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Presentation 3 - TesTable and GEOQUAL tools

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CAPFITOGEN Programme for the Strengthening of Capabilities in National Plant Genetic Resources Programmes, International Treaty on Plant Genetic Resources for Food and Agriculture - FAO

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Presentation 3 - TesTable and GEOQUAL tools

  1. 1. Mauricio Parra Quijano International Treaty on Plant Genetic Resources for Food and Agriculture CAPFITOGEN Program Coordinator http://www.capfitogen.net
  2. 2. TesTable Checks your table formats and optionally corrects them TesTable
  3. 3. 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)
  4. 4. ¿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)
  5. 5. Results TesTable save its results on “Pasaporte” folder
  6. 6. GEOQUAL Evaluates the quality of the geo-referencing at a given collecting site indicated in passport data
  7. 7. Geo-referencing and passport data 40° 20’ 33.4’’ N 03° 11’ 52.1’’ W
  8. 8. Why should we evaluate the geo-referencing quality? Coordinates True site x km 1030 75 100
  9. 9. Potential effects of poor geo-referencing 10 km 5 oC 6 oC 7 oC 8 oC 9 oC 1 km
  10. 10. 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
  11. 11. 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)
  12. 12. 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
  13. 13. 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)
  14. 14. > 30 km 10-20 km 5-10 km 0-1 km Ground level 0 20 Distance from the coastline SUITQUAL
  15. 15. Lower resolution Higher resolution zoom! SUITQUAL
  16. 16. 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
  17. 17. LOCALQUAL
  18. 18. TOTALQUAL = COORQUAL + SUITQUAL + LOCALQUAL VALUES FROM 0 TO 60 TOTALQUAL100 = (TOTALQUAL*60) /100 0 98 LOCALQUAL and TOTALQUAL100
  19. 19. 0 100 TOTALQUAL100: Unified value of the geo-referencing quality 80 90 Use of GEOQUAL

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