SchemaSpy Analysis of neotoma

Generated on Tue. Nov. 07 11:03 PST 2023

XML Representation
Insertion Order Deletion Order
Constraints 223
Anomalies 1
Routines 11

Database Properties

Database Type: PostgreSQL - 9.6.24


Table / View Children Parents Columns Rows Type Comments
aggregatesamples 0 2 4 553 Table

This table stores the samples in Aggregate Datasets.

aggregatesampleages 0 3 5 369 Table

This table stores the links to the ages of samples in an Aggregate Dataset. The table is necessary because samples may be from Collection Units with multiple chronologies, and this table stores the links to the sample ages desired for the Aggregate Dataset.

chroncontrols 5 4 13 100724 Table

This table stores data for Chronology Controls, which are the age-depth control points used for age models. These controls may be geophysical controls, such as radiocarbon dates, but include many other kinds of age controls, such as biostratigraphic controls, archaeological cultural associations, and volcanic tephras. In the case of radiocarbon dates, a Chronology Control may not simply be the raw radiocarbon date reported by the laboratory, but perhaps a radiocarbon date corrected for an old carbon reservoir, a calibrated radiocarbon date, or an average of several radiocarbon dates from the same level. A common control for lake-sediment cores is the age of the top of the core, which may be the year the core was taken or perhaps an estimate of 0 BP if a few cm of surficial sediment were lost.

elementportions 3 0 4 54 Table
datasetdoi 0 0 4 43796 Table
accumulationrates 0 3 6 1089 Table
radiocarboncalibration 0 0 2 45101 Table

Radiocarbon calibration table. This table is intended for quick calibration of age-model radiocarbon dates. These calibrated dates are for perusal and data exploration only. Please see Section 2.5 for a full discussion.

publications 13 1 26 13466 Table

This table stores publication or bibliographic data. The table is designed with fields for bibliographic data so that bibliographies can be formatted in different styles and potentially exported to bibliographic software such EndNote®. In the constituent databases that were originally merged into Neotoma, bibliographic entries were not parsed into separate fields, but rather were stored as free-form text. Because complete parsing of these thousands of legacy bibliographic entries into individual fields would have been prohibitively time consuming, the existing bibliographic data were ingested “as is” with a PubTypeID = Other. However, for legacy publications, the year of publication was added to the Year field, and authors were parsed into the PublicationAuthors table and added to the Contacts table. In addition, some global changes were made. For example, «Pp.» was changed to «Pages», «Ed.» to «Editor», and «Eds.» to «Editors». Also for FAUNMAP entries, abbreviated journal names were changed to fully spelled out names.
The merged databases used different bibliographic styles, and data entry personnel working on the same database sometimes followed different conventions. Consequently, the current bibliographic entries are not stylistically uniform. Eventually, the legacy bibliographic data will be parsed into separate fields.
The Publications table has fields to accommodate a number of different types of publications. Some fields contain different kinds of data for different kinds of publications. For example, the BookTitle field stores the titles of books, but stores the journal name for journal articles. The Publisher field stores the name of the publisher for books, but the name of the university for theses and dissertations.
Authors are stored in the PublicationAuthors table. Editors are also stored in the PublicationAuthors table if the entire publication is cited. The PublicationAuthors table has a ContactID field, which links to the Contacts table, where full names and contact information is stored for authors and editors. The PubTypeID «Authored Book» or «Edited Book» indicates whether the Publication Authors records are authors or editors. If a book chapter or section is the primary bibliographic entry, then the book editors are stored in the PublicationEditors table, which does not have a ContactID field.

eventpublications 0 2 4 378 Table
samples 8 3 12 506105 Table

This table stores sample data. Samples belong to Analysis Units, which belong to Collection Units, which belong to Sites. Samples also belong to a Dataset, and the Dataset determines the type of sample. Thus, there could be two different samples from the same Analysis Unit, one belonging to a pollen dataset, the other to a plant macrofossil dataset.

isostratdata 0 3 6 634 Table
lithology 0 1 8 30155 Table

This table stores the lithologic descriptions of Collection Units.

fractiondated 1 0 4 29 Table
radiocarbonmethods 1 0 4 5 Table
isosamplepretreatments 0 2 6 1035 Table
geochronpublications 0 2 4 36183 Table

Publications in which Geochronologic measurements are reported. Many older radiocarbon dates are reported in the journal Radiocarbon. Dates may be reported in multiple publications. The “publication” could be a database such as the online Canadian Archaeological Radiocarbon Database.

