API to return gene ids in genome region

[KeywanHP]

Currently we have a REST endpoint that returns the number of genes within a region, like this: https://knetminer.com/araknet/countLoci?keyword=4-1000000-2000000

New graphql endpoints are needed to return the number of genes and list of genes in a genome region as defined via TAXID, Chromosome, BEGIN, END. All gene nodes in the graph will have following properties which can be filtered on.

http://knetminer-wheat.cyverseuk.org:7474/browser/

{
  "iri": "http://knetminer.org/data/rdf/resources/gene_at2g45720_locus_2043709",
  "identifier": "AT2G45720;locus:2043709",
  "TAXID": "3702",
  "Chromosome": "2",
  "END": "18836374",
  "comment": "PROTEIN_CODING",
  "ondexId": "493896",
  "BEGIN": "18833086",
  "altName": "F4I18.30",
  "prefName": "AT2G45720"
}

Following tests should be written: Input:

• TAXID: 3702
• Chromosome: 4
• BEGIN: 1000000
• END: 2000000

Output:

• Return count of 218 and list of all gene node ids

[ronupanchal]

Noted with thanks.

On Fri, 9 Jul 2021, 7:08 pm Keywan Hassani-Pak, @.***> wrote:

Here are the properties of a gene node:

{ "iri": "http://knetminer.org/data/rdf/resources/gene_at2g45720_locus_2043709", "identifier": "AT2G45720;locus:2043709", "TAXID": "3702", "Chromosome": "2", "END": "18836374", "comment": "PROTEIN_CODING", "ondexId": "493896", "BEGIN": "18833086", "altName": "F4I18.30", "prefName": "AT2G45720" }

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[ronupanchal]

I have done

[KeywanHP]

Here is another test example to use with the wheat Neo4j db: http://knetminer-wheat.cyverseuk.org:7474/browser/

Input

• TAXID 4565
• Chromosome: 1A
• BEGIN: 10000000
• END: 20000000

Output Return about 168 gene ids.