PBDB Data Service 1.2 v2 > Fossil occurrences > Taxonomy of fossil occurrences

DESCRIPTION

This operation returns the taxonomic hierarchy of a selected set of fossil occurrences. You can select the set of occurrences to be analyzed using any of the parameters that are valid for the occs/list operation. You can make requests using both both operations with identical parameters, which will give you both a list of occurrences and a summary tabulation by taxon. If you include the block subcounts, then each taxon record will include a count of the number of species, genera, etc. from the selected set of occurrences that are contained within that taxon.

The result of this operation reports every taxon appearing in the selected set of occurrences, in hierarchical order. It includes the number of occurrences specifically identified to each listed taxon, along with the total number of occurrences of the taxon including all subtaxa. It also includes the number of species, genera, families and orders within each taxon that appear within the selected set of occurrences. The parent taxon identifier is also reported for each taxon, so that you are able to organize the result records into their proper hierarchy.

USAGE

Here are some usage examples:

PARAMETERS

You can use the following parameter if you wish to retrieve taxonomic tree corresponding to the entire set of occurrence records entered in this database. Please use this with care, since the result set will contain more than 250,000 records and will be at least 50 megabytes in size. You may also select subsets of this list by specifying some combination of the parameters listed below.

all_records

Select all occurrences entered in the database, subject to any other parameters you may specify. This parameter does not require any value.

The following parameters can be used to query for occurrences by a variety of criteria. Except as noted below, you may use these in any combination. If you do not specify all_records, you must specify at least one selection parameter from the following list.

occ_id

A comma-separated list of occurrence identifiers. The specified occurrences are selected, provided they satisfy the other parameters given with this request. You may also use the parameter name id. You can also use this parameter along with any of the other parameters to filter a known list of occurrences according to other criteria.

coll_id

A comma-separated list of collection identifiers. All occurrences associated with the specified collections are selected, provided they satisfy the other parameters given with this request.

clust_id

Return only records associated with the specified geographic clusters. You may specify one or more cluster ids, separated by commas.

coll_match

A string which will be matched against the collection_name and collection_aka fields. Records will be returned only if they belong to a matching collection. This string may contain the wildcards % and _. In fact, it will probably not match anything unless you include a % at the beginning and/or the end.

coll_re

This is like coll_match, except that it takes a regular expression. You can specify two or more alternatives separated by the vertical bar character |, and you can use all of the other standard regular expression syntax including the backslash \.

base_name

Return only records associated with the specified taxonomic name(s), including all subtaxa and synonyms. You may specify multiple names, separated by commas. You may append one or more exclusions to any name, using the ^ character. For example, Osteichthyes^Tetrapoda would select the fish excluding the tetrapods.

taxon_name

Return only records associated with the specified taxonomic name(s), including any synonyms. You may specify multiple names, separated by commas. Names may include wildcards, but if more than one name matches then only the one with the largest number of occurrences in the database will be used.

match_name

Return only records associated with the specified taxonomic name(s). You may specify multiple names, separated by commas. Names may include the wildcards % and _, and occurrences associated with all matching names will be returned. Synonyms will be ignored. This is a syntactic rather than a taxonomic match.

immediate

You may specify this parameter along with base_name, base_id, or taxon_name. If you do, then synonyms of the specified name(s) will be ignored. No value is necessary for this parameter, just include the parameter name.

base_id

Return only records associated with the specified taxa, including all subtaxa and synonyms. You may specify multiple taxon identifiers, separated by commas. Note that you may specify at most one of taxon_name, taxon_id, base_name, base_id.

taxon_id

Return only records associated with the specified taxa, not including subtaxa or synonyms. You may specify multiple taxon identifiers, separated by commas.

exclude_id

Exclude any records whose associated taxonomic name is a child of the given name or names, specified by taxon identifier. This is an alternative to the use of the ^ character in names.

