Presentation 3 - TesTable and GEOQUAL tools
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Transcript of Presentation 3 - TesTable and GEOQUAL tools
ToolsTesTable and GEOQUAL
Mauricio Parra QuijanoInternational Treaty on Plant Genetic Resources for Food and Agriculture CAPFITOGEN Program Coordinator
http://www.capfitogen.net
INTRODUCTION TO
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)
GEOQUAL
Evaluates the quality of the geo-referencing at a given collecting site indicated in passport data
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)
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
TOTALQUAL = COORQUAL + SUITQUAL + LOCALQUAL
VALUES FROM 0 TO 60
TOTALQUAL100 = (TOTALQUAL*60) /100
0 98
LOCALQUAL and TOTALQUAL100