    Discussion with Arllet 19th June: To reduce the work, Arllet proposed to at least focus on the standard field book list. 1. Marie with help of Harold to provide to Arllet :
2. Arlett will :
FILES prepared by Marie 1- the list of the common concepts (commonConcepts.txt). This list corresponds to the exact matches resulting of the comparison of 2 or more ontologies. 2- the list of the methods and scales that have changed between 2 versions of the english version of the Common Bean TD (modifiedMethSc.csv). 3- excel file corresponding to the Crop Research Ontology. Part_of relationships were defined in the OBO file. I decided thus to process them as the is_a relationships from the Trait Dictionary Template. I created this file using a dedicated routine. 4- the routine to transform OBO files (the traits ones) into a Trait Dictionary. The routine is in fact a Perl routine. Indeed, I think the perl routine is easier to use than the java jar. To run the code, you have to execute the following command : perl obo2tabMAL.pl input.obo > output.csv The output is a tabulated file. In order to open it, you have to import it in Excel using the tab delimiter (and only the tab delimiter as comma can be used in the definitions). Discussion with Rebecca, 23 July: Test with Maize, Wheat and Rice for end of August The Crop Ontology API can provide access to the JSON dump of the DB TD can be obtained in OBO from the CO site Get the rate of use of traits, methods and scales from the BMS from historical data |
GCP Crop Ontology >