idreso

Select only occurrences that are identified to the specified taxonomic resolution, and possibly lump together occurrences of the same genus or family. Accepted values are:

species

Select only occurrences which are identified to a species.

genus

Select only occurrences which are identified to a genus or species.

family

Select only occurrences which are identified to a family, genus or species.

lump_genus

Select only occurrences identified as a genus or species, and also coalesce all occurrences of the same genus in a given collection into a single record.

lump_gensub

Select only occurrences identified as a genus or species, and also coalesce all occurrences of the same genus/subgenus in a given collection into a single record.

idtype

This parameter specifies how re-identified occurrences should be treated. Allowed values include:

latest

Select only the latest identification of each occurrence, and ignore any previous ones. This is the default.

orig

Select only the original identification of each occurrence, and ignore any later ones.

reid

Select all identifications of occurrences that have been reidentified, including the original. Ignore occurrences for which no reidentification has been entered in the database. This may result in multiple records being returned each occurrence. Note, however, that if you also specify a taxon name then identifications that do not fall under that name will be ignored. You can find these by specifically querying for the occurrences you are interested in by identifier, with idtype=all.

all

Select every identification that matches the other query parameters. This may result in multiple records being returned for a given occurrence. See also the note given for reid above.

idqual

This parameter selects or excludes occurrences based on their taxonomic modifiers. Allowed values include:

any

Select all occurrences regardless of modifiers. This is the default.

certain

Exclude all occurrences marked with any of the following modifiers: aff. / cf. / ? / "" / informal / sensu lato.

genus_certain

Like certain, but look only at the genus/subgenus and ignore species modifiers.

uncertain

Select only occurrences marked with one of the following modifiers: aff. / cf. / ? / "" / informal / sensu lato.

new

Select only occurrences marked with one of the following: n. gen. / n. subgen. / n. sp.

idmod

This parameter selects or excludes occurrences based on any combination of taxonomic modifiers. You can use this parameter and/or idgen and idspc if you need to select a combination of modifiers not available through idqual. You can specify one or more of the following codes, separated by commas. If the first one is preceded by ! then they are excluded. otherwise, only occurrences marked with at least one are included:

ns

n. sp.

ng

n. gen. or n. subgen.

af

aff.

cf

cf.

sl

sensu lato

if

informal

eg

ex gr.

qm

question mark (?)

qu

quotes ("")

idgenmod

This parameter selects or excludes occurrences based on any combination of taxonomic modifiers on the genus and/or subgenus name. See idmod above.

idspcmod

This parameter selects or excludes occurrences based on any combination of taxonomic modifiers on the species name. See idmod above.

abundance

This parameter selects only occurrences that have particular kinds of abundance values. Accepted values are:

count

Select only occurrences with an abundance type of 'individuals', 'specimens' 'grid-count', 'elements', or 'fragments'

coverage

Select only occurrences with an abundance type of '%-...'

any

Select only occurrences with some type of abundance information

You may also append a colon followed by a decimal number. This will select only occurrences whose abundance is at least the specified minimum value.

lngmin
lngmax

Return only records whose present longitude falls within the given bounds. If you specify one of these parameters then you must specify both. If you provide bounds outside of the range -180° to 180°, they will be wrapped into the proper range. For example, if you specify lngmin=270 & lngmax=360, the query will be processed as if you had said lngmin=-90 & lngmax=0 . In this case, all longitude values in the query result will be adjusted to fall within the actual numeric range you specified.

latmin

Return only records whose present latitude is at least the given value.

latmax

Return only records whose present latitude is at most the given value.

loc

Return only records whose present location (longitude and latitude) falls within the specified shape, which must be given in WKT format with the coordinates being longitude and latitude values.

plate

Return only records located on the specified geological plate(s). If the value of this parameter starts with !, then all records on the specified plates are instead excluded. If the value of this parameter continues with G, then the values will be interpreted as plate numbers from the GPlates model. If S, then they will be interpreted as plate numbers from the Scotese model. Otherwise, they will be interpreted according to the value of the parameter pgm. The remainder of the value must be a list of plate numbers.

