Access Keys:
Skip to content (Access Key - 0)

2011 TL1 Data Managers Workshop

Objectives

  1. ICIS implementation and few examples for curation?
  2. Update the data catalogue - (Specific to common Bean - from the CD)
  3. Fieldbook implementation and future plans
  4. Implementation of Zeus for the 4 TL1 crops?
  5. Management of molecular / genotyping data

Logistics

  • Dates: August 3 - 17, 2011
  • Venue: GCP, Mexico


Activities and Reports

August 3

  • Overview of the existing TL1 bean data (well organized foldering by Activity)
  • Installed and updated ICIS in Alberto's laptop


August 4

  • Training in using setgen to create nursery and trial list and using browse for COP


August 5

  • Training in using workbook and retriever
  • Practiced converting real trial data of bean into Workbook format


August 8

  • Alberto created some TL1 nursery and trial lists in SetGen


August 9/10

  • Alberto loaded some TL1 pheontyping data
  • used Retriever to create query


August 11

  • curation of chickpea germplasm information in a phenotyping study
  • - same RIL number for different generations (different GID and store RIL as alternative name)
  • - same germplasm tested in different locations (if stable line, use the same GID. However, if the seeds harvested from the different location are sent back to icrisat, it should have different GID
  • - same germplasm tested in different year (use same GID although in genebank, the seeds harvested in different year will have different GIDs)
  • ICRISAT Convention
  • ICC - genebank accession
  • ICX - cross
  • ICL - lines
  • Demo on how to load the chickpea data
  1. Load the list to SetGen using Import tool
  2. Add GID column in Description sheet of the existing Workbook template. Then do Setup->Observation Sheet
  3. Specify Property, Scale and Method of GID by Setup -> Variable Section -> Custom Setup
  4. Retrieve the GIDs by Addins->Retrieve Germplasm List
  • Suggested structure of study and list

Tropical Legumes 1
    |
    ----Activity 1
   |
    ----Activity 2
   |
    ----Activity 3
   |
    ----Activity 4
 

  • Suggested naming convention for Study
    TL1A<activity number><Location><Year><specific trial type>
    example: TL1A1_Kenya2008_Pheno
  • Discussion about the catalogue of TL1 data between Prasad and Alberto
  • - it is suggested to use the filename.sheetname or study name as title of the dataset in the Catalogue excel file for easy reference


August 12

  • Coordination among data managers and collaborators
  1. data managers to create germplasm lists
  2. data managers to create workbook template with trial list
  3. send it to collaborators
  4. collaborators to send workbook or fieldbook with data
  5. data managers to load to local
  6. data managers to upload local to central - annually preferably 3 months before TL meeting
  7. data managers to upload central database to ftp site managed by legumes data manager - annually 2 months before the TL1 meetinggv
  8. legumes data manager to update legumes website - updated before TL1 annual meeting
  • GDMS
  • Prasad demoed the installation of GDMS
  • tested loading bean primers and querying
  • Loaded sample bean SSR genotyping data - cannot be loaded
  • Issues about GDMS:
  • how to register primary investigators and users in the database
  • all marker and genotyping data will be stored in one database - the GID is not enough to uniquely identify the crop germplasm, probably the Unique ID crop system-userid-local GID should be used instead
  • will the mark be the same for some crops?
  • No GID column in the SSR genotyping data template
  • Tool to tranform data stored in parallel format to serial (template) format
  • when will be the manual available?
  • there was problem in loading SSR genotyping data
  • IB Fieldbook installation and demo


August 15

Continuation of loading pedigree and evaluation data to the database

August 16

  • Preparing the mySQL database for Zeus

Convert MSAccess to MySQLhttp://cropwiki.irri.org/icis/index.php/MS_Access_to_MySQL_conversion_of_ICIS_databases

Generate the warehouseshttp://www.cropinfo.org/icis/index.php/ICIS_Data_Warehouse_Creation_and_Maintenance

  • Discussion about GDMS (with Jean-Marcel, Graham, Ndeye, Claudio and Tito)
  • (CGM)what happen if there is mysql already? Discussion between ICRISAT and CIMMYT about the installion of the databases for fieldbook and GDMS so that it will be consistent.
  • Where are the templates stored? The templates are stored in a folder in the web server
  • (AMP)It was decided to have the genotyping data for TL1 to be centralized in ICRISAT. There will be a mirror site in iplant.
  • (CGM)Similar to phenotyping data which will be mirrored in iplant but the definitive copy will be in the CLC
  • (JM)But how about the idea of separate database for each crop. The genotyping data can grow fast and how will the retrieval with that big database.
  • (CA)CIMMYT needs a standalone tool as most of their partners in Africa don't have good internet access.
  • (JM)The concept of local databases specially for people with no access to internet should be considered. The GDMS can be installed locally, However, what will be the approach in uploading of databases from local installation to central. It needs to be prioritized.
  • (JM and CGM)how to retrieve data? The retrieval by genotype/marker is available but not the retrieval of the loaded dataset
  • (JM)How will QTL data stored? Shall we store the raw data of the mapping population or just store the QTL data? What kind of dataset we keep or store in the database? How to deal reference map. CMTV has a tool to use reference map and should this tool be considered for integration?


August 17

Prerequisites: mySQL, Apache, tomcat - assumed they are installed
Other to install: java, SVN, ant, maven, graphviz - demo

  1. install the pre requisites
  2. restore the dumped databases
  3. check out codes from repository
  4. edit the necesary files for customization
  5. build and deploy the application
  • Discussion about Ontology with Rosemary

    The ontology curation tools is available on this site http://www.cropontology-curationtool.org/
    The possibility of developing a tool to upload the Trait Dictionary file to OLS

Participants

  1. Alberto Guerrero
  2. Prasad Peteti
  3. Clarissa Pimentel
  4. Arllet Portugal
  5. Jay Consolacion/Rosemary Shrestha
  6. Graham McLaren
  7. Sandra Morales (logistics)

Adaptavist Theme Builder (3.3.3-conf210) Powered by Atlassian Confluence 2.10.3, the Enterprise Wiki.
Free theme builder license