{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T09:13:58Z","timestamp":1769850838368,"version":"3.49.0"},"reference-count":43,"publisher":"Springer Science and Business Media LLC","issue":"S3","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2013,10]]},"DOI":"10.1186\/1752-0509-7-s3-s9","type":"journal-article","created":{"date-parts":[[2013,10,16]],"date-time":"2013-10-16T15:03:24Z","timestamp":1381935804000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":43,"title":["A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks"],"prefix":"10.1186","volume":"7","author":[{"given":"Zuoshuang","family":"Xiang","sequence":"first","affiliation":[]},{"given":"Tingting","family":"Qin","sequence":"additional","affiliation":[]},{"given":"Zhaohui S","family":"Qin","sequence":"additional","affiliation":[]},{"given":"Yongqun","family":"He","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,10,16]]},"reference":[{"key":"1166_CR1","unstructured":"The PubMed database. [http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/]"},{"issue":"3","key":"1166_CR2","first-page":"265","volume":"88","author":"CE Lipscomb","year":"2000","unstructured":"Lipscomb CE: Medical Subject Headings (MeSH). Bull Med Libr Assoc. 2000, 88 (3): 265-266.","journal-title":"Bull Med Libr Assoc"},{"key":"1166_CR3","unstructured":"MeSH fact sheet. URL: http:\/\/www.nlm.nih.gov\/pubs\/factsheets\/mesh.html, accessed on March 23, 2013"},{"key":"1166_CR4","first-page":"60","volume-title":"Proc Int Conf Intell Syst Mol Biol","author":"C Blaschke","year":"1999","unstructured":"Blaschke C, Andrade MA, Ouzounis C, Valencia A: Automatic extraction of biological information from scientific text: protein-protein interactions. Proc Int Conf Intell Syst Mol Biol. 1999, 60-67."},{"issue":"1","key":"1166_CR5","first-page":"21","volume":"28","author":"TK Jenssen","year":"2001","unstructured":"Jenssen TK, Laegreid A, Komorowski J, Hovig E: A literature network of human genes for high-throughput analysis of gene expression. Nat Genet. 2001, 28 (1): 21-28.","journal-title":"Nat Genet"},{"issue":"4","key":"1166_CR6","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1093\/bioinformatics\/17.4.319","volume":"17","author":"DR Masys","year":"2001","unstructured":"Masys DR, Welsh JB, Lynn Fink J, Gribskov M, Klacansky I, Corbeil J: Use of keyword hierarchies to interpret gene expression patterns. Bioinformatics (Oxford, England). 2001, 17 (4): 319-326. 10.1093\/bioinformatics\/17.4.319.","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"3","key":"1166_CR7","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1016\/S0169-2607(98)00033-9","volume":"57","author":"NR Smalheiser","year":"1998","unstructured":"Smalheiser NR, Swanson DR: Using ARROWSMITH: a computer-assisted approach to formulating and assessing scientific hypotheses. Comput Methods Programs Biomed. 1998, 57 (3): 149-153. 10.1016\/S0169-2607(98)00033-9.","journal-title":"Comput Methods Programs Biomed"},{"key":"1166_CR8","first-page":"642","volume-title":"Proc AMIA Symp","author":"P Srinivasan","year":"2001","unstructured":"Srinivasan P: MeSHmap: a text mining tool for MEDLINE. Proc AMIA Symp. 2001, 642-646."},{"key":"1166_CR9","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1186\/1471-2105-4-61","volume":"4","author":"KG Becker","year":"2003","unstructured":"Becker KG, Hosack DA, Dennis G, Lempicki RA, Bright TJ, Cheadle C, Engel J: PubMatrix: a tool for multiplex literature mining. BMC Bioinformatics. 2003, 4: 61-10.1186\/1471-2105-4-61.","journal-title":"BMC Bioinformatics"},{"key":"1166_CR10","first-page":"391","volume-title":"Pac Symp Biocomput","author":"P Glenisson","year":"2003","unstructured":"Glenisson P, Antal P, Mathys J, Moreau Y, De Moor B: Evaluation of the vector space representation in text-based gene clustering. Pac Symp Biocomput. 2003, 391-402."},{"issue":"1","key":"1166_CR11","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1093\/bioinformatics\/bth464","volume":"21","author":"R Homayouni","year":"2005","unstructured":"Homayouni R, Heinrich K, Wei L, Berry MW: Gene clustering by latent semantic indexing of MEDLINE abstracts. Bioinformatics (Oxford, England). 2005, 21 (1): 104-115. 