pgm

Specify which paleogeographic model(s) to use when returning paleocoordinates. You may specify one or more from the following list, separated by commas. If you do not specify a value for this parameter, the default model is gplates.

gplates

Wright et. al., 2013; Towards community-driven paleogeographic reconstructions

scotese

Scotese, C.R., 2021. An Atlas of Paleogeographic Maps: The Seas Come In and the Seas Go Out, Annual Reviews of Earth and Planetary Sciences, v. 49, p. 669-718.

seton

Seton et. al., 2012; Global continental and ocean basin reconstructions since 200 Ma

pgs

Specify whether to return paleocoordinates from the beginning, middle, or end of the age range for each collection. Accepted values are: early, mid, late. You may specify more than one as a comma-separated list.

cc

Return only records whose location falls within the specified geographic regions. The value of this parameter should be one or more two-character country codes and/or three-character continent codes as a comma-separated list. If the parameter value starts with !, then records falling into these regions are excluded instead of included. Any country codes starting with ^ are subtracted from the filter. For example:

ATA,AU

Select occurrences from Antarctica and Australia

NOA,SOA,^AR,^BO

Select occurrences from North and South America, but not Argentina or Bolivia

!EUR,^IS

Exclude occurrences from Europe, except those from Iceland

state

Return only records from collections that are indicated as falling within the specified state or province. This information is not recorded for all collections, and has not been checked for accuracy. Given that state names are sometimes duplicated between countries, it is recommended to also specify the country using the cc parameter.

county

Return only records from collections that are indicated as falling within the specified county or other sub-state administrative division. This information is not recorded for all collections, and has not been checked for accuracy. Given that county names are often duplicated between states and countries, it is recommended that you also specify the state using the state parameter and the country using the cc parameter.

continent

Return only records whose geographic location falls within the specified continent or continents. The value of this parameter should be a comma-separated list of continent codes. This parameter is deprecated; use cc instead.

strat

Return only records that fall within the named geological stratum or strata. You may specify more than one, separated by commas. Names may include the standard SQL wildcards % and _, and may be followed by any of 'fm', 'gp', 'mbr'. If none of these suffixes is given, then all matching stratigraphic names will be selected. If the parameter value begins with !, then records associated with this stratum or strata are excluded instead of included. Note that this parameter is resolved through string matching only. Stratigraphic nomenclature is not currently standardized in the database, so misspellings may occur.

formation

Return only records that fall within the named stratigraphic formation(s). This parameter is deprecated; use strat instead.

stratgroup

Return only records that fall within the named stratigraphic group(s). This parameter is deprecated; use strat instead.

member

Return only records that fall within the named stratigraphic member(s). This parameter is deprecated; use strat instead.

lithology

Return only records recorded as coming from any of the specified lithologies and/or lithology types. If the paramter value string starts with ! then matching records will be excluded instead. If the symbol ^ occurs at the beginning of any lithology name, then all subsequent values will be subtracted from the filter. Example: carbonate,^bafflestone.

envtype

Return only records recorded as belonging to any of the specified environments and/or environmental zones. If the parameter value string starts with ! then matching records will be excluded instead. If the symbol ^ occurs at the beginning of any environment code, then all subsequent values will be subtracted from the filter. Examples: terr,^fluvial,lacustrine or !slope,^carbonate. You may specify one or more of the following values, as a comma-separated list:

terr

Any terrestrial environment

marine

Any marine environment

carbonate

Carbonate environment

silicic

Siliciclastic environment

unknown

Unknown or indeterminate environment

lacust

Lacustrine zone

fluvial

Fluvial zone

karst

Karst zone

terrother

Other terrestrial zone

marginal

Marginal marine zone

reef

Reef zone

stshallow

Shallow subtidal zone

stdeep

Deep subtidal zone

offshore

Offshore zone

slope

Slope/basin zone

marindet

Marine indeterminate zone

interval_id

Return only records whose temporal locality falls within the given geologic time interval or intervals, specified by numeric identifier. If you specify more than one interval, the time range used will be the contiguous period from the beginning of the earliest to the end of the latest specified interval.

