PLAZA

Notes given in the application form

Eligibility criteria

  • Must be an ELIXIR Service (i.e. part of an existing ELIXIR Node’s Service Delivery Plan, or is an ELIXIR Commissioned Service), or is in the official process/commitment of becoming one. (Required)
  • Must have evidence that it supports an interoperability activity, and has been deployed. (Required)
  • Must indicate how it supports the FAIR Principles. (Required)
  • Should fit into the EIP service framework in the ELIXIR 2019-2023 Scientific Programme for data interoperability or other activities relevant to the ELIXIR mission.

Additional notes

  • Please complete this form by adding information for your Interoperability Resource in the appropriate section below. Consult with Recommended Interoperability Resource (RIR) selection criteria documentation on details for each section below.
  • Where a panel/question is not relevant to your Interoperability Resource, please leave it blank or mark as “not applicable”, optionally with a brief explanation as to why.
  • Word limit guidance is noted for free text fields.
  • Please include urls to external resources, where useful.
  • Any questions, contact Sirarat Sarntivijai (sirarat.sarntivijai@elixir-europe.org).

1. Resource facilitation to scientific research

a. Interoperability Resource: Briefly describe the function of the Interoperability Resource

PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics. The PLAZA platform consists of multiple independent instances focusing on different plant clades, while also providing access to a consistent set of reference species. A user-friendly web interface provides access to the structural and functional gene annotations, gene family data and phylogenetic trees, and detailed gene colinearity information. All data included has been curated to ensure interoperability. The PLAZA Workbench enables users to analyze multiple genes together in an efficient manner, while bulk downloads and an API are available for expert users to perform customized large-scale analyses.

b. Scope statement: describe the scope , and the users of the resource. How is the Interoperability Resource positioned with respect to other similar Interoperability Resources? Include the base URL and, if relevant, the introductory or “about” page URL.

The PLAZA platform is currently focused on plant genomes as it was developed within Plant Systems Biology department of UGent-VIB, but all the tools and software are generic enough to be broadly applicable to other clades of eukaryotes as well.

The use of PLAZA is varied: non-bioinformaticians who want to explore single genes or gene families of interest; bioinformaticians downloading and using the structured data for their own analyzes; consortia using PLAZA as a reference in genome sequencing projects; and GALAXY admins that use PLAZA as a data repository where genome references can be accessed from.

Because PLAZA is dedicated to adhering to the FAIR principles (https://bioinformatics.psb.ugent.be/plaza/pages/fair_data), it can be used automatically with other web-based resources.

c. Resource url

https://bioinformatics.psb.ugent.be/plaza

d. Inter-organisational recognition: does the Interoperability Resource have community recognition? (e.g. demonstrated through a collaboration, geographical diversity in the source of the submissions, international diversity of delivery partners and/or funders)

The PLAZA platform has been used in multiple genome projects, both with and without collaboration agreements. Agreements with industry partners are also in place, giving them access to the software driving the PLAZA platform. The data gathered through Google Analytics show that the end-users are distributed globally. Very frequently questions are asked to the PLAZA team to either include a new genome, or to update a genome to the latest assembly/annotation version.

2. Community

a. Community impact: If applicable, provide documented evidence of community impact (e.g., publication citations, API calls, projects using the resource, etc.)

The PLAZA platform is commonly cited in the publications of plant genome projects, such as the genome of Orchid (https://www.nature.com/ng/journal/v47/n1/abs/ng.3149.html), the seagrass Zostera marina (https://www.nature.com/articles/nature16548), as well several algal genome projects (https://www.sciencedirect.com/science/article/pii/S0960982218310601 and https://advances.sciencemag.org/content/3/7/e1700239).

Furthermore, many studies that focus on the comparative analysis of a single gene or gene family make use of PLAZA as a reference platform. The large number of citations of the different PLAZA publications confirm this: the PLAZA 1.0 (2009), PLAZA 2.5 (2012) and PLAZA 3.0 (2015) papers are all cited more than 150 times. Equally important is the large number of international collaborating institutes: MPI Golm, Observatoire Oceanologique de Banyuls sur Mer, and the University of Marburg are examples of institutes with which extensive collaborations have resulted in additional data integration and data exchange. Data providers such as TAIR also provide linkouts to the PLAZA platform.

b. Potential usage: Describe other systems that could use this candidate resource, but currently do not.

UniProt comes to mind as one of the primary data sources that could use the PLAZA platform as a source for protein sequences and identifiers. Further integration with additional GALAXY systems worldwide, where the PLAZA platform is used as a homogeneous structured data resource for genome files, is another example where PLAZA could be used. As PlantEnsemble and Phytozome deliver similar, but not fully overlapping functions, co-operation here is key for the future.

c. Outreach & support: Provide resource support publication(s)/user documentation(s) describing the Interoperability Resource (e.g. scientific journal publications, community preprints, resource user’s documentations etc.), resource dissemination plan (e.g. workshops, conference presentations), and other equal-opportunity research support (if applicable).

