{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,20]],"date-time":"2025-10-20T10:11:17Z","timestamp":1760955077541},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Prokaryotic protein\u2013protein interactions are underrepresented in currently available databases. Here, we describe a \u2018gold standard\u2019 dataset (MPI-LIT) focusing on microbial binary protein\u2013protein interactions and associated experimental evidence that we have manually curated from 813 abstracts and full texts that were selected from an initial set of 36 852 abstracts. The MPI-LIT dataset comprises 1237 experimental descriptions that describe a non-redundant set of 746 interactions of which 659 (88%) are not reported in public databases. To estimate the curation quality, we compared our dataset with a union of microbial interaction data from IntAct, DIP, BIND and MINT. Among common abstracts, we achieve a sensitivity of up to 66% for interactions and 75% for experimental methods. Compared with these other datasets, MPI-LIT has the lowest fraction of interaction experiments per abstract (0.9) and the highest coverage of strains (92) and scientific articles (813). We compared methods that evaluate functional interactions among proteins (such as genomic context or co-expression) which are implemented in the STRING database. Most of these methods discriminate well between functionally relevant protein interactions (MPI-LIT) and high-throughput data.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.jcvi.org\/mpidb\/interaction.php?dbsource=MPI-LIT.<\/jats:p>\n               <jats:p>Contact: \u00a0raja@jcvi.org<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn481","type":"journal-article","created":{"date-parts":[[2008,9,12]],"date-time":"2008-09-12T00:33:58Z","timestamp":1221179638000},"page":"2622-2627","source":"Crossref","is-referenced-by-count":13,"title":["MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions"],"prefix":"10.1093","volume":"24","author":[{"given":"Seesandra V.","family":"Rajagopala","sequence":"first","affiliation":[{"name":"1 J Craig Venter Institute, Rockville, MD 20850, USA, 2Indgen Life Technologies, Bangalore - 560 004, Karnataka, India and 3Institute for Genetics, Forschungszentrum Karlsruhe, Karlsruhe, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Johannes","family":"Goll","sequence":"additional","affiliation":[{"name":"1 J Craig Venter Institute, Rockville, MD 20850, USA, 2Indgen Life Technologies, Bangalore - 560 004, Karnataka, India and 3Institute for Genetics, Forschungszentrum Karlsruhe, Karlsruhe, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"N.D. Deve","family":"Gowda","sequence":"additional","affiliation":[{"name":"1 J Craig Venter Institute, Rockville, MD 20850, USA, 2Indgen Life Technologies, Bangalore - 560 004, Karnataka, India and 3Institute for Genetics, Forschungszentrum Karlsruhe, Karlsruhe, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kumar C.","family":"Sunil","sequence":"additional","affiliation":[{"name":"1 J Craig Venter Institute, Rockville, MD 20850, USA, 2Indgen Life Technologies, Bangalore - 560 004, Karnataka, India and 3Institute for Genetics, Forschungszentrum Karlsruhe, Karlsruhe, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bj\u00f6rn","family":"Titz","sequence":"additional","affiliation":[{"name":"1 J Craig Venter Institute, Rockville, MD 20850, USA, 2Indgen Life Technologies, Bangalore - 560 004, Karnataka, India and 3Institute for Genetics, Forschungszentrum Karlsruhe, Karlsruhe, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arnab","family":"Mukherjee","sequence":"additional","affiliation":[{"name":"1 J Craig Venter Institute, Rockville, MD 20850, USA, 2Indgen Life Technologies, Bangalore - 560 004, Karnataka, India and 3Institute for Genetics, Forschungszentrum Karlsruhe, Karlsruhe, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sharmila S.","family":"Mary","sequence":"additional","affiliation":[{"name":"1 J Craig Venter Institute, Rockville, MD 20850, USA, 2Indgen Life Technologies, Bangalore - 560 004, Karnataka, India and 3Institute for Genetics, Forschungszentrum Karlsruhe, Karlsruhe, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Naresh","family":"Raviswaran","sequence":"additional","affiliation":[{"name":"1 J Craig Venter Institute, Rockville, MD 20850, USA, 2Indgen Life Technologies, Bangalore - 560 004, Karnataka, India and 3Institute for Genetics, Forschungszentrum Karlsruhe, Karlsruhe, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chetan S.","family":"Poojari","sequence":"additional","affiliation":[{"name":"1 J Craig Venter Institute, Rockville, MD 20850, USA, 2Indgen Life Technologies, Bangalore - 560 004, Karnataka, India and 3Institute for Genetics, Forschungszentrum