interval

Return only records whose temporal locality falls within the named geologic time interval or intervals, specified by name. You may specify more than one interval, separated by either commas or a dash. If you specify more than one interval, the time range used will be the contiguous period from the beginning of the earliest to the end of the latest specified interval.

min_ma

Return only records whose temporal locality is at least this old, specified in Ma.

max_ma

Return only records whose temporal locality is at most this old, specified in Ma.

timerule

Resolve temporal locality according to the specified rule, as listed below. This rule is applied to determine which occurrences, collections, and/or taxa will be selected if you also specify an age range using any of the parameters listed immediately above. For diversity output, this rule is applied to place each occurrence into one or more temporal bins, or to ignore the occcurrence if it does not match any of the bins. The available rules are:

contain

Select only records whose temporal locality is strictly contained in the specified time range. This is the most restrictive rule. For diversity output, this rule guarantees that each occurrence will fall into at most one temporal bin, but many occurrences will be ignored because their temporal locality is too wide to fall into any of the bins.

major

Select only records for which at least 50% of the temporal locality range falls within the specified time range. For diversity output, this rule also guarantees that each occurrence will fall into at most one temporal bin. Many occurrences will be ignored because their temporal locality is more than twice as wide as any of the overlapping bins, but fewer will be ignored than with the contain rule. This is the default timerule unless you specifically select one.

buffer

Select only records whose temporal locality overlaps the specified time range and also falls completely within a 'buffer zone' around this range. This buffer defaults to 12 million years for the Paleozoic and Mesozoic and 5 million years for the Cenozoic. You can override the buffer width using the parameters timebuffer and late_buffer. For diversity output, some occurrences will be counted as falling into more than one bin. Some occurrences will still be ignored, but fewer than with the above rules.

overlap

Select only records whose temporal locality overlaps the specified time range by any amount. This is the most permissive rule. For diversity output, every occurrence will be counted. Many will be counted as falling into more than one bin.

timebuffer

Override the default buffer period when resolving temporal locality. The value must be given in millions of years. This parameter is only relevant if timerule is set to buffer.

latebuffer

Override the default buffer period for the end of the time range when resolving temporal locality. This allows the buffer to be different on the late end of the interval than on the early end. The value must be given in millions of years. This parameter is only relevant if timerule is set to buffer.

The following parameters can be used to filter the selection. If you wish to use one of them and have not specified any of the selection parameters listed above, use all_records.

occs_created_before

Select only records associated with occurrences that were created before the specified date or date/time.

occs_created_after

Select only records associated with occurrences that were created on or after the specified date or date/time.

occs_modified_before

Select only records associated with occurrences that were last modified before the specified date or date/time.

occs_modified_after

Select only records associated with occurrences that were modified on or after the specified date or date/time.

occs_authorized_by

Select only records associated with occurrences that were authorized by the specified person, indicated by name or identifier

occs_entered_by

Select only records associated with occurrences that were entered by the specified person, indicated by name or identifier

occs_modified_by

Select only records associated with occurrences that were modified by the specified person, indicated by name or identifier

occs_touched_by

Select only records associated with occurrences that were either authorized, entered or modified by the specified person, indicated by name or identifier

occs_authent_by

Select only records associated with occurrences that were authorized or entered by the specified the specified person, indicated by name or identifier

taxa_created_before

Select only records associated with taxa that were created before the specified date or date/time.

taxa_created_after

Select only records associated with taxa that were created on or after the specified date or date/time.

taxa_modified_before

Select only records associated with taxa that were last modified before the specified date or date/time.

