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About Brassica Information Portal

The Brassica Information Portal is a web repository for population and trait scoring information related to the Brassica breeding community. It provides information about quantitative trait loci and links curated Brassica phenotype experimental data with genotype information stored in external data sources. Advanced data submission capabilities and APIs enable users to store and publish their own study results in our Portal. The repository can be easily browsed thanks to a set of user-friendly query interfaces.

BIP Portal follows our Terms of Use rules, so please check these when interested in using our service.

How to cite us

Citing BIP

Eckes AH, Gubała T, Nowakowski P et al. Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data [version 1; referees: awaiting peer review]. F1000Research 2017, 6:465 (doi: 10.12688/f1000research.11301.1)

Citing GWASSER

https://github.com/cyverseuk/GWASSER

Manuals and training

Most of operations at BIP is explained through context-sensitive help. In addition, detailed manuals explaining use of submission wizards are available below:

From the home page you may access a separate section dedicated to the API documentation where you find all information needed to write your own calls for programmatic data upload and retrieval.

We have organised number of practical training courses on using the BIP. All slides, hands-on tutorial and test data sets are available on github for you to follow in your own pace. Do not hesitate getting in touch should you have question regarding the tutorial content or beyond.

Feedback

If you have any feedback or question about the BIP, please contact us at

Licensing

Submitters are responsible to adhere with data policies of his/her institution or company. By default, submitted data falls under the CC BY 4.0 license, to ensure maximal re-use potential, while the data generator or submitter needs to be accredited. This is in accordance to the BBSRC, which has funded this infrastructure. Submitters can state their license preferences in the comments section during submission. If this is not explicitly done, the CC BY 4.0 license applies. BIP also hosts some historical data before BIP was setup. Please refer to the individual projects for license information.

Everyone can access publicly available data from BIP without an account. We encourage everyone reusing data to contact the data generator or submitter (this should be available in the metadata). In any case, it is compulsory to acknowledge data generator or submitter in any resulting publication.

Source Code licensing

The database itself is open source under the GPLv3 license and is available on github. We kindly ask any party that wishes to deploy a copy (modified or not) of BIP on their own servers, to contact us at . According to the license, contacting us is not a legally binding requirement, but it aims to help measure the software impact and stay in contact with users for continuous software improvement.

Authentication

Login for submission is managed by an external oauth service, ORCiD. If you already have an ORCiD id, you can use it to access every functionality (submission and analysis) of the Portal.

Data and metadata types we accept

We currently accept Brassica Crop trial and population (meta)data. Submitting population or trial data via the submission web interface, we ask for metadata to be filled into fields provided during several submission steps. Your data can be submitted using the automatically generated .csv templates that will vary depending on the metadata information you put in during previous steps. Using the api, we also accept input data and metadata in .json format. Please see the API documentation for more information. We also have a ruby client which helps with automatised API-based submissions of population or trial data, reading from a spreadsheet. You still need to provide metadata within the client script. How to do this is described in the manual for population submission.

During the wizard-based submissions, we are trying to provide content examples for each submission field. Every field content is also further described in the API documentation. However, if you have any questions, contact us at .

Data and metadata standards

We are putting a lot of effort into use of controlled vocabularies, ontologies and adherence to minimal requirements. For traits, we are developing the Brassica trait ontology (BRATO), which adheres to CropOntology standards. If you want to contribute, please do so! We currently use Plant and Trait Ontology as reference ontologies for plants and GR_tax ontology to cover Brassica taxonomy. Marker sequences are currently cross-referenced with resources such as Genebank (NCBI) and EnsemblPlants where possible, which will be expanded in the future.

Citing data from BIP

Your submitted data can be assigned a DOI after a one week grace period. To the DOI-assigned data, the same license is applied as for BIP hosted data. As we cannot assign DOIs ourselves, we use ZENODO as an external service to assign DOIs. In compliance with DataCite, a stable copy of the submission is then hosted on ZENODO. Please read more information about licensing in the section above.