PDBj Mine:XPath

• XPath
• Examples
• • Search for PDB ID (1GOF):
  • Search for Revision information for a pdbid named 1gof:
  • Search for entity_poly data with polypeptide(L) chain type:
  • Search for entity data with EC number 1.1.1.1:
  • Search for PDB title data:
  • Search for PDB header data:
  • Search for PDB sheet data:
  • Search for PDB compnd data:
  • Search for PDB helix data:
  • Search for PDB seqres data:
  • Search for the Pubmed IDs of primary citation:
  • Search for the scientific names of gene resources:
  • Search the scientific name of the gene resource for entity_id 1:
  • Search for entity_src_gen data the scientific name of gene resouce isArabidopsis thaliana:
  • Search for the EC number of entity 1:
  • Search for the Taxonomy ID of source organism:

[XPath]

XPath is a simple language used to extract parts of XML documents.

[Examples]

Search for PDB ID (1GOF):

/1gof/datablock

Search for Revision information for a pdbid named 1gof:

/1gof/datablock/database_PDB_revCategory/database_PDB_rev

Result

<PDBx:database_PDB_rev num="1">
  <PDBx:date>1994-01-31</PDBx:date>
  <PDBx:date_original>1993-09-30</PDBx:date_original>
  <PDBx:mod_type>0</PDBx:mod_type>
  <PDBx:replaces>1GOF</PDBx:replaces>
</PDBx:database_PDB_rev>
<PDBx:database_PDB_rev num="2">
  <PDBx:date>2003-04-01</PDBx:date>
  <PDBx:mod_type>1</PDBx:mod_type>
  <PDBx:replaces>1GOF</PDBx:replaces>
</PDBx:database_PDB_rev>
<PDBx:database_PDB_rev num="3">
  <PDBx:date>2009-02-24</PDBx:date>
  <PDBx:mod_type>1</PDBx:mod_type>
  <PDBx:replaces>1GOF</PDBx:replaces>
</PDBx:database_PDB_rev>
<PDBx:database_PDB_rev num="4">
  <PDBx:date>2011-07-13</PDBx:date>
  <PDBx:mod_type>1</PDBx:mod_type>
  <PDBx:replaces>1GOF</PDBx:replaces>
</PDBx:database_PDB_rev>

Search for entity_poly data with polypeptide(L) chain type:

/PDBID/datablock/entity_polyCategory[entity_poly/type='polypeptide(L)']

Search for entity data with EC number 1.1.1.1:

/PDBID/datablock/entityCategory[entity/pdbx_ec='1.1.1.1']

Search for PDB title data:

/PDBID/datablock/structCategory/struct/title

Search for PDB header data:

/PDBID/datablock/struct_keywordsCategory/struct_keywords/pdbx_keywords

Search for PDB sheet data:

/PDBID/datablock/struct_sheet_rangeCategory/struct_sheet_range

Search for PDB compnd data:

/PDBID/datablock/entityCategory/entity

Search for PDB helix data:

/PDBID/datablock/struct_confCategory/struct_conf

Search for PDB seqres data:

/PDBID/datablock/pdbx_poly_seq_schemeCategory/pdbx_poly_seq_scheme

Search for the Pubmed IDs of primary citation:

/PDBID/datablock/citationCategory/citation[@id='primary']/pdbx_database_id_PubMed

Search for the scientific names of gene resources:

/PDBID/datablock/entity_src_genCategory/entity_src_gen/pdbx_gene_src_scientific_name

Search the scientific name of the gene resource for entity_id 1:

/PDBID/datablock/entity_src_genCategory/entity_src_gen[@entity_id=1]/pdbx_gene_src_scientific_name

Search for entity_src_gen data the scientific name of gene resouce isArabidopsis thaliana:

/PDBID/datablock/entity_src_genCategory/entity_src_gen[pdbx_gene_src_scientific_name="Arabidopsis thaliana"]

Search for the EC number of entity 1:

/PDBID/datablock/entityCategory/entity[@id=1]/pdbx_ec

Search for the Taxonomy ID of source organism:

/PDBID/datablock/entity_src_natCategory/entity_src_nat/pdbx_ncbi_taxonomy_id