REST interface

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Many services accessible via the new web interface work via a REST interface. This REST interface is publicly available for users. Examples are also available.
The PDBj REST services are available under the /rest/ URL.

Search API

URLhttps://pdbj.org/rest/newweb/search/omni
Input
  • query: search query
  • fields: list of fields to search (optional, if none given searches all fields)
OutputReturns a JSON encoded list of matches per field (category)
DescriptionDoes a surface search (e.g. only IDs and titles and such) of all PDBj databases

URLhttps://pdbj.org/rest/newweb/search/pdb
Input
  • query: search query
  • limit: number of posts to get (optional)
  • offset: starting position (optional, used in combination with limit)
  • sortBy: sort by (1: hit score, 2: publication date asc, 3: publication date desc, 4: modification date asc, 5: modification date desc) (optional, default is 1)
  • lang: language version to request (optional, default is English, NB Japanese-->English translation is only available in lang=ja mode)
  • noro: does not return the actual results, but only the number of results
  • query: search all fields (optional)
  • pdbid: search pdbid field (optional)
  • title: search entry title field (optional)
  • c_authors: search citation authors field (optional)
  • c_title: search citation title field (optional)
  • c_name: search citation journal field (optional)
  • c_volume: search citation volume field (optional)
  • compound_info: search compound field (optional)
  • other_db_select: filter by external database (optional, valid values are "ec number", "embl", "emdb", "gb", "go", "pir", "pubmed id", "doi", "uniprot", "pfam")
  • other_db_field: external database id (optional, in conjunction with other_db_select, in case nothing is supplied here, all entries which have a non-null value for other_db will return)
  • ligand: filter by ligand field (optional)
  • source: filter by biological source field (optional)
  • host_species: filter by host species field (optional)
  • rdate_before: filter by release date before (optional)
  • rdate_after: filter by release date after (optional)
  • ddate_before: filter by deposition date before (optional)
  • ddate_after: filter by deposition date after (optional)
  • mdate_before: filter by modification date before (optional)
  • mdate_after: filter by modification date after (optional)
  • c_year: filter by citation year (optional)
  • chain_type_0: filter by chain type (optional, valid values are 1: contains, 2: does not contain)
  • chain_type_1:
  • chain_type_2:
  • chain_type_3:
  • chain_type_4:
  • chain_type_5:
  • chain_type_6:
  • chain_type_7:
  • chain_type_8:
  • chain_number_min: filter by number of chains (optional)
  • chain_number_max:
  • chain_length_min: filter by chain length (optional)
  • chain_length_max:
  • res_min: minimum resolution (Å)
  • res_max: maximum resolution (Å)
  • method: filter by method (optional, valid values are 1: xray diffraction, 2: neutron diffraction, 3: fiber diffraction, 4: electron crystallography, 5: electron microscopy, 6: solution nmr, 7: solid-state nmr, 8: solution scattering, 9: powder diffraction, 10: infrared spectroscopy, 11: epr, 12: fluorescence transfer, 13: theoretical model, 14: hybrid, 15: theoretical model (obsolete))
OutputJSON encoded object containing meta data (e.g. number of results) and a list of results (if noro=0)
DescriptionPDBj Mine PDB search

URLhttps://pdbj.org/rest/newweb/search/cc
Input
  • query: search query
  • limit: number of posts to get (optional)
  • offset: starting position (optional, used in combination with limit)
  • sortBy: sort by (1: hit score, 2: comp_id asc, 3: comp_id desc, 4: release date asc, 5: release date desc, 6: modification date asc, 7: modification date desc) (optional, default is 1)
  • lang: language version to request (optional, default is English, NB Japanese-->English translation is only available in lang=ja mode)
  • noro: does not return the actual results, but only the number of results
  • code: searches by comp_id (optional)
  • mol_name: searches by the name of the molecules (chem_comp.name) (optional)
  • formula: searches by the formula (chem_comp.formula) (optional)
  • smiles: fingerprint search using smiles (optional)
  • inchi: searches by inchi (optional)
  • format: select return format (), valid values are json, csv, tsv, jsonp (return as file)
OutputJSON encoded object containing meta data (e.g. number of results) and a list of results (if noro=0)
DescriptionQuick search PDBj Mine ligand

URLhttps://pdbj.org/rest/newweb/search/prd
Input
  • query: search query
  • limit: number of posts to get (optional)
  • offset: starting position (optional, used in combination with limit)
  • sortBy: sort by (1: hit score, 2: comp_id asc, 3: comp_id desc, 4: release date asc, 5: release date desc, 6: modification date asc, 7: modification date desc) (optional, default is 1)
  • lang: language version to request (optional, default is English, NB Japanese-->English translation is only available in lang=ja mode)
  • noro: does not return the actual results, but only the number of results
  • format: select return format (), valid values are json, csv, tsv, jsonp (return as file)
OutputJSON encoded object containing meta data (e.g. number of results) and a list of results (if noro=0)
DescriptionQuick search PDBj Mine BIRD

