Name | Type | URL | Summary |
---|---|---|---|
MALLET | ML | [48] | Framework for feature extraction, logistic regression models and inference |
SVMPerf | ML | [83] | Support Vector Machine software for optimizing multivariate performance measures |
Weka | ML | [64] | Collection of machine learning algorithms for data mining, useful for feature selection |
LIBSVM | ML | [84] | Software for support vector classification |
Matlab | ML | [85] | Data analysis, and numeric computation software |
Liblinear | ML | [86] | Linear classifier software |
MEGAM | ML | [87] | Software for maximum entropy model implementation |
C&C CCG parser | NLP | [55] | Parser and taggers are written in C++ |
TreeTagger | NLP | [88] | Part-of-speech tagger (trained on PENN treebank) |
SNOWBALL | NLP | [89] | Stemming program |
NooJ | NLP | [90] | Corpus processing and dictionary matching |
Lucene | NLP | [53] | Full-featured text search engine library |
LingPipe | NLP | [91] | Tool kit for processing text using computational linguistics |
PSI-MI | Lexical | [46] | Molecular Interaction Ontology used by PPI databases |
UMLS | Lexical | [47] | Unified Medical Language System which contains a large vocabulary database about biomedical and health-related concepts |
MeSH | Lexical | [92] | Vocabulary thesaurus used for indexing PubMed |
ChEBI | Lexical | [93] | Chemical Entities of Biological Interest |
BioLexicon | Lexical | [52] | Terminological resources integrating data from various bioinformatics collections |
Stop words | Lexical | [44] | Collection of words that are filtered out prior to processing of natural language data |
NLProt | BioNLP | [94] | SVM-based tool for recognition of protein-names in text |
OSCAR3 | BioNLP | [95] | Tool for recognition of chemical name mentions in text |
ABNER | BioNLP | [60] | Bio-Named entity recognition (proteins, genes, DNA, etc.) |