Chemical annotation data

Data sources

We currently obtain chemical annotation data from several data resources and keep them up-to-date, so that you don’t have to do it:

* key name: this is the key for the specific annotation data in a chemical object.

The most updated information can be accessed here.


Each data source may have its own usage restrictions. Please refer to the data source pages above for their specific restrictions.

Chemical object

Chemical annotation data are both stored and returned as a chemical object, which is essentially a collection of fields (attributes) and their values:

  "unii": {
    "_license": "",
    "ingredient_type": "INGREDIENT SUBSTANCE",
    "inn_id": "8031",
    "molecular_formula": "C29H31N7O",
    "ncit": "C62035",
    "preferred_term": "IMATINIB",
    "pubchem": "5291",
    "registry_number": "152459-95-5",
    "rxcui": "282388",
    "smiles": "CN1CCN(CC2=CC=C(C=C2)C(=O)NC3=CC(NC4=NC=CC(=N4)C5=CC=CN=C5)=C(C)C=C3)CC1",
    "unii": "BKJ8M8G5HI"

The example above omits many of the available fields. For a full example, check out this example chemical, or try the interactive API page.

_id field

Each individual chemical object contains an “_id” field as the primary key. Where possible, chemical objects use InChIKey (a 27 character hash of the International Chemical Identifier) as their “_id”. If an InChIKey isn’t available, any one of the following datasource IDs may be used:

_score field

You will often see a “_score” field in the returned chemical object, which is the internal score representing how well the query matches the returned chemical object. It probably does not mean much in chemical annotation service when only one chemical object is returned. In chemical query service, by default, the returned chemical hits are sorted by the scores in descending order.

Available fields

The table below lists all of the possible fields that could be in a chemical object, as well as all of their parents (for nested fields). If the field is indexed, it may also be directly queried.

Field Indexed Type Notes