orthology-api

API service for the orthology database

Usage of HTTP Verbs

The following table describes how the Orthology API interprets the HTTP verbs.

.HTTP Verbs

HTTP Verb	Usage
GET	GET is used to retrieve information without changing the state of the system.

Other verbs, such as DELETE, POST, UPDATE are not supported by Ortgology at present.

Pagination and Sorting

Most of the endpoints returning collections are paginated and can be sorted. If no parameters are specified, then the default ones are applied.

Pagination

The parameters to specify the pagination are:

Parameter	Description
page	Number of the page to retrieve. It starts with 0 (which is the default value).
size	Number of elements to retrieve.

ONE TO ONE ORTHOLOGS

This section describes the REST endpoints for one oto one in the system.

Orthology api provides GET endpoints that provides the one to one orthologs data for the essential genes and the reference database services

Fields

These are the fields you are going to see in the body of a request in a GET or in the payload for POST or PUT operations.

Path	Type	Description
humanGeneSymbol	String	Human Gene Symbol
hgncAccId	String	Human Gene Accession Id
humanSupportCountThreshold	Number	Human Support Count Threshold
humanCategoryForThreshold	String	Human Category For Threshold
humanOrthologsAboveThreshold	Number	Human Orthologs Above Threshold
category	String	Category
supportCount	Number	Support Count
isMaxHumanToMouse	String	Is Max Human To Mouse
isMaxMouseToHuman	String	Is Max Mouse To Human
mouseOrthologsAboveThreshold	Number	Mouse Orthologs Above Threshold
mouseCategoryForThreshold	String	Mouse Category For Threshold
mouseSupportCountThreshold	Number	Mouse Support Count Threshold
mgiGeneAccId	String	Mouse Gene Accession Id
mouseGeneSymbol	String	Mouse Gene Symbol

GET By Mouse Gene Symbol

Get All the one-to-one orthologs mapping by mouse gene symbol or symbol list. The mouse gene symbol list should be entered with , separated in the endpoint. Note:Parameter size can not be bigger than 600.

Example Request

 '/api/ortholog/one_to_one/find_by_mouse_genes?genes=A1cf' -i -X GET

Example Response

HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 405
 [
   {
      "humanGeneSymbol":"A1CF",
      "hgncAccId":"HGNC:24086",
      "humanSupportCountThreshold":5,
      "humanCategoryForThreshold":"one-to-one",
      "humanOrthologsAboveThreshold":1,
      "category":"GOOD",
      "supportCount":11,
      "isMaxHumanToMouse":"max",
      "isMaxMouseToHuman":"max",
      "mouseOrthologsAboveThreshold":1,
      "mouseCategoryForThreshold":"one-to-one",
      "mouseSupportCountThreshold":5,
      "mgiGeneAccId":"MGI:1917115",
      "mouseGeneSymbol":"A1cf"
   }
]

GET By Human Gene Symbol

Get All the one-to-one orthologs mapping by human gene symbol or symbol list. The human gene symbol list should be entered with , separated in the endpoint. Note:Parameter size can not be bigger than 600.

Example Request

 '/api/ortholog/one_to_one/find_by_human_genes?genes=A1CF' -i -X GET

Example Response

 HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 405
 [
   {
      "humanGeneSymbol":"A1CF",
      "hgncAccId":"HGNC:24086",
      "humanSupportCountThreshold":5,
      "humanCategoryForThreshold":"one-to-one",
      "humanOrthologsAboveThreshold":1,
      "category":"GOOD",
      "supportCount":11,
      "isMaxHumanToMouse":"max",
      "isMaxMouseToHuman":"max",
      "mouseOrthologsAboveThreshold":1,
      "mouseCategoryForThreshold":"one-to-one",
      "mouseSupportCountThreshold":5,
      "mgiGeneAccId":"MGI:1917115",
      "mouseGeneSymbol":"A1cf"
   }
]

GET By Mgi Accession Id

Get All the one-to-one orthologs mapping by mgi accession id or mgi accession id list. The mgi accession id list should be entered with , separated in the endpoint. Note:Parameter size can not be bigger than 600.

