Unverified Commit c3715a1a authored by Sreenath Sasidharan Nair's avatar Sreenath Sasidharan Nair Committed by GitHub
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Merge branch 'master' into development

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# How to contribute
#### Last updated 09 Feb 2022
## Ways of contributing
Everyone is welcome to contribute to this repository. We recommend the following steps:
### 1. Announce and discuss your proposal through GitHub “issues”
* Click on “Issues” in the top menu bar and look at the existing issues. See if your idea or suggestion is already being
discussed.
* If an issue exists, add your comments. If you want to edit the content discussed, let people know through the
comments.
* If no relevant issue exists, create a new issue by clicking on the green “New issue” button on the right, and
choose one of the issues templates. You can find more information on creating issues in the GitHub documentation.
* Discuss your idea with the editors through comments in the issues. You will be notified when others comment on your
issues. Read the comments and write your opinion/questions/answers in the “Leave a comment” box and click on the green
“Comment” button on the right.
### 2. Write your content and make a pull request
* Fork the repository by clicking on the "Fork" button, while logged into GitHub
* Make the changes to the code in your forked copy of the repository
* Test your code and ensure there is sufficient documentation
* Open a pull request and refer to the issue identifier
* A developer from our team will review your code and merge it into the main repository
## Contributor responsibilities
When writing for this repository keep in mind the following:
* For the sake of consistency, please follow the coding style of the original repository.
* We give great importance to authorship credit. If others were involved in your contribution, by writing up or by
providing resources such as diagrams or links, please make sure you acknowledge them in the contributors’ section of
your page.
## Attribution of the contributors
All contributors will be displayed in the contributors page of the repository.
......@@ -13,7 +13,7 @@ format and on a unified platform.
3D-Beacons consists of a Registry, a Hub and Beacons who host Clients. The Registry is used by
the [3D-Beacons Hub](https://github.com/3D-Beacons/3d-beacons-hub-api) to look up which API endpoints are supported by
the various Beacons. The Beacons provide data according to the 3D-Beacons data
specifications ([Current version: 0.3.1](https://app.swaggerhub.com/apis/3dbeacons/3D-Beacons/0.3.1)). The Hub collates
specifications ([GitHub link](https://github.com/3D-Beacons/3d-beacons-specifications/blob/production/oas3.yaml)). The Hub collates
the data from the Beacons and expose it via Hub API endpoints.
### Current 3D-Beacons
......@@ -47,7 +47,7 @@ Data providers who are interested in making their macromolecule structures avail
should follow the following steps:
1. Contact the 3D-Beacons consortium
2. Review the [API specifications](https://app.swaggerhub.com/apis/3dbeacons/3D-Beacons) for sharing metadata
2. Review the [API specifications](https://github.com/3D-Beacons/3d-beacons-specifications/blob/production/oas3.yaml) for sharing metadata
3. Implement API endpoints or set up an instance of
the [3D-Beacons Client](https://github.com/3D-Beacons/3d-beacons-client)
4. Review the `resources/registry.json` file in this repository
......@@ -63,11 +63,11 @@ To ensure that the network provides access to relevant data, we require new pros
before linking their data to 3D-Beacons. Please send an email to Sameer Velankar (sameer@ebi.ac.uk) or Christine
Orengo (c.orengo@ucl.ac.uk) to initiate discussions.
### 2. Review the [API specifications](https://app.swaggerhub.com/apis/3dbeacons/3D-Beacons) for sharing metadata
### 2. Review the [API specifications](https://github.com/3D-Beacons/3d-beacons-specifications/blob/production/oas3.yaml) for sharing metadata
The 3D-Beacons Network provides access to metadata regarding macromolecule structures in a unified format. This means
that every data provider has to expose information in the same data format. We define the accepted data schemas in the
[3D-Beacons API specification](https://app.swaggerhub.com/apis/3dbeacons/3D-Beacons) on SwaggerHub.
[3D-Beacons API specification](https://github.com/3D-Beacons/3d-beacons-specifications/blob/production/oas3.yaml) on GitHub.
