iHOP (database)

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iHOP ( i nformation H yperlinked O ver P roteins) was a freely accessible literature search engine, in Abstracts of Pubmed occurring -Artikeln gene and protein names used as hyperlinks, and thus the search for thematically related to each other life science products facilitated. Above all, a quick and easy search for interaction partners of gene products or for articles that describe corresponding interactions was made possible. There is also a carefully researched list of synonyms for names. iHOP and the author's homepage have been offline since 2018.

background

In contrast to conventional search engines, which provide a list of results, iHOP aimed to link related content (as is the case with Wikipedia, for example ). In the biomedical sciences - with the Pubmed access portal - genes or gene products (i.e. proteins) are natural information units. Pubmed can thus be viewed as a network of genes that can be hyperlinked and handled in a similar way to the Internet. The connection between the articles was established using gene names that appear in individual abstract sentences.

functionality

Once a month, gene names (from databases such as UniProt and LocusLink ) and abstracts of Pubmed articles were imported. The abstracts are automatically searched for gene synonyms and MeSH terms ( Medical Subject Headings ) (dictionary-based search). For each gene and each abstract, a source page was created containing the original text divided into sentences, with gene synonyms, MeSH terms and associated verbs highlighted. Gene pages contained additional information (such as about homologous genes). In response to user requests, the relevant source pages were presented as HTML pages.

Result

When searching for a gene or gene product (i.e. protein; no distinction is made between gene and protein), those sentences taken from abstracts are considered hits in which the name of the gene in question is combined with a MeSH term or with another gene name occurs (suggesting an interaction between the two gene products). An essential feature was the numerous synonym names for a gene that were compiled from various databases. The corresponding MeSH term can be used for a google or Pubmed search. The second gene mentioned in connection with the first gene, on the other hand, led as a hyperlink to a separate page on which the information for this gene was again collated (i.e. the connection to the corresponding MeSH terms or other genes; the interactions with the gene, via which one reached the corresponding page, listed first). This ability to use gene names as hyperlinks was the original idea and the real strength of iHOP ; it thus provided a quick overview of related gene products. The corresponding extracts from abstracts could be saved and the connections between the gene products could be shown graphically.

swell

  • R. Hoffmann, A. Valencia: A Gene Network for Navigating the Literature. In: Nature Genetics . 36, 2004, p. 664.
  • R. Hoffmann, A. Valencia: Implementing the iHOP concept for navigation of biomedical literature. In: Bioinformatics. 21 (suppl. 2), 2005, pp. Ii252-ii258.

Web links