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 category is assigned 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 filling out the term request google sheet, using the "Proteins tab: https://docs.google.com/spreadsheets/d/1wQwHbqMye_3VPNItqXRiS2svb6sXK13KzAHvBeBlzdI/edit?usp=sharing
Enter your name, date, PMID, structure name, and the exact location within the reference where the structure is described. The ChEBI curator must be able to look up the structure in that location. If the structure exists in a cited reference, enter the PMID for the reference where the structure is located.
4. Wait for the ChEBI assignments or pre-curate 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 (for example, E1A2 Ag, E1A4 Imm, etc). DO NOT click "curation complete" and DO NOT promote these references.
5. Once ChEBI assigns the correct ChEBI ID and adds it to the IEDB internal site, the google term request sheet will be updated.
6. Curate the reference or update the precurated reference and proceed as usual.
Identify Non-peptidic Structures
Is it a peptide? 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.
Non-peptide attached to a protein If the presence of the non-peptidic part is shown to be responsible for the reactivity, curate it as a non-peptidic epitope. The protein is considered a carrier. For example, if the protein alone is not recognized or is only weakly recognized without the non-peptidic part, but the immune reactivity is significant when the non-peptidic part is added, the non-peptidic portion is responsible for that reactivity. Minor differences should not be considered evidence for reactivity, only significant differences.
Determine if the epitope is a stand alone entity or a fragment of a larger structure before you start
Stand alone entities = Accession Non-Sequence Molecule
Are not part of anything else Has no source antigen May or may not have source organism Examples: penicillin, DNCB, nickel
Fragment of accession non sequence = Fragment of a Natural Non-Sequence Molecule
Are a small part of a bigger structure Has source antigen Has source organism Examples: specific carbohydrate moiety of LPS, specific small lipid moiety of larger LOS
Fragment of a Natural Non-Sequence Molecule (subtype Other)
Accession Non-Sequence Molecule (subtype Other)
Will have SRC or ChEBI ID
Will have SRC or ChEBI ID
Maybe protein (GenPept)??
Try to come up with one (preferred)
Use of species level is preferred (human, not mammal)
Use Immunogens and antigens tested for identity if not clear
Immunogen/Antigen Epitope Relationships
If the immunogen or antigen is the source antigen/organism - straightforward
Other structure from source organism – if the immunogen or antigen taxonomic id is the same as the epitope’s
Taxonomic parent, child sibling – does the immunogen or antigen have a source organism? If so, is it related to the epitope? Is it in the same taxonomic family? See https://www.ncbi.nlm.nih.gov/guide/taxonomy/ to determine which taxonomic family the epitope and the immunogen/antigen are in.
Structurally Related – If none of the above apply, this very common. Usually there is a reason they are testing the different structures against each other. but it can be hard to determine. See ChEBI ontology tree for hierarchy
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.
Bulking and Minimal Curation
How to Decide to bulk antigens
It can be hard to tell if an epitope was mapped or not
Use Abstract, Discussion & Conclusion to see what authors state is the minimal or optimal epitope for monoclonal data
- Curate the main mapped epitope, not all the structures tested
For polyclonal data, we usually curate all negative structures tested, but will stop doing this for nonpeptidics
- If many negative structures are tested, bulk under the negative structure that is most similar to the epitope
Always bulk positive structures if a specific epitope was mapped = Curate the best immunogen or Antigen tested per assay type
- If both immunogen and antigen can be epitopes, we usually curate the assays twice but will stop doing this for nonpeptidics
- If both immunogen and antigen can be epitopes, curate just the antigen as the epitope
For example, if an individual allergic to penicillin was tested for reactivity to amoxicillin, then: epitope=amoxicillin, immunogen = structurally related, penicillin, antigen = epitope
If you are not sure what to curate, ask Alex