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README.md
amigo.js

README.md

Welcome...

...to the experimental AmiGO JSON API server.

Setup/run

At the top of the amigo repo, assuming you have a decently recent version of node:

Then point your browser to: http://localhost:6455

You can also use gulpfile.js to reuse your amigo.yaml like:

  • gulp run-amigo-api

Or to override the target GOlr instance URL:

There is also a developer restart server setup with:

  • gulp develop-amigo-api

API

The general JSON API return envelope looks like:

{
    "service": "<SERVICE_NAME>",
    "status": "success|failure",
    "date": "<DATE_STRING>",
    "time": "<PROCESSING_TIME>",
    "arguments": null,
    "comments": [],
    "data": null
}

/api/term/<TERM_ID>

Given a term ID, find all information.

Example

/api/entity/term/GO:0022008

TOO LARGE

/api/terms

Given a list of term IDs, find all information.

Example

/api/entity/terms?entity=GO:0022008&entity=GO:0008150

TOO LARGE

/api/entity/bioentity/<BIOENTITY_ID>

Given a bioentity ID, find all information.

Example

/api/entity/bioentity/SGD:S000001666

TOO LARGE

/api/search/

Given a search personality and some parameters, find items that match.

Example 1

/api/search/ontology?q=neuro

TOO LARGE

Example 2

/api/search/annotation?q=nucleus&fq=assigned_by:%22MGI%22

TOO LARGE

/api/autocomplete/

The same as /api/search/, except with a lighter payload (using manager.lite(true)).

Example

/api/autocomplete/ontology?q=neuro

TOO LARGE

/api/statistics/gene-to-term

Given some gene IDs, find the number of terms associated with them by group, single counting a gene product / term relationship (i.e. all annotations count for "1").

You can optionally a one or more "species" parameters to filter counts by (transitive) species.

Example 1 (truncated)

/api/statistics/gene-to-term?bioentity=UniProtKB:F1M4Q5&bioentity=UniProtKB:F1M4Q5&bioentity=UniProtKB:E1BYP4

{
    "service": "/api/statistics/gene-to-term",
    "status": "success",
    "arguments": {
        "bioentity": [
            "UniProtKB:F1M4Q5",
            "UniProtKB:E1BYP4"
        ],
        "species": []
    },
    "comments": [],
    "data": {
        "gene-to-term-summary-count": {
            "GO:0008150": 2,
            "GO:0009987": 2,
            "GO:0003674": 2,
            "GO:0006464": 1,
            "GO:0006470": 1,
            "GO:0006793": 1,
            "GO:0006796": 1,
        }
    },
    "time": 0,
    "date": "2016-02-25T14:02:50"
}

Example 2 (with impossible species filter)

/api/statistics/gene-to-term?bioentity=UniProtKB:F1M4Q5&bioentity=UniProtKB:F1M4Q5&bioentity=UniProtKB:E1BYP4&species=NCBITaxon:9606

{
    "service": "/api/statistics/gene-to-term",
    "status": "success",
    "arguments": {
        "bioentity": [
            "UniProtKB:F1M4Q5",
            "UniProtKB:E1BYP4"
        ],
        "species": [
            "NCBITaxon:9606"
        ]
    },
    "comments": [],
    "data": {
        "gene-to-term-summary-count": null
    },
    "time": 0,
    "date": "2016-02-25T14:02:24"
}

/api/statistics/term-to-gene

Given some term IDs, find the number of the number of gene products associated with each one.

You can optionally a one or more "species" parameters to filter counts by (transitive) species.