taxa_modified_after

Select only records associated with taxa that were modified on or after the specified date or date/time.

taxa_authorized_by

Select only records associated with taxa that were authorized by the specified person, indicated by name or identifier

taxa_entered_by

Select only records associated with taxa that were entered by the specified person, indicated by name or identifier

taxa_modified_by

Select only records associated with taxa that were modified by the specified person, indicated by name or identifier

taxa_touched_by

Select only records associated with taxa that were either authorized, entered or modified by the specified person, indicated by name or identifier

taxa_authent_by

Select only records associated with taxa that were authorized or entered by the specified the specified person, indicated by name or identifier

The following parameters can also be used to filter the result list based on taxonomy:

taxon_status

Selects only records associated with taxa that have the specified status. The default is all. Accepted values include:

all

Select all taxonomic names matching the other specified criteria. This is the default.

valid

Select only taxonomically valid names

accepted

Select only taxonomically valid names that are not junior synonyms

junior

Select only taxonomically valid names that are junior synonyms

invalid

Select only taxonomically invalid names, e.g. nomina dubia

pres

This parameter indicates whether to select records associated with taxa that are identified as ichnotaxa, form taxa, or regular taxa. The default is all, which will select all records that meet the other specified criteria. You can specify one or more of the following values as a list:

regular

Select regular taxa

form

Select form taxa

ichno

Select ichnotaxa

all

Select all taxa

rank

Return only records associated with taxonomic names at the specified rank, e.g. genus.

depth

Return only taxa no more than the specified number of levels below the base taxon or taxa in the hierarchy.

extant

Selects only records associated with extant or with non-extant taxa. Accepted values are: yes, no.

The following parameters can be used to generate data archives. The easiest way to do this is by using the download generator form.

archive_title

A value for this parameter directs that an archive be created with the specified title unless one already exists.

archive_replace

A true value for this parameter directs that if there is an existing archive with the specified title then its contents should be replaced by the output of the current request. Without this parameter, the error code E_EXISTING will be returned if the specified title matches an existing record. If the existing record has a DOI, the error E_IMMUTABLE will be returned and this cannot be overridden.

archive_authors

The value of this parameter, if any, is put into the 'authors' field of the created or updated archive record.

archive_desc

The value of this parameter, if any, is put into the 'description' field of the created or updated archive record.

You can use the following parameters to select extra information you wish to retrieve, and the order in which you wish to get the records:

show

This parameter is used to select additional information to be returned along with the basic record for each taxon. Its value should be one or more of the following, separated by commas:

full

This is a shortcut for including all of the information that defines this record. Currently, this includes the following blocks: attr, app, common, parent size, class, ecospace, otaph, etbasis, refattr. If we subsequently add new data fields to this record then full will include those as well. So if you are publishing a URL, it might be a good idea to include show=full.

attr

The attribution of this taxonomic name (author and year)

app

The age of first and last appearance of this taxon from all of the occurrences recorded in this database

occapp

The age of first and last appearance of each taxon from the set of occurrences being analyzed (not the absolute first and last occurrence ages).

common

The common name of this taxon, if one is entered in the database.

parent

If the classification of this taxon has been entered into the database, the name of the parent taxon, or its senior synonym if there is one.

immparent

You can use this instead of parent if you wish to know the immediate parent taxon. If the immediate parent is a junior synonym, both it and its senior synonym will be displayed.

acconly

Only return accepted names, and suppress the fields difference, accepted_name, accepted_rank, and accepted_no, because they are only relevant for non-accepted names.

size

The number of subtaxa appearing in this database, including the taxon itself.

class

The classification of this taxon: phylum, class, order, family, genus. Also includes the type taxon, if one is entered in the database. This information is also included in the nav block, so do not specify both at once.

classext

Like class, but also includes the relevant taxon identifiers.

subcounts

The number of subtaxa known to this database, summarized by rank.

ecospace

Information about ecological space that this organism occupies or occupied. This has only been filled in for a relatively few taxa. Here is a list of values.

