Bundles/pdb
Bundle: pdb Graph: http://purl.org/science/graph/pdb
From the protein data bank (PDB), a selection of approximately 290 structures relevant to the HLA system were chosen (by keyword search on "HLA" with some refinement.
Structure records are related to structures by <http://purl.obofoundry.org/obo/IAO_0000136> (is about); structures are related to complexes by <http://purl.org/science/owl/sciencecommons/has_grain>; complexes are related to chains by <http://www.ifomis.org/bfo/1.1/ro#has_part>.
For example:
Molecular description for 1K5N
PREFIX dc: <http://purl.org/dc/elements/1.1/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX sc: <http://purl.org/science/owl/sciencecommons/> prefix IAO: <FIXME://example/IAO_terms#> prefix ro: <http://www.ifomis.org/bfo/1.1/ro#> select distinct ?Molecule ?Type ?Length where { ?record rdfs:label "1K5N"; <http://purl.obofoundry.org/obo/IAO_0000136> ?struct. ?struct sc:has_grain [ ro:has_part ?chain ]. ?chain rdfs:label ?Molecule; sc:sequence_length ?Length; rdf:type [ rdfs:label ?Type] } order by ?chain
| Molecule | Type | Length |
|---|---|---|
| major histocompatibility complex molecule HLA-B*2709 | protein polypeptide chain | 276 |
| beta-2-microglobulin, light chain | protein polypeptide chain | 100 |
| nonameric model peptide m9 | protein polypeptide chain | 9 |
Contents |
Chains and Residues
http://purl.org/science/owl/sciencecommons/sequence http://purl.org/science/owl/sciencecommons/sequence_length
@@ <http://purl.org/science/owl/sciencecommons/uniprot>
Contact Points
http://purl.org/science/owl/sciencecommons/chain_contact
Features
@@
http://purl.org/science/owl/sciencecommons/cath_id http://purl.org/science/owl/sciencecommons/pfam_id http://purl.org/science/owl/sciencecommons/scop_id
Citations
Each structure record is related to its primary citation by <http://purl.org/science/owl/sciencecommons/pdb_primary_citation> to a pubmed article (@@more about pubmed article URIs... surely this is already documented somewhere?)
Misc
not sure whether these others are features to document: <http://purl.org/science/owl/sciencecommons/pdb_keywords_description>, <http://purl.org/science/owl/sciencecommons/pdb_keywords>, <http://purl.obofoundry.org/obo/IAO_0000142> for alleles,
http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/1999/02/22-rdf-syntax-ns#value
not sure where these are used... gotta check@@ http://www.w3.org/2000/01/rdf-schema#comment http://www.w3.org/2000/01/rdf-schema#label http://www.w3.org/2000/01/rdf-schema#seeAlso
