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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/rest/quick_search
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

URL/rest/webSearch
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: pdbid asc, 3: pdbid desc, 4: deposition date asc, 5: deposition date desc, 6: release date asc, 7: release date desc, 8: resolution asc) (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 searches PDBj mine.

URL/rest/ligandSearch
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 ligand

URL/rest/statusSearch
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)
  • exclude_WDRN: exclude WDRN entries (optional, valid values 0/1, default 0)
  • author_release_sequence: filter by sequence status (optional)
  • d_date_year_after: filter between deposition date after, year (optional)
  • d_date_month_after: filter between deposition date after, month (optional)
  • d_date_day_after: filter between deposition date after, day (optional)
  • d_date_year_before: filter between deposition date before, year (optional)
  • d_date_month_before: filter between deposition date before, month (optional)
  • d_date_day_before: filter between deposition date before, day (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)
URL/rest/searchBlog
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

URL/rest/advancedSearch
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
  • format: select return format (optional, default is format=json), valid values are json, csv, tsv, jsonp (return as file)
  • keyword: search keyword field (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)
  • r_date_year_after: filter by release date (optional)
  • r_date_month_after:
  • r_date_day_after:
  • r_date_year_before:
  • r_date_month_before:
  • r_date_day_before:
  • d_date_year_after: filter by deposition date (optional)
  • d_date_month_after:
  • d_date_day_after:
  • d_date_year_before:
  • d_date_month_before:
  • d_date_day_before:
  • m_date_year_after: filter by modification date (optional)
  • m_date_month_after:
  • m_date_day_after:
  • m_date_year_before:
  • m_date_month_before:
  • m_date_day_before:
  • 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 advanced search (PDB)

URL/rest/mine2_xpath/XPATH_QUERY
InputXPath query (XPATH_QUERY)
OutputXPath results (XML)
DescriptionRuns an XPath query against the PDB

URL/rest/mine2_sql
Input
  • q: SQL query
  • limit: number of posts to get (optional)
  • offset: starting position (optional, used in combination with limit)
  • format: select return format (optional, default is json), valid values are json, xml, tsv, csv
  • OutputQuery results in the selected format
    DescriptionPerforms a SQL query against the Mine 2 RDB

    URL/rest/helpy_search
    Input
    • query: search query
    • lang: language version to request (optional, default is English)
    OutputJSON encoded list of matching entries (in the serviceBrowser.json file)
    DescriptionSearches the service browser index

    Mine entry (PDB & ligand) Expl. API

    URL/rest/displayPDBfile
    Input
    OutputRequested file (as a stream) given a PDBID
    DescriptionDownloads a file for viewing given a PDBID

    URL/rest/downloadPDBfile
    Input
    OutputRequested file (as a file) given a PDBID
    DescriptionDownloads a file given a PDBID

    URL/rest/displayCOMPfile
    Input
    OutputRequested file (as a stream) given a comp_id
    DescriptionDownloads a file for viewing given a comp_id

    URL/rest/downloadCOMPfile
    Input
    OutputRequested file (as a file) given a comp_id
    DescriptionDownloads a file given a comp_id

    URL/rest/pdbResources
    Input
    • pdbid: PDBID
    OutputJSON encoded list of additional resources
    DescriptionDownload additional resources which are not part of pdbx (e.g. files, links to other databases)

    URL/rest/getLigandResources
    Input
    • comp_id:
    OutputJSON encoded list of additional resources
    DescriptionDownload additional resources which are not part of pdbx (ligandbox)

    Blog API

    URL/rest/blogPostsHandler/requestItems
    Input
    • IIDs: PID to request (multiple combinations of IIDs=*** can be added to the URL to request multiple items)
    • lang: language version to request (optional, default is English)
    OutputJSON encoded list of blog entries corresponding the requested ID(s). For each entry a list of key-value pairs is provided which describe the various fields of a blog entry (meta data and content).
    DescriptionGets one or multiple blog posts from the newweb system by PID.

    URL/rest/blogPostsHandler/requestSummariesForCategory
    Input
    • CID: CID of the category
    • limit: number of posts to get (optional)
    • offset: starting position (optional, used in combination with limit)
    • cDateSort: sort by publication date (optional, valid values are 0/1, default is 0 (and sort by modification date instead))
    • lang: language version to request (optional, default is English)
    OutputJSON encoded list of post entries with meta data and description content
    DescriptionGet a list of posts and their descriptions for a given category.

    URL/rest/blogPostsHandler/getPostByURL
    Input
    • URL: alternative URL of the blog post
    • lang: language version to request (optional, default is English)
    OutputSame as for /rest/blogPostsHandler/requestItems
    DescriptionGets meta data and content for a single blog posts for an alternate URL.

    Misc API

    URL/rest/momIndex
    Input(none)
    OutputJSON encoded list of MoM entries
    DescriptionGet the all meta data (e.g. desc, category, publication date, etc) of Molecule of the Month articles. To get an individual article including main text, please use /rest/blogPostsHandler/getPostByURL?lang=ja&url=mom%2F[mom article ID].

    URL/rest/displayPromodeEfile
    Input
    • id: promode id (pdbid + chain id)
    • format: file format
    OutputRequested file (as a stream) given a promode id
    DescriptionDownloads a file for viewing given a promode id

    URL/rest/downloadPromodeEfile
    Input
    • id: promode id (pdbid + chain id)
    • format: file format
    OutputRequested file (as a file) given a promode id
    DescriptionDownloads a file given a promode id
    2014-08-21 (last edited: more than 1 year ago)2015-03-31
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