ttaph

Information about the taphonomy of this organism. You can also use the alias taphonomy. Here is a list of values.

etbasis

Annotates the output block ecospace, indicating at which taxonomic level each piece of information was entered.

seq

The sequence numbers that mark this taxon's position in the tree.

img

The identifier of the image (if any) associated with this taxon. These images are sourced from phylopic.org.

ref

The reference from which this taxonomic name was entered, as formatted text.

refattr

The author(s) and year of publication of the reference. Note that this may be different from the attribution of the name itself, if the reference is a secondary source.

ent

The identifiers of the people who authorized, entered and modified this record

entname

The names of the people who authorized, entered and modified this record

crmod

The created and modified timestamps for the collection record

order

This parameter is currently nonfunctional. It will eventually allow you to to set the order in which the taxa are returned.

You can also use any of the special parameters with this request

METHODS

This data service accepts the following HTTP methods: GET, HEAD

RESPONSE

The response to an HTTP request with this operation will consist of fields from the following list. The block basic is always present. The others may be selected using the parameter show.

Field nameBlockDescription
pbdbcom
orig_no oid basic

A unique identifier for this taxonomic name

taxon_no vid basic

A unique identifier for the selected variant of this taxonomic name. By default, this is the variant currently accepted as most correct.

record_type typ basic

The type of this object: txn for a taxon.

flags flg basic

This field will be empty for most records. Otherwise, it will contain one or more of the following letters:

B

This taxon is one of the ones specified explicitly in the query. If the result is a subtree, this represents the 'base'.

E

This taxon was specified in the query as an exclusion.

V

This taxonomic name is a variant that is not currently accepted.

I

This taxon is an ichnotaxon.

F

This taxon is a form taxon.

taxon_rank rnk basic

The rank of this taxon, ranging from subspecies up to kingdom

taxon_name nam basic

The scientific name of this taxon

taxon_attr att attr

The attribution (author and year) of this taxonomic name

common_name nm2 common, full

The common (vernacular) name of this taxon, if any

difference tdf basic

If this name is either a junior synonym or is invalid for some reason, this field gives the reason. The fields accepted_no and accepted_name then specify the name that should be used instead.

tax_status n/a basic

The taxonomic status of this name, in the Darwin Core vocabulary. This field only appears if that vocabulary is selected.

nom_status n/a basic

The nomenclatural status of this name, in the Darwin Core vocabulary. This field only appears if that vocabulary is selected.

accepted_no acc basic

If this name is either a junior synonym or an invalid name, this field gives the identifier of the accepted name to be used in its place. Otherwise, its value will be the same as orig_no. In the compact vocabulary, this field will be omitted in that case.

accepted_rank acr basic

If accepted_no is different from orig_no, this field gives the rank of the accepted name. Otherwise, its value will be the same as taxon_rank. In the compact voabulary, this field will be omitted in that case.

accepted_name acn basic

If accepted_no is different from orig_no, this field gives the accepted name. Otherwise, its value will be the same as taxon_name. In the compact vocabulary, this field will be omitted in that case.

parent_no par basic

The identifier of the parent taxon, or of its senior synonym if there is one. This field and those following are only available if the classification of this taxon is known to the database.

parent_name prl parent, immparent

The name of the parent taxon, or of its senior synonym if there is one.

immpar_no ipn immparent

The identifier of the immediate parent taxon, even if it is a junior synonym.

immpar_name ipl immparent

The name of the immediate parent taxon, even if it is a junior synonym.

container_no ctn basic

The identifier of a taxon from the result set containing this one, which may or may not be the parent. This field will only appear in the result of the occs/taxa operation, where no base taxon is specified. The taxa reported in this case are the "classical" ranks, rather than the full taxonomic hierarcy.

ref_author aut refattr, refattr

The author(s) of the reference from which this name was entered. Note that the author of the name itself may be different if the reference is a secondary source.