Example Request

 '/api/ortholog/one_to_one/find_by_mgi_ids?mgiIds=MGI:1917115' -i -X GET

Example Response

 HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 405
 [
   {
      "humanGeneSymbol":"A1CF",
      "hgncAccId":"HGNC:24086",
      "humanSupportCountThreshold":5,
      "humanCategoryForThreshold":"one-to-one",
      "humanOrthologsAboveThreshold":1,
      "category":"GOOD",
      "supportCount":11,
      "isMaxHumanToMouse":"max",
      "isMaxMouseToHuman":"max",
      "mouseOrthologsAboveThreshold":1,
      "mouseCategoryForThreshold":"one-to-one",
      "mouseSupportCountThreshold":5,
      "mgiGeneAccId":"MGI:1917115",
      "mouseGeneSymbol":"A1cf"
   }
]

GET By Hgnc Accession Id

Get All the one-to-one orthologs mapping by hgnc accession id or hgnc accession id list. The hgnc accession id list should be entered with , separated in the endpoint. Note:Parameter size can not be bigger than 600.

Example Request

 '/api/ortholog/one_to_one/find_by_hgnc_ids?hgncIds=HGNC:24086' -i -X GET

Example Response

 HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 405
 [
   {
      "humanGeneSymbol":"A1CF",
      "hgncAccId":"HGNC:24086",
      "humanSupportCountThreshold":5,
      "humanCategoryForThreshold":"one-to-one",
      "humanOrthologsAboveThreshold":1,
      "category":"GOOD",
      "supportCount":11,
      "isMaxHumanToMouse":"max",
      "isMaxMouseToHuman":"max",
      "mouseOrthologsAboveThreshold":1,
      "mouseCategoryForThreshold":"one-to-one",
      "mouseSupportCountThreshold":5,
      "mgiGeneAccId":"MGI:1917115",
      "mouseGeneSymbol":"A1cf"
   }
]

GET All Orthologs

Get All the one-to-one ortholog

Example Request

 '/api/ortholog/find_all' -i -X GET

Example Response

 HTTP/1.1 200 OK
Content-Type: application/hal+json
Content-Length: 600
{
   "_embedded":{
      "orthologDtoList":[
         {
            "humanGeneSymbol":"A1CF",
            "hgncAccId":"HGNC:24086",
            "humanSupportCountThreshold":5,
            "humanCategoryForThreshold":"one-to-one",
            "humanOrthologsAboveThreshold":1,
            "category":"GOOD",
            "supportCount":11,
            "isMaxHumanToMouse":"max",
            "isMaxMouseToHuman":"max",
            "mouseOrthologsAboveThreshold":1,
            "mouseCategoryForThreshold":"one-to-one",
            "mouseSupportCountThreshold":5,
            "mgiGeneAccId":"MGI:1917115",
            "mouseGeneSymbol":"A1cf"
         }
      ]
   },
   "_links":{
      "self":{
         "href":"/api/ortholog/find_all?page=0&size=20"
      }
   },
   "page":{
      "size":20,
      "totalElements":1,
      "totalPages":1,
      "number":0
   }
}

ONE TO MANY ORTHOLOGS

GET By Mgi Accession Id

Get All the orthologs mapping by mgi accession id or mgi accession id list. The mgi accession id list should be entered with , separated in the endpoint. Note:Parameter size can not be bigger than 650.

Example Request

 '/api/ortholog/find_all_by_mgi_ids?mgiIds=MGI:1917115' -i -X GET

Example Response

 HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 405
 [
   {
      "humanGeneSymbol":"A1CF",
      "hgncAccId":"HGNC:24086",
      "humanSupportCountThreshold":5,
      "humanCategoryForThreshold":"one-to-one",
      "humanOrthologsAboveThreshold":1,
      "category":"GOOD",
      "supportCount":11,
      "isMaxHumanToMouse":"max",
      "isMaxMouseToHuman":"max",
      "mouseOrthologsAboveThreshold":1,
      "mouseCategoryForThreshold":"one-to-one",
      "mouseSupportCountThreshold":5,
      "mgiGeneAccId":"MGI:1917115",
      "mouseGeneSymbol":"A1cf"
   }
]

GET All Orthologs As Tsv File

Get All the orthologs as tsv file

Example Request

 '/api/ortholog/write_to_tsv_file' -i -X GET

GET All One To One Impc Orthologs As Tsv File

Get All the one-to-one Impc orthologs as tsv file

Example Request

 '/api/ortholog/one_to_one/Impc/write_to_tsv_file' -i -X GET

Lastest updates

• 2022-06-29: - one_to_one/impc/write_to_tsv_file endpoint added.
• 2022-06-15: - find_all_by_mgi_ids added.