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

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

URL	https://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))
Output	JSON encoded object containing meta data (e.g. number of results) and a list of results (if noro=0)
Description	PDBj Mine PDB search

URL	https://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)
Output	JSON encoded object containing meta data (e.g. number of results) and a list of results (if noro=0)
Description	Quick search PDBj Mine ligand

URL	https://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)
Output	JSON encoded object containing meta data (e.g. number of results) and a list of results (if noro=0)
Description	Quick search PDBj Mine BIRD

URL	https://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)
Output	JSON encoded object containing meta data (e.g. number of results) and a list of results (if noro=0)
Description	Search unreleased entries (status search)

URL	https://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)
Output	JSON encoded object containing meta data (e.g. number of results) and a list of results (if noro=0)
Description	Retrieves a list of matching blog posts matching a query

URL	https://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)
Output	Query results in the selected format
Description	Performs a SQL query against the Mine 2 RDB

Mine entry API

URL	https://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)
Output	Requested file (as a stream) given an entry ID
Description	Downloads a file for viewing given an entry ID

URL	https://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)
Output	Requested location of the file given an entry ID
Description	Returns the location of the file on within the PDBj data area for viewing given an entry ID

URL	https://pdbj.org/rest/newweb/fetch/batch-download-prep
Input	ids: comma seperated list of entry IDs formats: comma seperated list of file formats
Output	Download request objects (splitted)
Description	Returns an array of download requests objects (in JSON format) that can each be fed to /rest/newweb/batch-download

URL	https://pdbj.org/rest/newweb/fetch/batch-download
Input	payload: Download request object generated by /rest/newweb/batch-download-prep
Output	Download request objects (splitted)
Description	Returns an array of download requests objects that can each be fed to /rest/newweb/batch-download

URL	https://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)
Output	Requested data items for the requested entries in the requested format
Description	Extracts arbitrary metadata from the PDB (replaces the old CIF query service)

URL	https://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
Output	Requested tables/categories for the requested entries in mmjson format
Description	Extracts tables/categories of entries in mmjson format from the RDB

Misc API

URL	https://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)
Output	EDMap in ccp4 format
Description	Generates a local EDMap for a given entry

URL	https://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
Output	Results in custom json format
Description	Executes BLAST for a given pdbid/chainid or custom sequence

URL	https://pdbj.org/rest/newweb/seqnavi/cluster
Input	entryIds: entry IDs (pdbid+chainid pairs) dcut: cutoff for clusting similar sequences
Output	Results in custom json format
Description	Clusters given entries

URL	https://pdbj.org/rest/newweb/fetch/promode_tgz
Input	id: promode entry ID
Output	Raw promode elastic data in tgz compressed file
Description	Fetches the raw promode data file

URL	https://pdbj.org/rest/newweb/rss/news
Input	lang: Language to process
Output	Results in RSS format
Description	Fetches a list of news posts in RSS format

URL	https://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
Output	Results in JSON format
Description	Fetches a list of blog posts and files in JSON format

Created: 2018-06-22 (last edited: more than 1 year ago)