Gombe Mother-Infant Database Technical Specifications

Copyright Notices

Acknowledgments

The Gombe-MI Development Group

Karl O. Pinc
Book Author, System Design Lead, Implementation
Carson M. Murray, PhD.
Project Co-Leader, System Design Core Member
Elizabeth V. Lonsdorf, PhD.
Project Co-Leader, System Design Core Member
Karen Anderson
System Design Core Member, Copy Review, System Testing Lead
A. Catherine Markham, PhD.
System Design Participant
Margaret A. Stanton, PhD.
System Design Participant, System Testing Core Member
Edward Wilkerson, Jr.
System Design Participant

Funding and Support. We gratefully acknowledge the support of The National Institutes of Health grant R00HD057992 for the development of this system. We are also very grateful for the support given by The Leo S. Guthman Foundation, the Lincoln Park Zoo, Franklin & Marshall College, and The George Washington University.

Other Thanks. We would like to thank the myriad Free and Open Source communities, including those of PostgreSQL, the GNU Project, the Debian Project, Ubuntu, PhpPgAdmin, the Pyramid web framework, TeX and LaTeX, dblatex, DocBook, Babase, and many others unmentioned, for giving, gratis, billions of dollars[1] of work to the world, without which the Gombe-MI software and this book would not exist.

Any opinions, findings, conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Institutes of Health, The Leo S. Guthman Foundation, the Lincoln Park Zoo, Franklin & Marshall College, The George Washington University, or any other organization which has supplied support for this work.

