{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,8]],"date-time":"2025-12-08T22:07:30Z","timestamp":1765231650789},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The biomedical literature contains a wealth of information on associations between many different types of objects, such as protein\u2013protein interactions, gene\u2013disease associations and subcellular locations of proteins. When searching such information using conventional search engines, e.g. PubMed, users see the data only one-abstract at a time and \u2018hidden\u2019 in natural language text. AliBaba is an interactive tool for graphical summarization of search results. It parses the set of abstracts that fit a PubMed query and presents extracted information on biomedical objects and their relationships as a graphical network. AliBaba extracts associations between cells, diseases, drugs, proteins, species and tissues. Several filter options allow for a more focused search. Thus, researchers can grasp complex networks described in various articles at a glance.<\/jats:p>\n               <jats:p>Availability: \u00a0<\/jats:p>\n               <jats:p>Contact: \u00a0hakenberg@informatik.hu-berlin.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl408","type":"journal-article","created":{"date-parts":[[2006,7,27]],"date-time":"2006-07-27T00:58:50Z","timestamp":1153961930000},"page":"2444-2445","source":"Crossref","is-referenced-by-count":89,"title":["A<scp>li<\/scp>B<scp>aba<\/scp>: PubMed as a graph"],"prefix":"10.1093","volume":"22","author":[{"given":"Conrad","family":"Plake","sequence":"first","affiliation":[{"name":"Knowledge Management in Bioinformatics, Humboldt-Universit\u00e4t zu Berlin 1 \u00a0 1 \u00a0 \u00a0 Unter den Linden 6, 10099 Berlin, Germany"}]},{"given":"Torsten","family":"Schiemann","sequence":"additional","affiliation":[{"name":"Knowledge Management in Bioinformatics, Humboldt-Universit\u00e4t zu Berlin 1 \u00a0 1 \u00a0 \u00a0 Unter den Linden 6, 10099 Berlin, Germany"}]},{"given":"Marcus","family":"Pankalla","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Computer Science, Free University Berlin 2 \u00a0 2 \u00a0 \u00a0 Arnimallee 2-6, 14195 Berlin, Germany"}]},{"given":"J\u00f6rg","family":"Hakenberg","sequence":"additional","affiliation":[{"name":"Knowledge Management in Bioinformatics, Humboldt-Universit\u00e4t zu Berlin 1 \u00a0 1 \u00a0 \u00a0 Unter den Linden 6, 10099 Berlin, Germany"}]},{"given":"Ulf","family":"Leser","sequence":"additional","affiliation":[{"name":"Knowledge Management in Bioinformatics, Humboldt-Universit\u00e4t zu Berlin 1 \u00a0 1 \u00a0 \u00a0 Unter den Linden 6, 10099 Berlin, Germany"}]}],"member":"286","published-online":{"date-parts":[[2006,7,26]]},"reference":[{"key":"2023012409244004600_b1","doi-asserted-by":"crossref","first-page":"W783","DOI":"10.1093\/nar\/gki470","article-title":"GoPubMed: exploring PubMed with the Gene Ontology","volume":"33","author":"Doms","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012409244004600_b2","article-title":"Genic interaction extraction with alignments and finite state automata","author":"Hakenberg","year":"2005"},{"key":"2023012409244004600_b3","doi-asserted-by":"crossref","first-page":"3294","DOI":"10.1093\/bioinformatics\/bti493","article-title":"Discovering patterns to extract protein\u2013protein interactions from the literature: Part II","volume":"21","author":"Hao","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012409244004600_b4","doi-asserted-by":"crossref","first-page":"ii252","DOI":"10.1093\/bioinformatics\/bti1142","article-title":"Implementing the iHOP concept for navigation of biomedical literature","volume":"21","author":"Hoffmann","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012409244004600_b5","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1038\/nrg1768","article-title":"Literature mining for the biologist: from information retrieval to biological discovery","volume":"7","author":"Jensen","year":"2006","journal-title":"Nat. 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