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README.md
participants.md

README.md

ProtVista (protein annotation viewer) extension using Bioschemas data

### Representative: Gustavo Salazar

Community


ELIXIR Interoperability platform, Bioschemas

Leads


Gustavo Salazar
Leyla Garcia
Rafael Jimenez
Xavier Watkins

Background information


Back in the days, the Distributed Annotation Protocol (DAS) provided protein annotation from multiple resources in a uniform format. Such data was fed to DASTY, a protein annotation viewer that could be embedded on any website. DASTY was used in UniProt to display annotations coming from other data resources. Bioschemas can take place of DAS as it provides a specification for marking up protein annotations on web pages. As for the visualization, ProtVista provides a highly modular, reusable and extensible set of web components to visualize protein annotation. Sources not fully compliant with the data model are supported via adapters. We propose to combine Bioschemas data with ProtVista in order to support protein annotation visualization.

Expected outcomes


  • ProtVista adapter to use Bioschemas data
  • ProtVista extension to display Bioschemas protein annotations from multiple sources
  • Integration with BioJS (if possible)

Expected audience


People interested in

  • Bioschemas
  • Visualization, BioJS
  • Web components
  • Protein annotations
    Expected hacking days: 4 days

Related works and references


  1. Integrating biological data --the Distributed Annotation System
  2. Dasty3, a web framework for DAS
  3. Bioschemas
  4. ProtVista: visualization of protein sequence annotations

GitHub or any other public repositories of your FOSS products (if any)


ProtVista web components

Roadmap


  1. Review and understand the Bioschemas BioChemEntity type, identify whether any change is required
  2. Review and adjust the Bioschemas Protein profile as needed
  3. Review and adjust the Bioschemas ProteinAnnotation profile as needed
  4. Get some protein related sources marked up with the Bioschemas Protein profile, e.g., InterPro, UniProt, CATH, in order to get information about the sequence and so (at least the sequence is needed by ProtVista)
  5. Get some protein related sources marked up with the Bioschemas ProteinAnnotation profile, e.g., InterPro, UniProt, CATH
  6. Implement a way to retrieve protein annotations from marked up resources, maybe crawler, indexer or so
  7. Implement a ProtVista adapter to transform Bioschemas ProteinAnnotation data. See ProtVista web components repo, particularly those packages ending on -adapter, e.g., protvista-structure-adapter
  8. Implement a proof-of-concept using at least one Bioschemas ProteinAnnotation source and the adapter to render a protvista-track with real or mocked up data

Notes:

  • Tasks 4 and 5 require 1, 2 and 3
  • Task 6 requires 4 or 5
  • Task 7 can be done with mocked data just to see how the adapter works
  • Task 8 requires 7
  • Ideally 1, 2 and 3 should be achieved during the BioHackathon, great if we get at least one marked up resource for 4 and 5, amazing if some advances on 6 are done, and wonderful if we get to 7 and 8!

Skills


  • Bioschemas
  • JavaScript, web components, lerna
  • ProtVista
  • For marking up resources, crawling and indexing, skills vary but all require software development knowledge

How to participate


  • Go to the participants list
  • Add your name with GitHub user, skills, and tasks you want to participate at
  • Have a quick chat with Gustavo to coordinate activities

Thanks for collaborating!