Splitting setgen into two use cases
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Splitting Setgen into two use cases?. Ruaraidh Sackville Hamilton International Rice Research Institute Los Baños, Philippines. Use cases. Parents managed by user: Entry point = parents; Setgen good Making crosses Making selections Bulking up seed

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Splitting Setgen into two use cases?

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Splitting setgen into two use cases

Splitting Setgen into two use cases?

Ruaraidh Sackville Hamilton

International Rice Research Institute

Los Baños, Philippines


Use cases

Use cases

  • Parents managed by user:Entry point = parents;Setgen good

    • Making crosses

    • Making selections

    • Bulking up seed

  • Parents managed by others:Entry point = offspring;Data quality problems with Setgen

    • Incoming seeds received from others

    • (Entering historical data)

ICIS developers' workshop


Case 1 user manages parents

Case 1. User manages parents

Step 1: Before trial, create list of existing parental GIDs to be included

Step 2: After trial, create list of new progeny GIDs to be created

Step 3: Create data for progeny

ICIS developers' workshop


Use case 1 sub cases making selections vs bulking seed

Use case 1 - sub-cases:Making selections vs bulking seed

Number of progeny GIDs per parent:

  • Making selections

    • 0, 1 … N = number of offspring liked by the breeder

    • DER

  • Bulking seed

    • 0 = failure of seed increase

    • 1 = normal successful seed increase

      • Usually MAN

    • (N>1: for the special case of splitting mixed accessions into uniform components)

ICIS developers' workshop


Selection and seed increase features of germplsm

Selection and seed increase:Features of GERMPLSM

ICIS developers' workshop


Selection and seed increase features of names

Selection and seed increase:Features of NAMES

  • Typically one name per progeny GID

    • = Preferred name, NSTAT=1

    • Also functions as preferred ID ( ≡ NSTAT=8)

    • NVAL assigned automatically as f(parental name)

    • User-specific rules for assigning NVAL:

      • Selection by IRRI breeder: = NVAL of preferred name of GPID2 & “-N”

      • Seed increase by IRRI GRC: = NVAL of preferred ID of MGID & “:YYYYSS”

ICIS developers' workshop


Selection and seed increase features of names1

Selection and seed increase:Features of NAMES

ICIS developers' workshop


Use case 1 summary

Use Case 1 summary

  • Sub-cases for selection and seed multiplication very similar

    • One Setgen suitable

    • User-defined customisation to handle the differences

    • User-defined customisation for ease of use

  • Setgen Cf GRIMS

    • Setgen = just workflow for parent  offspring GIDs

    • GRIMS = whole workflow for selecting, growing, processing the harvest, storing the harvest

    • Setgen is just one element of the workflow controlled by GRIMS

    • Should Setgen be extended to handle the whole workflow?

ICIS developers' workshop


Case 2 user receives seed from others

Case 2. User receives seed from others

1: Initial data on batch: LISTNMS, EVENTMEM

Need fast routine entry of data without need for expert judgements quick release by SHU

2: Initial data on new GIDs as orphans

3: Upload to central (for external receipts processed by SHU)

4: Search central for existing GIDs representing the parents

5: Update data for new GIDs with parents already in central

6: Create GIDs for parents not already in central

7: Update data for the new GIDs from those parents

8: Scan / file / deposit original documents  FILELINK

ICIS developers' workshop


Case 2 step 1 batch data

Case 2 step 1: batch data

  • LISTNMS

  • EVENTMEM links to PERSONS, INSTITUT

    • Batch ID, batch description, date received, donor person, donor institute

    • IP conditions e.g. SMTA, SMTA with additional restrictions, other restrictions

  • FILELINK

    • To point to original documentation:e-files;Scanned paper documents

ICIS developers' workshop


2 initial data entry for new gids germplsm

2: Initial data entry for new GIDs:GERMPLSM

ICIS developers' workshop


2 initial data entry for new gids names

2: Initial data entry for new GIDs:NAMES

  • Germplasm provider may provide:

    • ± pedigree info

    • 0, 1 … N names

  • Choose name values to enter as

    • ENTRYCD, SOURCE, DESIG, GRPNAME

    • Enter in LISTDATA

  • Create NAMES records

    • Preferred ID (if specified by user’s rules)

      • Automatically assigned NVAL by user’s rules

      • NSTAT=8, NLOCN=GLOCN, NDATE=today, NTYPE=user-specified)

    • Names provided by provider

      • With missing NSTAT, NLOCN, NDATE, NTYPE

ICIS developers' workshop


4 searching central for gpid2

4: Searching central for GPID2

  • Does central already have a GID representing the provider’s sample?

