ToolsTesTable and GEOQUAL

Mauricio Parra QuijanoInternational Treaty on Plant Genetic Resources for Food and Agriculture CAPFITOGEN Program Coordinator

http://www.capfitogen.net

INTRODUCTION TO

TesTable

Checks your table formats and optionally corrects them

TesTable

Type of tables

• Passport (similar to MCPD V.2) with /without additional fields (availability, 5 quality GEOQUAL fields, etc.)

• External sources (for Representa tool)

• Genotype data (for DIVmapas tool)

• Phenotype data (for DIVmapas tool)

• Type of phenotype variables (for DIVmapas tool)

¿How does TesTable work?

Tables in .txt format are introduced (they must be located on “Pasaporte” folder)

TesTable checks every important field (name, location in the table, content format)

TesTable creates an error report

TesTable may produce a new corrected table (without overwrite/replace the original table)

Results

TesTable save its results on “Pasaporte” folder

GEOQUAL

Evaluates the quality of the geo-referencing at a given collecting site indicated in passport data

Geo-referencing and passport data

40° 20’ 33.4’’ N03° 11’ 52.1’’ W

Why should we evaluate the geo-referencing quality?

Coordinates

True site

x km

1030

75

100

Potential effects of poor geo-referencing

10 km

5 oC6 oC

7 oC 8 oC 9 oC

1 km

Level Value

ORIGCTY CRI

ADM1 Punta Arenas

ADM2 Buenos Aires

ADM3 NA

ADM4 NA

Level Value

ORIGCTY CRI

ADM1 Punta Arenas

ADM2 Pérez Zeledón

ADM3 NA

ADM4 NA

Description of the collecting site

Error describing the collecting sites

GEOQUAL features

•GEOQUAL is a tool which assigns a quality value to the passport data of a germplasm collection that include coordinates.

•The user enters the passport data in FAO-Bioversity 2012 format.

•GEOQUAL calculates three parameters COORQUAL, LOCALQUAL and SUITQUAL along with other sub-parameters.

•The parameters are summarized to generate both TOTALQUAL (0-60 range) and TOTALQUAL100 (0-100 range)

Parameter that determines the intrinsic quality of the coordinates included in the passport data. Values from 0 to 20. Sub-parameters.:

• ERRORES: Values beyond the coordinate frame

• PRECIS: Accuracy level. Measured in degrees, minutes or seconds (sexagesimal)

• GEORBLE: Probability of correct coordinates from site description

• INTERTEMP: Quality of coordinates by collection year

• * GEOREFMETH: System by which coordinates are assigned

COORQUAL

SUITQUAL

Parameter that assigns a quality value to the coordinates according to the appropriateness of the collection site for plant growth. Values from 0 to 20.

• Difference between cultivated and wild plants (SAMPSTAT)

• It uses information on land use from Global Land Cover map (1 km)

> 30 km

10-20 km

5-10 km

0-1 km

Ground level

0 20

Distance from the coastline

SUITQUAL

Lower resolution

Higher resolution

zoom!

SUITQUAL

LOCALQUAL

Parameter that comes from the comparison of the site (locality) description and administrative data coming from the coordinates, both from user’s passport data.

• The administrative geo-referenced information is extracted from the GADM database

• The comparison is between character strings, generating a distance (Levenshtein). Insertions, deletions and changes are determined, to assume that a string is equal to another. Function "agrep" in R

• According to the number of correct matches, a value ranging from 0 to 20 is assigned.

Passport description

GADM from Coordinates

GADM (second option)

ORIGCTY ISO

ADM1 NAME1 VARNAME1

ADM2 NAME2 VARNAME2

ADM3 NAME3 VARNAME3

ADM4 NAME4 VARNAME4

LOCALQUAL

TOTALQUAL = COORQUAL + SUITQUAL + LOCALQUAL

VALUES FROM 0 TO 60

TOTALQUAL100 = (TOTALQUAL*60) /100

0 98

LOCALQUAL and TOTALQUAL100

0 100

TOTALQUAL100: Unified value of the geo-referencing quality

80 90

Use of GEOQUAL