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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 BIP. The repository can be easily browsed thanks to a set of user-friendly query interfaces.

BIP shows impact

Further information on the Projects related to the Brassica Information Portal can be found in the BIP project description. The Brassica Information Portal has received a lot of attention after our press release. The Eastern Daily Press and Agri-Tech East wrote articles in response to the press release. The Brassica Information Portal was also presented in the Arabidopsis community newsletter (GARNish_25). A blog entry explains to the public why Brassica crops are important and brilliant- have a look at Brilliant Brassica.

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. The first workshop on how to use the database has been held on the 7.09.2016. All slides, hands-on tutorial and test data sets are available on github for you to follow in your own pace.

Authentication

Login for submission is managed by an external OAuth service, ORCiD. Registration is very quick and registered users can access every functionality (submission and analysis) of the Portal.

Feedback

If you have any queries or suggestions related to the software, data, documentation and training, please contact us at

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

Licensing

Citing data deposited in BIP

It is required for everyone using published data sets to acknowledge authors and organisations that generated and submitted it. In order to make this process easy, BIP allows storage of detailed author contact details, data set DOIs and publication meta-data (Pubmed ID; article DOI). Data set submitted to BIP can be cited by the unique identifier assigned to the complete data set. We also recommend to generate DOIs for specific parts of the original submission. We use ZENODO as an external service to assign DOIs. Please read more information about our data sharing policy below.

Source Code

The BIP framework is open source under the GPLv3 license and is available on github. BIP is a community project, we kindly welcome any contributions to improve existing and add new functionalities. If you wish to deploy a copy of BIP (for Brassica or any other crop) on your own servers, don’t hesitate to contact us in case you need our assistance. Contacting us also helps measuring the software impact and planning future developments.

Data model

Our data model is developed based on CropStoreDB and is presented in this diagram.

Data and metadata types we accept

We currently accept Brassica crops 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 provides an example of submission of population data with API. It requires an input data in csv format and additional metadata within the client script. Follow the manual for population submission where examples for each submission field are provided. Content of every field is further described in the API documentation.

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 have or are aware of other trait types that we do not cover yet, please get in touch or add them to BRATO directly. Your contributions are most welcome! 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 Sequence Read Archive (NCBI) and EnsemblPlants where possible.

Data privacy

You can submit data to BIP without publicly releasing it straight away. For example, it is possible to submit your data prior to publication, and removing the embargo post- publication. Be advised that you cannot obtain a DOI to cite your dataset in the paper without public release. In order to obtain a DOI, your data needs to be publicly available and stable. Submitter is given a week of grace period during which the content may be retracted or the status of the data may be changed from public to private and subsequently modified. Once made public, and after the grace period expired you cannot modify or delete your record. If you wish to this please contact us.

Data sharing

Submitters are responsible to adhere with data policies of his/her institution or company. If not stated otherwise, 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. Submitters can provide licensing information during the submission process. If this is not explicitly done, the CC BY 4.0 license applies. If you plan to reuse previously generated data sets please refer to the individual projects for license information.

Availability and liability

BIP is hosted on NBI infrastructure that has a good record of keeping servers up and running. However, we cannot guarantee the availability of our services to the users at all time. Assistance is available during business hours London time, please contact us at

BIP Portal follows Earlham Institute Terms of Use rules.