RCSB PDB Sequence Coordinates API changes
Migrating from the 1D Coordinates Service to the Sequence Coordinate Service involves updating your endpoint URLs to call the new service and modifying your applications to account for breaking changes introduced in the new API.
HTTP Request
The Sequence Coordinates Service API only support HTTP POST requests.
End Points
Endpoint alignment
has been renamed to alignments
.
1D Coordinates Service | Sequence Coordinates Service |
---|---|
query UniProt2PDB{ alignment( from:UNIPROT, to:PDB_ENTITY, queryId:"P01112" ){ query_sequence target_alignment { target_id } } } |
query UniProt2PDB{ alignments( from:UNIPROT, to:PDB_ENTITY, queryId:"P01112" ){ query_sequence target_alignments { target_id } } } |
Endpoint group_alignment
has been renamed to group_alignments
.
1D Coordinates Service | Sequence Coordinates Service |
---|---|
query UP_GROUP{
group_alignment(
group: matching_uniprot_accession
groupId: "P01112"
) {
target_alignment {
target_id
}
}
} |
query UP_GROUP{
group_alignments(
group: MATCHING_UNIPROT_ACCESSION
groupId: "P01112"
) {
target_alignments {
target_id
}
}
} |
End Points Arguments
Endpoint group_annotations
boolean argument histogram
has been removed.
Its functionality has been replaced by a new endpoint group_annotations_summary
with the same signature.
1D Coordinates Service | Sequence Coordinates Service |
---|---|
query UP_GROUP_FEATURES{ group_annotations( group: matching_uniprot_accession groupId: "P01112" sources: [PDB_INSTANCE] histogram: true ) { target_id features{ type } } } |
query UP_GROUP_FEATURES{
group_annotations_summary(
group: MATCHING_UNIPROT_ACCESSION
groupId: "P01112"
sources: [PDB_INSTANCE]
) {
target_id
features{
type
}
}
} |
Enumerated values of GroupReference are now screaming snake case
>- MATCHING_UNIPROT_ACCESSION
- SEQUENCE_IDENTITY
1D Coordinates Service | Sequence Coordinates Service |
---|---|
query UP_GROUP{ group_alignment( group: matching_uniprot_accession groupId: "P01112" ) { target_alignment { target_id } } } query SEQ_GROUP{ group_alignment( group: sequence_identity groupId: "507_30" ) { target_alignment { target_id } } } |
query UP_GROUP{ group_alignments( group: MATCHING_UNIPROT_ACCESSION groupId: "P01112" ) { target_alignments { target_id } } } query SEQ_GROUP{ group_alignments( group: SEQUENCE_IDENTITY groupId: "507_30" ) { target_alignments { target_id } } } |
Query Fields
Field target_alignment
has been renamed to target_alignments
.
1D Coordinates Service | Sequence Coordinates Service |
---|---|
query UniProt2PDB{ alignment( from:UNIPROT, to:PDB_ENTITY, queryId:"P01112" ){ query_sequence target_alignment { target_id } } } |
query UniProt2PDB{ alignments( from:UNIPROT, to:PDB_ENTITY, queryId:"P01112" ){ query_sequence target_alignments { target_id } } } |
Field target_alignment_subset
has been removed.
The motivation of this field was to request a subset of alignment based on offset and length arguments.
This functionality has been moved to target_alignments
field that accepts optional arguments as the removed field.
1D Coordinates Service | Sequence Coordinates Service |
---|---|
query UP_GROUP{ group_alignment( group: matching_uniprot_accession groupId: "P01112" ) { target_alignment_subset(after: "5", first:3) { edges { node { target_id } } } } } |
query UP_GROUP{ group_alignments( group: MATCHING_UNIPROT_ACCESSION groupId: "P01112" ) { target_alignments(offset:5, first:3) { target_id } } } |
Type Names
GraphQL type name changes. This only affects programmatic users that build types from GraphQL schema
FilterInput
type has been renamed toAnnotationFilterInput
Source
type has been renamed toAnnotationReference
AlignmentResponse
type has been renamed toSequenceAlignments
AnnotationFeatures
type has been renamed toSequenceAnnotations
AdditionalProperties
type has been renamed toFeaturesAdditionalProperties
Type
type has been renamed toFeaturesType
FeaturePositions
type has been renamed toFeaturesFeaturePositions
AlignedRegion
type has been renamed toAlignedRegions
Feature
type has been renamed toFeatures
Contact Us
Contact info@rcsb.org with questions or feedback about this service.