ONTOLOGY IN BMS


Synchronization between BMS and Ontology

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 :
  • a comparative list of method & scales that have changed - take one crop as an example
  • a list of concepts that are in common for all 10 crops + soybean, pearl millet and lentil - the definition must be provided to check if this si exactly the same trait
  • The Java routine in jar file for the conversion of OBO files into TD template in Excel. To be used by Arlett for Maize and Wheat.

2. Arlett will :
  • send screenshots of the new BMS/fieldbook to show how the ontology is managed and clarify how users can now access methods and scales for a given trait
  • Will contact Rebecca to clarify the purpose of the scripts she mentioned and share with us if the routine is relevant to the sync process.
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


Ĉ
Elizabeth Arnaud,
Jul 23, 2014, 1:21 AM
ĉ
Elizabeth Arnaud,
Jul 23, 2014, 1:21 AM
ċ
commonConcepts.txt
(15k)
Elizabeth Arnaud,
Jul 23, 2014, 1:21 AM
Ĉ
Elizabeth Arnaud,
Jul 23, 2014, 1:21 AM
ċ
modifiedMethSc.csv
(67k)
Elizabeth Arnaud,
Jul 23, 2014, 1:21 AM
ċ
obo2tabMAL.pl
(9k)
Elizabeth Arnaud,
Jul 23, 2014, 1:21 AM
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