PBDB Data Service: Documentation

A fossil occurence represents the occurrence of a particular organism at a particular location in time and space. Each occurrence is a member of a single fossil collection, and has a taxonomic identification which may be more or less specific. The fossil occurrence records are the core data concept around which this database is built.

A fossil collection is somewhat loosely defined as a set of fossil occurrences that are co-located geographically and temporally. Each collection has a geographic location, stratigraphic context, and age estimate.

Many of the fossil occurrences in the database are based on specimens that can be examined and measured. There are also specimens entered into the database for which no information was available as to the location and context in which they were found.

The taxonomic names stored in the database are arranged hierarchically. Our tree of life is quite complete down to the class level, and reasonably complete down to the suborder level. Below that, coverage varies. Many parts of the tree have been completely entered, while others are sparser.

The taxonomic hierarchy in our database is computed algorithmically based on a constantly growing set of taxonomic opinions. These opinions are ranked by publication year and basis, yielding a 'consensus taxonomy' based on the latest research.

The database lists almost every geologic time interval in current use, including the standard set established by the International Commission on Stratigraphy (2013-01).

The collections and specimens in the database are associated with specific geographic locations, which can be queried separately from other operations.

Most of the fossil collections in the database are categorized by the formation from which each was collected, and many by group and member.

Each fossil occurrence, collection, specimen, taxonomic name, and opinion in the database is associated with one or more bibliographic references, identifying the source from which this information was entered.

Research papers that make major use of data from this database can be submitted for consideration as official publications. The operations in this section provide a list of official publication records and information about individual records.

Database members can archive data downloads, preserving them on the server so that they or others can later retrieve the exact same result set. This facility can be used to document the research process. Additionally, you can request that a DOI be generated for significant archives so that they can be quoted in research papers.

This operation provides information about the structure, encoding and organization of the information in the database. It is designed to enable the easy configuration of client applications.

The operations in this group provide access to multiple types of data records, including auto-completion for client applications.

Auxiliary operations to support the frontend Navigator application.

Statistical summaries of database information

Data entry operations for educational resource records.

Data entry operations for specimen and measurement records.

Data entry operations for official publication records.

Data entry operations for data archive records.

Records retrieved from the data service can be identified either by using the numeric identifiers from the underlying database records (i.e. 'occurrence_no'), or using an extended identifier syntax.

The data service accepts taxonomic names using several different parameters, and there are modifiers that you can add in order to precisely specify which taxa you are interested in.

The ecology of organisms and the taphonomy of their fossil remains are described by several different data fields with an associated vocabulary.

You can retrieve records based on when they were modified and/or created.

Each piece of data entered into the database is linked to the bibliographic reference from which it was entered.

The basis and precision of geographic locations is specified by a set of code values.

You can get the results of query operations in a variety of formats, and with the field names expressed in any of the available vocabularies.

There are a number of special parameters which you can use with almost any data service operation. These constrain or alter the response in various ways.

The initial part of the URL specifies the server to be contacted, and the protocol (http or https) to be used in the transaction.

The first component of the URL path indicates which data service you wish to use. There are multiple data service versions available from this server, and you need to specify which one you are talking to. The advantage of this approach is that you can store URLs that use a particular version of the data service, and they will continue to be valid even as we add new versions.

The rest of the URL path indicates the operation to be carried out. For a GET request, it specifies the class of information to be retrieved.

The path suffix indicates the format in which the results will be returned. In this case, the result will be expressed in Javascript Object Notation.

Some of the parameters are used to construct a database query that will retrieve the desired information. This one selects a particular taxonomic name.

Other parameters change or augment the set of information returned. This one specifies that in addition to basic information about the taxonomic name the result should also include the name's attribution.

The JSON format is intended primarily to support client applications, including the PBDB Navigator. Response fields are named using compact 3-character field names.

The text formats (txt, tsv, csv) are intended primarily for researchers downloading data from the database. These downloads can easily be loaded into spreadsheets or other analysis tools. The field names are taken from the PBDB Classic interface, for compatibility with existing tools and analytical procedures.

The text formats (txt, tsv, csv) are intended primarily for researchers downloading data from the database. These downloads can easily be loaded into spreadsheets or other analysis tools. The field names are taken from the PBDB Classic interface, for compatibility with existing tools and analytical procedures.

The text formats (txt, tsv, csv) are intended primarily for researchers downloading data from the database. These downloads can easily be loaded into spreadsheets or other analysis tools. The field names are taken from the PBDB Classic interface, for compatibility with existing tools and analytical procedures.

This format is used for operations that replace the old Larkin data service, written in Javascript, that was used to provide data to the frontend website. This format is designed to produce the same output as the old data service.

The RIS format is a common format for bibliographic references.

The PNG suffix is used with a few URL paths to fetch images stored in the database.

The PBDB vocabulary is derived from the underlying field names and values in the database, augmented by a few new fields. For the most part any response that uses this vocabulary will be directly comparable to downloads from the PBDB Classic interface. This vocabulary is the default for text format responses.

The Compact vocabulary is a set of 3-character field names designed to minimize the size of the response message. This is the default for JSON format responses. Some of the field values are similarly abbreviated, while others are conveyed in their entirety. For details, see the documentation for the individual response fields.

The BibJSON vocabulary uses the field names and value formats defined for BibTeX, which is the vocabulary used for BibJSON.