so, then a comment must be made. See the section on [[Curation Manual2.0#Host Organism]] for more details.

'''Sex'''
Choices are M, F, or blank. Always capture the sex if possible.

'''Age'''
This is a free text field to enter the age(s) or range of the hosts. Always capture when provided.

'''MHC Types Present'''
In cases where the peptide is recognized in the context of an indistict MHC group (HLA-DR), this field may be used to further describe the MHC present (HLA-DRB1). Additionally, when restriction is not known, the MHC Types present field should be used to describe the alleles present among the responding hosts.

=====In vivo Process=====
In order to capture an in vivo process, the organism from which the antibody(ies) were derived must have been exposed to a relevant immunogen in vivo prior to harvesting the antibody(ies) from the animal. 

======1st In Vivo Process Type======
Select from the drop down menu the most applicable type. See the section on [[Curation Manual2.0#Process Types]] for further details.

'''Disease State'''
If the host organism has/had a disease that is/was the result of exposure to the immunogen being curated, use the Disease Finder to select the appropriate disease from those listed by ICD10 or generated by the IEDB. Be sure to follow the guidelines for Disease State for the in vivo Process type which was selected [[Curation Manual2.0#Process Types]]. Refer to the section on [[Curation Manual2.0#Disease State and Stage]] for further details.

'''Disease Stage'''
If disease state is filled, stage must also be filled and vice versa. The choices are:
*Acute
*Chronic
*Other
*Post
*Unknown
Refer to the section on [[Curation Manual2.0#Disease State and Stage]] for further details.

'''Immunogen Reference Name'''
This field is used to describe situations where the reference provides additional information regarding the immunogen such as life stage, fixation state, etc, than the object name as it appears in the object fields. 

'''Immunogen'''
The immunogen is entered via the object editor. First the relationship of the immunogen to the epitope must be selected. This drop down list is generated based upon the object type of the epitope to which the assay is associated. For example, if the epitope is of the object type Sequence molecule, no natural source, then the Immunogen Epitope Relation drop down list will not contain "Source Organism" as a choice because the epitope is not natural and therefore, it does not have a source organism. See the sections on [[Curation Manual2.0#Object Types and Subtypes]] and [[Curation Manual2.0#Epitope Relations]] for full explanations.

'''Immunogen Evidence Code'''

This drop down menu is used to describe how certain the curator is of the object he/she assigned as the immunogen. In some cases authors will provide exactly the accession ID for the immunogen, while in other cases, the exact immunogen may be vague.


*'''Author provided Identifier'''-Select this when the authors provide a Uniprot/Genbank ID or NCBI Taaxonomy ID for the immunogen.


*'''Exact match to reference information'''-Use this selection when the source name and organism name exactly match the text and there is no doubt regarding the immunogen object being the one intended by the authors.


*'''Representative selection''' (based on incomplete info)-Use this selection when there are several potential matches to the author provided source name and/or organism name and you must select among them.


*'''Imperfect match'''-Use this evidence code when the closest match to the immunogen name in the reference is a source and/or organism strain that differs from exactly what the manuscript refers to. Do not assign sources across organism species. Because internal identifiers can be created, this is only to be used when the SRC would only be used  for this one case, and therefore will not be generated. An example is when a very specific lab strain was used.


*'''Internal Identifier-no external match available'''-This choice is to be made every time an internal IEDB source (SRC source) is selected.


'''Immunogen Containing Object'''

The object editor is used to create the object that acts as a carrier, a delivery mechanism, or an expression mechanism for the immunogen. There is no need to repeat information regarding the immunogen unless it helps explain the carrier construct. For example, when the immunogen appears in the middle of a longer peptide construct, you may want to enter the entire peptide sequence. 

The possible object types for container objects are as follows:

*'''Recombinant Organism'''-Enter both the organism which is recombinant and the insert that has been engineered into it.
*'''Plasmid'''-Only enter information regarding the insert that is expressed by the plasmid.
*'''Infected Cell'''-Select the cell type which is infected. 
*'''Transfected Cell'''-Select the cell type and describe what is transfected into it.
*'''Pulsed Cell'''-Select the cell type and describe what is pulsed onto it.
*'''Display Library'''-Select from the subtypes of Phage display, Yeast display, Bacterial display, and Ribosomal display.
*'''Complexed Molecules'''-Select from a list of subtypes which allows the entry of peptide sequences, proteins, and all nonsequence molecule types. Peptide conjugate, Protein conjugate, and Multi-Antigenic Peptide (MAP) are commonly used subtypes.


