PBDB Download Generator

Download Records

This form allows you to download data of all types from the Paleobiology Database. Use the various fields and selectors to specify which information you are looking for, and the form will generate a URL that will retrieve that specific set of records using the data service API.

To learn more about the various parts of this form, use the buttons. Be sure to read the data service documentation for a full explanation of what each field that you download contains.

What do you want to download?

Occurrences
Specimens / Measurements
Geological strata
Collections
Diversity over time
Taxa
Opinions
Bibliographic references / Taxa by ref

Comma-separated values (csv)
Tab-separated values (tsv)
JSON
RIS

Include non-public data
Public data only

Show all available parameters
Simple form

Using the left column of radio buttons, you can select any of the various kinds of data records available from the database. Using the middle column, you can choose from the available data formats. With few exceptions, you can select any type of record based on any criteria specified in the bottom section of this form. If you ask for taxa, opinions, or references, then your query will be evaluated using the full set of taxa known to the database if you specify only taxonomic criteria. Otherwise, it will be evaluated based on the table of fossil occurrences, using only the taxa which are associated with occurrences matching the criteria you specify.

If you are logged in, you can also choose to include non-public data in your result set (the default) or to retrieve public data only. This choice is found in the middle column. Unless you change this setting, the download will contain all matching data that you have permission to view, including your own embargoed data and any embargoed data whose authorizer has given you permission. Please be aware that in this case the generated URL will only work if used when you are logged in! If you share this URL with another member of the PaleoBioDB community, it will only work when they are logged in, and then they will only see the data that they have permission to view. So if you are planning to publish a URL or share it with someone who is not a database contributor, or if you want to generate a URL that will work even when you are not logged in, you must select the "public data only" option.

If you wish to get a list of bibliographic references according to some criteria and also find out which taxa are listed from each reference, you must download both "bibliographic references" and "taxa by ref" and match up the reference_no values between the two files yourself. Likewise, if you wish to get a list of specimens and their associated measurements, you must download both "specimens" and "measurements" and match up the specimen_no values yourself.

URL

Use one or more of the following sections to select a set of records and choose output options. If you close a section, you remove those parameters from the download URL until the section is opened again.

Opinion type:

By default, you will get all opinions concerning the taxa selected by whatever criteria you specify below. You can choose instead to just get the opinions that were selected algorithmically as classification opinions, or you can choose to just retrieve opinions which declare valid names, or junior synonyms, or invalid names. If you want, for example, just the classification opinions which declare junior synonyms, choose "classification opinions only" and then choose "junior synonyms" using the "Taxonomic status" meny below.

Reference types:
By selecting from this list of checkboxes, you can choose among the various types of references known to the database selected according to the criteria you specify in the subsequent sections of this form. For more information, you can read the documentation on bibliographic references.

Select by taxonomy

Taxon or taxa to include:
Select records associated with the specified taxa plus all subtaxa. Subgroups can be excluded using the ^ symbol. Homonyms can be resolved using the : symbol. For more information, you can read the instructions on specifying taxonomic names. Examples: Dinosauria Theropoda, Sauropoda Dinosauria ^Aves Gastropoda:Ficus Plant:Ficus
Taxonomic resolution: Taxonomic resolution: Taxonomic rank(s):		Show accepted names only
You can select only occurences that are identified at least to the level of genus, family, etc. If you choose one of the "lump by" options, then only one record is reported for each occurrence of a given genus and/or subgenus in a given collection. If you check "Show accepted names only", then the exact name by which an occurrence was identified will not be shown; only the corresponding accepted taxonomic name will be returned.
You can select only specimens that are identified at least to the level of genus, family, etc. The "lump by" options have no effect for specimens. If you check "Show accepted names only", then the exact name by which a specimen was identified will not be shown; only the corresponding accepted taxonomic name will be returned.
You can select only collections containing an occurrence that is identified at least to the level of genus, family, etc. The "lump by" options and "show accepted names only" have no effect for collections.
You can select only strata containing an occurrence that is identified at least to the level of genus, family, etc. The "lump by" options and "show accepted names only" have no effect for strata.
You can select the diversity metric you wish to use, in other words, the taxonomic level at which to count. The option "genera + subgenera" counts subgenera as if they were genera.
You can select any range of taxonomic ranks using the "rank" parameter. A set of useful choices is given in this menu. Note that unranked clades that match the specification (i.e. "genera through orders") will be returned. If you check "Show accepted names only", that is equivalent to choosing "accepted" from the Taxonomic status menu.
Taxonomic status:		Show obsolete name variants
By default, all taxonomic names matching the criteria you specify are returned. You can also choose to get only accepted names, only valid names (this includes junior synonyms), only junior synonyms, or only invalid names. If you check "show obsolete name variants", then all variants of the names matching the other criteria will be returned. All but the current variant will be marked with the flag "V".
Preservation:		Identification:
The preservation parameter lets you choose whether to return information about ichnotaxa, form taxa and/or regular taxa.
The identification parameter affects only occurrences that have more than one identification recorded in the database. If you choose "all", then occurrences that have been reidentified will generate a separate record for each identification that matches the other filters you have specified (i.e. are subtaxa of the specified base name). If you choose "orig" then only the original identification of each occurrence is reported and reidentifications will be ignored. If you choose "reidentifications" then all identifications of occurrences that have been reidentified will be returned, each as a separate record. Occurrences that have not been reidentified will be ignored.
Modifiers:
	Genus:
	Species:
You can choose to exclude uncertain identifications, specifically the following: aff. / cf. / ? / "" / informal / sensu lato. You can also exclude these modifiers only when applied to genera, or alternatively select identifications that have them. You can also choose to show only newly identified taxa. Finally, you can create a custom filter by selecting any subset of these.

