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Manoj Pandian Sakthivel edited this page Apr 7, 2020 · 19 revisions

Open questions:

  • How do we retrieve homeologues?
  • How do we retrieve orthologues?
  • How do we retrieve alternative_alleles?
  • How are we going to handle all the external references that doesn't exist anymore?
  • How are we going to build the working URI for external references? ( The current site does this but most of the links don't work anymore)

Previous discussions:

  • How do we specifically retrieve all the external references from the metadata?

    • External references will either part of the metadata or be a thing on its own. We are still not very sure whether it will have to be handled separately for it to have it's own type.

  • How do we get the display name for biotypes?

    • One solution that was discussed is to make the GraphQL server retrieve the displayName by sending a request to Sequence Ontology lookup while preparing the response for the client

  • What are the other attributes? Do we need to display them all?

    • The will be a lot of junk in the other attributes section if we need to display them all. Instead, we need to make a selected list of all the high-level attributes and display those instead.

Current GraphQL Schema:

type Assembly { id: String! species: Species! } type Species { scientific_name: String! name: String! [MISSING] strains: [Strain!] } type Allele = { allele_name: String!, stable_id: String! } type Homeologue = { type: string, stable_id: string } type Strain = { strain_name: string, stable_id: string } type Attribute = { description: String! displayName: String! code: String! } type Source { name: String! uri: String // not all sources will have urls } type Metadata { key: String! // e.g. "external_reference" value: String! // e.g. "ENSG00000139618" description: String source_uri: String // e.g. url to entity in Expression Atlas source: Source! // e.g. Expresion Atlas object } // reference to given entity in other source // or use Metadata ? type ExternalReference { source: Source! value: String! source_uri: String } type Attribute { code: String! // protein coding label: String! // Protein Coding } type Slice { region: Region! } type Region { name: String! strand: Strand assembly: String! } type SequenceOntologyTerm: { id: String! code: String! display_name: String! } type Transcript { stable_id: String! metadata: [Metadata!] } type Publication { title: String authors: String[] source: Source source_url: String }; type OtherAssembly { assembly: Assembly stable_id: String! } type Gene { symbol: String! so_term: SequenceOntologyTerm name: String! alternative_symbols: [String!] function: { value: String!, source_url: String!, source: Source } external_references: [ExternalReference] publications: [Publications] other_assemblies: [OtherAssembly] homeologues: [Homeologue] relationships: { alternative_alleles: [], homeologues: [] } transcripts: [Transcript] }

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