• 1 Acknowledgements
  • 2 Introduction
    • 2.1 Whence Neotoma
    • 2.2 Rationale
    • 2.3 History of the Constituent Databases
      • 2.3.1 Global Pollen Database
      • 2.3.2 North American Plant Macrofossil Database
      • 2.3.3 FAUNMAP
      • 2.3.4 BEETLE
    • 2.4 Who Will Use Neotoma?
  • 3 Working with the Raw Data
    • 3.1 Using the Database Locally
  • 4 Using R
  • 5 Searching for Sites
    • 5.1 Site names: sitename="%Lago%"
      • 5.1.1 Code
      • 5.1.2 3.1.1.2. Result
    • 5.2 3.1.2. Location: loc=c()
      • 5.2.1 3.1.2.1. Code
      • 5.2.2 3.1.2.2. Result
  • 6 SQL Quickly
    • 6.1 SQL Example
      • 6.1.1 SQL Query
    • 6.2 Table Keys
    • 6.3 Data Types
      • 6.3.1 Query
  • 7 Database Design Concepts
    • 7.1 Sites, Collection Units, Analysis Units, Samples, and Datasets
    • 7.2 Taxa and Variables
    • 7.3 Taxonomy and Synonymy
    • 7.4 Taxa and Ecological Groups
    • 7.5 Chronology
    • 7.6 Sediment and Depositional Environments
    • 7.7 Date Fields
  • 8 Anatomy of a Neotoma Dataset
    • 8.1 The Minimum Object
  • 9 Neotoma Tables
    • 9.1 Site Related Tables
    • 9.2 Dataset & Collection Related Tables
    • 9.3 Chronology & Age Related Tables
    • 9.4 Sample Related Tables
    • 9.5 Specimen Related Tables
    • 9.6 Taxonomy Related Tables
    • 9.7 Individual Related Tables
    • 9.8 Publication Related Tables
    • 9.9 Supporting Resources
    • 9.10 Isotope Data Management
  • 10 Contact and Individual Related Tables
    • 10.1 collectors
      • 10.1.1 SQL Example
    • 10.2 contacts
    • 10.3 contactstatuses
  • 11 Dataset & Collection Related Tables
    • 11.1 accumulationrates
    • 11.2 aggregatedatasets
    • 11.3 aggregateordertypes
    • 11.4 collectiontypes
    • 11.5 collectionunits
    • 11.6 contextsdatasettypes
    • 11.7 datasetdatabases
    • 11.8 datasetdoi
    • 11.9 datasetpis
    • 11.10 datasetpublications
    • 11.11 datasets
      • 11.11.1 SQL Example
      • 11.11.2 SQL Example
    • 11.12 datasetsubmissions
    • 11.13 datasetsubmissiontypes
      • 11.13.1 SQL Example
    • 11.14 datasettaxagrouptypes
    • 11.15 datasettaxonnotes
    • 11.16 datasettypes
    • 11.17 datasetvariables
    • 11.18 depenvttypes
      • 11.18.1 SQL Example
      • 11.18.2 SQL Example
      • 11.18.3 SQL Example
  • 12 Publication Related Tables
    • 12.1 publicationauthors
      • 12.1.1 SQL Example
    • 12.2 publicationeditors
    • 12.3 publications
    • 12.4 publicationtypes
      • 12.4.1 Legacy
      • 12.4.2 Journal Article
      • 12.4.3 Book Chapter
      • 12.4.4 Authored Book
      • 12.4.5 Edited Book
      • 12.4.6 Master’s Thesis
      • 12.4.7 Doctoral Dissertation
      • 12.4.8 Authored Report
      • 12.4.9 Edited Report
      • 12.4.10 Other Authored Publication
      • 12.4.11 Other Edited Publication
  • 13 Sample Related Tables
    • 13.1 aggregatesamples
    • 13.2 analysisunits
    • 13.3 data
      • 13.3.1 SQL Example
    • 13.4 depagents
    • 13.5 depagenttypes
    • 13.6 faciestypes
    • 13.7 keywords
    • 13.8 lithology
    • 13.9 sampleages
      • 13.9.1 SQL Example
    • 13.10 sampleanalysts
    • 13.11 samplekeywords
      • 13.11.1 SQL Example
    • 13.12 samples
      • 13.12.1 SQL Example
  • 14 Site Related Tables
    • 14.1 geopoliticalunits
      • 14.1.1 SQL Example
      • 14.1.2 SQL Example
    • 14.2 lakeparameters
      • 14.2.1 SQL Example
    • 14.3 lakeparametertypes
      • 14.3.1 SQL Example
    • 14.4 sitegeopolitical
      • 14.4.1 SQL Example
    • 14.5 siteimages
    • 14.6 sites
      • 14.6.1 SQL Example
  • 15 Taxonomy Related Tables
    • 15.1 ecolgroups
      • 15.1.1 SQL Example
      • 15.1.2 SQL Example
    • 15.2 ecolgrouptypes
    • 15.3 ecolsettypes
    • 15.4 synonyms
    • 15.5 synonymtypes
      • 15.5.1 SQL Example
    • 15.6 taxa
    • 15.7 taxagrouptypes
    • 15.8 variables
      • 15.8.1 SQL Example
      • 15.8.2 SQL Example
      • 15.8.3 SQL Example
    • 15.9 variablecontexts
    • 15.10 variableelements
    • 15.11 variablemodifications
    • 15.12 variableunits
    • 15.13 repositoryinstitutions
    • 15.14 repositoryspecimens
      • 15.14.1 SQL Example
    • 15.15 specimendates
  • 16 Chronology & Age Related Tables
    • 16.1 agetypes
    • 16.2 aggregatechronologies
    • 16.3 chroncontrols
    • 16.4 chroncontroltypes
    • 16.5 chronologies
      • 16.5.1 SQL Example
      • 16.5.2 SQL Example
    • 16.6 aggregatesampleages
      • 16.6.1 SQL Example
      • 16.6.2 SQL Example
    • 16.7 geochronology
      • 16.7.1 SQL Example
    • 16.8 geochronpublications
    • 16.9 geochrontypes
    • 16.10 relativeagepublications
    • 16.11 relativeages
      • 16.11.1 SQL Example
    • 16.12 radiocarboncalibration
    • 16.13 relativeagescales
    • 16.14 relativeageunits
    • 16.15 relativechronology
    • 16.16 tephrachronology
    • 16.17 tephras
  • 17 Views and Materialized Views
    • 17.1 About Views (Briefly)
    • 17.2 Neotoma Views
      • 17.2.1 Schema ap
      • 17.2.2 Schema da
      • 17.2.3 Schema ‘db’
      • 17.2.4 Schema ndb
      • 17.2.5 Schema ti
      • 17.2.6 Schema ts
    • 17.3 Neotoma Materialized Views
      • 17.3.1 Schema ap
  • 18 References

