Iedb Tools

Configuration File: iedb_tools.json Tool Type: Local Tools Count: 8

This page contains all tools defined in the iedb_tools.json configuration file.

Available Tools

iedb_get_epitope_antigens (Type: IEDBTool)

Given an epitope structure_id, get linked antigens (IEDB Query API). Returned rows contain `par…

iedb_get_epitope_antigens tool specification

Tool Information:

• Name: iedb_get_epitope_antigens

• Type: IEDBTool

• Description: Given an epitope structure_id, get linked antigens (IEDB Query API). Returned rows contain parent_source_antigen_iri (an antigen identifier) that you can use in other filters/searches.

Parameters:

• structure_id (integer) (required) IEDB epitope structure ID (from iedb_search_epitopes).

• limit (integer) (optional) Maximum number of rows to return.

• offset (integer) (optional) Pagination offset.

• order (string) (optional) Optional PostgREST order clause.

• select (unknown) (optional) Optional projection list (comma-separated string or array of field names).

• filters (object) (optional) Advanced PostgREST filters mapping column -> filter expression.

Example Usage:

query = {
    "name": "iedb_get_epitope_antigens",
    "arguments": {
        "structure_id": 10
    }
}
result = tu.run(query)

iedb_get_epitope_mhc (Type: IEDBTool)

Given an epitope structure_id, get linked MHC restriction association rows (IEDB Query API). Re…

iedb_get_epitope_mhc tool specification

Tool Information:

• Name: iedb_get_epitope_mhc

• Type: IEDBTool

• Description: Given an epitope structure_id, get linked MHC restriction association rows (IEDB Query API). Returned rows include elution_id for the association.

Parameters:

• structure_id (integer) (required) IEDB epitope structure ID (from iedb_search_epitopes).

• limit (integer) (optional) Maximum number of rows to return.

• offset (integer) (optional) Pagination offset.

• order (string) (optional) Optional PostgREST order clause.

• select (unknown) (optional) Optional projection list (comma-separated string or array of field names).

• filters (object) (optional) Advanced PostgREST filters mapping column -> filter expression.

Example Usage:

query = {
    "name": "iedb_get_epitope_mhc",
    "arguments": {
        "structure_id": 10
    }
}
result = tu.run(query)

iedb_get_epitope_references (Type: IEDBTool)

Given an epitope structure_id, get linked references (IEDB Query API). Returned rows include `r…

iedb_get_epitope_references tool specification

Tool Information:

• Name: iedb_get_epitope_references

• Type: IEDBTool

• Description: Given an epitope structure_id, get linked references (IEDB Query API). Returned rows include reference_id; use iedb_search_references to retrieve titles and PubMed IDs for those reference IDs.

Parameters:

• structure_id (integer) (required) IEDB epitope structure ID (from iedb_search_epitopes).

• limit (integer) (optional) Maximum number of rows to return.

• offset (integer) (optional) Pagination offset.

• order (string) (optional) Optional PostgREST order clause.

• select (unknown) (optional) Optional projection list (comma-separated string or array of field names).

• filters (object) (optional) Advanced PostgREST filters mapping column -> filter expression.

Example Usage:

query = {
    "name": "iedb_get_epitope_references",
    "arguments": {
        "structure_id": 10
    }
}
result = tu.run(query)

iedb_search_antigens (Type: IEDBTool)

Search antigen-related rows (IEDB Query API). This is mainly useful for discovering antigen IRIs/…

iedb_search_antigens tool specification

Tool Information:

• Name: iedb_search_antigens

• Type: IEDBTool

• Description: Search antigen-related rows (IEDB Query API). This is mainly useful for discovering antigen IRIs/IDs to use in other filters.

Tip: use select to request only a few fields (smaller + faster responses).

Parameters:

• limit (integer) (optional) Maximum number of rows to return.

• offset (integer) (optional) Pagination offset.

• order (string) (optional) Optional PostgREST order clause.

• select (unknown) (optional) Optional projection list (comma-separated string or array of field names).

• filters (object) (optional) Advanced PostgREST filters mapping column -> filter expression.