ref_pubyr pby refattr, refattr

The year of publication of the reference from which this name was entered. Note that the publication year of the name itself may be different if the reference is a secondary source.

reference_no rid basic

The identifier of the reference from which this name was entered.

is_extant ext basic

True if this taxon is extant on earth today, false if not, not present if unrecorded

n_occs noc basic

The number of fossil occurrences in this database that are identified as belonging to this taxon or any of its subtaxa.

firstapp_max_ma fea app

The early age bound for the first appearance of this taxon in the database

firstapp_min_ma fla app

The late age bound for the first appearance of this taxon in the database

lastapp_max_ma lea app

The early age bound for the last appearance of this taxon in the database

lastapp_min_ma lla app

The late age bound for the last appearance of this taxon in the database

early_interval tei app

The name of the interval in which this taxon first appears, or the start of its range.

late_interval tli app

The name of the interval in which this taxon last appears, if different from early_interval.

firstocc_max_ma foa occapp

The early age bound for the first appearance of this taxon in the set of occurrences being analyzed.

firstocc_min_ma fpa occapp

The late age bound for the first appearance of this taxon in the set of occurrences being analyzed.

lastocc_max_ma loa occapp

The early age bound for the last appearance of this taxon in the set of occurrences being analyzed.

lastocc_min_ma lpa occapp

The late age bound for the last appearance of this taxon in the set of occurrences being analyzed.

taxon_size siz size

The total number of taxa in the database that are contained within this taxon, including itself

extant_size exs size

The total number of extant taxa in the database that are contained within this taxon, including itself

phylum phl class

The name of the phylum in which this taxon is classified

phylum_no phn classext

The identifier of the phylum in which this taxon is classified. This is only included with the block classext.

class cll class

The name of the class in which this taxon is classified

class_no cln classext

The identifier of the class in which this taxon is classified. This is only included with the block classext.

order odl class

The name of the order in which this taxon is classified

order_no odn classext

The identifier of the order in which this occurrence is classified. This is only included with the block classext.

family fml class

The name of the family in which this taxon is classified

family_no fmn classext

The identifier of the family in which this occurrence is classified. This is only included with the block classext.

genus gnl class

The name of the genus in which this taxon is classified. A genus may be listed as occurring in a different genus if it is a junior synonym; a species may be listed as occurring in a different genus than its name would indicate if its genus is synonymized but no synonymy opinion has been entered for the species.

genus_no gnn classext

The identifier of the genus in which this occurrence is classified. This is only included with the block classext.

subgenus_no sgn classext

The identifier of the subgenus in which this occurrence is classified, if any. This is only included with the block classext.

type_taxon ttl class

The name of the type taxon for this taxon, if known.

type_taxon_no ttn classext

The identifier of the type taxon for this taxon, if known.

n_orders odc subcounts

The number of orders within this taxon. For lists of taxa derived from a set of occurrences, this will be the number of orders that appear within that set. Otherwise, this will be the total number of orders within this taxon that are known to the database.

n_families fmc subcounts

The number of families within this taxon, according to the same rules as n_orders above.

n_genera gnc subcounts

The number of genera within this taxon, according to the same rules as n_orders above.

n_species spc subcounts

The number of species within this taxon, according to the same rules as n_orders above.

taxon_environment jev ecospace

The general environment or environments in which this life form is found. See ecotaph vocabulary.

environment_basis jec ecospace

Specifies the taxon from which the environment information is inherited.

motility jmo ecospace

Whether the organism is motile, attached and/or epibiont, and its mode of locomotion if any. See ecotaph vocabulary.

motility_basis jmc etbasis

Specifies the taxon for which the motility information was set. The taphonomy and ecospace information are inherited from parent taxa unless specific values are set.

life_habit jlh ecospace

The general life mode and locality of this organism. See ecotaph vocabulary.