Karlsruhe, Karlsruhe, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Srinivas","family":"Ramachandra","sequence":"additional","affiliation":[{"name":"1 J Craig Venter Institute, Rockville, MD 20850, USA, 2Indgen Life Technologies, Bangalore - 560 004, Karnataka, India and 3Institute for Genetics, Forschungszentrum Karlsruhe, Karlsruhe, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Svetlana","family":"Shtivelband","sequence":"additional","affiliation":[{"name":"1 J Craig Venter Institute, Rockville, MD 20850, USA, 2Indgen Life Technologies, Bangalore - 560 004, Karnataka, India and 3Institute for Genetics, Forschungszentrum Karlsruhe, Karlsruhe, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephen M.","family":"Blazie","sequence":"additional","affiliation":[{"name":"1 J Craig Venter Institute, Rockville, MD 20850, USA, 2Indgen Life Technologies, Bangalore - 560 004, Karnataka, India and 3Institute for Genetics, Forschungszentrum Karlsruhe, Karlsruhe, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julia","family":"Hofmann","sequence":"additional","affiliation":[{"name":"1 J Craig Venter Institute, Rockville, MD 20850, USA, 2Indgen Life Technologies, Bangalore - 560 004, Karnataka, India and 3Institute for Genetics, Forschungszentrum Karlsruhe, Karlsruhe, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Uetz","sequence":"additional","affiliation":[{"name":"1 J Craig Venter Institute, Rockville, MD 20850, USA, 2Indgen Life Technologies, Bangalore - 560 004, Karnataka, India and 3Institute for Genetics, Forschungszentrum Karlsruhe, Karlsruhe, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,9,11]]},"reference":[{"key":"2023020212225308000_B1","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1093\/bioinformatics\/btl140","article-title":"Improved scoring of functional groups from gene expression data by decorrelating GO graph structure","volume":"22","author":"Alexa","year":"2006","journal-title":"Bioinformatics"},{"issue":"Database issue","key":"2023020212225308000_B2","doi-asserted-by":"crossref","first-page":"D418","DOI":"10.1093\/nar\/gki051","article-title":"The biomolecular interaction network database and related tools 2005 update","volume":"33","author":"Alfarano","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2023020212225308000_B3","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1101\/gr.4527806","article-title":"Large-scale identification of protein--protein interaction ofEscherichia coliK-12","volume":"16","author":"Arifuzzaman","year":"2006","journal-title":"Genome Res"},{"key":"2023020212225308000_B4","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1038\/nature03239","article-title":"Interaction network containing conserved and essential protein complexes inEscherichia coli","volume":"433","author":"Butland","year":"2005","journal-title":"Nature"},{"issue":"Database issue","key":"2023020212225308000_B5","doi-asserted-by":"crossref","first-page":"D572","DOI":"10.1093\/nar\/gkl950","article-title":"MINT: the molecular interaction database","volume":"35","author":"Chatr-aryamontri","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023020212225308000_B6","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1016\/S0168-9525(02)02763-4","article-title":"Bridging structural biology and genomics: assessing protein interaction data with known complexes","volume":"18","author":"Edwards","year":"2002","journal-title":"Trends Genet"},{"key":"2023020212225308000_B7","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/340245a0","article-title":"A novel genetic system to detect protein-protein interactions","volume":"340","author":"Fields","year":"1989","journal-title":"Nature"},{"key":"2023020212225308000_B8","doi-asserted-by":"crossref","first-page":"1743","DOI":"10.1093\/bioinformatics\/btn285","article-title":"MPIDB: the microbial protein interaction database","volume":"24","author":"Goll","year":"2008","journal-title":"Bioinformatics"},{"key":"2023020212225308000_B9","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1038\/nature02555","article-title":"Evidence for dynamically organized modularity in the yeast protein\u2013protein interaction network","volume":"430","author":"Han","year":"2004","journal-title":"Nature"},{"key":"2023020212225308000_B10","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/1741-7007-5-44","article-title":"Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions","volume":"5","author":"Kerrien","year":"2007","journal-title":"BMC Biol"},{"issue":"Database issue","key":"2023020212225308000_B11","doi-asserted-by":"crossref","first-page":"D561","DOI":"10.1093\/nar\/gkl958","article-title":"IntAct--open source resource for molecular interaction