The PLAZA platform has been published in several high impact journals (e.g. https://www.ncbi.nlm.nih.gov/pubmed/20040540 and https://www.ncbi.nlm.nih.gov/pubmed/29069403). In addition, user guidelines have been published separately (https://www.ncbi.nlm.nih.gov/pubmed/27987171). Furthermore, over the course of the last 10 years, multiple workshops have been organized, both local and abroad. In these workshops the focus is mainly on non-bioinformaticians, to teach them how to get the most out of their data using the website. Finally, extensive user documentation is available on the website. Here we also ensure that the documentation is available for the latest and older versions, in order to ensure maximum reliability.

d. Dependency of other resources: How is this resource critical to the user(s)? Do other resources depend on the resource described here to provide downstream service? Please list, or provide a link to a diagram.

The PLAZA platform is critical for the Belgian GALAXY platform, as PLAZA provides the genome references for the plant species.

PLAZA is also currently the only data platform to provide an ensemble method for orthology predictions in plants. As orthology is a very complex issue in plants, due to the multiple independent genome duplications, and orthology is often used as a proxy for function similarity, having a resource that provides high quality orthology predictions is key for many users to have an idea what the role is of genes in non-model species. Therefore, PLAZA is a critical resource for people who want to study to function of genes in non-model species, due to its unique and extensive integrative orthology.

3. Quality of resource

a. Uptime: Average percentage uptime/month during the last 12 months, response time of the resource. In case of ontology/standards production, interval of update/release, adaptability of ontology design patterns to evolving data. Provide information where applicable: uptime of resource, software release cycle (please state week/month etc), update frequency.

Uptime of resource: Not measured. But in the order of 99% (in 2019: single day outage due to database server crash)

Software release cycle (please state week/month etc): Software development is a continuous ongoing process, without a set release cycle. Agile programming is applied, with features being continuously updated or added. Major data releases are often accompanied with a description of the list of software improvements that have taken place between the data releases.

Update frequency (data underlying resource, if applicable): PLAZA instances are released quite often, with major releases about once every year. Building a full PLAZA instance takes a substantial amount of time (~1 month), and as such care is put into ensuring that the input data is high quality.

b. Accessibility: what are resource retrieval mechanisms? Does the resource provide web-based user interface, application programmable interface (API), containers, and/or other channels? Please list resource access mechanism, provide URLs as applicable.

  1. Web based user interface (accessible from https://bioinformatics.psb.ugent.be/plaza/ where users can select the instance they are looking for)
  2. API based data retrieval through a REST API interface per PLAZA instance (documentation available here https://bioinformatics.psb.ugent.be/plaza/documentation/api )
  3. Bulk downloads through an FTP server, with the data organized per PLAZA instance (data available here ftp://ftp.psb.ugent.be/pub/plaza/)

c. Maintenance quality: Is there a maintenance SOP or plan, reflecting sustainability and scalability? Does it align with guidelines for sustainable software development? Please include a resource commitment statement (description text or URL).

The PLAZA platform is documented in several ways: 1) user documentation, 2) internal build documentation using Atlassian Confluence, 3) internal issue tracker using Atlassian Jira, 4) software repository using Atlassian Stash, 5) extensive within-code documentation.

Currently major efforts are ongoing to further improve the installability and buildability of the PLAZA platform, by moving the entire operation to the cloud, allowing end-users to build their own PLAZA platform. To fully commit to this, all guidelines for sustainable software development will be followed.

d. Support quality: Please list support mechanisms (e.g., point of contact, request ticketing, resource’s response time where a solution is identified, etc.), and methods to collect user feedback. If available, list tutorial documentations or tutorial materials and format, including linking on the ELIXIR’s Training Portal (TeSS) (or other training platforms) where applicable.

Several contact email addresses are provided on the website, to help users with technical or legal issues, to provide feedback, etc. Furthermore, we keep track of all issues, both user provided and internal, using the Atlassian Jira issue tracker. Going forward, after releasing the PLAZA Cloud solution, a public issue tracker will also be provided.

4. Legal framework, funding, and governance

a. Legal framework: What are the resource’s license/terms of use? Can the license facilitate Open Science? Please include the url for the license the resource uses.

The data license for the PLAZA resource is the CC BY-NC-SA 4.0 license:

b. Privacy/Ethics policy: If applicable, is there a publicly available privacy policy in which use and security around personal data are described (e.g. the EU General Data Protection Regulation (GDPR), ELIXIR Ethics Policy, other relevant ELIXIR Policies)? Please include the url of the privacy/ethics policy, if applicable.

c. Funding & sustainability plan: List of funding sources supporting the resource, and sustainability plan.

  1. Funded in the framework of ELIXIR Belgium: 2019-2022 (1FTE).
  2. Industrial income (circa 0.5FTE per year)
  3. Diverse research projects include development of features in PLAZA.

d. Governance: Describe the Resource’s QA/QC plan that guarantees similar quality governance to that of ELIXIR. Please link SAB members, if applicable.

No such QA/QC plan is currently in place. This can be setup in the future.