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Table 3 Feature comparison among PESCADOR, iHOP, STRING and AliBaba.

From: PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries

Feature

PESCADOR

iHOP

STRING

AliBaba

Input

PubMed

(user selection or query)

Protein/Gene ID

Protein/Gene ID

PubMed

(query)

Biological concepts

Customized

Fixed

Fixed

Fixed

Literature corpus

Selected PubMed

Whole PubMed

Whole PubMed

Selected PubMed

Co-occurrence context

Sentence/whole abstract

Sentence

Whole abstract

Sentence

Target protein display filters

Biological concept;

Biointeraction term;

Co-occurring pair;

Co-occurrence structure.

Co-occurring pair.

Co-occurring pair;

Confidence;

Degree.

Co-occurring pair;

Confidence;

Degree.

Manual validation of co-occurring pairs

Yes

Yes

No

No

Co-occurrence validation sharing among users

Yes

No

No

No

Network building

Automatically on-the-fly

Manually stepwise

Automatically on-the-fly

Automatically on-the-fly