More research links on mutation extraction

(Curated state of the art until 2016 Q1)

Methods:

tmVar http://www.ncbi.nlm.nih.gov/pubmed/23564842 MutationFinder http://bioinformatics.oxfordjournals.org/content/23/14/1862.abstract?keytype=ref&ijkey=sUzKV8EBYZu4j1w

Corpora: osiris corpus & method L. I. Furlong, H. Dach, M. Hofmann-Apitius, and F. Sanz. “OSIRISv1. 2: a named entity recognition system for sequence variants of genes in biomedical literature.” In: BMC bioinformatics 9.1 (2008 seth corpus & method P. Thomas, T. Rocktäschel, Y. Mayer, and U. Leser. SETH: SNP Extraction Tool for Human Variations. http://rockt.github.io/SETH/ . 2014. EMU Prostate Cancer set (PCa) SNP Corpus (Thomas et al) http://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/research-development/information-extraction-semantic-text-analysis/named-entity-recognition/snp-normalization-corpus.html

New: [MAP] MutationMapper 2013 - SNP only, normalization and grounding to protein sequence. They use MutationFinder for recognition, and pure keyword searching from UniProt provided names. No full text but did study a bit. No corpus http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3739722/ [MAP] MutD 2015 reuse MutationFinder and tmVar for SNPs then use other tools to link proteins-mutation-diseases. No full text. http://www.ncbi.nlm.nih.gov/pubmed/26047637 EMU SNPs and normalization to genes http://www.ncbi.nlm.nih.gov/pubmed/21138947/ Verspoor combination of methods http://www.ncbi.nlm.nih.gov/pubmed/25285203.2 Benchmarking infrastructure for mutation text mining http://www.ncbi.nlm.nih.gov/pubmed/24568600 PolySearch 2008 SNPs only links mutations to genes to diseases http://www.ncbi.nlm.nih.gov/pubmed/18487273 SETH 2013 all types of mutations no NL, just follow HGVS + MutationFinder http://rockt.github.io/SETH/ OSIRISv1.2 2008 only SNPs http://www.ncbi.nlm.nih.gov/pubmed/18251998 OpenMutationMiner http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3395893/

Support:

DISEASES http://www.sciencedirect.com/science/article/pii/S1046202314003831 http://www.ncbi.nlm.nih.gov/pubmed/23962656 OntoMate http://www.ncbi.nlm.nih.gov/pubmed/25619558 Nagel Corpus http://bionlp-corpora.sourceforge.net/proteinresidue/ MutationFinder Corpus http://bionlp-corpora.sourceforge.net/proteinresidue/ Tari L 2014 - not free and likely just combination of diff methods http://www.ncbi.nlm.nih.gov/pubmed/25946883 wKinMut they essentially reuse SNP2L which reuses MutationFinder http://www.ncbi.nlm.nih.gov/pubmed/24289158 Extraction of human kinase mutations from literature, databases and genotyping studies -- Reuse MutationFinder - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745582/ Valencia 2012 Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining. http://www.ncbi.nlm.nih.gov/pubmed/23055974 Valencia 2010 Analysis of biological processes and diseases using text mining approaches. http://www.ncbi.nlm.nih.gov/pubmed/19957157 SNP Corpus http://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/research-development/information-extraction-semantic-text-analysis/named-entity-recognition/snp-normalization-corpus.html Intrinsic evaluation of text mining tools may not predict performance on realistic tasks. http://www.ncbi.nlm.nih.gov/pubmed/18229722 Tools, resources and databases for SNPs and indels in sequences: a review. -- not free -- but not important http://www.ncbi.nlm.nih.gov/pubmed/24794070 MetaRanker 2.0: a web server for prioritization of genetic variation data. http://www.ncbi.nlm.nih.gov/pubmed/23703204 HIVmut.org http://www.ncbi.nlm.nih.gov/pubmed/25474213 http://www.ncbi.nlm.nih.gov/pubmed/20539892 http://www.ncbi.nlm.nih.gov/pubmed/?term=%22text+mining%22+sequence+variations http://www.ncbi.nlm.nih.gov/pubmed/?term=%22text+mining%22+sequence+mutations http://www.ncbi.nlm.nih.gov/pubmed/18172931 http://www.ncbi.nlm.nih.gov/pubmed/26813965 http://www.ncbi.nlm.nih.gov/pubmed/?term=%22text+mining%22+mutations http://www.ncbi.nlm.nih.gov/pubmed/26047637 http://www.ncbi.nlm.nih.gov/pubmed/20920264 http://www.ncbi.nlm.nih.gov/pubmed/19515247 http://www.ncbi.nlm.nih.gov/pubmed/18058827 http://www.ncbi.nlm.nih.gov/pubmed/25484337 http://www.ncbi.nlm.nih.gov/pubmed/?term=%2Btext+%2Bmining+%2Bmutations+%2Bmethod http://www.ncbi.nlm.nih.gov/pubmed/24260124

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[2007Sawyer] http://www.pnas.org/content/104/16/6504 http://www.hindawi.com/journals/bmri/2014/240403/