Neotoma Paleoecology Manual v2.0

10 Contact and Individual Related Tables

10.1 collectors

The collectors table lists the people who were responsible for collecting a particular collection unit. This is part of the complete set of individuals who collect, analyze, publish and process the data for contribution to Neotoma. Other related tables include publicationsauthors, sampleanalysts, and datasetsubmissions.

  • collectorid (primary key): An arbitrary Collector identification number.
  • collectionunitid (foreign key)]: The collectionunitid for the record that was collected. Field links to the collectionunits table.
  • contactid (foreign key): Person who collected the CollectionUnit. Multiple individuals are listed in separate records. Field links to the contacts table.
  • collectororder: Order in which the collectors should be listed.

10.1.1 SQL Example

We want to see the top contributors for each constitutent database, so we calculate the sum of each appearance of a contributor/database, and then return the COUNT(*). The DISTINCT ON pattern allows us to select a single instance of the field db.databasename, that has been ordered by the descending COUNT(*) per individual, and database. This then ensures we have the top collectionunit collector for each constituent database.

SELECT DISTINCT ON (db.databasename)
       ct.contactname, 
       db.databasename,
       COUNT(*)
FROM ndb.contacts AS ct
INNER JOIN ndb.collectors AS co ON co.contactid = ct.contactid
INNER JOIN ndb.collectionunits AS cu ON cu.collectionunitid = co.collectionunitid
INNER JOIN ndb.datasets AS ds ON ds.collectionunitid = cu.collectionunitid
INNER JOIN ndb.datasetdatabases AS dsdb ON dsdb.datasetid = ds.datasetid
INNER JOIN ndb.constituentdatabases AS db ON db.databaseid = dsdb.databaseid
GROUP BY db.databasename, ct.contactname
ORDER BY db.databasename, COUNT(*) DESC;
Table 10.1: Displaying records 1 - 10
contactname databasename count
USEPA and Collaborators Academy of Natural Sciences of Drexel University 2546
Scott, Louis African Pollen Database 71
West, Dixie L. Alaskan Archaeofaunas 22
Tinner, Willy Alpine Palynological Database 153
Delorme, Denis Canadian Museum of Nature-Delorme Ostracoda-Surface Samples 9024
Li, Jianyong Chinese Pollen Database 3
Revelles-López, Jordi Deep-Time Palynology Database 1
Wise, Robert Diatom Paleolimnology Data Cooperative (DPDC) 4952
Visset, Lionel European Pollen Database 159
Cannon, Aubrey Faunal Isotope Database 10

10.2 contacts

This table lists persons and organizations. The table is referenced through Foreign Keys in the following tables: * Chronologies, * Collectors, * DatasetPIs, * DatasetSubmissions, * Projects, * PublicationAuthors, * SampleAnalysts, and * SiteImages tables.

  • contactid (primary key): An arbitrary contactid number.
  • aliasid (foreign key): The contactid of a person’s current name. If the aliasid is different from the contactid, the contactid refers to the person’s former name. For example, if J. L. Bouvier became J. B. Kennedy, the contactid for J. B. Kennedy is the aliasid for J. L. Bouvier.
  • contactname: Full name of the person, last name first (e.g. Simpson, George Gaylord) or name of organization or project (e.g. Great Plains Flora Association).
  • contactstatusid (foreign key): Current status of the person, organization, or project. Field links to the contactstatuses lookup table.
  • familyname: Family or surname name of a person.
  • leadinginitials**: leading initials for given or forenames **without spaces (e.g. G.G.).
  • givennames: Given or forenames of a person (e.g. George Gaylord). Initials with spaces are used if full given names are not known (e.g. G. G).
  • suffix: Suffix of a person’s name (e.g. «Jr.», «III»).
  • title: A person’s title (e.g. «Dr.», «Prof.», «»).
  • phone: Telephone number.
  • fax: Fax number.
  • email: Email address.
  • url: Universal Resource Locator, an Internet World Wide Web address.
  • address: Full mailing address.
  • notes: Free form notes or comments about the person, organization, or project.

10.3 contactstatuses

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

  • contactstatusid (primary key): An arbitrary Contact Status identification number.
  • contactstatus: Status of person, organization, or project.
  • statusdescription:
    • Description of the status. The following statuses exist (with descriptions):
      • active: Person, project, or organization is active in the field
      • deceased: Person is deceased
      • defunct: Project or organization is defunct or non-operational
      • extant: Project or organization is extant
      • inactive: Person is inactive in the field
      • retired: Person is retired
      • unknown: Status is unknown