Table of Contents

1. Gombe-MI System Architecture
Databases
The gombemi Database
The gombemi_test Database
The gombemi_copy Database
Roles and Database Permissions
The gombemi_readers role
The gombemi_editors role
Administrative (Superuser) Users
Schemas
The gombemi schema
The gombemi_something_views schemas
The sandbox schema
The devel schema
The per-user schemas
Tables, A Definition
Queries
2. An Overview Of The Gombe-MI Data
Support Table Overview
Main Table Overview
ER Diagrams
ER Diagrams Explained
Gombe-MI Entity Relationship Diagrams
An Overview Of The Views
Indexes
3. Main Tables
Demography Related Tables
ADOPTIONS
BIOGRAPHY_DATA (Copy of the Master Biography Access Table)
CHIMPIDS (Virtual and Real Chimp Identifiers)
COMMUNITY_MEMBERSHIP (Copy of the Master Community_Membership Table)
TWINS
Follow Mechanics Related Tables
FIELDFOLLOWS
FOLLOWPARTS (Follow Participants)
FOLLOWS
INTERVALS (Follow Observation Time Intervals)
SHEETS (Follow Template Sheets)
Follow Event Related Tables
EATS (Food Eaten)
EVENTS (Behavioral Events)
FISHED (Food Fished For)
PARTS (Behavioral Participants)
PLAYS (Playing Detail)
RESTS (Resting Detail)
RIDES (Riding Detail)
VOCS (Vocalization Detail)
Follow Distance Related Tables
DISTANCEPARTS (Follow Participants Between Whom Distance Was Measured)
DISTANCES (Distances Between Follow Participants)
Group Related Tables
GROUPMEMBERS (Individuals Found in Group Composition Survey Analysis)
GROUPS (Group Composition Surveys)
RAW_GROUPMEMBERS (Raw Data on Individuals in Group Composition Surveys)
RAW_GROUPS (Raw Data on Group Composition Surveys)
4. Support Tables
Demography Related Support Tables
BDDISTS (Birth Date Probability Distributions)
ENTRYTYPES (Entrytype codes)
DEPARTTYPES (Departtype codes)
Follow Mechanics Related Support Tables
BEHAVIOR_TRANS (Behavior Translation Table)
DISTANCE_TRANS (Distance Translation Table)
FOLLOWROLES (Roles of Follow Participants)
FOLLOWTYPES (Follow Data Entry Sheet Types)
FOODPART_TRANS (Food Part Translation Table)
GC_TRANS (Group Composition Translation Table)
PEOPLE
PLAY_TRANS (Play Translation Table)
VOC_TRANS (Vocalization Translation Table)
Follow Event Related Support Tables
BEHAVIORS
FISHING_RESULTS
FOODKINDS
FOODPARTS
POSITIONS
PLAY_TYPES
RESTING_POSTURES
RIDING_POSTURES
VOCALIZATIONS
Follow Distance Related Support Tables
DISTANCECODES
Group Related Support Tables
GCSTATUSES
GM_ORIGINS
5. The Gombe-MI Views
Demography Related Views
BIOGRAPHY
BIOGRAPHY_UPLOAD (Upload into BIOGRAPHY_DATA)
CHIMPS (Real and Virtual Chimpanzees)
COMMUNITY_MEMBERSHIP_UPLOAD (Upload COMMUNITY_MEMBERSHIP)
Follow Mechanics Related Views
FOCAL_FOLLOWS (Follows and their Focals)
DATASHEETS (A Field Datasheet-Like Report)
DATASHEET_EVENTS (A Field Datasheet-Like Report Of Behavioral Events)
FOLLOW_DURATIONS (Duration of the Follow)
FOLLOW_INTERVALS (Follows and their Intervals)
UPLOAD_BEHAVIORS (Facility for uploading follow data)
Follow Event Related Views
ACTOR_ACTEES (Dyadic Directed Behavioral Events)
ACTOR_ACTEES_W_BABOONS (Dyadic Directed Behavioral Events w. Baboons)
ASOCIAL_EVENTS (Non-Social Behavioral Events)
EVENT_BOUTS (Analysis of the focals' Behavioral Bouts, per Minute)
EVENT_BOUT_AGGS (Analysis of the focals' Behavioral Bouts, per Bout)
FAMILY_EVENTS (Behavioral Events With the Focals Identified by Column)
FOCAL_EVENTS (All Behavioral Events With the Focals Distinguished)
FOCAL_SOCIAL_EVENTS (Dyadic Behavioral Events Involving a Focal)
NOOBS (Times During Which a Focal has no Behavioral Observations)
SOCIAL_BOUTS (Analysis of the focals' Behavioral Bouts, per Partner, per Minute)
SOCIAL_BOUT_AGGS (Analysis of Social Bouts, per Social Partner per Bout)
SOCIAL_EVENTS (Dyadic Behavioral Events Involving Chimpanzees)
SOCIAL_EVENTS_W_BABOONS (Dyadic Behavioral Events Including Baboons)
Follow Distance Related Views
DISTS (Distance Measurements Between Chimpanzees)
FAMILY_DISTS (Inter-Chimp Distance Measurements, Focals Identified by Column)
Group Related Views
6. The Gombe-MI Functions
Query Functions
followfunc — return the function (role) of a chimp in a follow
followrole — return the role of a chimp in a follow
Utility Functions
add_social_partners — Ensure that all social interaction partners are in the group composition data
delete_gc — Delete a follow's group composition data
infants_in_gc — Ensure that the (biological or adopted) young infants of a mom are the group composition data
infer_gc — Infer group composition from social relationships
mom_in_gc — Ensure that the (biological or adoptive) mother of a young chimp, and all the mom's young infants, are in the group composition data
7. Data Entry
Data Entry Overview
Automatically Generated IDs
8. The Gombemi-MI Custom Programs
Data Maintenance Programs
UPLOAD_BEHAVIORS: View to upload follow data
Upload: Upload Into Any Table or View
Upload_GC: Upload Group Composition Data
Logout: Logout From Gombe-MI Custom Programs
Wwwdiff: World Wide Web based Difference program
System Management Programs
Add_User: Create a database user
Copy_Schema: Copy Schemas Between Databases
A. Restrictions: Things Not To Do
B. Database Transactions Explained
C. One Minute Interval Assumptions
D. The Warning Sub-System
Introduction to the Warning Sub-System
An Overview of the Warning Sub-System Data Structures
The Warning Sub-System Tables
The Warning Sub-System Support Tables
Warning Sub-System ER Diagrams
The Warning Sub-System Main Tables
INTEGRITY_QUERIES
INTEGRITY_WARNINGS (Warning Sub-System Results)
Warning Sub-System Support Tables
IQTYPES (Integrity Query Types)
WARNING_REMARKS (Remarks Regards Warning Results)
The Warning Sub-System Functions (Activating The Warning Sub-System)
run_integrity_queries — execute one or more of the queries stored in the INTEGRITY_QUERIES table
E. GNU Free Documentation License
F. GNU General Public License version 3