data","volume":"35","author":"Kerrien","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023020212225308000_B12","doi-asserted-by":"crossref","first-page":"1178","DOI":"10.1016\/j.febslet.2008.02.072","article-title":"A text-mining perspective on the requirements for electronically annotated abstracts","volume":"582","author":"Leitner","year":"2008","journal-title":"FEBS Lett"},{"key":"2023020212225308000_B13","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1093\/bioinformatics\/bti749","article-title":"Biothesaurus: a web-based thesaurus of protein and gene names","volume":"22","author":"Liu","year":"2006","journal-title":"Bioinformatics"},{"key":"2023020212225308000_B14","doi-asserted-by":"crossref","first-page":"R130","DOI":"10.1186\/gb-2007-8-7-r130","article-title":"A proteome-wide protein interaction map forCampylobacter jejuni","volume":"8","author":"Parrish","year":"2007","journal-title":"Genome Biol"},{"key":"2023020212225308000_B15","doi-asserted-by":"crossref","first-page":"2363","DOI":"10.1101\/gr.1680803","article-title":"Development of human protein reference database as an initial platform for approaching systems biology in humans","volume":"13","author":"Peri","year":"2003","journal-title":"Genome Res"},{"key":"2023020212225308000_B16","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1093\/nar\/29.1.123","article-title":"The comprehensive microbial resource","volume":"29","author":"Peterson","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"2023020212225308000_B17","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1038\/35051615","article-title":"The protein\u2013protein interaction map ofHelicobacter pylori","volume":"409","author":"Rain","year":"2001","journal-title":"Nature"},{"key":"2023020212225308000_B18","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1038\/msb4100166","article-title":"The protein network of bacterial motility","volume":"3","author":"Rajagopala","year":"2007","journal-title":"Mol. Syst. Biol"},{"key":"2023020212225308000_B19","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/jbiol36","article-title":"Comprehensive curation and analysis of global interaction networks inSaccharomyces cerevisiae","volume":"5","author":"Reguly","year":"2006","journal-title":"J. Biol"},{"issue":"Database issue","key":"2023020212225308000_B20","doi-asserted-by":"crossref","first-page":"D449","DOI":"10.1093\/nar\/gkh086","article-title":"The database of interacting proteins: 2004 update","volume":"32","author":"Salwinski","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023020212225308000_B21","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/dnares\/dsm021","article-title":"A large-scale protein protein interaction analysis inSynechocystis sp. PCC6803","volume":"14","author":"Sato","year":"2007","journal-title":"DNA Res"},{"key":"2023020212225308000_B22","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1186\/1471-2105-7-360","article-title":"A direct comparison of protein interaction confidence assignment schemes","volume":"7","author":"Suthram","year":"2006","journal-title":"BMC Bioinform"},{"key":"2023020212225308000_B23","doi-asserted-by":"crossref","first-page":"e2292","DOI":"10.1371\/journal.pone.0002292","article-title":"The binary protein interactome ofTreponema pallidum\u2013the syphilis spirochete","volume":"3","author":"Titz","year":"2008","journal-title":"PLoS ONE"},{"issue":"Database issue","key":"2023020212225308000_B24","first-page":"D190","article-title":"The universal protein resource (uniprot)","volume":"36","author":"UniProt-Consortium","year":"2008","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"2023020212225308000_B25","doi-asserted-by":"crossref","first-page":"D358","DOI":"10.1093\/nar\/gkl825","article-title":"STRING 7\u2013recent developments in the integration and prediction of protein interactions","volume":"35","author":"von Mering","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023020212225308000_B26","doi-asserted-by":"crossref","first-page":"e16","DOI":"10.1371\/journal.pbio.0050016","article-title":"The sorcerer II global ocean sampling expedition: expanding the universe of protein families","volume":"5","author":"Yooseph","year":"2007","journal-title":"PLoS Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/22\/2622\/49055422\/bioinformatics_24_22_2622.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/22\/2622\/49055422\/bioinformatics_24_22_2622.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T14:47:10Z","timestamp":1675349230000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/22\/2622\/184682"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,9,11]]},"references-count":26,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2008,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn481","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,11,15]]},"published":{"date-parts":[[2008,9,11]]}}}