epitope


Description

The Epitope table describes the epitopes extracted from IEDB.

Columns

Column Type Size Nulls Auto Default Children Parents Comments
epitope_id serial 10 √ nextval('epitope_epitope_id_seq'::regclass)
epitope_2697049_e_envelope_.iedb_epitope_id Implied ConstraintR
epitope_2697049_m_membrane_.iedb_epitope_id Implied ConstraintR
epitope_2697049_n_nucleocap.iedb_epitope_id Implied ConstraintR
epitope_2697049_ns3_orf3a_p.iedb_epitope_id Implied ConstraintR
epitope_2697049_ns6_orf6_pr.iedb_epitope_id Implied ConstraintR
epitope_2697049_ns7a_orf7a_.iedb_epitope_id Implied ConstraintR
epitope_2697049_ns7b_orf7b.iedb_epitope_id Implied ConstraintR
epitope_2697049_ns8_orf8_pr.iedb_epitope_id Implied ConstraintR
epitope_2697049_nsp10.iedb_epitope_id Implied ConstraintR
epitope_2697049_nsp11.iedb_epitope_id Implied ConstraintR
epitope_2697049_nsp12_rna_d.iedb_epitope_id Implied ConstraintR
epitope_2697049_nsp13_helic.iedb_epitope_id Implied ConstraintR
epitope_2697049_nsp14_3_to_.iedb_epitope_id Implied ConstraintR
epitope_2697049_nsp15_endor.iedb_epitope_id Implied ConstraintR
epitope_2697049_nsp16_2_o_r.iedb_epitope_id Implied ConstraintR
epitope_2697049_nsp1_leader.iedb_epitope_id Implied ConstraintR
epitope_2697049_nsp2.iedb_epitope_id Implied ConstraintR
epitope_2697049_nsp3.iedb_epitope_id Implied ConstraintR
epitope_2697049_nsp4.iedb_epitope_id Implied ConstraintR
epitope_2697049_nsp5_3c_lik.iedb_epitope_id Implied ConstraintR
epitope_2697049_nsp6.iedb_epitope_id Implied ConstraintR
epitope_2697049_nsp7.iedb_epitope_id Implied ConstraintR
epitope_2697049_nsp8.iedb_epitope_id Implied ConstraintR
epitope_2697049_nsp9.iedb_epitope_id Implied ConstraintR
epitope_2697049_orf10_prote.iedb_epitope_id Implied ConstraintR
epitope_2697049_orf1a_polyp.iedb_epitope_id Implied ConstraintR
epitope_2697049_orf1ab_poly.iedb_epitope_id Implied ConstraintR
epitope_2697049_spike_surfa.iedb_epitope_id Implied ConstraintR
epitope_fragment.epitope_id epitope_fragment_epitope_id_fkeyR
epitope_iri varchar 2147483647 √ null

Identifies the single epitope within the IEDB system (ID) and allows to resort to its information
iedb_epitope_id int4 10 √ null

Identifies the single epitope within the IEDB system (IRI) and allows to resort to its information
virus_id int4 10 null
virus.virus_id epitope_virus_id_fkeyR
host_id int4 10 null
host_specie.host_id epitope_host_id_fkeyR
protein_name varchar 2147483647 √ null
cell_type varchar 2147483647 √ null

Indicates the target of the experiment (allowing values are ‘T cell’, ‘B cell’, ‘MHC ligand’)
mhc_class varchar 2147483647 √ null

Indicates the general classes of alleles provided in the previous field (possible values are ‘I’, ‘II’, or ‘I,II’ if both class I and II alleles are considered)
response_frequency_pos float4 8,8 √ null

On IEDB this measure is defined as the number of positively responded subjects (R) divided by the total number of those tested (N), summed up by mapped epitopes; however, to compensate for epitopes that are identified by a low number of assays, we employ a corrected formula (proposed in Carrasco et al., 2015), where the importance of corrections decreases as the number of assays increases.
epitope_sequence varchar 2147483647 √ null

Indicates the general classes of alleles provided in the previous field (possible values are ‘I’, ‘II’, or ‘I,II’ if both class I and II alleles are considered).
epi_annotation_start int4 10 √ null

Start coordinate of epitope on protein
epi_annotation_stop int4 10 √ null

Stop coordinate of epitope on protein
external_link varchar 2147483647 √ null

References the publication where the epitope was first reported (and manually collected by IEDB curation team).
prediction_process varchar 2147483647 √ null

Prediction process used for the epitope (now they are all imported from IEDB)
is_linear bool 1 √ null

Defines continuous (true) or discontinuous (false) epitopes, composed of amino acid residues that may be located on different protein regions – brought together by protein folding
source_host_name varchar 2147483647 √ null
source_host_iri varchar 2147483647 √ null
mhc_allele varchar 2147483647 √ null

Also referred to as ‘mhc_allele’, it indicates the list of the class (e.g., ‘HLA Class I’), or lists of alleles (e.g., ‘HLA-B*35:01, HLA-B*15:01’) to which the epitope is restricted-this is relevant only for T-cell and MHC Ligand assays
assay_type varchar 2147483647 √ null

Indicates the outcome - considering possibly multiple experiments (we have ‘positive’, ‘negative’, and ‘both’, when positive and negative outcomes were included)

Indexes

Constraint Name Type Sort Column(s)
epitope_pkey Primary key Asc epitope_id

Relationships

Close relationships within degrees of separation