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Fixed some links on germplasm-data and added Data Storage Model page
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carolyncaron committed Dec 14, 2023
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8 changes: 5 additions & 3 deletions _docs/curation/germplasm-data.md
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Expand Up @@ -9,9 +9,11 @@ This module package enhances germplasm support in Tripal Core with support for b

** *Placeholder for Lacey, who will give an idea of the breeder workflow and why there are different importers* **

## [Germplasm Accessions](germplasm-data/germplasm-accessions-importer.md)
## [Germplasm Accessions](germplasm-data/germplasm-accessions-importer)
The Germplasm Accessions Importer is used for specific germplasm samples which are often maintained by genebanks. These accessions often serve as the seed source for various experiments and may also be used as parents in breeding crosses. Genebanks will generally maintain public passport data on these accessions, which is captured by this importer with the Genebank being specified as the "External Database". In addition to these passport data, this importer optionally collects BrAPI-suggested information such as breeding institution, breeding method, pedigree and synonyms where they are available and applicable.

## [Germplasm Crosses](germplasm-data/germplasm-crosses-importer.md)
## [Germplasm Crosses](germplasm-data/germplasm-crosses-importer)

## [Germplasm Collections](germplasm-data/germplasm-collections-importer.md)
## [Germplasm Collections](germplasm-data/germplasm-collections-importer)

## [Data Storage Model](germplasm-data/data-storage-model)
25 changes: 25 additions & 0 deletions _docs/curation/germplasm-data/data-storage-model.md
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---
title: Data Storage Model
tags:
- germplasm
- importers
description: This is documentation pertaining to how germplasm data is stored in the Chado database.
---

## Data Storage Model for Germplasm

### Germplasm Accessions
Germplasm accessions and their corresponding metadata are stored in the following chado tables: `stock`, `stockprop`, `stock_relationship`, `db`, `dbxref`, `synonym` and `stock_synonym`:

- The organism of one accession is determined by the genus, species and subtaxa (optional)
- Germplasm accessions are loaded into the table `stock`,
- The external database (eg: genebank) is stored in `dbxref` and `db`
- Properties are loaded into the table `stockprop`
- Synonyms are loaded into the tables `synonym`, `stock_synonym` and `stock_relationship`

### Germplasm Crosses
Germplasm crosses and their corresponding metadata are stored in the following chado tables: `stock`, `stockprop`, and `stock_relationship`:

- Germplasm crosses are loaded into the table `stock`
- Properties for each germplasm are loaded into table `stockprop`
- The relationship between germplasm and its parents is loaded into the table `stock_relationship`

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