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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