Learn to use iHOP, or Information Hyperlinked Over Proteins; a sophisticated, next generation, text-mining database. It provides comprehensive, up-to-date information on specific genes and proteins by automatically scanning millions of PubMed abstracts each day. iHOP will selectively present only the information on genes and proteins you want. The control over the reliability and relevance of the retrieved information always remains in the hands of the user. Use iHOP to get improved results from all your scientific literature searches more efficiently.

You will learn:

  • to understand the four main iHOP views
  • ways of filtering your searches to optimize results to your needs
  • how to use iHOP Gene Model to keep track of interesting sentences
  • how to download data from iHOP


This tutorial is a part of the tutorial group Text-related tools. You might find the other tutorials in the group interesting:

PubMatrix: PubMatrix, an on-line tool for multiplex literature mining of the PubMed database.

STRING: known and predicted protein-protein interactions

Textpresso: Text-mining the biological literature

Gene Ontology: Gene Ontology controlled vocabularies in biology

XplorMed: eXploring Medline abstracts

GoMiner: Ascribe biological significance to large lists of genes by annotating them with their corresponding GO categories

Controlled Vocabularies: Standardized term lists that can enhance interactions with biological databases

DAVID: A tool that analyzes large lists of genes to provide biological meaning

Entrez Overview: Overview of NCBI's Entrez Search Resource

PubMed: PubMed access to biomedical research literature


Literature and Text Mining : Tools which are related to scientific literature. Repositories, query tools, and mining resources are included.


Tip of the Week: BioGPS for expression data and more: This week's tip introduces BioGPS, or Gene Portal System. We get a lot of questions about two things that BioGPS can help you to tackle: what do I do with a list of genes to find out what they are? An...

Mining figure legends. Huh.: Every so often something comes up in your weekly literature search that makes you go: huh. That happened to me today with a paper on text mining. Now, I have used a variety of text-mining tools (Textpr...

New Online Tutorial for iHOP from OpenHelix: Comprehensive tutorial on the publicly available iHOP database enables researchers to quickly and effectively use this invaluable next-generation resource. Seattle, WA,  August 10, 2009 -- OpenHelix to...

Navigating the literature: We have a slide we like to present at some trainings showing the rise in the amount of raw sequence data and number of complete genomes over the last 18 years. There is another slide we show that indic...


Recent BioMed Central research articles citing this resource

Razfar Mojtaba et al., On robustness of physical layer network coding to pollution attack. EURASIP Journal on Wireless Communications and Networking (2017) doi:10.1186/s13638-016-0788-9

Hu Yanjun et al., Linear system construction of multilateration based on error propagation estimation. EURASIP Journal on Wireless Communications and Networking (2016) doi:10.1186/s13638-016-0657-6

Chen Weiqi et al., Joint QoS provisioning and congestion control for multi-hop wireless networks. EURASIP Journal on Wireless Communications and Networking (2016) doi:10.1186/s13638-016-0519-2

Son Van Vu et al., Co-channel interference cancellation using precoding for bi-direction multiple hops MIMO relay systems. EURASIP Journal on Wireless Communications and Networking (2016) doi:10.1186/s13638-015-0493-0

Xiong Wei et al., Minimum node degree of k -connected vehicular ad hoc networks in highway scenarios. EURASIP Journal on Wireless Communications and Networking (2016) doi:10.1186/s13638-016-0529-0