Chemical Named Entity Recognizer

This services annotates chemical named entities using the open source OSCAR4 tagger.

More details on OSCAR4, including a number of example texts, can be found in this publication. One simple example, from that paper would be "The quick brown ethyl acetate jumps over the lazy bromine" which results in two annotations over ethyl acetate and bromine.

THe tagger produces annotations of a single type, namely ChemicalNE. These annotations have the following features:

type: the type of NE. Usually 'compound'
Std_InChI: The standard International Chemical Identifier for the recognised NE.
Std_InChiKey: A hashed version of the Std_InChi key useful for web searches etc.
SMILES: The named entity described using the simplified molecular-input line-entry system (SMILES)

1,200 free requests / day

Larger batches £0.80 / CPU hour

Use this pipeline

Single documents

You can process up to 1,200 documents per day free of charge using the REST API, at an average rate of 2 documents/sec. Higher quotas are available for research users by arrangement, contact us for details.

The API endpoint for this pipeline is:

https://cloud-api.gate.ac.uk/process/oscar4

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Batches of documents

You can process any amount of data with this pipeline on a pay-as-you-go basis, for £0.80 per hour. This can be data you upload yourself, data you collected from Twitter, or the results of a previous job.

Reserve a job