This meeting provided a ton of useful feedback on GOBii and the GDM platform. This document focuses on the suggestions for improvement provided at that meeting.
CIMMYT
Overall
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Benefits
centralized, searchable institutional record genotype data
not dependent on external services
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Category | Feedback | Reporter | Notes | GSD |
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General | Can’t complete genotyping analysis workflows smoothly | CIMMYT | ||
“run and maintain” mode at CIMMYT pending GOBii / EBS integration |
Loader
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Benefits
Flexible
Templates
Challenges
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CIMMYT | ||
Loader | Loader validations stricter than db req’s Can’t load 2 dnaruns for the same sample |
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CIMMYT | CIMMYT uses same experiment / project for all datasets | |
Diagnosing errors - over- |
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reliance on help desk | CIMMYT | ||
Lacking useful transformations during loading Update marker names that are based on sequence positions |
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CIMMYT | |||
Steep learning curve | CIMMYT | ||
No tool for SNP recalling (for KASP markers – but unclear where/how |
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this could happen) |
Extractor
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Benefits
Fast
Email notifications
Can aggregate some data across datasets
Challenges:
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Query system inflexible
Can’t select multiple dataset types for download
Can’t extract by multiple factors - e.g. intersect of markers and samples
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CIMMYT | |||||||||||||
Manual mapping is tedious different fields from different service providers | IRRI | ||||||||||||
Errors with certain characters when importing sample files generated by B4R | IRRI | ||||||||||||
Indels not supported unless encoded as +/- | IRRI |
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Data often requires cleaning prior to upload | IRRI | ||||||||||||
Requirement to associate data with PI | IRRI | ||||||||||||
Extractor | Inflexible query system Can’t select multiple dataset types for download Can’t extract by multiple factors - e.g. intersect of markers and samples | CIMMYT | |||||||||||
File delivery system convoluted | CIMMYT |
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Challenges
QC” stats from KDC not provided to users during download |
CAST
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Benefits
Consensus call functionality
Splitting on multiple criteria
Some combining of data across datasets
CIMMYT | ||||
CAST | Cannot combine data from same samples in different datasets into one row | CIMMYT | ||
Does not facilitate the selection of marker groups to use in analyses | CIMMYT | |||
Timescope |
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Benefits:
Provides important functionalities to enable the “safe” deleting of datasets, markers, and samples
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Requires deployment of another tool instead of combining all CRUD functionalities in one tool | CIMMYT | |||
Separate authentication system, not linked to institutional authentication system |
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Data
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Benefits
Large data storage for common data types
Flexible properties facilitate metadata storage
Marker groups allow the storage of different haplotypes associated with the same group of markers
Challenges
CIMMYT | |||
Data | Some data dependencies have led to unplanned processes |
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sample linkage to |
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project and UUID implementation have caused CIMMYT to use one project for all datasets | CIMMYT | ||
Variants have not been implemented to facilitate analyses for the “same” marker used in different platforms, potentially with different names, over time | CIMMYT | ||
Marker groups are based on markers instead of variants |
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not linked to traits, phenotypes, etc. | CIMMYT | ||
Current data structure |
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seems to prevent the storage of data linked to each genotypic call or data point |
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QC values can’t be associated with data points VCF data apart from GT isn’t preserved | CIMMYT | ||
Allele frequency data cannot be stored or retrieved easily | CIMMYT | ||
Across ST and GOBii no clear model for how to store “consensus” calls or “reference” genotype or fingerprint constructed from different samples over time | CIMMYT | ||
In an integrated system, many fields of information may be duplicated and sometimes have different “IDs” e.g. ID for germplasm in CB and new ID for germplasm in GOBii |
IRRI
Loader
Challenges
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Manual mapping is tedious
different fields from different service providers
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Errors with certain characters in sample files generated by B4R
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Indels not supported unless encoded as +/-
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Data often requires cleaning prior to upload
CIMMYT |
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