GGCE Server issueshttps://gitlab.croptrust.org/grin-global/grin-global-server/-/issues2020-07-29T03:58:54+02:00https://gitlab.croptrust.org/grin-global/grin-global-server/-/issues/64Acquisition: Checking for Duplicates2020-07-29T03:58:54+02:00Grace CapilitAcquisition: Checking for DuplicatesAfter documenting incoming materials to the Genebank, we want to check whether we already have a copy of these newly received materials in the Genebank, either as registered seeds (accession) or unregistered samples (from another incomin...After documenting incoming materials to the Genebank, we want to check whether we already have a copy of these newly received materials in the Genebank, either as registered seeds (accession) or unregistered samples (from another incoming batch with TemporaryID only)
This function will search the database for similar entries by name (cultivar name, DonorID, CollNo, etc) using algorithms for
* exact match
* edistance
* soundex
Checking for duplicates can be done
1) by batch where the user can either specify/choose the BatchID of the incoming materials to be compared or upload list from a file or
2) by entry where a name is entered in the search boxGrace CapilitGrace Capilithttps://gitlab.croptrust.org/grin-global/grin-global-server/-/issues/62Acquisition: Evaluating Incoming samples for Inclusion in the Processing2020-08-05T09:15:30+02:00Grace CapilitAcquisition: Evaluating Incoming samples for Inclusion in the ProcessingThis will enable Genebank managers to document evaluation of incoming materials that will guide succeeding actions on the sample.
Will use accession_action to record
1) the incoming seed status
| Code | Description ...This will enable Genebank managers to document evaluation of incoming materials that will guide succeeding actions on the sample.
Will use accession_action to record
1) the incoming seed status
| Code | Description |
|------|---------------------------------------------------|
| REP | REPLACEMENT |
| MIS | MISSING SAMPLE/PACKET |
| HLD | HOLD |
| DUPY | PROBABLE DUPLICATE (INCLUDE IN SEED PROCESSING) |
| SHP | WITH SEED HEALTH PROBLEM |
| EXC | TO BE EXCLUDED IN SEED PROCESSING/PLANTING |
| INC | TO BE INCLUDED IN SEED PROCESSING/PLANTING |
| SUF | SUFFICIENT, FOR DIRECT ACCNO ASSIGNMENT |
| DUPN | EXACT DUPLICATE (NOT INCLUDED IN SEED PROCESSING) |
| MIX | MIXED SAMPLE (INSUFFICIENT AMOUNT) |
| MXS | MIXED SAMPLE (SUFFICIENT AMOUNT) |
2) viability (non-viable, weak, viable)
3) planting material availability (sufficient, insufficient)
4) remnant status (sufficient, insufficient, no remnants)
quantitative data
5) population structure (1, 2, 3, etc)
-indicates the number of population, >1 when mixed
6) number of rows that can be plantedGrace CapilitGrace Capilithttps://gitlab.croptrust.org/grin-global/grin-global-server/-/issues/42Genebank reporting2020-06-16T18:31:13+02:00Nora Castaneda-AlvarezGenebank reportingWe want to enable partners to report on several genebank management aspects, using information recorded in GG. Partners should be able to report on:
* Availability of selected crop collections - accession level.
* Security (safety dupl...We want to enable partners to report on several genebank management aspects, using information recorded in GG. Partners should be able to report on:
* Availability of selected crop collections - accession level.
* Security (safety duplication) - accession level.
* Data availability - accession level.
* Distribution - accession level.
Some considerations to look upon are:
1. Availability is estimated on four variables:
* health - conducted at inventory level.
* viability - conducted at inventory level.
* quantity sufficiency - conducted at inventory level.
* legal status - defined at accession level.
2. Distribution: we also ask genebanks to report on:
* type of recipient
* country of recipient
* distinguish between internal vs. external recipients (same institution or not)
* exclude material sent to safety duplication
* type of germplasm (SAMPSTAT)
* distribution of subsets
* purpose of the requestor
3. Storage: we ask genebanks about the storage of inventory/accessions.
4. Security: we ask genebanks to report on the places where they have sent material for safety duplication.
How to summarize inventory level to report at accession level?
5. We also want to know how many viability tests are conducting per year.
6. We want to know the number of accessions/inventory (?) regenerated and characterized per year.
7. We want to know the number of requests received annually.
8. We want to know the total number of accessions and number of unique accessions distributed annually.
Here is the table of indicators and targets applicable to Seeds for Resilience (indicators 1,2,3,5,11 are potentially estimated through GG):
| | **Indicator** | **Target at year 5** |
|----|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------:|
| 1 | **Availability:** % collection which is clean of pathogens of quarantine risk, viable, and in sufficient quantity to be immediately available for international distribution from medium-term storage (or local distribution for some tree species). | 90% accessions available |
| 2 | **Security:** For seed crops: % collection held in long-term storage at two locations and also in Svalbard Global Seed Vault (except for tree species). For clonal crops: % of the collection held in long-term storage or cryopreservation at two locations; % of the collection held in slow growth conditions in vitro at two locations | 90% seed accessions safety duplicated 50% clonal accessions in cryo-preservation; Intermediate target 90% accessions duplicated in in vitro |
| 3 | **Data availability** | Passport: PDCI >6 Characterization: 100% accessions with characterization data |
| 5 | **Distribution:** % of annual requests for seed samples from users successfully serviced | 80% relevant requests serviced annually |
| 11 | Number of user requests for seed samples | 100 |Matija ObrezaMatija Obreza