Commit 4d08d93c authored by Célia Michotey's avatar Célia Michotey
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Add About, Help and How to join documents. GNP-5519.

parent 12534586
# About this application
# About this data portal
The purpose of this portal is to facilitate the discoverability of public data on plant biology from a federation of established data repositories.
It is based on the [Breeding API (BrAPI)](https://brapi.org/) specifications and facilitates the access to genotype and phenotype datasets for crop and forest plants through an easy to use web interface.
It also provides a standard interface that can be accessed programatically through [web services](https://urgi.versailles.inra.fr/faidare/swagger-ui.html).
It is an extension of the generic [Data-Discovery portal](https://forgemia.inra.fr/urgi-is/data-discovery), a web portal that allows finding any type of data across several databases through a lightweight keyword based search.
FAIDARE offers more detailed search and data retrieval capabilities and it takes advantage of the growing adoption of the BrAPI.
It has been developed by [INRA-URGI](http://urgi.versailles.inra.fr/) in collaboration with [**Elixir Plant**](https://elixir-europe.org/communities/plant-sciences), [**Phenome-Emphasis.fr**](https://www.phenome-emphasis.fr/phenome_eng/Methodological-projects/MCP2-Distributed-Information-system) and [**Elixir-fr/IFB**](https://www.france-bioinformatique.fr).
If you want to join the FAIDARE federation, please read the [HOW TO JOIN guide](HOW-TO-JOIN.md) and [contact us](mailto:urgi-contact@inra.fr?subject=%5BFAIDARE%5D).
# Help section
> Note: this application is responsive, meaning that its rendering will adapt to the screen's size of your device, hence location of items below can be different than stated.
You can find data by building your own query using the fields available in the two tabs of the form:
* The `Germplasm` tab allow you to add criteria on plant material/germplasm (_e.g._ its name, genus or species).
* The `Trait` tab allow you to add criteria on trait(s) and/or variable(s) name(s).
In each field, one or several term(s) can be entered.
As you begin to type, a list of relevant suggestions is proposed to guide you in your search.
The query is launched as soon as at least one parameter is selected in the form.
The results are automatically updated if a parameter is added or removed.
To refine your search, you can add more specific filters by using the facets/categories on the left side.
> Note: applying several filters in the same facet/category will search for documents related to any of the selected terms (resulting in a `OR` operator between all the category's terms).
> In contrary, applying filters in different facets/categories will search for documents having both filters (resulting in an `AND` operator for the different facets).
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# How to join FAIDARE federation?
If you want your information system to be part of the FAIDARE federation, we invite you to [contact us](mailto:urgi-contact@inra.fr?subject=%5BFAIDARE%5D) as soon as possible so that we can follow your progress and assist you if needed.
You will need to create a new `source` corresponding to your information system.
For this, you will have to set up your own [BrAPI](https://brapi.org/) endpoint and reference it in the sources of [Elixir's FAIDARE harvester](https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis).
General information and considerations can be found on the [**Elixir Plant**](https://elixir-europe.org/communities/plant-sciences) web page.
## Creation of a BrAPI endpoint
To create a new endpoint, you should implement the BrAPI calls needed to give access to the data of your information system.
Those calls are documented in various formats on the [Developer resources](https://www.brapi.org/developers#) section of the BrAPI web site.
The BrAPI calls currently used by FAIDARE are:
* germplasm
* location
* ontology
* program
* study
* study/{studyDbId}/observationVariable
* study/{studyDbId}/germplasm
* study/{studyDbId}/observationUnit (can be resource intensive and therefore not implemented)
* trial
> Note that since the tool makes a backlink to your information system, we need a URL in the `DocumentationURL` field of the BrAPI for researchers to get more detailed information about the indexed entry directly in your information system.
To ensure the quality of your BrAPI endpoint, you can use the validation tools provided by the BrAPI community, especially [Brava](http://webapps.ipk-gatersleben.de/brapivalidator/).
If you have any question or need help implementing BrAPI calls, you can [contact the BrAPI community](https://brapi.org/).
## Referencement of a BrAPI endpoint
For your endpoint to be visible on FAIDARE, you have to declare it in the sources of [Elixir's FAIDARE harvester](https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis).
To do this, you only have to create your own configuration file, according to the following template, and add it to the [`sources`](https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis/tree/master/sources)` directory of the harvester:
```
{
"@context": {
"schema": "http://schema.org/",
"brapi": "https://brapi.org/"
},
"@type": "schema:DataCatalog",
"@id": "[information system URL]",
"schema:identifier": "[BrAPI endpoint name]",
"schema:name": "[information system name]",
"brapi:endpointUrl": "[BrAPI endpoint URL]"
}
```
Example: [URGI.json](https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis/blob/master/sources/URGI.json)
```
{
"@context": {
"schema": "http://schema.org/",
"brapi": "https://brapi.org/"
},
"@type": "schema:DataCatalog",
"@id": "https://urgi.versailles.inra.fr/gnpis",
"schema:identifier": "URGI",
"schema:name": "URGI GnpIS",
"brapi:endpointUrl": "https://urgi.versailles.inra.fr/faidare/brapi/v1/"
}
```
If you have any question or need help referencing your endpoint, you can [contact us](mailto:urgi-contact@inra.fr?subject=%5BFAIDARE%5D).
## Data availability & update
[Elixir's FAIDARE harvester](https://github.com/elixir-europe/plant-brapi-etl-data-lookup-gnpis) extract the metadata available from all declared sources (_i.e._ BrAPI endpoint) and index it into a centralised Elasticsearch cache.
The sources are reindexed regularly (once a month maximum) but if you want a reindexation following a major update on your side, please [inform us](mailto:urgi-contact@inra.fr?subject=%5BFAIDARE%5D).
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