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