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Support GFF3 format #1007

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heuermh opened this Issue Apr 20, 2016 · 4 comments

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heuermh commented Apr 20, 2016

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@tdanford tdanford self-assigned this Apr 20, 2016

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heuermh Apr 20, 2016

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For bdg-formats changes I was thinking

record ExternalIdentifier // could replace Dbxref?
{
  string db; // or database, or authority, or namespace
  string id; // or identifier, or accession
  string version;
}
record OntologyTerm
{
  string id; // or identifier
  union { null, string } term = null; // or concept
  union { null, string } sourceName = null; // or authority
  union { null, string } sourceVersion = null;
}
record Feature
{
- array<string> parentIds = [];
+ union { null, string } parentId = null; // not sure about this

+ array<string> childIds = [];

- union { null, string } featureType = null;
+ union { null, OntologyTerm } featureType = null;
}

And then some way of adding OntologyTerm and ExternalIdentifier as value types in attributes, either as separate maps

record Feature
{
  map<string> attributes = {};

+ map<OntologyTerm> ontologyTerms = {};  // Map<String, OntologyTerm> in avro, right?

- array<Dbxref> dbxrefs = [];
+ map<ExternalIdentifiers> externalIdentifiers = {};
}

or something like the Attributes record in GA4GH

record Attributes
{
  map<array<union {string, ExternalIdentifier, OntologyTerm}>> values = {};
}
record Feature
{
- map<string> attributes = {};
+ union { null, Attributes } attributes = null;
}
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heuermh commented Apr 20, 2016

For bdg-formats changes I was thinking

record ExternalIdentifier // could replace Dbxref?
{
  string db; // or database, or authority, or namespace
  string id; // or identifier, or accession
  string version;
}
record OntologyTerm
{
  string id; // or identifier
  union { null, string } term = null; // or concept
  union { null, string } sourceName = null; // or authority
  union { null, string } sourceVersion = null;
}
record Feature
{
- array<string> parentIds = [];
+ union { null, string } parentId = null; // not sure about this

+ array<string> childIds = [];

- union { null, string } featureType = null;
+ union { null, OntologyTerm } featureType = null;
}

And then some way of adding OntologyTerm and ExternalIdentifier as value types in attributes, either as separate maps

record Feature
{
  map<string> attributes = {};

+ map<OntologyTerm> ontologyTerms = {};  // Map<String, OntologyTerm> in avro, right?

- array<Dbxref> dbxrefs = [];
+ map<ExternalIdentifiers> externalIdentifiers = {};
}

or something like the Attributes record in GA4GH

record Attributes
{
  map<array<union {string, ExternalIdentifier, OntologyTerm}>> values = {};
}
record Feature
{
- map<string> attributes = {};
+ union { null, Attributes } attributes = null;
}
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heuermh commented May 10, 2016

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heuermh May 18, 2016

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@tdanford could we have another round of discussion on this one?

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heuermh commented May 18, 2016

@tdanford could we have another round of discussion on this one?

@heuermh heuermh modified the milestone: 0.20.0 Jun 5, 2016

@heuermh heuermh added the enhancement label Jun 5, 2016

@heuermh heuermh referenced this issue Jun 7, 2016

Closed

Release ADAM version 0.20.0 #1048

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heuermh Jun 28, 2016

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Fixed by #998

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heuermh commented Jun 28, 2016

Fixed by #998

@heuermh heuermh closed this Jun 28, 2016

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