10.1093\/bioinformatics\/bth464.","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"1","key":"1166_CR12","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1152\/physiolgenomics.00155.2003","volume":"18","author":"JF Challacombe","year":"2004","unstructured":"Challacombe JF, Rechtsteiner A, Gottardo R, Rocha LM, Browne EP, Shenk T, Altherr MR, Brettin TS: Evaluation of the host transcriptional response to human cytomegalovirus infection. Physiol Genomics. 2004, 18 (1): 51-62. 10.1152\/physiolgenomics.00155.2003.","journal-title":"Physiol Genomics"},{"key":"1166_CR13","first-page":"76","volume-title":"Pac Symp Biocomput","author":"AG Maguitman","year":"2006","unstructured":"Maguitman AG, Rechtsteiner A, Verspoor K, Strauss CE, Rocha LM: Large-scale testing of bibliome informatics using Pfam protein families. Pac Symp Biocomput. 2006, 76-87."},{"issue":"4","key":"1166_CR14","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1016\/j.gde.2004.06.015","volume":"14","author":"AG Fraser","year":"2004","unstructured":"Fraser AG, Marcotte EM: Development through the eyes of functional genomics. Curr Opin Genet Dev. 2004, 14 (4): 336-342. 10.1016\/j.gde.2004.06.015.","journal-title":"Curr Opin Genet Dev"},{"issue":"10","key":"1166_CR15","doi-asserted-by":"publisher","first-page":"1314","DOI":"10.1093\/bioinformatics\/btp158","volume":"25","author":"LC Tsoi","year":"2009","unstructured":"Tsoi LC, Boehnke M, Klein RL, Zheng WJ: Evaluation of genome-wide association study results through development of ontology fingerprints. Bioinformatics (Oxford, England). 2009, 25 (10): 1314-1320. 10.1093\/bioinformatics\/btp158.","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"1","key":"1166_CR16","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT: Gene ontology, et al: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25 (1): 25-29. 10.1038\/75556.","journal-title":"Nat Genet"},{"issue":"5","key":"1166_CR17","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1016\/0306-4573(88)90021-0","volume":"24","author":"G Salton","year":"1988","unstructured":"Salton G, Buckley C: Term-weighting approaches in automatic text retrieval. Information Processing and Management. 1988, 24 (5): 513-523. 10.1016\/0306-4573(88)90021-0.","journal-title":"Information Processing and Management"},{"key":"1166_CR18","volume-title":"Introduction to Modern Information Retrieval","author":"G Salton","year":"1983","unstructured":"Salton G: Introduction to Modern Information Retrieval. 1983, New York: McGraw-Hill"},{"issue":"18","key":"1166_CR19","doi-asserted-by":"publisher","first-page":"2298","DOI":"10.1093\/bioinformatics\/btl388","volume":"22","author":"J Lewis","year":"2006","unstructured":"Lewis J, Ossowski S, Hicks J, Errami M, Garner HR: Text similarity: an alternative way to search MEDLINE. Bioinformatics (Oxford, England). 2006, 22 (18): 2298-2304. 10.1093\/bioinformatics\/btl388.","journal-title":"Bioinformatics (Oxford, England)"},{"key":"1166_CR20","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1086\/282436","volume":"100","author":"HS Horn","year":"1966","unstructured":"Horn HS: Measurement of \"overlap\" in comparative ecological studies. Am Naturalist. 1966, 100: 419-424. 10.1086\/282436.","journal-title":"Am Naturalist"},{"key":"1166_CR21","volume-title":"Data Mining: Practical Machine Learning Tools and Techniques","author":"IH Witten","year":"2005","unstructured":"Witten IH, Frank E: Data Mining: Practical Machine Learning Tools and Techniques. 2005, Morgan Kaufmann, 2","edition":"2"},{"issue":"Database issue","key":"1166_CR22","first-page":"D120","volume":"36","author":"S Gama-Castro","year":"2008","unstructured":"Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, et al: RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res. 2008, 36 (Database issue): D120-124.","journal-title":"Nucleic Acids Res"},{"issue":"4857","key":"1166_CR23","doi-asserted-by":"publisher","first-page":"1285","DOI":"10.1126\/science.3287615","volume":"240","author":"JA Swets","year":"1988","unstructured":"Swets JA: Measuring the accuracy of diagnostic systems. Science. 1988, 240 (4857): 1285-1293. 10.1126\/science.3287615.","journal-title":"Science"},{"issue":"11","key":"1166_CR24","doi-asserted-by":"publisher","first-page":"1943","DOI":"10.1016\/j.biochi.2011.07.016","volume":"93","author":"CK Vanderpool","year":"2011","unstructured":"Vanderpool CK, Balasubramanian D, Lloyd CR: Dual-function RNA regulators in bacteria. Biochimie. 