life_habit_basis jhc etbasis

Specifies the taxon for which the life habit information was set. See motility_basis above. These fields are only included if the ecospace block is also included.

vision jvs ecospace

The degree of vision possessed by this organism. See ecotaph vocabulary.

vision_basis jvc etbasis

Specifies the taxon for which the vision information was set. See motility_basis above. These fields are only included if the ecospace block is also included.

diet jdt ecospace

The general diet or feeding mode of this organism. See ecotaph vocabulary.

diet_basis jdc etbasis

Specifies the taxon for which the diet information was set. See motility_basis above. These fields are only included if the ecospace block is also included.

reproduction jre ecospace

The mode of reproduction of this organism. See ecotaph vocabulary.

reproduction_basis jrc etbasis

Specifies the taxon for which the reproduction information was set. See motility_basis above. These fields are only included if the ecospace block is also included.

ontogeny jon ecospace

Briefly describes the ontogeny of this organism. See ecotaph vocabulary.

ontogeny_basis joc etbasis

Specifies the taxon for which the ontogeny information was set. See motility_basis above. These fields are only included if the ecospace block is also included.

ecospace_comments jcm ecospace

Additional remarks about the ecospace, if any.

composition jco ttaph

The composition of the skeletal parts of this organism. See taphonomy vocabulary.

architecture jsa ttaph

An indication of the internal skeletal architecture. See taphonomy vocabulary.

thickness jth ttaph

An indication of the relative thickness of the skeleton. See taphonomy vocabulary.

reinforcement jsr ttaph

An indication of the skeletal reinforcement, if any. See taphonomy vocabulary.

taphonomy_basis jtc etbasis

Specifies the taxon for which the taphonomy information was set. See motility_basis above. These fields are only included if the otaph block is also included.

lft lsq seq

This number gives the taxon's position in a preorder traversal of the taxonomic tree.

rgt rsq seq

This number greater than or equal to the maximum of the sequence numbers of all of this taxon's subtaxa, and less than the sequence of any succeeding taxon in the sequence. You can use this, along with lft, to determine subtaxon relationships. If the pair lft,rgt for taxon <A> is bracketed by the pair lft,rgt for taxon <B>, then A is a subtaxon of B.

image_no img img

If this value is non-zero, you can use it to construct image URLs using taxa/thumb and taxa/icon.

primary_reference ref ref

The primary reference associated with this record (as formatted text)

authorizer_no ati ent, entname

The identifier of the person who authorized the entry of this record

enterer_no eni ent, entname

The identifier of the person who actually entered this record.

modifier_no mdi ent, entname

The identifier of the person who last modified this record, if it has been modified.

authorizer ath entname

The name of the person who authorized the entry of this record

enterer ent entname

The name of the person who actually entered this record

modifier mdf entname

The name of the person who last modified this record, if it has been modified.

created dcr crmod

The date and time at which this record was created.

modified dmd crmod

The date and time at which this record was last modified.

The summary block will consist of fields from the following list.

Field nameBlockDescription
pbdbcom
n_occs noc summary

The number of occurrences that were scanned in the process of computing this taxonomic tree.

missing_taxon mtx summary

The number of occurrences skipped because the taxonomic hierarchy in this database is incomplete. For example, some genera have not been placed in their proper family, so occurrences in these genera will be skipped if you are counting families.

FORMATS

The following response formats are available for this operation. You must select the desired format for a request by adding the appropriate suffix to the URI path.

FormatSuffixDocumentation
JSON .json

JSON format

Comma-separated text .txt

Text formats

Comma-separated text .csv

Text formats

Tab-separated text .tsv

Text formats

VOCABULARIES

The following response vocabularies are available for this operation. If you wish your responses to be expressed in a vocabulary other than the default for your selected format, you can use the vocab parameter with the appropriate vocabulary name.

VocabularyNameDefault forDescription
PaleobioDB field names pbdb txt, csv, tsv

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.

Compact field names com json

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.

 

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