{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T18:17:19Z","timestamp":1783102639032,"version":"3.54.6"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T00:00:00Z","timestamp":1782345600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"BMBF-funded de"},{"name":"NBI Cloud within the German Network for Bioinformatics Infrastructure","award":["031A532B"],"award-info":[{"award-number":["031A532B"]}]},{"name":"NBI Cloud within the German Network for Bioinformatics Infrastructure","award":["031A533A"],"award-info":[{"award-number":["031A533A"]}]},{"name":"NBI Cloud within the German Network for Bioinformatics Infrastructure","award":["031A533B"],"award-info":[{"award-number":["031A533B"]}]},{"name":"NBI Cloud within the German Network for Bioinformatics Infrastructure","award":["031A534A"],"award-info":[{"award-number":["031A534A"]}]},{"name":"NBI Cloud within the German Network for Bioinformatics Infrastructure","award":["031A535A"],"award-info":[{"award-number":["031A535A"]}]},{"name":"NBI Cloud within the German Network for Bioinformatics Infrastructure","award":["031A537A"],"award-info":[{"award-number":["031A537A"]}]},{"name":"NBI Cloud within the German Network for Bioinformatics Infrastructure","award":["031A537B"],"award-info":[{"award-number":["031A537B"]}]},{"name":"NBI Cloud within the German Network for Bioinformatics Infrastructure","award":["031A537C"],"award-info":[{"award-number":["031A537C"]}]},{"name":"NBI Cloud within the German Network for Bioinformatics Infrastructure","award":["031A537D"],"award-info":[{"award-number":["031A537D"]}]},{"name":"NBI Cloud within the German Network for Bioinformatics Infrastructure","award":["031A538A"],"award-info":[{"award-number":["031A538A"]}]},{"DOI":"10.13039\/501100004189","name":"Max Planck Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004189","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Organisms within ecological systems often engage in molecular interactions that mediate key biological processes, such as protein\u2013protein interactions involved in host\u2013pathogen recognition and symbiosis. Characterization of these interactions at a molecular level is essential for understanding the mechanistic, evolutionary, and functional basis of interspecies interactions, as well as for informing potential therapeutic interventions. However, progress in this field is significantly impeded by the lack of a comprehensive database of interacting species at molecular resolution and the limited availability of experimental data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduce the Interacting Species Database (ISDB), a comprehensive resource that catalogs interspecies interactions, annotated with NCBI taxonomic identifiers, interaction types and known molecular interactions. The ISDB encompasses 858\u00a0229 interacting species pairs and 171\u00a0713 interspecies protein-protein interactions within 261\u00a0287 organisms. ISDB is designed to support researchers in searching for, downloading, and depositing interspecies interaction data, which facilitates the study of ecological dynamics across diverse research domains.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The ISDB is available via a web interface (https:\/\/www.elhabashylab.org\/isdb), open-source code on GitHub (https:\/\/github.com\/ElhabashyLab\/ISDB) under the MIT license and is archived on Zenodo (Version v1.0.1, DOI: 10.5281\/zenodo.20162385).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag419","type":"journal-article","created":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T11:50:59Z","timestamp":1782301859000},"source":"Crossref","is-referenced-by-count":0,"title":["Interacting Species Database (ISDB): comprehensive resource for interspecies interactions at the molecular level"],"prefix":"10.1093","volume":"42","author":[{"given":"Michael","family":"Mederer","sequence":"first","affiliation":[{"name":"Department for Internal Medicine I (Gastroenterology, Hepatology, Endocrinology, and Metabolism), Medical University of Innsbruck , Innsbruck A-6020 ,","place":["Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anupam","family":"Gautam","sequence":"additional","affiliation":[{"name":"Institute for Bioinformatics and Medical Informatics, University of T\u00fcbingen , Maria-von-Linden-Str. 6 , T\u00fcbingen 72076,","place":["Germany"]},{"name":"Department of Microbiome Science, Max Planck Institute for Biology T\u00fcbingen , Max-Planck-Ring 5 , T\u00fcbingen 72076,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1739-4598","authenticated-orcid":false,"given":"Oliver","family":"Kohlbacher","sequence":"additional","affiliation":[{"name":"Institute for Bioinformatics and Medical Informatics, University of T\u00fcbingen , Maria-von-Linden-Str. 6 , T\u00fcbingen 72076,","place":["Germany"]},{"name":"Department of Computer Science, University of T\u00fcbingen , Maria-von-Linden-Str. 1 , T\u00fcbingen 72076,","place":["Germany"]},{"name":"Institute for Translational Bioinformatics, University Hospital T\u00fcbingen , Schaffhausenstra\u00dfe 77 , T\u00fcbingen 72072,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1959-4836","authenticated-orcid":false,"given":"Andrei","family":"Lupas","sequence":"additional","affiliation":[{"name":"Department of Protein Evolution, Max Planck Institute for Biology T\u00fcbingen , Max-Planck-Ring 5 , T\u00fcbingen 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