formtaxa 0 3 7 3 Table
faciestypes 1 0 4 103 Table

Lookup table of Facies Types. Table is referenced by the AnalysisUnits table.

chroncontrolranks 0 5 9 0 Table
synonymtypes 1 0 4 20 Table

Lookup table of Synonym Types. Table is referenced by the Synonyms table.

summarydatataphonomy 0 2 4 42956 Table
chronologies 3 3 13 31133 Table

This table stores Chronology data. A Chronology refers to an explicit chronology assigned to a Collection Unit. A Chronology has Chronology Controls, the actual age-depth control points, which are stored in the ChronControls table. A Chronology is also based on an Age Model, which may be a numerical method that fits a curve to a set of age-depth control points or may simply be individually dated Analysis Units.
A Collection Unit may have more than one Chronology, for example one in radiocarbon years and another in calibrated radiocarbon years. There may be a Chronology developed by the original author and another developed by a later research project. Chronologies may be stored for archival reasons, even though they are now believed to have problems, if they were used for an important research project. One Chronology per Age Type may be designated the default Chronology, which is the Chronology currently preferred by the database stewards.
Based upon the Chronology, which includes the Age Model and the Chron Controls, ages are assigned to individual samples, which are stored in the SampleAges table.
A younger and older age bounds are assigned to the Chronology. Within these bounds the Chronology is regarded as reliable. Ages may be assigned to samples beyond the reliable age bounds, but these are not considered reliable

datasetsubmissiontypes 1 0 4 9 Table

Lookup table of Dataset Submission Types. Table is referenced by the DatasetSubmissions table.

taxa 17 4 14 46322 Table

This table lists all taxa in the database. Most taxa are biological taxa; however, some are biometric measures and some are physical parameters.

contactstatuses 1 0 5 7 Table

Lookup table of Contact Statuses. Table is referenced by the Contacts table.

sampleanalysts 0 2 6 304119 Table

This table lists the Sample Analysts.

isostandardtypes 1 0 5 20 Table
embargo 1 0 3 0 Table
chroncontrolaccuracydirections 1 0 4 3 Table
taxagrouptypes 4 0 4 55 Table

Lookup table for Taxa Group Types. This table is referenced by the Taxa table.

specimendates 1 6 10 2662 Table

This table enables queries for dated specimens of individual taxa. Although the MaterialDated field in the Geochronology table may list the taxa dated, this protocol is not enforced, and the field is not linked to the taxa table.

analysisunitaltdepths 0 2 5 7395 Table
unitsdatasettypes 0 2 4 657 Table
isovariablescaletypes 0 2 4 14 Table
chroncontrolaccuracyranks 1 0 4 8 Table
isomatanalsubstrate 0 2 4 19 Table
repositoryinstitutions 2 0 6 387 Table

A lookup table of institutions that are repositories for fossil specimens. Table is referenced by the RepositorySpecimens table.

siteimages 0 2 9 9 Table

This table stores hyperlinks to jpeg images of sites.

elementtaxagroupmaturities 0 2 4 40 Table
repositoryspecimens 0 2 5 6405 Table

This table lists the repositories in which fossil specimens have been accessioned or reposited. The inventory in Neotoma is by Dataset, which is the collection of specimens from a Collection Unit. Occasionally, specimens from a single Collection Unit have been reposited at different institutions, in which case multiple records for that Dataset occur in the table.

specimens 4 8 17 3351 Table
agetypes 5 0 6 5 Table

Lookup table of Age Types or units. This table is referenced by the Chronologies and Geochronology tables.

taphonomictypes 2 1 6 81 Table
sites 4 0 13 21776 Table

The Sites table stores information about sites or localities, including name, geographic coordinates, and description. Sites generally have an areal extent and can be circumscribed by a latitude-longitude box. However, site data ingested from legacy databases have included only point locations. The lat-long box can be used either to circumscribe the aerial extent of a site or to provide purposeful imprecision to the site location. Site location may be imprecise because the original description was vague, e.g. «a gravel bar 5 miles east of town», or because the investigators, land owner, or land management agency may not want the exact location made public, perhaps to prevent looting and vandalism. In the first case, the lat-long box can be made sufficiently large to encompass the true location and in the second case to prevent exact location.

aggregateordertypes 1 0 5 7 Table

Lookup table for Aggregate Order Types. Table is referenced by the AggregateDatasets table.

