Non-peptidic Specific Rules
Non-peptidic epitopes include lipids, carbohydrates, and a variety of drugs and chemicals. Rules to specific groups or individual compounds have been agreed upon. Please follow them to ensure consistency across all curations.
Process for Curating Non-peptidic References
1. When you find a non-peptidic reference in any abstract queue, first make sure the non-peptidic box is checked to allow for accurate statistics.
2. Read the entire manuscript and determine every needed non-peptidic structure used in the paper. This includes all immunogens, antigens, carriers, and epitopes.
3. Request the identified structures by emailing the following to email@example.com: PMID, structure name, and the exact location within the reference where the structure is described.
4. Wait for the ChEBI assignments or precurate using "filler" object IDs. If you use "fillers", you MUST enter the correct epitope name,immunogen and antigen reference names, and write clearly on the coversheet everywhere that the ID will need to be updated in the future. DO NOT click "curation complete" and DO NOT promote these references.
5. Once ChEBI assigns the correct ChEBI ID and it is pushed to their external site, checked, and added to the IEDB internal site, you will be notified.
6. Curate the reference or update the precurated reference and proceed as usual.
Identify Non-peptidic Structures
In most cases, it is clear what is a peptidic vs a non-peptidic epitope, but for modified peptides, such as glycopeptides, some confusion may arise. In the case of a peptide plus any other structure, curate the entire structure as a peptidic epitope plus a modification. Do not curate a peptidic epitope using a CHEBI identifier.
See the section on how to curate modifications: http://curationwiki.iedb.org/wiki/index.php/Curation_Manual2.0#Modified_Amino_Acids.
These haptens are curated with the epitope being the DNP or TNP groups (CHEBI:53018, CHEBI:53067). The exact compound used as immunogen or antigen is captured in the immunogen/antigen fields as being structurally related. Commonly tested immunogen and antigens are DNCB/Dinitrochlorobenzene (CHEBI:34718), DNFB/1-fluoro-2,4-dinitrobenzene (CHEBI:53049), etc.
In the event the immunogen or antigen is the DNP or TNP group, the carrier molecule (typically a protein, sometimes a cell) should also be described.
Although most assayed forms of cardiolipin consist of a mixture of different isoforms of bovine heart cardiolipin, the IEDB has decided to curate this structure because if the mixtures are not curated, extremely little data regarding cardiolipin will be entered into the database.
To assign the source organism of cardiolipin, only assign a source when the authors state they purified it from or used a specific source of the cardiolipin. Otherwise, leave the source organism field blank. Note that if there is no source organism for an epitope, there should be no epitope evidence code.
Epitope Structure Defines:
For cardiolipin, this field should be Epitope containing region/antigenic site.