Please review this specification, and identify the schemas that fit the data you would like to make accessible via
3D-Beacons. For example, if you want to make your structures discoverable based on a UniProt identifier, then the
......@@ -82,7 +82,7 @@ pre-packaged and ready-to-use implementation of certain API endpoints. For more
### 4. Review the `resources/registry.json` file in this repository
Once your metadata is exposed via API endpoints that comply with the [3D-Beacons API specification](https://app.swaggerhub.com/apis/3dbeacons/3D-Beacons), you should review the `resources/registry.json` file in this repository. This file contains all the information needed by the [3D-Beacons Hub API](https://github.com/3D-Beacons/3d-beacons-hub-api) for linking your API endpoints to the 3D-Beacons Network.
Once your metadata is exposed via API endpoints that comply with the [3D-Beacons API specification](https://github.com/3D-Beacons/3d-beacons-specifications/blob/production/oas3.yaml), you should review the `resources/registry.json` file in this repository. This file contains all the information needed by the [3D-Beacons Hub API](https://github.com/3D-Beacons/3d-beacons-hub-api) for linking your API endpoints to the 3D-Beacons Network.
The registry has two main data blocks: 1.) `providers` and 2.) `services`.
......@@ -128,7 +128,7 @@ the `resources/registry.json` file by adding a new item in the `providers` list
Finally, please create a pull request so that we can merge your version of the `resources/registry.json` file to our `development` branch. We will then test the updated file, and also test all the API endpoints you specified in the `services` list of the `resources/registry.json` file.
As part of testing the API endpoints, we will perform stress testing of all the API endpoints you provide. We will also validate the data format against the [3D-Beacons API specification](https://app.swaggerhub.com/apis/3dbeacons/3D-Beacons), and test if the [3D-Beacons Hub API](https://github.com/3D-Beacons/3d-beacons-hub-api) can concatenate data.
As part of testing the API endpoints, we will perform stress testing of all the API endpoints you provide. We will also validate the data format against the [3D-Beacons API specification](https://github.com/3D-Beacons/3d-beacons-specifications/blob/production/oas3.yaml), and test if the [3D-Beacons Hub API](https://github.com/3D-Beacons/3d-beacons-hub-api) can concatenate data.
Once done, we proceed to merge the updates into the `master` branch, at which point your data resource will become officially linked to the 3D-Beacons Network.
......
......@@ -57,21 +57,30 @@
{
"providerId": "alphafill",
"providerName": "AlphaFill Model Data Bank",
"providerDescription": "AlphaFill is a databank of AlphaFold models enriched with ligands, cofactors, and ions that are transplanyed from homologous experimental structure models.",
"providerDescription": "AlphaFill is a databank of AlphaFold models enriched with ligands, cofactors, and ions that are transplanted from homologous experimental structure models.",
"providerUrl": "https://alphafill.eu/",
"baseServiceUrl": "https://alphafill.eu/v1/aff/",
"devBaseServiceUrl": "https://alphafill.eu/v1/aff/",
"providerLogo": "https://alphafill.eu/images/alphafill-logo.svg"
},
{
{
"providerId": "hegelab",
"providerName": "hegelab.org",
"providerDescription": "Membrane Protein Research Group, Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary",
"providerUrl": "http://www.hegelab.org/",
"baseServiceUrl": "https://3dbeacon.hegelab.org/",
"baseServiceUrl": "https://3dbeacon.hegelab.org/",
"devBaseServiceUrl": "https://dev.3dbeacon.hegelab.org/",
"providerLogo": "http://www.hegelab.org/images/logo.png"
}
},
{
"providerId": "modelarchive",
"providerName": "ModelArchive",
"providerDescription": "ModelArchive is the archive for structural models which are not based on experimental data and complements the PDB archive for experimental structures and PDB-Dev for integrative structures.",
"providerUrl": "https://modelarchive.org",
"baseServiceUrl": "https://modelarchive.org/3d-beacons/",
"devBaseServiceUrl": "https://modelarchive.org/3d-beacons/",
"providerLogo": "https://modelarchive.org/app/assets/styles/logos/MA_logo.png"
}
],
"services": [
{
......@@ -114,10 +123,16 @@
"provider": "alphafill",
"accessPoint": "3d-beacon/"
},
{
{
"serviceType": "summary",
"provider": "hegelab",
"accessPoint": "uniprot/summary/"
}
},
{
"serviceType": "summary",
"provider": "modelarchive",
"accessPoint": "uniprot/summary/"
}
]
}
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