geopoliticalunits 3 0 7 10097 Table

Lookup table of GeoPoliticalUnits. Table is referenced by the SiteGeoPolitical table. These are countries and various subdivisions. Countries and subdivisions were acquired from the U.S. Central Intelligence Agency World Factbook8 and the ISO 3166-1 and ISO 3166-2 databases9.
Each GeoPolitical Unit has a rank. GeoPolitical Units with Rank 1 are generally countries. There are a few exceptions, including Antarctica and island territories, such as Greenland, which although a Danish territory, is geographically separate and distinct. Rank 2 units are generally secondary political divisions with various designations: e.g. states in the United States, provinces in Canada, and regions in France. For some countries, the secondary divisions are not political but rather distinct geographic entities, such as islands. The secondary divisions of some island nations include either groups of islands or sections of more highly populated islands; however, the actual island on which a site is located is more important information. Some countries also have Rank 3 units, e.g. counties in the United States and metropolitan departments in France. In addition to purely political units, various other administrative regions and geographic entities can be contained in this table. Examples of administrative regions are National Parks and Forests. It might be quite useful, for example, to have a record of all the sites in Yellowstone National Park. These additional units are Rank 4, and they can be added to the database as warranted.

datataxonnotes 0 2 7 0 Table
isoinstrumentationtypes 1 0 4 4 Table
variablecontexts 2 0 4 83 Table

Variable Contexts lookup table. Table is referenced by the Variables table.

relativeagepublications 0 2 4 115 Table

This table stores Publications in which Relative Ages are reported for CollectionUnits.

externalpublications 0 2 5 1317 Table
isometadata 0 4 13 4893 Table
radiocarbon 0 1 12 31854 Table
collectionunits 6 4 20 32827 Table

This table stores data for Collection Units.

isosampleorigintypes 0 0 4 6 Table
isomaterialanalyzedtypes 2 0 4 12 Table
samplekeywords 0 2 4 17904 Table

This table lists the Sample Analysts.

depagents 0 2 4 5273 Table

Deposition Agents for Analysis Units. Individual Analysis Units may be listed multiple times with different Deposition Agents.

specimentaphonomy 0 2 4 452 Table
lithostrat 2 2 6 16 Table
relativeagescales 1 0 4 9 Table

Lookup table of Relative Age Scales. Table is referenced by the RelativeAges table.

rocktypes 2 1 6 206 Table
synonymy 0 5 11 37992 Table

The synonymy table links dataset-level synonymies to particular publications or contacts. This allows users to maintain the original taxonomic information within a table, but tie it to newer and more authoritative taxonomic information.

variables 7 4 7 55155 Table

This table lists Variables, which always consist of a Taxon and Units of measurement. Variables can also have Elements, Contexts, and Modifications. Thus, the same taxon with different measurement units (e.g. present/absent, NISP, MNI) are different Variables.

depagenttypes 1 0 4 19 Table

Lookup table of Depositional Agents. Table is referenced by the DepAgents table.

synonyms 0 3 6 2821 Table

This table lists common synonyms for taxa in the Taxa table. No effort has been made to provide a complete taxonomic synonymy, but rather to list synonyms commonly used in recent literature. This table is not the same as the Synonomy table, also present in Neotoma, which links a specific synonymy to a dataset

keywords 1 0 4 5 Table

Lookup table of Keywords referenced by the SampleKeywords table. The table provides a means to identify samples sharing a common attribute. For example, the keyword «modern sample» identifies modern surface samples in the database. These samples include individual surface samples, as well as core tops. Although not implemented, a «pre-European settlement» keyword would be a means to identify samples just predating European settlement.

contacts 17 1 17 13247 Table

This table lists persons and organizations referenced by the Chronologies, Collectors, DatasetPIs, DatasetSubmissions, Projects, PublicationAuthors, SampleAnalysts, and SiteImages tables.

sitegeopolitical 0 2 5 53305 Table

This table lists the GeoPolitical units in which sites occur.

events 3 1 12 371 Table
elementtaxagroupsymmetries 0 2 4 446 Table
datasetdatabases 0 2 4 47689 Table
isobiomarkerbandtypes 0 1 5 9 Table
sampleages 1 2 8 591749 Table

This table stores sample ages. Ages are assigned to a Chronology. Because there may be more than one Chronology for a Collection Unit, samples may be assigned different ages for different Chronologies. A simple example is one sample age in radiocarbon years and another in calibrated radiocarbon years. The age units are an attribute of the Chronology.

isostandards 0 3 6 0 Table
datasettaxagrouptypes 0 2 4 184 Table
publicationtranslators 0 1 8 4 Table
publicationtypes 1 0 4 13 Table

Lookup table of Publication Types. This table is referenced by the Publications table.