Example 1

/api/statistics/term-to-gene?term=GO:0022008&term=GO:0008150

{
    "service": "/api/statistics/gene-to-term",
    "status": "success",
    "arguments": {
        "term": [
            "GO:0022008",
            "GO:0008150"
        ],
        "species": []
    },
    "comments": [],
    "data": {
        "term-to-gene-summary-count": {
            "GO:0022008": 14541,
            "GO:0008150": 812745
        }
    },
    "time": 0,
    "date": "2016-02-25T14:02:52"
}

Example 2 (with species filter)

/api/statistics/term-to-gene?term=GO:0022008&term=GO:0008150&species=NCBITaxon:9606

{
    "service": "/api/statistics/gene-to-term",
    "status": "success",
    "arguments": {
        "term": [
            "GO:0022008",
            "GO:0008150"
        ],
        "species": [
            "NCBITaxon:9606"
        ]
    },
    "comments": [],
    "data": {
        "term-to-gene-summary-count": {
            "GO:0022008": 1269,
            "GO:0008150": 34063
        }
    },
    "time": 0,
    "date": "2016-02-25T14:02:10"
}

/api/overview

Get an overview of the total database counts.

You can optionally a one or more "species" parameters to filter gene production and annotation counts by (transitive) species.

Example 1

/api/statistics/overview

{
    "service": "/api/statistics/overview",
    "status": "success",
    "arguments": {
        "species": []
    },
    "comments": [],
    "data": {
        "term-count": 171943,
        "gene-product-count": 952303,
        "annotation-count": 6233301
    },
    "time": 0,
    "date": "2016-02-25T14:02:26"
}

Example 2 (with species filter)

/api/statistics/overview?species=NCBITaxon:9606

{
    "service": "/api/statistics/overview",
    "status": "success",
    "arguments": {
        "species": [
            "NCBITaxon:9606"
        ]
    },
    "comments": [],
    "data": {
        "term-count": 171943,
        "gene-product-count": 48753,
        "annotation-count": 503780
    },
    "time": 0,
    "date": "2016-02-25T14:02:43"
}

/api/disambiguation/bioentity

Try and resolve the identifiers of one or more string entities in a "bioentity" document.

In addition to one or more "entity" parameters, you need to have a single "species" parameter.

Example 1

Failure to have any entities to disambiguate.

/api/disambiguation/bioentity?species=NCBITaxon:3037

{
  "date": "2016-11-14T19:11:28",
  "time": 0,
  "data": null,
  "comments": [
    "Death by lack of entities."
  ],
  "arguments": {
    "species": [
      "NCBITaxon:3037"
    ],
    "entity": []
  },
  "status": "failure",
  "service": "/api/disambiguation/bioentity"
}

Example 2

Empty return on an unknown species.

/api/disambiguation/bioentity?species=NCBITaxon:99999&entity=pacA&entity=UniProtKB:Q76L33

{
  "date": "2016-11-15T13:11:18",
  "time": 0,
  "data": {
    "ugly": [],
    "bad": [
      {
        "results": [],
        "input": "pacA"
      },
      {
        "results": [],
        "input": "UniProtKB:Q76L33"
      }
    ],
    "good": []
  },
  "comments": [],
  "arguments": {
    "species": [
      "NCBITaxon:99999"
    ],
    "entity": [
      "pacA",
      "UniProtKB:Q76L33"
    ]
  },
  "status": "success",
  "service": "/api/disambiguation/bioentity"
}

Example 3

Resolve a synbol and an id for "Euglena longa".

/api/disambiguation/bioentity?species=NCBITaxon:3037&entity=pacA&entity=UniProtKB:Q76L33

{
  "date": "2016-11-15T13:11:07",
  "time": 0,
  "data": {
    "ugly": [],
    "bad": [],
    "good": [
      {
        "results": [
          {
            "matched": "bioentity_label",
            "id": "UniProtKB:Q76L34"
          }
        ],
        "input": "pacA"
      },
      {
        "results": [
          {
            "matched": "bioentity",
            "id": "UniProtKB:Q76L33"
          }
        ],
        "input": "UniProtKB:Q76L33"
      }
    ]
  },
  "comments": [],
  "arguments": {
    "species": [
      "NCBITaxon:3037"
    ],
    "entity": [
      "pacA",
      "UniProtKB:Q76L33"
    ]
  },
  "status": "success",
  "service": "/api/disambiguation/bioentity"
}