Table 2.
IE frameworks, tools and toolkits used in the included publications.
| Name | Description | License | Website | No. of Papers |
|---|---|---|---|---|
| Frameworks | ||||
| UIMA | Software framework for the analysis of unstructured contents like: text, video and audio data | Apache | https://uima.apache.org/ | 31 |
| GATE | Java-based open-source software for various NLP tasks such as information extraction and semantic annotation | GNU Lesser General Public License | https://gate.ac.uk/ | 5 |
| Protégé | Open-source ontology editor and framework for building intelligent systems | MIT License | http://protege.stanford.edu/ | 1 |
| Tools | ||||
| cTAKES | Open-source NLP system based on UIMA framework for extraction of information from electronic health records unstructured clinical text | Apache | http://ctakes.apache.org/ | 26 |
| MetaMap | National Institutes of Health (NIH)-developed NLP tool that maps biomedical text to UMLS concepts | UMLS Metathesaurus | https://metamap.nlm.nih.gov/ | 12 |
| MedLEE | NLP system that extracts, structures, and encodes clinical information from narrative clinical notes | NLP International for commercial use | http://zellig.cpmc.columbia.edu/medlee/ | 10 |
| KnowledgeMap Concept Indexer (KMCI) | NLP system that identifies biomedical concepts and maps them to UMLS concepts | Vanderbilt License | https://medschool.vanderbilt.edu/cpm/center-precision-medicine-blog/kmci-knowledgemap-concept-indexer | 4 |
| HITEx | Open-source NLP tool built on top of the GATE framework for various tasks such as principal diagnoses extraction and smoking status extraction | i2b2 Software License Agreement | https://www.i2b2.org/software/projects/hitex/hitex_manual.html | 4 |
| MedEx | NLP tool used to recognize drug names, dose, route, and frequency from free-text clinical records | Apache | https://medschool.vanderbilt.edu/cpm/center-precision-medicine-blog/medex-tool-finding-medication-information | 4 |
| MedTagger | Open-source NLP pipeline based on UIMA framework for indexing based on dictionaries, information extraction, and machine learning–based named entity recognition from clinical text | Apache | http://ohnlp.org/index.php/MedTagger | 3 |
| ARC | Automated retrieval console (ARC) is an open- source NLP pipeline that converts unstructured text to structured data such as Systematized Nomenclature of Medicine – Clinical Terms (SNOMED CT) or UMLS codes | Apache | http://blulab.chpc.utah.edu/content/arc-automated-retrieval-console | 2 |
| Medtex | Clinical NLP software that extracts meaningful information from narrative text to facilitate clinical staff in decision-making process | No license information available | https://aehrc.com/research/projects/medical-free-text-retrieval-and-analytics/#medtex | 2 |
| CLAMP | NLP software system based on UIMA framework for clinical language annotation, modeling, processing and machine learning | Software Research License | https://sbmi.uth.edu/ccb/resources/clamp.htm | 1 |
| MedXN | A tool to extract comprehensive medication information from clinical narratives and normalize it to RxNorm | Apache | http://ohnlp.org/index.php/MedXN | 1 |
| MedTime | A tool to extract temporal information from clinical narratives and normalize it to the TIMEX3 standard | GNU General Public License | http://ohnlp.org/index.php/MedTime | 1 |
| PredMED | NLP application developed by IBM to extract full prescriptions from narrative clinical notes | Commercial | 1 | |
| SAS Text Miner | A plug-in for SAS Enterprise Miner environment provides tools that enable you to extract information from a collection of text documents and uncover the themes and concepts that are concealed in them. | Commercial | 1 | |
| Toolkits | ||||
| WEKA | Open source toolkit that contains various machine learning algorithms for data-mining tasks | GNU General Public License | http://www.cs.waikato.ac.nz/ml/weka/ | 5 |
| MALLET | Java-based package for various NLP tasks such as document classification, information extraction, and topic modeling | Common Public License | http://mallet.cs.umass.edu/ | 4 |
| OpenNLP | Open-source machine learning toolkit for processing of natural language text | Apache | https://opennlp.apache.org/ | 1 |
| NLTK | Python-based NLP toolkit for natural language text | Apache | http://www.nltk.org/ | 1 |
| SPLAT | Statistical parsing and linguistic analysis toolkit (SPLAT) is a linguistic analysis toolkit for natural language developed by Microsoft research | Commercial | https://www.microsoft.com/en-us/research/project/msr-splat/ | 1 |