'''Adjuvants'''
Select from an alphabetical drop down list that contains commonly used adjuvants. For rare adjuvants, select "Other" and use the Immunization Comments field to explain what was used.


'''Route'''
Select from an alphabetical list of commonly used routes. For rare routes, select "Other" and use the Immunization Comments field to explain how the immunization was performed.


'''Dose Schedule'''
This field should be filled with a very short description of dosage and number of doses. See standardized text for appropriate text, but be sure to remove the brackets that are contained in the standardized text.


======2nd In Vivo Process Type======
In cases where the organism was immunized with a second, different, but relevant immunogen in vivo prior to assay, utilize the second in vivo process fields. These fields are identical to the fields for 1st in vivo process.
See the section on [[Curation Manual2.0#Process Types]] for further details.

====='''Adoptive Transfer'''=====
==Guidelines on B cell Assays==


'''Adoptive Transfer'''

The adoptive transfer fields are used to curate assays performed on epitope specific antibody material derived from an animal which received an adoptive transfer of immune material.

In cases where adoptive transfer was performed in a curatable in vivo assay, select the appropriate in vivo assay type of the subtype "after adoptive transfer" and use the adoptive transfer comments field to capture the details of what material was transferred and any procedures performed on the recipient animal.

*In order to be curated, this assay must be epitope relevant, that is, the transferred material must be epitope specific.


'''Adoptive Transfer Comments'''

Explain the adoptive transfer procedure in complete concise sentences.


If the assay is in vitro:

try to bulk the assay under another similar assay without an AT step using the assay comments.

if there is no other assay to bulk it under, select the correct in vitro assay type and be sure to explain the AT steps in the AT comments field.

====='''Assay Information'''=====

'''Assay'''

The '''Assay Finder''' is used to select the '''Assay Type''', '''Assay Type Group''', and '''Assay Type Units'''. 
Be sure to utilize the correct units for the assay you are entering.

'''Qualitative Measurement'''
The <u>Qualitative Measurement</u> field is a '''''required field '''''. Select the appropriate response based upon the figures and text provided in the manuscript. All assay contexts in the database must be labeled as either positive or negative. At times, this can be controversial. The overriding rule is to follow what the author states, however, data may be present without comment from the authors regarding the result. For truly confusing data, the author may be contacted for clarification. For data that can be reasonably considered negative or positive based upon other information provided in the manuscript, the curator may make a judgment. 

It consist of a drop down menu of:
*Positive
*Positive-Low
*Positive-Intermediate
*Positive-High
*Negative


'''Measurement Inequality'''
These selections may be used in order to add additional information regarding the quantitative value. 

'''Quantitative Measurement'''
Certain B cell assays usually have quantitative values that should be captured. Be sure to select the appropriate units and check your math if conversions are required.

'''Number of Subjects Tested'''
Use this field to enter the number of subjects that were tested or the number of distinct subjects that effector cells were assayed from.	

'''Number of Subjects Responded'''	
Of the number tested, enter the number that responded by recognition of the assay antigen.

'''Response Frequency (%)'''
This field will be calculated for you if you enter the above two values. If the percentage of subjects that responded is known, but the number tested and number responded is not known, enter the response frequency here.


======'''Assayed Antibody'''======

'''Assayed Antibody Source Material'''

This field clarifies the origin and purification status of the antibody used. Values such as serum, purified immunoglobulin, etc are available through a pull down menu.

In the event the antibody binding domain (Fab, Fv, VHH, etc) is artificially displayed on a construct or phage, <Displayed Ab(s)> is selected.


'''Assayed Antibody Immunoglobulin Domain'''	

*When the isotype of the antibody is not specified in the reference, but a known secondary antibody is used, the isotype of the primary antibody may be inferred from the secondary antibody used in the assay. In most of the cases, the '''Chain 1 Isotype''' field will capture the heavy chain and the '''Chain 2 Isotype''' field will capture the light chain.

'''Assayed Antibody Purification Status'''
This field captures if the antibody(ies) tested is monoclonal or polyclonal. Polyclonal monospecific is to be used when the antibody was selected by binding to a specific peptide or when the immunization was performed with a single epitope.


'''Assayed Antibody Name'''

Assayed Antibody Heavy Chain Type	
Assayed Antibody Light Chain Type	
Assayed Antibody

Chimeric antibodies are generated from more than one species.
A description of the multiple species the antibody was derived from is included in the <u>Comments on Assay</u> field.