collectiontypes 1 0 4 11 Table

This table is a lookup table for types of Collection Units, or Collection Types. Table is referenced by the CollectionUnits table.

taphonomicsystemsdatasettypes 0 2 4 11 Table
eventchronology 0 3 7 271 Table
aggregatechronologies 1 2 10 7 Table

This table stores metadata for Aggregate Chronologies. An Aggregate Chronology refers to an explicit chronology assigned to a sample Aggregate. The individual Aggregate Samples have ages assigned in the AggregateSampleAges table. An Aggregate Chronology would be used, for example, for a set of packrat middens assigned to an AggregateDataset. The Aggregate Chronology is analogous to the Chronology assigned to samples from a single Collection Unit.
An Aggregate may have more than one Aggregate Chronology, for example one in radiocarbon years and another in calibrated radiocarbon years. One Aggregate Chronology per Age Type may be designated the default, which is the Aggregate Chronology currently preferred by the database stewards.

relativechronology 0 3 7 4625 Table

This table stores relative chronologic data. Relative Ages are assigned to Analysis Units, The Relative Age data along with any possible Geochronology and Tephrachronology data are used to create a chronology.

leadmodelbasis 0 0 2 3 Table
aggregatedatasets 3 1 6 11 Table

Aggregate Datasets are aggregates of samples of a particular data type. Some examples:
* Plant macrofossil samples from a group of packrat middens collected from a particular valley, mountain range, or other similarly defined geographic area. Each midden is from a different Site or Collection Unit, but they are grouped into time series for that area and are published as a single dataset.
* Samples collected from 32 cutbanks along several km of Roberts Creek, northeast Iowa. Each sample is from a different site, but they form a time series from 0-12,510 14C yr BP, and pollen, plant macrofossils, and beetles were published and graphed as if from a single site.
* A set of pollen surface samples from a particular region or study that were published and analyzed as a single dataset and submitted to the database as a single dataset.
The examples above are datasets predefined in the database. New aggregate datasets could be assembled for particular studies, for example all the pollen samples for a given time slice for a given geographic region.

collectors 0 2 6 46892 Table

The Collectors table lists the people who collected Collection Units.

taxaalthierarchy 0 3 3 0 Table
elementmaturities 3 0 4 12 Table
specimendomesticstatustypes 1 0 4 4 Table
publicationeditors 0 1 8 1466 Table

This table stores the editors of publications for which chapters or sections are the primary bibliographic entries. Chapter authors are stored in the PublicatonAuthors table, where they are linked to the Contacts table. However, publication editors are not cross-referenced in the Contacts table, because chapter authors are the principal citation.

isosrmetadata 0 2 6 14 Table
specimendatescal 0 3 10 2605 Table
calibrationcurves 2 1 5 15 Table
sitestemp 0 0 13 18853 Table
isosubstratetypes 2 0 4 11 Table
chroncontrolprecisionranks 1 0 4 8 Table
contextsdatasettypes 0 2 4 190 Table
datasets 17 3 8 48328 Table

This table stores the data for Datasets. A Dataset is the set of samples for a particular data type from a Collection Unit. A Collection Unit may have multiple Datasets for different data types, for example one dataset for pollen and another for plant macrofossils. Every Sample is assigned to a Dataset, and every Dataset is assigned to a Collection Unit. Samples from different Collection Units cannot be assigned to the same Dataset (although they may be assigned to Aggregate Datasets).

calibrationprograms 2 0 5 73 Table
chroncontrolaccuracydistributions 1 0 4 4 Table
elementsymmetries 3 0 4 8 Table
lakeparametertypes 1 0 6 21 Table
relativeageunits 1 0 4 12 Table

Lookup table of RelativeAgeUnits. Table is referenced by the RelativeAges table.

lakeparameters 0 2 5 23072 Table
data 7 2 6 10039985 Table

The primary data table in the database. Each occurrence of a Variable in a sample comprises a record in the Data table.

ecolsettypes 1 0 4 23 Table

Lookup table of Ecological Set Types. Table is referenced by the EcolGroups table.

