Table 7

Overview of tools and resources. Collection of external tools and resources used for the PPI tasks by participating teams.

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.)

Krallinger et al. BMC Bioinformatics 2011 12(Suppl 8):S3   doi:10.1186/1471-2105-12-S8-S3