Example Usage:

query = {
    "name": "iedb_search_antigens",
    "arguments": {
    }
}
result = tu.run(query)

iedb_search_bcell (Type: IEDBTool)

Search B-cell assay rows (IEDB Query API). Use this to discover bcell_id values and related epi…

iedb_search_bcell tool specification

Tool Information:

• Name: iedb_search_bcell

• Type: IEDBTool

• Description: Search B-cell assay rows (IEDB Query API). Use this to discover bcell_id values and related epitope structure_id values.

Tip: use select to request only a few fields (smaller + faster responses).

Parameters:

• limit (integer) (optional) Maximum number of rows to return.

• offset (integer) (optional) Pagination offset.

• order (string) (optional) Optional PostgREST order clause.

• select (unknown) (optional) Optional projection list (comma-separated string or array of field names).

• filters (object) (optional) Advanced PostgREST filters mapping column -> filter expression.

Example Usage:

query = {
    "name": "iedb_search_bcell",
    "arguments": {
    }
}
result = tu.run(query)

iedb_search_epitopes (Type: IEDBTool)

Search immune epitopes (IEDB Query API). Use this to discover epitope structure_id values, then…

iedb_search_epitopes tool specification

Tool Information:

• Name: iedb_search_epitopes

• Type: IEDBTool

• Description: Search immune epitopes (IEDB Query API). Use this to discover epitope structure_id values, then use the epitope linking tools (e.g., iedb_get_epitope_references) to retrieve related references, MHC, antigens, etc.

Tips: - Use select to request only a few fields (smaller + faster responses). - For advanced filtering, pass filters with values like eq.123 or ilike.*KVF*.

Parameters:

• sequence_contains (string) (optional) Sequence fragment to search within linear_sequence using a contains match. Example: ‘KVF’ finds epitopes containing that motif.

• structure_type (string) (optional) Filter by epitope structure type. Example: ‘Linear peptide’.

• limit (integer) (optional) Maximum number of rows to return.

• offset (integer) (optional) Pagination offset.

• order (string) (optional) Optional PostgREST order clause (e.g., ‘structure_id.asc’).

• select (unknown) (optional) Optional projection list to reduce payload size. Provide a comma-separated string or an array of field names (e.g., [‘structure_id’,’linear_sequence’]).

• filters (object) (optional) Advanced PostgREST filters mapping column -> filter expression (e.g., {“linear_sequence”:”ilike.*KVF*”}).

Example Usage:

query = {
    "name": "iedb_search_epitopes",
    "arguments": {
    }
}
result = tu.run(query)

iedb_search_mhc (Type: IEDBTool)

Search MHC-related assay rows (IEDB Query API). Use this to discover epitope structure_id value…

iedb_search_mhc tool specification

Tool Information:

• Name: iedb_search_mhc

• Type: IEDBTool

• Description: Search MHC-related assay rows (IEDB Query API). Use this to discover epitope structure_id values involved in MHC restriction.

Tip: use select to request only a few fields (smaller + faster responses).

Parameters:

• limit (integer) (optional) Maximum number of rows to return.

• offset (integer) (optional) Pagination offset.

• order (string) (optional) Optional PostgREST order clause.

• select (unknown) (optional) Optional projection list (comma-separated string or array of field names).

• filters (object) (optional) Advanced PostgREST filters mapping column -> filter expression.

Example Usage:

query = {
    "name": "iedb_search_mhc",
    "arguments": {
    }
}
result = tu.run(query)

iedb_search_references (Type: IEDBTool)

Search references/citations (IEDB Query API). Use this to discover reference_id values, PubMed …

iedb_search_references tool specification

Tool Information:

• Name: iedb_search_references

• Type: IEDBTool

• Description: Search references/citations (IEDB Query API). Use this to discover reference_id values, PubMed IDs, and paper titles.

Tip: use select to request only a few fields (smaller + faster responses).

Parameters:

• limit (integer) (optional) Maximum number of rows to return.

• offset (integer) (optional) Pagination offset.

• order (string) (optional) Optional PostgREST order clause.

• select (unknown) (optional) Optional projection list (comma-separated string or array of field names).

• filters (object) (optional) Advanced PostgREST filters mapping column -> filter expression.

Example Usage:

query = {
    "name": "iedb_search_references",
    "arguments": {
    }
}
result = tu.run(query)

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