PhenoMiner statistics

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Protocols

PhenoMiner specifications

Information


Unique identifier OMICS_07088
Name PhenoMiner
Restrictions to use None
Community driven Yes
Data access Browse
User data submission Allowed
Maintained No

Taxon


  • Rodents
    • Rattus norvegicus

Documentation


Maintainer


This tool is not available anymore.

Publications for PhenoMiner

PhenoMiner citations

 (6)
library_books

Identifying genotype phenotype relationships in biomedical text

2017
J Biomed Semantics
PMCID: 5719522
PMID: 29212530
DOI: 10.1186/s13326-017-0163-8

[…] ationships that include entities that are named implicitly will not be identified in the test set, reducing the precision and recall slightly. The phenotypes at the cellular level are labelled in the Phenominer corpus. Our work on genotype-phenotype relationships does not consider this type of phenotype because the linguistic context is different from relationships involving the non-cellular level […]

library_books

Novel bioinformatic developments for exome sequencing

2016
Hum Genet
PMCID: 4883269
PMID: 27075447
DOI: 10.1007/s00439-016-1658-6

[…] ge and facilitate the use of phenotype information. PhenoDB (Hamosh et al. ) and PhenoTips (Girdea et al. ) are platforms that allow clinicians to enter, store and analyze structured phenotypic data. Phenominer is a tool able to extract phenotype contexts from simple text to identify relationships between human diseases described in OMIM and literature (Collier et al. ). In the future even the act […]

library_books

The Disease Portals, disease–gene annotation and the RGD disease ontology at the Rat Genome Database

2016
PMCID: 4805243
PMID: 27009807
DOI: 10.1093/database/baw034

[…] st of disease-related genes. The rat, mouse and human JBrowse and GBrowse genome browsers can be utilized to view disease-related genes, QTLs and congenic strains in their larger genomic context. The PhenoMiner tool is employed to find quantitative phenotypes for a list of disease-related strains and the Variant Visualizer is used to locate possible disease-causing and strain-specific variants in […]

library_books

Disease, Models, Variants and Altered Pathways—Journeying RGD Through the Magnifying Glass

2015
Comput Struct Biotechnol J
PMCID: 4700298
PMID: 27602200
DOI: 10.1016/j.csbj.2015.11.006

[…] ontology (CMO), the measurement method ontology (MMO) or the experimental condition ontology (XCO). However, in these cases, it would be interesting to view the quantitative phenotype data, using the PhenoMiner. […]

call_split

PhenoMiner: from text to a database of phenotypes associated with OMIM diseases

2015
PMCID: 4622021
PMID: 26507285
DOI: 10.1093/database/bav104
call_split See protocol

[…] information from unstructured texts. Recent use cases include the ShARE/CLEF () EPR curation and BioCreative gene curation challenges () which provide controlled test suites for system developers.The PhenoMiner (PM) system pipeline is outlined in . The principal modules are now briefly discussed. Data sampling: As described in Data Sampling section;Data cleansing: split and tokenize the sentences […]

library_books

The digital revolution in phenotyping

2015
Brief Bioinform
PMCID: 5036847
PMID: 26420780
DOI: 10.1093/bib/bbv083

[…] literature as a source, several groups have been active in developing approaches explicitly for phenotypes. These include the Bio-LarK system, which has been applied to skeletal dysplasia [] and the PhenoMiner system, which has been applied to the cardiovascular and autoimmune systems []. Work by Khordad et al. [] has looked at a more mixed domain using the Unified Medical Language System (UMLS) […]

Citations

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PhenoMiner institution(s)
Human and Molecular Genetics Center, Medical College of Wisconsin, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
PhenoMiner funding source(s)
Supported by the National Heart, Lung and Blood Institute on behalf of the National Institutes of Health (HL64541).

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