====='''Antigen'''=====

'''Antigen Reference Name'''
This field is used to describe situations where the reference provides additional information regarding the antigen such as life stage, fixation state, etc, other than the object name as it appears in the object fields.


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

'''Native''' Select <Native> when the 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.

The following will be considered enough evidence for choosing Antigen Conformation Recognized = Native:

Antigen = Source Antigen
 
OR

Antigen = Source Organism

'''AND'''

Assay Type = Neutralization
Antibody dependent Cytotoxicity Assay
Challenge Assay
Cytopathic Effect Assay (CPE)
Hemagglutination-Inhibition
Calorimetry
Colony Immunoblot
Inhibition Assay

'''Non-native/unknown'''  Select <Non-native/unknown> 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.  This value also includes antigens for which the physical nature of the antigen is neither stated by the author, nor decipherable from the paper (unknown).

<u style="color:red">'''Important Note:'''</u> When authors’ state the conformation of the antigen is native, and it is reasonable to believe so, the conformation should be entered as Native, even when the above criteria are not met. Examples of such situations are when assembled viral particles or sporozoites are used in an ELISA and the authors’ specify recognition of native antigen.

<u style="color:red">'''Important Note:'''</u> Assays having different antigen conformations may be bulk curated if the outcome is the same. Bulk curate under the native conformation.


'''Antigen'''
The antigen is entered via the object editor. 
First the relationship of the antigen to the epitope must be selected. This drop down list is generated based upon the object type of the epitope to which the assay is associated. For example, if the epitope is of the object type Sequence molecule, no natural source, then the Antigen Epitope Relation drop down list will not contain "Source Organism" as a choice because the epitope is not natural and therefore, it does not have a source organism. See the sections on [[Curation Manual2.0#Object Types and Subtypes]] and [[Curation Manual2.0#Epitope Relations]] for full explanations.


'''Antigen Evidence Code'''

This drop down menu is used to describe how certain the curator is of the object he/she assigned as the antigen. In some cases authors will provide exactly the accession ID for the antigen, while in other cases, the exact antigen may be vague.


*'''Author provided Identifier'''-Select this when the authors provide a Uniprot/Genbank ID or NCBI Taaxonomy ID for the antigen.


*'''Exact match to reference information'''-Use this selection when the source name and organism name exactly match the text and there is no doubt regarding the antigen object being the one intended by the authors.


*'''Representative selection''' (based on incomplete info)-Use this selection when there are several potential matches to the author provided source name and/or organism name and you must select among them.


*'''Imperfect match'''-Use this evidence code when the closest match to the antigen name in the reference is a source and/or organism strain that differs from exactly what the manuscript refers to. Do not assign sources across organism species. Because internal identifiers can be created, this is only to be used when the SRC would only be used  for this one case, and therefore will not be generated. An example is when a very specific lab strain was used.


*'''Internal Identifier-no external match available'''-This choice is to be made every time an internal IEDB source (SRC source) is selected.


'''Antigen Containing Object'''

The object editor is used to create the object that acts as a carrier, a delivery mechanism, or an expression mechanism for the antigen. There is no need to repeat information regarding the antigen unless it helps explain the carrier construct. For example, when the antigen appears in the middle of a longer peptide construct, you may want to enter the entire peptide sequence. 

The possible object types for container objects are as follows:

*'''Recombinant Organism'''-Enter both the organism which is recombinant and the insert that has been engineered into it.
*'''Plasmid'''-Only enter information regarding the insert that is expressed by the plasmid.
*'''Infected Cell'''-Select the cell type which is infected. 
*'''Transfected Cell'''-Select the cell type and describe what is transfected into it.
*'''Pulsed Cell'''-Select the cell type and describe what is pulsed onto it.
*'''Display Library'''-Select from the subtypes of Phage display, Yeast display, Bacterial display, and Ribosomal display.
*'''Complexed Molecules'''-Select from a list of subtypes which allows the entry of peptide sequences, proteins, and all nonsequence molecule types. Peptide conjugate, Protein conjugate, and Multi-Antigenic Peptide (MAP) are commonly used subtypes.


===='''Assay Comments'''====
This field is used to enter comments relevant to the T cell assay. If bulking different assays, there should be a comment. If neither the immunogen nor the antigen are the epitope, there should be a comment. As with all comments fields, this field should only be used when necessary. The comments should be a complete “stand alone” concept written in proper English and must provide information of value that would otherwise be lost given the current IEDB fields.