URLhttps://pdbj.org/rest/newweb/search/status
Input
  • limit: number of posts to get (optional)
  • offset: starting position (optional, used in combination with limit)
  • sortBy: sort by (1: hit score, 2: pdbid asc, 3: pdbid desc, 4: deposition date asc, 5: deposition date desc, 6: status code asc, 7: status code desc) (optional, default is 1)
  • lang: language version to request (optional, default is English, NB Japanese-->English translation is only available in lang=ja mode)
  • noro: does not return the actual results, but only the number of results
  • keyword/query: search all fields (optional)
  • pdbid: search pdbid field (optional)
  • authors: search author field (optional)
  • title: search title field (optional)
  • status_code: search status_code field (optional)
  • author_release_sequence: filter by sequence status (optional)
  • exclude_WDRN: exclude WDRN entries (optional, valid values 0/1, default 0)
  • ddate_after: filter between deposition date after (optional)
  • ddate_before: filter between deposition date before (optional)
OutputJSON encoded object containing meta data (e.g. number of results) and a list of results (if noro=0)
DescriptionSearch unreleased entries (status search)
URLhttps://pdbj.org/rest/newweb/search/blog
Input
  • query: search query
  • limit: number of posts to get (optional)
  • offset: starting position (optional, used in combination with limit)
  • sortBy: sort by (1: hit score, 2: publication date asc, 3: publication date desc, 4: modification date asc, 5: modification date desc) (optional, default is 1)
  • lang: language version to request (optional, default is English, NB Japanese-->English translation is only available in lang=ja mode)
  • noro: does not return the actual results, but only the number of results
  • CID: selects to search only in a single category (optional, integer)
OutputJSON encoded object containing meta data (e.g. number of results) and a list of results (if noro=0)
DescriptionRetrieves a list of matching blog posts matching a query

URLhttps://pdbj.org/rest/newweb/search/sql
Input
  • q: SQL query
  • limit: number of posts to get (optional)
  • offset: starting position (optional, used in combination with limit)
  • OutputQuery results in the selected format
    DescriptionPerforms a SQL query against the Mine 2 RDB

    Mine entry API

    URLhttps://pdbj.org/rest/newweb/fetch/file
    Input
    • id: entry ID, for BU assembly id, specify in the form of xxxx.y, where xxxx is the PDBID and y the assembly id
    • type: file format
    • version: file version (default 0)
    OutputRequested file (as a stream) given an entry ID
    DescriptionDownloads a file for viewing given an entry ID
    URLhttps://pdbj.org/rest/newweb/fetch/file-loc
    Input
    • id: entry ID, for BU assembly id, specify in the form of xxxx.y, where xxxx is the PDBID and y the assembly id
    • type: file format
    • version: file version (default 0)
    OutputRequested location of the file given an entry ID
    DescriptionReturns the location of the file on within the PDBj data area for viewing given an entry ID
    URLhttps://pdbj.org/rest/newweb/fetch/batch-download-prep
    Input
    • ids: comma seperated list of entry IDs
    • formats: comma seperated list of file formats
    OutputDownload request objects (splitted)
    DescriptionReturns an array of download requests objects (in JSON format) that can each be fed to /rest/newweb/batch-download

    URLhttps://pdbj.org/rest/newweb/fetch/batch-download
    Input
    • payload: Download request object generated by /rest/newweb/batch-download-prep
    OutputDownload request objects (splitted)
    DescriptionReturns an array of download requests objects that can each be fed to /rest/newweb/batch-download

    URLhttps://pdbj.org/rest/newweb/fetch/batch-data-fetch
    Input
    • ids: comma seperated list of entry IDs
    • schema: schema to select from (e.g. pdb, cc)
    • items: comma seperated list of data items (table.column / category.dataname) to fetch
    • format: data format of results (mmjson, mmcif, json-column, json-row)
    OutputRequested data items for the requested entries in the requested format
    DescriptionExtracts arbitrary metadata from the PDB (replaces the old CIF query service)

    URLhttps://pdbj.org/rest/newweb/fetch/rdb
    Input
    • entryId: comma seperated list of entry IDs
    • schemaName: schema to select from (e.g. pdb, cc)
    • tables: comma seperated list of tables/categories to fetch
    OutputRequested tables/categories for the requested entries in mmjson format
    DescriptionExtracts tables/categories of entries in mmjson format from the RDB

    Misc API

    URLhttps://pdbj.org/rest/newweb/edmap
    Input
    • pdbid: PDBID for the entry to process
    • mode: map type mode (2fo-fc/fo-fc)
    • xyz: list of xyz coordinates in JSON format specifying around which atoms to generate the map
    • border: size of the map around the atoms to generate (default 10)
    OutputEDMap in ccp4 format
    DescriptionGenerates a local EDMap for a given entry

    URLhttps://pdbj.org/rest/newweb/seqnavi
    Input
    • pdbid: PDBID for the entry to process
    • chainid: assymetric chain id of the entry to process
    • type: chain type (prot/nucl)
    • seq: custom sequence input
    OutputResults in custom json format
    DescriptionExecutes BLAST for a given pdbid/chainid or custom sequence

    URLhttps://pdbj.org/rest/newweb/seqnavi/cluster
    Input
    • entryIds: entry IDs (pdbid+chainid pairs)
    • dcut: cutoff for clusting similar sequences
    OutputResults in custom json format
    DescriptionClusters given entries

    URLhttps://pdbj.org/rest/newweb/fetch/promode_tgz
    Input
    • id: promode entry ID
    OutputRaw promode elastic data in tgz compressed file
    DescriptionFetches the raw promode data file

    URLhttps://pdbj.org/rest/newweb/rss/news
    Input
    • lang: Language to process
    OutputResults in RSS format
    DescriptionFetches a list of news posts in RSS format

    URLhttps://pdbj.org/rest/newweb/cms/list
    Input
    • recursive: set to also process all subdirectories
    • limit: number of results to fetch
    • offset: fetch offset
    • year: limit publication date to specific year
    • sort: sort by ctime or mtime
    OutputResults in JSON format
    DescriptionFetches a list of blog posts and files in JSON format


    Created: 2018-06-22 (last edited: 4 days ago)2021-06-10
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    PDB entries from 2021-06-09