Skip to content

Genolink User Guide

Genolink is middleware designed to seamlessly connect passport data from Genesys-PGR with genotype data in databases such as Gigwa, enabling easy search, filtering, and retrieval of relevant genebank accessions.

Genolink is developed by the AGG Strategic Partnership in collaboration with The Crop Trust. You can access Genolink and contribute to its development by visiting the official GitHub repository:
Genolink GitHub Repository

Genolink provides the following search options that can be combined to refine searches and ensure only relevant accessions are retrieved.

Genolink main interface
Figure 1: Genolink main interface

Applying Genesys-PGR filters

Refine your search by passport descriptors (date of collection, crop, taxonomy, institute, country of origin, biological status, storage type).

Passport Data Filter
Figure 2: Passport Data Filter

Wild Text Search

The wild text search allows you to query across multiple fields of the passport data.
You can:
- Use double quotes for exact phrases (e.g., "rice")
- Use the OR operator (|) for multiple terms (e.g., rice | leaf)
- Use asterisks for prefix searches (e.g., rice*)
- Use parentheses for grouping

The example below shows a query for rice | leaf. The search returns records that match either term across different fields, such as accession name, taxonomy, or remarks.

Wild text search results example
Figure 3: Example results for query rice | leaf

Enter one or multiple accession numbers directly.

Accession number search using direct input
Figure 4: Accession number search using direct input

Enter multiple accession numbers by uploading a text file. Once uploaded, click Browse.

Accession number search using file upload
Figure 5: Accession number search using file upload

Please upload a text file with your list of accessions, with each accession entered on a separate line.

Text file format for accession number upload
Figure 6: Text file format for accession number upload

After the upload, the filter will be applied when you press Search.

Search results after uploading accession list
Figure 7: Search results after uploading accession list

Note: Your file must be a plain text file (.txt).

The GenotypeID filter works the same way as the Accession Number Search (direct input or file upload).
Please refer to the Accession Number Search section for detailed steps and examples.

The only difference is that, in the text file, you must provide a list of GenotypeIDs (one per line) instead of accession numbers.

Filtering for Genotyped Accessions

To restrict results to genotyped accessions only, tick the Check for genotype checkbox in the filter panel and then press Search.
This will return only those accessions with genotype data available.

Filtering results by selecting the "Check for genotype" option
Figure 8: Filtering results by selecting the "Check for genotype" option

Requesting Genotype Data

To request genotype data for your filtered accession records:

  1. Select accessions from the table by checking the boxes in the first column.
  2. Once selected, the server(s) containing the genotype data for those records will be displayed.
  3. You can identify which accessions have genotype data by checking the AGG-SP Status column.
  4. Accessions with genotype data show Status = Completed.
  5. These records also include a specific GenotypeID value.

Selecting accessions and requesting genotype data
Figure 9: Selecting accessions and identifying genotype data availability

  1. After selecting the accessions and clicking Lookup Data, a summary will be shown.
  2. It indicates how many of the selected accessions have genotype data in the Gigwa server.
  3. It also shows how many of them are registered in the Genolink internal database.
  4. The summary lists the Gigwa datasets that contain genotype data for those accessions.

Lookup Data summary for selected accessions
Figure 10: Summary showing genotype data availability in Gigwa and internal database

  1. After selecting the dataset, you can further refine the genotype data search in two ways:

Genotype Data Based on Genomic Region

  • Filter results by specific chromosomes
  • Define genomic positions (start–end ranges)

Filtering genotype data by chromosome and position
Figure 11: Refining genotype data search using chromosome and position filters

Genotype Data Based on Marker Names

  • Filter results using Variant IDs that correspond to specific genomic regions.

Filtering genotype data by Variant IDs
Figure 12: Refining genotype data search using Variant IDs

All Markers

If you do not apply any of the above filters (chromosome, position, or variant ID), Genolink will return genotype results for all chromosomes and all positions.

Note: This may generate very large result sets and could affect performance.

After configuring your filters (or leaving them empty), click Search Genotype to retrieve the results.
If you want to restart or run a new genotype search with different filters, click the Reset button to clear the current selections.

Genotype results table
Figure 13: Example of genotype search results

Exporting to VCF

After retrieving your genotype results, you can select the server from which you want to export the data.
Once the server is chosen, click the Export VCF button to download the genotype data as a VCF file.

Exporting genotype data as VCF
Figure 14: Exporting genotype data in VCF format