List of Figures

2.1. Key to the Gombe-MI Entity Relationship Diagrams
2.2. Gombe-MI Demography Entity Relationship Diagram
2.3. Gombe-MI Essentials of a Follow Entity Relationship Diagram
2.4. Gombe-MI Follow Distance Entity Relationship Diagram
2.5. Gombe-MI Follow Events Entity Relationship Diagram
2.6. Gombe-MI Behavior Event Detail Entity Relationship Diagram
2.7. Gombe-MI Group Membership Entity Relationship Diagram
2.8. Gombe-MI Follow Detailed Entity Relationship Diagram
2.9. Gombe-MI Data Collection Templates Entity Relationship Diagram
5.1. Query Defining the BIOGRAPHY View
5.2. Entity Relationship Diagram of the BIOGRAPHY View
5.3. Query Defining the BIOGRAPHY_UPLOAD View
5.4. Entity Relationship Diagram of the BIOGRAPHY_UPLOAD View
5.5. Query Defining the CHIMPS View
5.6. Entity Relationship Diagram of the CHIMPS View
5.7. Query Defining the COMMUNITY_MEMBERSHIP_UPLOAD View
5.8. Entity Relationship Diagram of the COMMUNITY_MEMBERSHIP_UPLOAD View
5.9. Query Defining the FOCAL_FOLLOWS View: Part I
5.10. Query Defining the FOCAL_FOLLOWS View: Part II
5.11. Entity Relationship Diagram of the FOCAL_FOLLOWS View
5.12. Query Defining the DATASHEETS View: Part I
5.13. Query Defining the DATASHEETS View: Part II
5.14. Query Defining the DATASHEETS View: Part III
5.15. Query Defining the DATASHEETS View: Part IV
5.16. Entity Relationship Diagram of the DATASHEETS View
5.17. Query Defining the DATASHEET_EVENTS View: Part I
5.18. Query Defining the DATASHEET_EVENTS View: Part II
5.19. Query Defining the DATASHEET_EVENTS View: Part III
5.20. Query Defining the DATASHEET_EVENTS View: Part IV
5.21. Query Defining the DATASHEET_EVENTS View: Part V
5.22. Query Defining the DATASHEET_EVENTS View: Part VI
5.23. Entity Relationship Diagram of the DATASHEET_EVENTS View
5.24. Query Defining the FOLLOW_DURATIONS View
5.25. Entity Relationship Diagram of the FOLLOW_DURATIONS View
5.26. Query Defining the FOLLOW_INTERVALS View
5.27. Entity Relationship Diagram of the FOLLOW_INTERVALS View
5.28. Query Defining the UPLOAD_BEHAVIORS View: Part I
5.29. Query Defining the UPLOAD_BEHAVIORS View: Part II
5.30. Entity Relationship Diagram of the UPLOAD_BEHAVIORS View
5.31. Query Defining the ACTOR_ACTEES View
5.32. Entity Relationship Diagram of the ACTOR_ACTEES View
5.33. Query Defining the ACTOR_ACTEES_W_BABOONS View: Part I
5.34. Query Defining the ACTOR_ACTEES_W_BABOONS View: Part II
5.35. Entity Relationship Diagram of the ACTOR_ACTEES_W_BABOONS View
5.36. Query Defining the ASOCIAL_EVENTS View
5.37. Entity Relationship Diagram of the ASOCIAL_EVENTS View
5.38. Query Defining the EVENT_BOUTS View: Part I
5.39. Query Defining the EVENT_BOUTS View: Part II
5.40. Query Defining the EVENT_BOUTS View: Part III
5.41. Query Defining the EVENT_BOUTS View: Part IV
5.42. Query Defining the EVENT_BOUTS View: Part V
5.43. Query Defining the EVENT_BOUTS View: Part VI
5.44. Entity Relationship Diagram of the EVENT_BOUTS View
5.45. Query Defining the EVENT_BOUT_AGGS View
5.46. Entity Relationship Diagram of the EVENT_BOUT_AGGS View
5.47. Query Defining the FAMILY_EVENTS View: Part I
5.48. Query Defining the FAMILY_EVENTS View: Part II
5.49. Entity Relationship Diagram of the FAMILY_EVENTS View
5.50. Query Defining the FOCAL_EVENTS View
5.51. Entity Relationship Diagram of the FOCAL_EVENTS View
5.52. Query Defining the FOCAL_SOCIAL_EVENTS View
5.53. Entity Relationship Diagram of the FOCAL_SOCIAL_EVENTS View
5.54. Query Defining the NOOBS View
5.55. Entity Relationship Diagram of the NOOBS View
5.56. Query Defining the SOCIAL_BOUTS View: Part I
5.57. Query Defining the SOCIAL_BOUTS View: Part II
5.58. Query Defining the SOCIAL_BOUTS View: Part III
5.59. Query Defining the SOCIAL_BOUTS View: Part IV
5.60. Query Defining the SOCIAL_BOUTS View: Part V
5.61. Query Defining the SOCIAL_BOUTS View: Part VI
5.62. Query Defining the SOCIAL_BOUTS View: Part VII
5.63. Query Defining the SOCIAL_BOUTS View: Part VIII
5.64. Entity Relationship Diagram of the SOCIAL_BOUTS View
5.65. Query Defining the SOCIAL_BOUT_AGGS View
5.66. Entity Relationship Diagram of the SOCIAL_BOUT_AGGS View
5.67. Query Defining the SOCIAL_EVENTS View
5.68. Entity Relationship Diagram of the SOCIAL_EVENTS View
5.69. Query Defining the SOCIAL_EVENTS_W_BABOONS View: Part I
5.70. Query Defining the SOCIAL_EVENTS_W_BABOONS View: Part II
5.71. Query Defining the SOCIAL_EVENTS_W_BABOONS View: Part III
5.72. Entity Relationship Diagram of the SOCIAL_EVENTS_W_BABOONS View
5.73. Query Defining the DISTS View
5.74. Entity Relationship Diagram of the DISTS View
5.75. Query Defining the FAMILY_DISTS View: Part I
5.76. Query Defining the FAMILY_DISTS View: Part II
5.77. Entity Relationship Diagram of the FAMILY_DISTS View
D.1. Warning Sub-System Entity Relationship Diagram

