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ProMiner specifications


Unique identifier OMICS_17136
Name ProMiner
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Juliane Fluck

Additional information

Add info: Access available upon request.

Publication for ProMiner

ProMiner citations


A method for named entity normalization in biomedical articles: application to diseases and plants

BMC Bioinformatics
PMCID: 5640957
PMID: 29029598
DOI: 10.1186/s12859-017-1857-8

[…] because biological entities (1) have many synonyms; (2) are often referred to using abbreviations; (3) are described by phrases; and (4) are mixtures of alphabets, figures, and punctuation marks. The ProMiner [] system follows a dictionary-based approach based on an approximate string-matching method; it was designed to detect and normalize gene and protein names. This system uses preprocessed dic […]


Neuroimaging Feature Terminology: A Controlled Terminology for the Annotation of Brain Imaging Features

PMCID: 5611802
PMID: 28731430
DOI: 10.3233/JAD-161148

[…] ing it over figure captions and full-text articles using SCAIView. For this, we converted the OWL file into a dictionary (.syn) file using a java program. The resulting dictionary was incorporated in ProMiner, which is a rule-based entity recognition system []. The hierarchical structure of the OWL file was converted into an XML tree so that NIFT can be navigated within the SCAIView environment an […]


Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL)

PMCID: 4995071
PMID: 27554092
DOI: 10.1093/database/baw113
call_split See protocol

[…] lable at is an information retrieval system that incorporates PubMed documents and annotations, created for various entity classes (e.g. HGNC, MGI and ChEBI) by the NER tool ProMiner, within a Lucene-based search index. The API method searches the sentences that contain the two entities and a trigger word matching the relationship type. The resulting sentences are sorted […]


PIPE: a protein–protein interaction passage extraction module for BioCreative challenge

PMCID: 4983456
PMID: 27524807
DOI: 10.1093/database/baw101

[…] were proteins. Unlike the above corpora, HPRD50 was constructed by taking 50 random abstracts referenced by the Human Protein Reference Database [HPRD ()]. Human proteins and genes were identified by ProMiner () software, while direct physical interactions, regulatory relations as well as modifications were annotated by experts. The corpus was developed as a test set for the RelEx () system, conta […]


Protein protein interaction extraction with feature selection by evaluating contribution levels of groups consisting of related features

BMC Bioinformatics
PMCID: 4965725
PMID: 27454611
DOI: 10.1186/s12859-016-1100-z

[…] nd proteins, 30 other abstracts without PPIs were added to AIMed as negative instances. HPRD50 is comprised of 50 abstracts, in which the human gene and protein names were automatically identified by ProMiner software. IEPA was created from 303 PubMed abstracts, each of which contains a specific pair of co-occurring chemicals. The LLL corpus contains 77 sentences and was the shared dataset for the […]


NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease

J Biomed Semantics
PMCID: 4939021
PMID: 27392431
DOI: 10.1186/s13326-016-0079-8

[…] e expression, we focus our current research on MTIs and PPIs.In order to harvest AD-specific knowledge from the literature, we used our in-house state-of-the-art named entity recognition (NER) system ProMiner [] and the semantic search engine SCAIView []. Identification of genes/proteins and disease mentions was accomplished using dictionaries. The disease dictionary was built using MeSH [], MedDR […]


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ProMiner institution(s)
Fraunhofer Institute SCAI, Schloss Birlinghoven, Sankt Augustin, Germany; Institute for Informatics, Ludwig-Maximilians-Universität München, München, Germany
ProMiner funding source(s)
Supported by Aventis Pharma, Frankfurt (project BEX) and the German ministry for research and education (project BOA).

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