{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T19:44:13Z","timestamp":1740167053430,"version":"3.37.3"},"reference-count":6,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2018,6,11]],"date-time":"2018-06-11T00:00:00Z","timestamp":1528675200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["P41GM103504"],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"Identifier Mapping, the association of terms across disparate taxonomies and databases, is a common hurdle in bioinformatics workflows. The idmapper<\/ns4:italic> app for Cytoscape simplifies identifier mapping for genes and proteins in the context of common biological networks. This app provides a unified interface to different identifier resources accessible through a right-click on the table's column header. It also provides an OSGi programming interface via Cytoscape Commands<\/ns4:italic> and CyREST<\/ns4:italic> that can be utilized for identifier mapping in scripts and other Cytoscape apps, and supports integrated Swagger documentation.<\/ns4:p>","DOI":"10.12688\/f1000research.14807.1","type":"journal-article","created":{"date-parts":[[2018,6,11]],"date-time":"2018-06-11T09:05:09Z","timestamp":1528707909000},"page":"725","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Identifier Mapping in Cytoscape: idmapper"],"prefix":"10.12688","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9659-6926","authenticated-orcid":false,"given":"Adam","family":"Treister","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5706-2163","authenticated-orcid":false,"given":"Alexander R.","family":"Pico","sequence":"additional","affiliation":[]}],"member":"2560","published-online":{"date-parts":[[2018,6,11]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"2366-2382","DOI":"10.1038\/nprot.2007.324","article-title":"Integration of biological networks and gene expression data using Cytoscape.","volume":"2","author":"M Cline","year":"2007","journal-title":"Nat Protoc."},{"key":"ref-2","doi-asserted-by":"publisher","first-page":"2498-2504","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks.","volume":"13","author":"P Shannon","year":"2003","journal-title":"Genome Res."},{"key":"ref-3","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/1471-2105-11-5","article-title":"The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services.","volume":"11","author":"M van Iersel","year":"2010","journal-title":"BMC Bioinformatics."},{"key":"ref-4","doi-asserted-by":"publisher","first-page":"148","DOI":"10.12688\/f1000research.4521.1","article-title":"BridgeDb app: unifying identifier mapping services for Cytoscape [version 1; referees: 2 approved].","volume":"3","author":"J Gao","year":"2014","journal-title":"F1000Res."},{"key":"ref-5","doi-asserted-by":"publisher","first-page":"D362-D368","DOI":"10.1093\/nar\/gkw937","article-title":"The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.","volume":"45","author":"D Szklarczyk","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref-6","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.1246814","article-title":"cytoscape\/idmapper: 3.6.3 (Version 3.6.3).","author":"A Treister","year":"2018","journal-title":"Zenodo."}],"updated-by":[{"updated":{"date-parts":[[2018,8,6]],"date-time":"2018-08-06T00:00:00Z","timestamp":1533513600000},"DOI":"10.12688\/f1000research.14807.2","type":"new_version","source":"publisher","label":"New version"}],"container-title":["F1000Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/f1000research.com\/articles\/7-725\/v1\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/7-725\/v1\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/7-725\/v1\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,12,6]],"date-time":"2018-12-06T05:31:17Z","timestamp":1544074277000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/articles\/7-725\/v1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,6,11]]},"references-count":6,"URL":"https:\/\/doi.org\/10.12688\/f1000research.14807.1","relation":{"has-review":[{"id-type":"doi","id":"10.5256\/f1000research.16116.r34906","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.16116.r34907","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.16116.r34908","asserted-by":"subject"}]},"ISSN":["2046-1402"],"issn-type":[{"type":"electronic","value":"2046-1402"}],"subject":[],"published":{"date-parts":[[2018,6,11]]},"assertion":[{"value":"Indexed","URL":"https:\/\/f1000research.com\/articles\/7-725\/v1#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.16116.r34908, Ruth Isserlin, Donnelly Centre for Cellular and Biomolecular Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada, 12 Jun 2018, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/7-725\/v1#referee-response-34908","order":0,"name":"referee-response-34908","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"Alexander Pico<\/b>; \nPosted: 26 Jun 2018<\/i>; Ruth, thank you so much for your thorough review. These clarifications, fixes and additions have greatly improved the article. Version 2 should be released soon, addressing all the issues you raised. We decided not to include the regular expressions in Table 1, however. They are messy and are what you'd expect from the example identifiers provided, which we feel do a better job of communicating what to expect from each data source. We hope you'll have a chance to look over version 2 and find that it meets your expectations.","URL":"https:\/\/f1000research.com\/articles\/7-725\/v1#referee-comment-3766","order":1,"name":"referee-comment-3766","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.16116.r34906, Augustin Luna, cBio Center, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA, 03 Jul 2018, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/7-725\/v1#referee-response-34906","order":2,"name":"referee-response-34906","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"Alexander Pico<\/b>; \nPosted: 03 Jul 2018<\/i>; Augustin, thanks for the review.1. The regular expressions come from BridgeDb (which in turn gets them from identifiers.org). If there isn't a match to the regular expressions (or if more than one system is matched), then it just picks the first option in the list. A few of the system types aren't well specified. It's a simple matter to override this in the UI. We will add a sentence or two in the next version of the paper in response to all reviewers.2. Right. RCy3 supports both a generic function call and a specific mapTableColumn function call. Since this is a "core" app, the RCy3 package supports custom convenience functions to make this operation easier to use and better documented. We will add a more detailed description and contrasting example in the next version of the paper.","URL":"https:\/\/f1000research.com\/articles\/7-725\/v1#referee-comment-3795","order":3,"name":"referee-comment-3795","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.16116.r34907, Nadezhda T. Doncheva, Novo Nordisk Foundation Center for Protein Research & Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark, 19 Jul 2018, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/7-725\/v1#referee-response-34907","order":4,"name":"referee-response-34907","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"Alexander Pico<\/b>; \nPosted: 22 Jul 2018<\/i>; Nadya, thank you for the review. We have prepared a version 2 of the paper that addresses your main comments and corrections. A couple additional notes that are not reflected in the updated text: The R and Python library projects are independently developed, so coordinating on parameter names is impossible and in many cases not desired since consistency within each is much more important than across them, i.e., most users will pick one or the other and want maximum consistency with the conventions of that language, etc. Figure 2 is a requirement for all Cytoscape Automation papers. Even for cases like ours where there is just one operation. It's our fault for making such a simple app! Thanks for the bug reports. We will try to reproduce and fix these for future releases of the app.","URL":"https:\/\/f1000research.com\/articles\/7-725\/v1#referee-comment-3849","order":5,"name":"referee-comment-3849","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"We would like to acknowledge funding from National Institute of General Medical Sciences [P41GM103504 (ARP, AT)]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":6,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}