Table 4 General purpose biomedical semantic annotation tools (Part II)

Modularity/configuration options

Semantic types (i.e. types of entities to annotate)

pre-built pipelines for several biomedical types (see Specific features)

Text processing pipeline;

Term matching options and strategies

Modular text processing pipeline

Disambiguation of terms

No information available

Not supported

Not supported

Instead of through WSD, it uses a set of heuristics rules to identify and remove annotations of lower importance

Vocabulary (terminology)

Custom built vocabulary by using concepts from multiple sources, such as UMLS, NCBI BioSystems, ChEBI, and the Gene Ontology.

The use of the vocabulary depends on the type of entity a pipeline is specialized for (e.g. NCBI KB for species, or Gene Ontology for genes)

General purpose dictionary lookup tool, not tied to any vocabulary

Not tied to any particular vocabulary

Speed^a

Suitable for real-time processing

Suitable for real-time processing

Suitable for real-time processing

Suitable for real-time processing

Implementation form

Software (Python) library;

RESTful Web service;

Javascript widget

SOAP Web service

Software (Java) library; part of the UIMA NLP framework [28]

RESTful Web service

Availability

open source;

available under Attribution-NonCommercial 3.0 Unported license

closed source, but

freely available

open source;

available under Apache License, v.2.0

open source;

available under Attribution-NonCommercial 3.0 Unported license

Specific features

Primarily aimed for annotation of biomedical research papers; focused on annotation of several (11) types of biomedical entities, including species, microRNAs, enzymes, chemicals, drugs, diseases, etc.

Offers several pre-built pipelines for specific entity types; e.g. whatizitGO identifies proteins based on the Gene Ontology (GO), while whatizitChemical annotates chemical entities based on ChEBI

Not specifically developed for the biomedical domain, but is a general purpose dictionary lookup tool

Includes modules for both ML and dictionary-based annotation; can automatically combine annotations generated by different modules

URL

http://bioinformatics.ua.pt/becas/

http://www.ebi.ac.uk/webservices/whatizit

https://uima.apache.org/sandbox.html#concept.mapper.annotator

https://github.com/BMDSoftware/neji