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Table 3 Comparison of features between LAITOR, STRING and iHOP.

From: LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships

Features LAITOR STRING iHOP
Software type Command-line script Website application Website application
Information sources Any type of text loaded by the user (e.g. PubMed, OMIM, Wikipedia) PubMed, SGD, OMIM, The Interactive Fly. PubMed
Text limit Any type of tagged text Only abstracts Only abstracts
Protein name tagging Depends of external software (NLPROT), confers against loaded dictionary YES, filtered by selected organism YES, filtered by selected organism
List of used synonyms Flexible user-based dictionary input Variety of pre-compiled dictionaries Entrez Gene, FlyBase, UniProt and HUGO Nomenclature Committee
Explores biological concepts YES, finds user loaded concepts linked to a co-occurring pair at sentence level. NOT YES, searches species names, MeSH and compound terms
Extracts co-occurrences among proteins YES, considering whole text and isolated sentences YES, limited to the whole abstract YES, at sentence level only
Extracts interactions among proteins YES, considering a biointeractions dictionary defined by the user NOT YES, considering a pre-compiled biointeractions dictionary
Terms co-occurrences YES, extracts terms mentioned in the full text or in isolated sentences at different structures which are scored differently YES, extract terms mentioned together in abstracts, more often than what would be expected by chance based on their overall occurrence YES, extracts terms mentioned in isolated sentences
Semantic understanding YES, extracts the biointeractions and concepts linked to an extracted pair at sentence level in different co-occurrence types NOT, only checks co-occurrences of terms YES, extracts the biointeractions and concepts linked to an extracted pair at sentence level
Co-occurrence frequency report YES, displays the frequency that a pair co-occurred in general sentences, and for each found biointeraction YES, only the number of times that a pair co-occurred in each abstract NOT
Outputs network YES, in tabular format and in pre-compiled formats for third-part applications (ARENA3D, MEDUSA) YES, displays the network in the browser from selected abstracts YES, users can build a network by adding a set of nodes per time by selecting desired abstracts