  • Issue:

    • Many GIDs may share the same name

    • Nothing to indicate what each GID represents

      •  New field GREPRESENTS??

    • Guidance from GLOCN, NLOCN, NTYPE, NSTAT, and same fields of candidate’s GPID2 & GPID1

      • ot easily seen in GMS_Search

    • Many errors in GLOCN, NLOCN, NTYPE, NSTAT

      • IRTP 456: 15 GIDs, 48 errors, 9 missing GIDs

      • Azucena: 74 GIDs, 27 missing, 10 unidentifiable, > 60% of GPID1-GPID2 values wrong

      • Inconsistent / inadequate user understanding

      • Inadequate data validation

ICIS developers' workshop


Grepresents values proposed in 2009

GRepresents values proposed in 2009

  • Good candidates for GPID2

    • Accession conserved in genebank at GLocN

    • Breeder's selection or other line produced at GLocN

    • Sample maintained at GLocN for testing in nurseries

    • Copy of a genebank accession or breeder's line held informally at GLocN

  • Possible candidates

    • Notional GID required for historical pedigree

    • Inconsistent data

    • Unvalidated

  • Not possible as candidates

    • Cross made at GLocN

    • Sample collected from field or market at GLocN

      • Except for new direct accession from field

ICIS developers' workshop


4 searching central for gpid21

4: Searching central for GPID2

  • Perfect match:

    • Provider specifies own preferred ID

      • Provider uses same ICIS central

        • Gives GID of own sample

      • Sample from provider’s curated collection

        • Gives preferred name & ID as separate identifiers

      • Sample bred by provider

        • Line name is only name, serving as ID and name

    • Candidate GID has

      • (GID represents sample managed by donor)

      • GNPGS < 0

      • GLOCN = donor’s locid

      • Name with matching NVAL and:

        • Name with NLOCN=GLOCN

        • Only one name, or name with NSTAT=8

ICIS developers' workshop


4 searching central for gpid22

4: Searching central for GPID2

  • Super perfect match = perfect match plus

    • Provider specifies their donor’s preferred ID

      • Candidate GID has GPID2 with single name or with preferred ID matching provider’s donor’s preferred ID

    • Provider specifies the original collected sample ID

      • Candidate GID has GPID1 with preferred ID having NTYPE=9 and NVAL=collected sample ID

    • Provider specifies the pedigree

      • Candidate GID has the same pedigree

ICIS developers' workshop


4 searching central for gpid23

4: Searching central for GPID2

  • Imperfect match:

    • Provider does not specify own preferred ID

      • Not professional germplasm manager

      • E.g. Provides only cultivar name or pedigree

    • Partial match; “matching” name (allowing variants):

      • “GID represents” not specified

      • GLOCN ≠ donor’s locid

      • NLOCN ≠ donor’s locid

      • Multiple names, none with NSTAT=8

      • Provider = genebank, gives accession ID, but no NID with NTYPE=1, NSTAT=8

    • Data reliability

      • Multiple NIDs with same NVAL but inconsistent NLOCN, NDATE, NSTAT, NTYPE, GPID1, GPID2

         Potentially unreliable

ICIS developers' workshop


4 searching central for gpid24

4: Searching central for GPID2

  • Search:

    • Calculate % match to donor’s sample

    • Sort by % match

    • Calculate reliability

ICIS developers' workshop


5 successful search for gpid2

5: Successful search for GPID2

  • Assign

    • GPID2 := selected candidate

    • GPID1 := GPID1 of GPID2

  • Display reliability and all recorded distinct values of NLOCN, NDATE, NSTAT, NTYPE, GPID1, GPID2 for same NVAL

    • Expert user corrects wrong data for GPID2 & GPID1

  • After correcting GPID2, new GID:

    • Inherits NLOCN and NDATE of GPID2

    • Is assigned NTYPE and NSTAT by user-rules

      • May be directly inherited e.g. NSTAT=1

      • May be changed: e.g. NSTAT=8 for GPID2  NSTAT=0 for new GID

ICIS developers' workshop


6 unsuccessful search for gpid2

6: Unsuccessful search for GPID2

  • Repeat

    • Step 3, create GIDs with partial data to represent GPID2

    • Steps 4-6, look for and use or created source of GPID2

  • Iteration finishes with

    • Successful search for source of source, or

    • Source of source = GPID1

ICIS developers' workshop


Intermediate cases

Intermediate cases

  • Transfers of seed between users of the same ICIS central

    • For recipient, like handling incoming seed, but with parent GIDs already defined in provider’s list

  • Seed increase of mixed accessions, splitting into uniform components as new accessions

    • Initially like seed increase, but then like receiving new accession

ICIS developers' workshop


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