1. Search
  2. Entry access
  3. Deposition

Search

Currently the following search parameters are supported by the COD search endpoint in https://www.crystallography.net/cod/result:

  • id – a string containing one or more COD IDs separated by a comma (",") or a new line ("\n") symbol. The percent ("%") wild card symbol can be used to specify a range of IDs.
  • smarts – a substructure query in SMILES arbitrary target specification.
  • text – a keyword that must be contained in the metadata of the entry. The metadata search covers data such as the bibliographic information of the associated publication, common and systematic name of the sample compound and the name of the sample mineral.
  • format – the format in which the results will be returned. Supported formats:
    • html – a html web page displaying the list of COD entries.
    • csv – a csv file containing information about the COD entries. The provided information matches the one provided by the COD MySQL database.
    • json – a json file containing information about the COD entries. The provided information matches the one provided by the COD MySQL database.
    • lst – a txt file containing a list of COD IDs.
    • urls – a txt file containing a list of URLs pointing to the COD CIF files.
    • zip – a zip archive containing CIF files. Please note that there is a limit of how many entries can be returned using this format. In case this limit is reached, a html page with an error message is returned instead.
    • count – the number of COD entries that match the search criteria.
  • formula – the empirical chemical formula of the crystal. Chemical element symbols in the formula must be ordered according to the Hill notation and separated by a space symbol, e.g. "C8 H10 N4 O2".
  • el1, el2, ..., el8 – chemical element symbols that must appear in the chemical formula.
  • nel1, nel2, ..., nel4 – chemical element symbols that must not appear in the chemical formula.
  • strictmin, strictmax – the minimum/maximum number of distinct chemical elements that must appear in the chemical formula.
  • spacegroup – the Hermann–Mauguin space group symbol or the superspace group symbol.
  • space_group_number – the space group number as assigned in International Tables for Crystallography Vol. A.
  • amin, amax – the minimum/maximum value of the lattice parameter a.
  • bmin, bmax – the minimum/maximum value of the lattice parameter b.
  • cmin, cmax – the minimum/maximum value of the lattice parameter c.
  • alpmin, alpmax – the minimum/maximum value of the lattice parameter alpha.
  • betmin, betmax – the minimum/maximum value of the lattice parameter beta.
  • gamin, gamax – the minimum/maximum value of the lattice parameter gamma.
  • vmin, vmax – the minimum/maximum volume of the lattice.
  • minZ, maxZ – the minimum/maximum Z value of the lattice.
  • minZprime, maxZprime – the minimum/maximum Z' value of the lattice.
  • journal – the name of the journal in which the scientific paper describing the crystal structure was published.
  • year – the year of publication of the crystal structure.
  • volume – the volume of the journal where the scientific paper describing the crystal structure was published.
  • issue – the issue of the journal where the scientific paper describing the crystal structure was published.
  • doi – the DOI that links to the online paper in which the crystal structure was published.
  • has_fobs – flag value denoting that entries must have an associated X-ray reflection files (Fobs or Iobs data) in the COD which contain the original reflection intensities used to determine the structures.
  • include_duplicates – flag value denoting that entries that are marked as duplicates of other entries in the COD should not be excluded.
  • include_errors – flag value denoting that entries that are marked as having errors should not be excluded.
  • include_theoretical – flag value denoting that entries that are marked as theoretical should not be excluded.

Entry access

Each database entry can be accessed by appending its ID to https://www.crystallography.net/cod/ and postfixing it by the format, for example, request https://www.crystallography.net/cod/1000000.cif results in retrieval of CIF contents of COD entry 1000000.

Supported formats:

  • cif.
  • hkl – diffraction data (if an entry has associated diffraction data).
  • html – HTML information table for the entry.
  • rdf – entry data in Resource Description Framework format.

Entry access will always return the newest version of the data. Specific revisions could be accessed for CIF and HKL formats by appending revision number preceded by "@", for example, request https://www.crystallography.net/cod/1000000.cif@1 results in retrieval of CIF contents of COD entry 1000000 as of revision 1.

Deposition

Data can be deposited to the COD by posting (HTTP POST) data to deposition endpoint https://www.crystallography.net/cod/cgi-bin/cif-deposit.pl.

Mandatory fields:

  • username – depositor's username.
  • password – depositor's password.
  • user_email – depositor's email address.
  • deposition_type – deposition type: published, ?prepublication or personal.
  • cif – contents of the deposited CIF file. Multiple data blocks are allowed. Please note that this field is a file upload field, not a string with CIF contents.

Optional fields:

  • hkl – diffraction data associated with the deposited CIF file. Please note that this field is a file upload field, not a string with HKL contents.
  • output_mode – format of the output, html by default, stdout is also accepted, resulting in more plain-looking output.
  • progress – if set to 1, outputs more verbose information about the deposition process.

Mandatory fields for prepublication and personal communication depositions:

  • author_name – name of the author as given in the CIF file.
  • author_email – email address to contact the author.

Optional fields for prepublication depositions:

  • journal – name of the journal in which the structures are intended to be published.
  • hold_period – number of months by which the structure hold period should be extended. Value range: [0-12]. Default: '6' for the initial deposition, '0' for all sequential depositions.

Mandatory fields for redeposition (update/change of data already in the COD):

  • replace – set to 1 to indicate that an existing COD entry should be replaced by the provided file.
  • message – log message describing the performed changes. Ignored when the replace field is not set to 1.

The outcome of the deposition is reported in structured both human- and computer-readable format (this will hopefully change in the future to ease the automated processing of the output). Three outcomes are possible:

  • Success. In html format newly deposited/updated COD entry numbers are presented in <span class="assignedDatabaseID">...</span> HTML elements (may be more than one COD ID).
  • Duplicate. In html format COD entries already having the deposited data are presented in <span class="duplicateDatabaseID">...</span> HTML elements (may be more than one COD ID).
  • Error. In html format errors are presented in structured both human- and computer-readable manner.