geochroncontrols 0 2 4 42293 Table
publicationauthors 0 2 9 30625 Table

This table lists authors as their names are given in publications. Only the initials are stored for authors’ given names. The ContactID links to the author’s full name and contact data in the Contacts table. Thus, for a bibliographic entry, Charles Robert Darwin is listed as C. R. Darwin, or as C. Darwin if the publication did not include his middle name. Book editors are also stored in this table if the entire book is cited. However, if a book chapter or section is cited, authors are stored in this table, but the book editors are stored in the PublicationEditors table. Thus, for the following reference, G. C. Frison is stored in the PublicationAuthors table.
Frison, G. C., editor. 1996. The Mill Iron site. University of New Mexico Press, Albuquerque, New Mexico, USA.
Whereas for the following publication, L. S. Cummings is listed in the PublicationAuthors table, and G. C. Frison is listed in the PublicationEditors table.
Cummings, L. S. 1996. Paleoenvironmental interpretations for the Mill Iron site: stratigraphic pollen and phyrolith analysis. Pages 177-193 in G. C. Frison, editor. The Mill Iron site. University of New Mexico Press, Albuquerque, New Mexico, USA.

specimengenbank 0 1 2 3 Table
chroncontroltypes 3 1 5 99 Table

Lookup table of Chronology Control Types. This table is referenced by the ChronControls table.

isosampleintrosystemtypes 1 0 4 4 Table
analysisunitaltdepthscales 1 1 7 55 Table
datasetpublications 0 2 5 58986 Table

This table lists the publications for datasets.

taxaalthierarchytypes 1 0 3 1 Table
geochrontypes 1 0 4 18 Table

Lookup table for Geochronology Types. Table is referenced by the Geochronology table.

chroncontrolscal14c 0 3 5 6591 Table
depenvttypes 2 1 5 222 Table

Lookup table of Depositional Environment Types. Table is referenced by the CollectionUnits table.

geochronology 3 3 14 39608 Table

This table stores geochronologic data. Geochronologic measurements are from geochronologic samples, which are from Analysis Units, which may have a depth and thickness. Geochronologic measurements may be from the same or different Analysis Units as fossils. In the case of faunal excavations, geochronologic samples are typically from the same Analysis Units as the fossils, and there may be multiple geochronologic samples from a single Analysis Unit. In the case of cores used for microfossil analysis, geochronologic samples are often from separate Analysis Units; dated core sections are often thicker than microfossil Analysis Units.

isopretreatmenttypes 1 0 5 40 Table
relativeages 2 2 11 642 Table

Lookup table of RelativeAges. Table is referenced by the RelativeChronology table.

constituentdatabases 3 1 6 37 Table
elementtaxagroupportions 0 2 4 411 Table
specimensextypes 1 0 4 3 Table
ecolgroups 0 3 5 43776 Table

Taxa are assigned to Sets of Ecological Groups. A taxon may be assigned to more than one Set of Ecological Groups, representing different schemes for organizing taxa.

elementtaxagroups 3 2 5 1010 Table
dataprocessors 0 2 4 60649 Table
contactreferences 0 2 3 662 Table
analysisunits 9 2 11 449200 Table

This table stores the data for Analysis Units.

datasettaxonnotes 0 3 7 1668 Table
ecolgrouptypes 1 0 4 193 Table

Lookup table of Ecological Group Types. Table is referenced by the EcolGroups table.

isospecimendata 0 2 6 5193 Table
isoscaletypes 1 0 5 8 Table
eventtypes 1 1 5 9 Table
elementtypes 5 0 4 926 Table
sysdiagrams 0 0 5 0 Table
lithostratunits 1 0 5 5 Table
variableelements 1 4 8 967 Table

Lookup table of Variable Elements. Table is referenced by the Variables table.

analysisunitlithostrat 0 2 4 0 Table
tephras 0 2 6 148 Table

Tephras lookup table. This table stores recognized tephras with established ages. Referenced by the Tephrachronology table.

taphonomicsystems 2 0 5 9 Table
taxonpaths 0 1 2 0 Table
datasettypes 6 0 4 41 Table

Lookup table for Dataset Types. Table is referenced by the Datasets table.

geopaths 0 1 2 9997 Table
datasetpis 0 2 5 124861 Table
externaltaxa 0 2 6 46858 Table
datasetsubmissions 0 4 9 57403 Table

Submissions to the database are of Datasets. Submissions may be original submissions, resubmissions, compilations from other databases, or recompilations. See the description of the DatasetSubmissionTypes table.

isoinstrumentation 0 4 10 156 Table
externaldatabases 3 0 6 9 Table
elementdatasettaxagroups 0 2 5 1448 Table
isobiomarkertypes 1 0 4 4 Table
variableunits 4 0 4 209 Table

Lookup table of Variable Units. Table is referenced by the Variables table.

datasetvariables 0 2 5 0 Table
dsageranges 0 2 4 0 View
dslinks 0 2 3 0 View
geopoldepth 0 1 5 0 View
dsdatasample 0 3 4 0 View
pubtsv 0 1 2 0 View
dssampdata 0 1 3 0 View