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Anni specifications

Information


Unique identifier OMICS_07921
Name Anni
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Version 2.1
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Publications for Anni

Anni citations

 (27)
library_books

Internal driving factors leading to extrahepatic manifestation of the hepatitis C virus infection

2017
PMCID: 5716440
PMID: 29039494
DOI: 10.3892/ijmm.2017.3175

[…] The association between a gene and the HCV infection was analyzed using the online tool Anni 2.1 (http://biosemantics.org/index.php/software/anni). The calculation was performed as previously described (). The entry of each pathway, such as map04010 for mitogen-activated protein kinases […]

library_books

A mononucleotide repeat in PRRT2 is an important, frequent target of mismatch repair deficiency in cancer

2016
Oncotarget
PMCID: 5351611
PMID: 27907910
DOI: 10.18632/oncotarget.13464

[…] R sequences in PC346C, which were 6 nucleotides or longer. We excluded LOC annotated gene symbols and genes already known to be associated with MMR deficiency or MSI by using the text mining software Anni 2.0. (http://biosemantics.org/index.php/software/anni). We identified over 35 mutated genes in PC346C, which were already known as targets of MSI or are associated with MMR deficiency including T […]

library_books

Building a glaucoma interaction network using a text mining approach

2016
BioData Min
PMCID: 4857381
PMID: 27152122
DOI: 10.1186/s13040-016-0096-2

[…] he next generation of text mining approaches have to deal with the construction of complete text mining systems to aid the inference of interactions or associations between bio entities. OntoGene [], Anni [], RLISM [], and CRAB [] are examples of such next generation systems. In terms of usage, OntoGene is considered the most integrative because it allows the detection of entities and relationship […]

library_books

Tissue Restricted Splice Junctions Originate Not Only from Tissue Specific Gene Loci, but Gene Loci with a Broad Pattern of Expression

2015
PLoS One
PMCID: 4695084
PMID: 26713731
DOI: 10.1371/journal.pone.0144302

[…] To investigate whether tissue-specific splice junctions were from genes with known tissue associations, text mining was performed with the tool Anni 2.1 []. Anni can take two sets of concepts, such as a user supplied list of genes and either GO biological processes or tissue (both supplied as predefined concept sets in Anni), and can derive a […]

library_books

Transcriptomic Characterization of C57BL/6 Mouse Embryonic Stem Cell Differentiation and Its Modulation by Developmental Toxicants

2014
PLoS One
PMCID: 4172731
PMID: 25247782
DOI: 10.1371/journal.pone.0108510

[…] ld >10 for KEGG pathways. The statistically enriched GO terms were grouped and counted after classification according to GO Slim using the freely available web tool CateGOrizer . The text-mining tool Anni was also used to explore matching concept profiles of gene clusters with concept profiles of biological processes in the GO database. The program calculates the overall matching score, the cohes […]

library_books

Structuring research methods and data with the research object model: genomics workflows as a case study

2014
J Biomed Semantics
PMCID: 4177597
PMID: 25276335
DOI: 10.1186/2041-1480-5-41

[…] y and gene associations that are available via the KEGG REST Services []. The second workflow mines the text-mining based database of associations between GO biological processes and genes behind the Anni 2.1 tool [] that are available via the concept profile mining Web services []. We also created a workflow to list all possible concept sets in the concept profile database, to encourage reuse of […]

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Anni institution(s)
Department of Medical Informatics, Erasmus MC University Medical Center, Dr. Molewaterplein, Rotterdam, The Netherlands; Department of Pathology, Erasmus MC University Medical Center, Dr. Molewaterplein, Rotterdam, The Netherlands; Department of Urology, Erasmus MC University Medical Center, Dr. Molewaterplein, Rotterdam, The Netherlands
Anni funding source(s)
Supported by an ErasmusMC Breedtestrategie grant, INFOBIOMED, 6th R&D Framework, EC (IST 2002 507585), and by the Biorange project sp 4.1.1 of the Netherlands Bioinformatics Centre.

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