2011, 93 (11): 1943-1949. 10.1016\/j.biochi.2011.07.016.","journal-title":"Biochimie"},{"issue":"18","key":"1166_CR25","doi-asserted-by":"publisher","first-page":"6179","DOI":"10.1128\/JB.186.18.6179-6185.2004","volume":"186","author":"RA Lease","year":"2004","unstructured":"Lease RA, Smith D, McDonough K, Belfort M: The small noncoding DsrA RNA is an acid resistance regulator in Escherichia coli. J Bacteriol. 2004, 186 (18): 6179-6185. 10.1128\/JB.186.18.6179-6185.2004.","journal-title":"J Bacteriol"},{"issue":"24","key":"1166_CR26","doi-asserted-by":"publisher","first-page":"8317","DOI":"10.1128\/JB.186.24.8317-8325.2004","volume":"186","author":"H Ogasawara","year":"2004","unstructured":"Ogasawara H, Teramoto J, Hirao K, Yamamoto K, Ishihama A, Utsumi R: Negative regulation of DNA repair gene (ung) expression by the CpxR\/CpxA two-component system in Escherichia coli K-12 and induction of mutations by increased expression of CpxR. J Bacteriol. 2004, 186 (24): 8317-8325. 10.1128\/JB.186.24.8317-8325.2004.","journal-title":"J Bacteriol"},{"issue":"Pt 8","key":"1166_CR27","doi-asserted-by":"publisher","first-page":"2518","DOI":"10.1099\/mic.0.2007\/006312-0","volume":"153","author":"LD Tatar","year":"2007","unstructured":"Tatar LD, Marolda CL, Polischuk AN, van Leeuwen D, Valvano MA: An Escherichia coli undecaprenyl-pyrophosphate phosphatase implicated in undecaprenyl phosphate recycling. Microbiology. 2007, 153 (Pt 8): 2518-2529.","journal-title":"Microbiology"},{"issue":"11","key":"1166_CR28","doi-asserted-by":"publisher","first-page":"5298","DOI":"10.1128\/IAI.00652-07","volume":"75","author":"AT Anfora","year":"2007","unstructured":"Anfora AT, Haugen BJ, Roesch P, Redford P, Welch RA: Roles of serine accumulation and catabolism in the colonization of the murine urinary tract by Escherichia coli CFT073. Infect Immun. 2007, 75 (11): 5298-5304. 10.1128\/IAI.00652-07.","journal-title":"Infect Immun"},{"key":"1166_CR29","unstructured":"E. coli gene clustering based on GenoMesh analysis. http:\/\/genomesh.hegroup.org\/downloads\/files\/E_coli_clusters_Sqrt_Cosine_coefficient.pdf, accessed on March 29. 2013"},{"issue":"1","key":"1166_CR30","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1016\/S0092-8674(00)81141-1","volume":"93","author":"DJ DeRosier","year":"1998","unstructured":"DeRosier DJ: The turn of the screw: the bacterial flagellar motor. Cell. 1998, 93 (1): 17-20. 10.1016\/S0092-8674(00)81141-1.","journal-title":"Cell"},{"key":"1166_CR31","volume-title":"Biochim Biophys Acta","author":"D Apel","year":"2007","unstructured":"Apel D, Surette MG: Bringing order to a complex molecular machine: The assembly of the bacterial flagella. Biochim Biophys Acta. 2007"},{"issue":"12","key":"1166_CR32","doi-asserted-by":"publisher","first-page":"7053","DOI":"10.1128\/IAI.71.12.7053-7060.2003","volume":"71","author":"P Lestrate","year":"2003","unstructured":"Lestrate P, Dricot A, Delrue RM, Lambert C, Martinelli V, De Bolle X, Letesson JJ, Tibor A: Attenuated signature-tagged mutagenesis mutants of Brucella melitensis identified during the acute phase of infection in mice. Infect Immun. 2003, 71 (12): 7053-7060. 10.1128\/IAI.71.12.7053-7060.2003.","journal-title":"Infect Immun"},{"issue":"8","key":"1166_CR33","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1111\/j.1462-5822.2005.00543.x","volume":"7","author":"RM Delrue","year":"2005","unstructured":"Delrue RM, Deschamps C, Leonard S, Nijskens C, Danese I, Schaus JM, Bonnot S, Ferooz J, Tibor A, De Bolle X, et al: A quorum-sensing regulator controls expression of both the type IV secretion system and the flagellar apparatus of Brucella melitensis. Cell Microbiol. 2005, 7 (8): 1151-1161. 10.1111\/j.1462-5822.2005.00543.x.","journal-title":"Cell Microbiol"},{"issue":"1","key":"1166_CR34","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1046\/j.1365-2958.1998.00913.x","volume":"29","author":"A Sola-Landa","year":"1998","unstructured":"Sola-Landa A, Pizarro-Cerda J, Grillo MJ, Moreno E, Moriyon I, Blasco JM, Gorvel JP, Lopez-Goni I: A two-component regulatory system playing a critical role in plant pathogens and endosymbionts is present in Brucella abortus and controls cell invasion and virulence. Mol Microbiol. 