PBDB Data Service 1.2 v1 > General documentation > Bibliographic references

DESCRIPTION

This page describes the character and usage of bibliographic references in this data service. It describes the various roles that references play in the database, the parameters used to select them, and the values that are used to report these different roles.

REFERENCES

Every piece of data entered into the Paleobiology Database comes from a source, which may be either published or unpublished. Each of these sources is entered into the References table in the database, and every occurrence, collection, specimen, taxon, and opinion record contains a field named reference_no which links it to the record for its source in the References table.

When querying for any of these other data types, you can always ask for just those records that are linked to a particular reference, or to references from a particular publication or with particular authors. When querying for references themselves, you can ask specifically for references that are linked to occurrences, opinions, and so on. The parameters used for this are described below.

It is important to remember that the author of a taxonomic name or opinion may not be the same as the author of the linked reference. The reference may be a secondary source, which quotes or mentions the actual author of the name or opinion. There is a separate set of parameters for querying for taxa and opinions by author.

Reference parameters

The following parameters are available when querying for occurrences, specimens, collections, taxa, and opinions. You can also use them when querying for references, in which case they select which references to return. If you use two or more of these parameters together in the same query, they are conjoined. That is, a data record is selected only if it is linked to a reference that satisfies all of the given parameters together, or a reference is selected only if it satisfies all of them together.

ref_id

Return data records that are linked to one of the specified references. The value of this parameter should be one or more reference identifiers, as a comma-separated list.

ref_author

Return data records that are linked to any reference with one of the specified authors. You may specify more than one, as a comma-separated list. You may specify authors using any of the following patterns:

Smith

Return records linked to any reference with an author whose last name is "Smith"

J. Smith

Return records linked to any reference with an author whose first name starts with "J" and whose last name is "Smith"

J. Smith and F. Jones

Return records linked to any reference with both "J. Smith" and "F. Jones" as authors (in any order). You can also specify this as just "Smith and Jones" if you do not know the first names. There is currently no way to search for three or more authors together, but this could be added if people ask for it.

ref_primary

Return data records that are linked to any reference whose primary author is one of the specified names. You may specify names using the same patterns as with ref_author. If you use a name like Smith and Jones, you will get back records that are linked to any reference for which Smith is the primary author and Jones is also an author.

ref_title

Return data records that are linked to a reference whose title matches the specified string. You can use % and _ as wildcards, but the value of this parameter must contain at least one letter.

pub_title

Return data records that are linked to a reference whose "publication title" matches the specified string. You can use % and _ as wildcards, but the value of this parameter must contain at least one letter. You can use this field, for example, to select all articles from a particular journal or monograph series.

ref_pubyr

Return data records that are linked to a reference that was published during the indicated year or range of years. The parameter value must match one of the following patterns:

2000

Return records linked to any reference published in the year 2000

1990-2000

Return records linked to any reference published between 1990 and 2000, inclusive

1990-

Return records linked to any reference published in 1990 or after

-2000

Return records linked to any reference published in 2000 or before

The following parameter is used only when querying for references themselves, using any of the operations listed here:

ref_type

Return references that have any of the specified roles in the database. The value of this parameter should be one or more of the following, as a comma-separated list. If you are selecting references using the new download form, the second column of this table gives the label of the corresponding checkbox on the form.

If your query also includes other parameters such as a base taxon name, occurrence location, and so on, then references are only selected if their linked records satisfy those parameters.

auth authority references

Select references that provide the authority for taxonomic names. Note that such a reference may either be the published source of the name, or it may quote an earlier source.

class classification references

Select references which provide classification opinions. Out of all the opinions entered for each taxonomic name, one is automatically selected as the classification opinion for that name. This classification opinion gives the name its position in the consensus taxonomic hierarchy.

taxonomy --

This is a shortcut for auth,class.

ops opinion references

Select references from which taxonomic opinions were entered into the database, including opinions that are not selected as classification opinions.

occs occurrence references

Select references from which fossil occurrences were entered into the database.

spec specimen references

Select references from which fossil specimens were entered into the database.

colls collection references

Select references that are indicated as the primary reference for one or more fossil collections.

Reference types

When you query for references, the resulting records will contain a field named ref_type (rtp in the compact vocabulary). This field will contain a list of one or more of the the following codes, separated by commas:

PBDB valueCompact valueDescription
auth A

A reference of this type provides the authority for at least one taxonomic name. It may either be the published source of the name, or it may quote an earlier source.

class C

A reference of this type provides at least one classification opinion.

unsel U

A reference of this type provides at least one opinion that is not selected as a classification opinon.

occ O

A reference of this type has at least one fossil occurrence entered from it.

spec S

A reference of this type has at least one fossil specimen entered from it.

prim P

A reference of this type is the primary reference for at least one fossil collection.

ref R

A reference of this type plays an unspecified role in the database.

Associated counts

If you want to know exactly how many opinions, occurrences, taxa, etc. were entered from each reference, you can include the output block counts. This will include the following set of output fields. Note that all counts are restricted to just those taxa, occurrences, specimens, and collections which match the parameters given in the query. In other words, these counts do not necessarily reflect the total number of taxa, occurrences, etc. entered from each reference.

PBDBCompactDescription
n_taxa ntx

The number of distinct taxa associated with this reference

n_auth nau

The number of taxa for which this reference provides the authority

n_class ncl

The number of classification opinions entered from this reference

n_unclass nuc

The number of opinions not selected for classification entered from this reference

n_occs noc

The number of occurrences entered from this reference

n_specs nsp

The number of specimens entered from this reference

n_colls nco

The number of collections for which this is the primary reference

 

This service is provided by the Paleobiology Database, hosted by the Department of Geoscience at the University of Wisconsin-Madison.

If you have questions about this data service, or wish to report a bug, please contact the database administrator at admin@paleobiodb.org