This document discusses linking three ecological databases - HIFP, KBSP, and ETS - used at the French Institute of Pondicherry (IFP) by creating common reference tables for taxonomy and geography. It identifies that the three databases have completely different structures and examines approaches to standardize location names and taxonomic classifications to facilitate linking information between the databases. Key challenges include resolving issues of same locations having different names, different names referring to the same place, and lack of geographical coordinates for some location records.

1. Pl@ntGhats
Linking HIFP, KBSP, and ETS databases
to common reference tables
French Institute of Pondicherry (IFP)
July 2013
Rainer Zaiss
IRD UMR AMAP

2. 1. Create links between different ecological databases that are in
use at IFP
2. Develop a data management system to
1. display,
2. query,
3. manage and
4. share
the information
Pl@ntGhats

3. 1. IFP herbarium database
 17000 observations
 24000 sheets (3400 are scanned)
 Spread over around 2000 locations
 4700 taxons
Pl@ntGhats HIFP database
OBSERVATION
DETERMINATION
SHEET
IMAGE1 : N
1 : N
1 : N

4. 2. Endemic tree species database
 12000 observations
 356 taxons
 Spread over around 2500 locations
http://www.ifpindia.org/ecrire/upload/digital_database/Site/Endemic_Tree_Species/html/main.htm
Pl@ntGhats ETS database
Observation … … … … …

5. 2. Endemic tree species database compiled from different sources
Pl@ntGhats ETS database
REFERENCE ENDEMIC TREE SPECIES DATABASE NBR
IFP HIFP herbarium database 1158
Blater Herbarium, St. Xaviers' College, Mumbai, Maharashtra, India. 132
Botanical Survey of India, Southern Circle, Coimbatore, Tamil Nadu, India. 2354
Botanical Survey of India, Western Circle, Pune, Maharashtra, India. 894
Central National Herbarium, Howrah, West Bengal, India. 117
Centre for Taxonomic Studies, Bangalore, Karnataka, India. 627
Forest College, Coimbatore, Tamil Nadu India. 16
Kerala Forest Research Institute, Pechi, Kerala, India. 284
Rapinat Herbarium, Tiruchirapali, Tamil Nadu, India. 102
Royal Botanic Gardens, Kew, United Kingdom. 156
Tropical Botanic Garden and Research Institute, Palode, Kerala, India. 173
Herbarium
UNKNOWN 9
Induchoodan field work 1071
Literature 884
Literature unprecise 47
Map field work 2328
Others field work 20
Pascal field work 932
Uppangala field work 32

6. 3. Karnataka sampling plots 1996 -1997
 96 sampling plots in central Western
Ghats region
 Macroplots
 Abundance of trees
gbh >=10 cm
 61,965 individuals
 Microplots (combined)
 Abundance of trees
gbh < 10 cm but above 1m height
 14,863 individuals
Pl@ntGhats KBSP database
Macroplot
Microplots
http://www.ifpindia.org/biodiversityportal/index.php?option=com_content&view=article&id=57&Itemid=65&lang=en

7. Three databases with a completely different database structure
Pl@ntGhats database link
HIFP
KBSP
ETS
…
How to
proceed to
link the
databases ?

8. Three databases with a completely different database structure
Pl@ntGhats database link
HIFP
KBSP
ETS
…
TAXONOMY
REFERENCEDATABASE

9. Three databases with a completely different database structure
Pl@ntGhats database link
HIFP
KBSP
ETS
…
TAXONOMY
REFERENCEDATABASE
GEOGRAPHY
REFERENCEDATABASE

10. Pl@ntGhats Taxonomy reference database
APGiii familiesIFP classification (Cronquist)
Acorus
Cronquist system: Araceae
APG3 : Acoraceae
Example GENUS

11. Persons : Author(s), collector(s), determiner(s)
Pl@ntGhats Taxonomy reference database
Person groups
Abbreviation Groups
Standard Abbreviation
Person
1. From Brahms
2. New persons from HIFP
3. New persons from ETS
One line for each botanists

12. Persons : Author(s), collector(s), determiner(s)
Pl@ntGhats Taxonomy reference database
Author abbreviation : Gmelina arborea Roxb.
Author abbreviation groups Gomphandra tetrandra (Wall. ex Roxb.) Sleumer

13. Persons : Author(s), collector(s), determiner(s)
Pl@ntGhats Taxonomy reference database
Author abbreviation : Gmelina arborea Roxb.
Author abbreviation groups Gomphandra tetrandra (Wall. ex Roxb.) Sleumer
Collector Ramesh, B.R.
Collector groups Ramesh, B.R., Ayyappan, N., Aravajy, S.
Determiner Ramesh, B.R.
Determiner groups Ramesh, B.R., Zaiss, R.

14. Pl@ntGhats Geography reference table
I’am located ?
here

15. 3. What is a location?
 A point
 Fixed on the earth surface by it’s geographical
coordinates
45°05'00''E -23°12'00''S
 Based on the datum WGS84
 The point has a certain horizontal precision
30 meters, 5 km, …
Is this a good idea ?????
Pl@ntGhats Geography reference table

16. Is this a good idea ?????
YES if we use a GPS receiver to locate the sample !!!
BUT IN OUR CASE WE HAVE MAINLY HISTORICAL DATA
Pl@ntGhats Geography reference table
+ =

17. 3. What are the problems?
 Same locations (Lon./Lat.) carrying
different names ?
 Different locations carrying different
names
 We just have the name but not the
geographical coordinates of the
location
 We just have the coordinates of the
location but we do not know the
name of the location
 + all other combinations that you
can imagine…..
Pl@ntGhats Geography reference table
We have location names that designate geographical regions…
We have location names that designate ????
We do not know the source of the coordinates ?

18. 3. What are the problems?
 Same locations (Lon./Lat.) carrying
different names ?
 Different locations carrying the same
name
 We just have the name of the
location but not the geographical
coordinates
 We just have the coordinates of the
location but we do not know the
name
 …
Pl@ntGhats Geography reference table
We have location names that designates geographical regions…
We have location names that designates ????
We do not know the source of the coordinates ?

19. 3. What are the advantages to work with point locations
Pl@ntGhats Geography reference table
POINT INSIDE POLYGON
We can use geographical joins to relate
the points with all kind of geographical
subdivisions
Administrative subdivision
Forest division
Biodiversity hot spots

20. It looks very easy, where are the problems ?
Pl@ntGhats database link
HIFP
KBSP
ETS
…
TAXONOMY
REFERENCEDATABASE
GEOGRAPHY
REFERENCEDATABASE

21. The three databases are available at the IFP server
http://182.72.114.106:5984/_start
The herbarium database is not up to date
The main challenge is to build up a localities reference table
THANK YOU
Pl@ntGhats Where do we stand ?

22. It looks very easy, where are the problems ?
In order to create the links we have
to define and follow standards !!!
Standards are necessary in order to go ahead !!!!!!
Pl@ntGhats database link