1998, 29 (1): 125-138. 10.1046\/j.1365-2958.1998.00913.x.","journal-title":"Mol Microbiol"},{"issue":"5","key":"1166_CR35","doi-asserted-by":"publisher","first-page":"2873","DOI":"10.1128\/IAI.73.5.2873-2880.2005","volume":"73","author":"JM Gee","year":"2005","unstructured":"Gee JM, Valderas MW, Kovach ME, Grippe VK, Robertson GT, Ng WL, Richardson JM, Winkler ME, Roop RM: The Brucella abortus Cu, Zn superoxide dismutase is required for optimal resistance to oxidative killing by murine macrophages and wild-type virulence in experimentally infected mice. Infect Immun. 2005, 73 (5): 2873-2880. 10.1128\/IAI.73.5.2873-2880.2005. 2","journal-title":"Infect Immun"},{"issue":"1-4","key":"1166_CR36","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/S0378-1135(02)00214-6","volume":"90","author":"JP Gorvel","year":"2002","unstructured":"Gorvel JP, Moreno E: Brucella intracellular life: from invasion to intracellular replication. Vet Microbiol. 2002, 90 (1-4): 281-297. 10.1016\/S0378-1135(02)00214-6.","journal-title":"Vet Microbiol"},{"issue":"1","key":"1166_CR37","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1186\/1471-2105-7-347","volume":"7","author":"Z Xiang","year":"2006","unstructured":"Xiang Z, Zheng W, He Y: BBP: Brucella genome annotation with literature mining and curation. BMC Bioinformatics. 2006, 7 (1): 347-10.1186\/1471-2105-7-347.","journal-title":"BMC Bioinformatics"},{"issue":"Database issue","key":"1166_CR38","doi-asserted-by":"publisher","first-page":"D412","DOI":"10.1093\/nar\/gkn760","volume":"37","author":"LJ Jensen","year":"2009","unstructured":"Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, et al: STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res. 2009, 37 (Database issue): D412-416.","journal-title":"Nucleic Acids Res"},{"key":"1166_CR39","doi-asserted-by":"crossref","unstructured":"He Y, Cowell L, Diehl AD, Mobley HL, Peters B, Ruttenberg A, Scheuermann RH, Brinkman RR, Courtot M, Mungall C: VO: Vaccine Ontology. The 1st International Conference on Biomedical Ontology (ICBO 2009): July 24-26 2009; Buffalo, NY, USA. Nature Precedings. [http:\/\/precedings.nature.com\/documents\/3552\/version\/1]","DOI":"10.1038\/npre.2009.3553"},{"issue":"1","key":"1166_CR40","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1186\/2041-1480-3-17","volume":"3","author":"Y Lin","year":"2012","unstructured":"Lin Y, He Y: Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses. J Biomed Semantics. 2012, 3 (1): 17-10.1186\/2041-1480-3-17.","journal-title":"J Biomed Semantics"},{"key":"1166_CR41","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1186\/1471-2172-12-49","volume":"12","author":"J Hur","year":"2011","unstructured":"Hur J, Xiang Z, Feldman EL, He Y: Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network. BMC Immunol. 2011, 12: 49-10.1186\/1471-2172-12-49.","journal-title":"BMC Immunol"},{"issue":"7","key":"1166_CR42","doi-asserted-by":"publisher","first-page":"R150","DOI":"10.1186\/gb-2007-8-7-r150","volume":"8","author":"Z Xiang","year":"2007","unstructured":"Xiang Z, Tian Y, He Y: PHIDIAS: a pathogen-host interaction data integration and analysis system. Genome Biol. 2007, 8 (7): R150-10.1186\/gb-2007-8-7-r150.","journal-title":"Genome Biol"},{"issue":"22","key":"1166_CR43","doi-asserted-by":"publisher","first-page":"7577","DOI":"10.1093\/nar\/gkm740","volume":"35","author":"PD Karp","year":"2007","unstructured":"Karp PD, Keseler IM, Shearer A, Latendresse M, Krummenacker M, Paley SM, Paulsen I, Collado-Vides J, Gama-Castro S, Peralta-Gil M, et al: Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res. 2007, 35 (22): 7577-7590. 10.1093\/nar\/gkm740.","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-7-S3-S9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T01:48:19Z","timestamp":1630547299000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-7-S3-S9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,10]]},"references-count":43,"journal-issue":{"issue":"S3","published-print":{"date-parts":[[2013,10]]}},"alternative-id":["1166"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-7-s3-s9","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,10]]},"assertion":[{"value":"16 October 2013","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S9"}}