List of Examples

1.1. Creating table foo in the sandbox schema
1.2. Granting permission to table foo in the sandbox schema
1.3. Creating table foo in user mylogin's schema
1.4. Using AS in an SQL query: Counting simultaneous self-grooming
5.1. Deleting The Mother's VOCS Row
5.2. Changing A Vocalization
5.3. Changing a Vocalization: Changing focal and vocalization
5.4. Changing a Behavior to a Fishing Behavior
5.5. Unconditionally Inserting a FISHED Row For the Mother
5.6. Deleting The Mother's PARTS Row
5.7. Inserting A PARTS Row For The Mother
5.8. Changing Non-Focal Participant In A PARTS Row
5.9. Deleting the Infant's PARTS row and Inserting a New PARTS Row for the Sibling
5.10. Changing an Infant's PARTS row Into A PARTS Row for the Sibling
5.11. Deleting The Mother's DISTANCEPARTS Row
5.12. Inserting A DISTANCEPARTS Row For The Mother
5.13. Changing A Inter-Familial Distance Measurement Participant In A DISTANCEPARTS Row
5.14. Deleting Infant's DISTANCEPARTS row and Inserting a New Row for the Sibling
5.15. Changing an Infant's DISTANCEPARTS row Into A DISTANCEPARTS Row for the Sibling
6.1. Deleting Automatically Generated Group Compositions
6.2. Inferring the group composition of follows that have none
D.1. Inserting a query into INTEGRITY_QUERIES using dollar quoting
D.2. Executing all INTEGRITY_QUERIES
D.3. Executing a single INTEGRITY_QUERIES.Query
D.4. Executing INTEGRITY_QUERIES of the bdate type

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