Select by time

Interval or Ma range:	through
You can specify an interval or a range of intervals by name. The selected records will range from the beginning of the earliest specified interval to the end of the latest, regardless of the order in which you specify them. Alternatively, you can specify a maximun and/or minimum age in units of Ma.
Time rule:	Time buffer in Ma:
The contain time rule is the strictest. It selects occurrences whose temporal range is contained in the specified interval. The major time rule (default) is more permissive and selects occurrences for which a majority of their temporal range overlaps the specified interval. The buffer time rule selects occurrences whose temporal range overlaps the specified interval and is contained inside a buffer zone around the interval. The default buffer is 5 Ma outside of the interval for the Cenozoic, 12 Ma for the earlier eras. The overlap time rule is the most permissive and selects all occurrences whose temporal range overlaps the specified interval by any amount. The contain time rule is the strictest. It counts each occurrence in the bin (interval) that contains the occurrence's temporal range, if one exists. Each occurrence will be counted at most once, many will not be counted at all because their temporal range overlaps two or more bins. The major time rule (default) bins each occurrence into an interval overlapped by a majority of the occurrence's temporal range, if one exists. Each occurrence will be counted at most once, some will not be counted at all but fewer than with the 'contain' rule. The buffer time rule counts each occurrence in every interval that overlaps its temporal range, provided the temporal range is contained in a buffer zone around the interval. The default buffer is 5 Ma for the Cenozoic, 12 Ma for the earlier eras. This rule may count some occurrences more than once; fewer will be left uncounted than with the above rules. The overlap time rule is the most permissive. It counts each occurrence in every interval that overlaps its temporal range. This guarantees that every occurrence will be counted, but many will be counted more than once.
Temporal resolution:	Assume extant taxa range through to present
You can select the temporal resolution at which to tabulate the results. Each bin will be an interval of the selected type.

Select by location

Each row in this section is applied separately to the query. If you specify values in more than one row, then only data records that satisfy all of them together will be selected.

Continent: Country:

Countries:

If you specify one or more countries but not a continent, then just those countries will be selected or excluded. To specify multiple countries, you must type a list of the 2-letter codes.

State/province: County:

You can specify or exclude one or more states or counties, separated by commas. If you do this, you must specify the country.

Longitude: min max Latitude: min max

Paleogeography model: Plate(s):
Comparison model:

You can select any of the available paleogeography models, and can choose to show paleocoordinates computed at the beginning, middle, or end of each collection's age range. These choices will be used if you select the paleolocation block under Choose output options or if you specify one or more plate numbers here. You can choose to compare multiple models and age selectors using the second set of menus. The text field above allows you to enter one or more plate numbers from your selected model. This will restrict the result to collections and occurrences that lie on one or more of these plates, according that model. The available models are:

Latitude and Longitude are specified in decimal degrees. You can use a minus sign for W/S, or you can append N or S to the latitude and E or W to the longitude values.

Select by geological context

Select by specimen

Select by metadata

Collection name/description (regex):

Anything you put in this field will be applied as a regular expression to the collection_name and collection_aka fields. Records will be returned only if they are associated with a matching collection. If you just put in regular text, it will match any collection with that text anywhere in either field. You can also use any of the standard regular expression syntax, including the backslash character and vertical bar.

identifier(s):

You may select only records associated with a specified record or records, such as all taxa from a specified set of collections, or all collections from a specified geographic cluster. You may enter one or more record identifiers, as a comma-separated list. These can be specified either as numbers, or as Paleobiology Database external identifiers such as "col:1003" or "occ:54023". In the latter case, the identifier must match the type selected in the dropdown menu.

Bibliographic reference

You may select only records associated with a specified bibliographic reference or references. You may specify these using reference identifiers, either as a number or as an identifier of the form "ref:1027". Alternately, you can specify a title, publication title, primary author, or any author.

Specimens

Occurrences

Collections

Taxa

Opinions

References

Dates should be entered either as yyyy-mm-dd, or as a number of "days ago", "months ago", etc. These are documented here. Names can be entered with or without first initial, as in "Alroy" or "J. Alroy".

Select all records of this type in the database

If you check this box, then all records of the selected type in the database will be returned. Any other criteria you specify are still applied. Please do this only if you are able to accept a download that might be well over 100 MB in size.

Choose output options

Choose archive options

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Lithology:
You can choose one or more of these lithology types, and either select or exclude fossils that were extracted from them. This is evaluated on a per-collection basis.
Environment:

You can select any combination of the major environments from the top row, then modify this selection using the bottom rows. This set of major and minor environment types is the same as was used with the old download form. Note: The lithology and environment information are entered separately, and for any particular collection it is possible that either, both, or none of this information has been entered.

If you fill in the Archive title field below, then the selected data will be stored in an archive file on our server instead of being immediately downloaded. When you click the "Archive" button above, you will be directed to the Archive Management web app. This will allow you to edit the descriptive fields, download the data, and apply for a DOI that you can use to publish your archive.
Archive title:
You may fill in either or both of the following fields, and you may add or update this information later using the Archive Management web app. If you later apply for a DOI and publish this archive, these fields will be reported in conjunction with it. You may want to fill in the Authors field with the names of the author(s) of the paper(s) that this archive is intended to be published with.
Authors:
Description:

Abundance:	Minimum:
You can select only occurrences for which an abundance is reported given in terms of number of specimens or individuals in the collection, or for which an abundance is reported in terms of percent coverage, or for which any kind of abundance information is given. You can also specify a minimum abundance value.