diff --git a/content/03.02.data-management.md b/content/03.02.data-management.md index 7298530..d8330a5 100644 --- a/content/03.02.data-management.md +++ b/content/03.02.data-management.md @@ -62,3 +62,8 @@ BIMS (Breeding Information Management System) [@doi:10.1093/database/baab054] is [Germinate](https://ics.hutton.ac.uk/get-germinate/) [@doi:10.1002/csc2.20248] is an open-source plant genetic resources database that combines and integrates various kinds of plant breeding data including genotypic data, phenotypic trials data, passport data, images, geographic information and climate data into a single repository. Germinate is tightly linked to the BrAPI specification and supports a majority of BrAPI endpoints for querying, filtering and submission. Germinate integrates and connects with other BrAPI-enabled tools such as GridScore for phenotypic data collection, Flapjack for genotypic data visualization and Helium for pedigree visualization, but, due to the nature of BrAPI, Germinate can act as a data repository for any BrAPI-compatible tool. Thanks to the interoperability provided by BrAPI the need for manual data handling becomes a rarity with the direct benefit of faster data processing, fewer to no human errors, data security and integrity. + +#### MGIS + + +The Musa Germplasm information system, [MGIS](https://www.crop-diversity.org/mgis/), serves as a comprehensive community portal dedicated to banana diversity, a crop critical to global food security [@doi:10.1093/database/bax046]. MGIS offers detailed information on banana germplasm, focusing on the collections held by the CGIAR International Banana Genebank (ITC) [@doi:10.1186/s43170-020-00015-6]. It is built on the Build on the Drupal/Tripal technology, like BIMS and Florilège. Since its inception, MGIS developers have actively participated in the Breeding API (BrAPI) community, pushing for the integration of Multicrop Passport Data (MCPD) into Germplasm module call of the API. MGIS thus provides passport data information on ITC banana genebank accessions (with GLIS DOI), synchronized with [Genesys](https://www.genesys-pgr.org/a/overview/v2YdWZGrZjD), but also enriches it by incorporating additional data from other germplasm collections worldwide. All those germplasm data are available through BrAPI germplasm module calls implementations. For genotyping data, MGIS incorporates GIGWA [@doi:10.1093/gigascience/giz051], which provides tailored implementations for BrAPI genotyping module calls. Furthermore, MGIS supports the implementation of a set of BrAPI phenotyping module calls, facilitating the exposing of morphological descriptors and trait information supported by ontologies like the Crop Ontology [@doi:10.1093/aobpla/plq008]. It is integrated with the Trait Selector BrAPP, developed as part of a project involving Breedbase [@doi:10.1093/g3journal/jkac078]. Uses cases between the Musa implementation of Breedbase, MusaBase, and MGIS to interlink genebank and breeding data. diff --git a/content/03.06.samples-and-genotypes.md b/content/03.06.samples-and-genotypes.md index 8230a78..e4c3f7a 100644 --- a/content/03.06.samples-and-genotypes.md +++ b/content/03.06.samples-and-genotypes.md @@ -10,11 +10,6 @@ The DArT genotyping lab is heavily used world wide when it comes to plant genotyping. Developers at DArT have worked with the BrAPI community to establish a standard API for sending sample metadata to the lab before genotyping. This eliminates much of the human error involved with sending samples to en external lab. -#### MGIS - - -MGIS has germplasm and genotype data stored for many musa accessions. Through BrAPI, users are able to access this data directly from MusaBase, for use in specific experiments. - #### GIGWA Gigwa is a JEE web application providing means to centralize, share, finely filter, and visualize high-throughput genotyping data [@doi:10.1093/gigascience/giz051]. Built on top of MongoDB, it is scalable and can support working smoothly with datasets containing billions of genotypes. Installable from docker images or all-in-one bundle archives, it is pretty straightforward to deploy on servers or local computers and has thus been adopted by numerous research institutes from around the world. Notably, Gigwa serves as a collaborative management tool and/or a portal for exposing the data for genebanks and breeding programs for some CGIAR centers [@doi:10.1002/ppp3.10187]. Thus, the amount of data hosted and made widely accessible using this system has kept growing over the last few years. diff --git a/content/metadata.yaml b/content/metadata.yaml index 7ada10d..140d4fc 100644 --- a/content/metadata.yaml +++ b/content/metadata.yaml @@ -276,7 +276,15 @@ authors: orcid: 0000-0003-0903-6811 email: v.guignon@cgiar.org affiliations: - - The Alliance of Bioversity International and CIAT (CGIAR) + - Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France + corresponding: false + - name: Mathieu Rouard + initials: MR + github: mrouard + orcid: 0000-0003-0284-1885 + email: m.rouard@cgiar.org + affiliations: + - Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France corresponding: false - name: Asis Hallab initials: AH