{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T05:07:58Z","timestamp":1772168878055,"version":"3.50.1"},"reference-count":13,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2018,3,29]],"date-time":"2018-03-29T00:00:00Z","timestamp":1522281600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009497","name":"University of Texas at Arlington","doi-asserted-by":"publisher","award":["Startupfund"],"award-info":[{"award-number":["Startupfund"]}],"id":[{"id":"10.13039\/100009497","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns4:p>\n                    We developed a Gene Annotation Easy Viewer (GAEV) that integrates the gene annotation data from the KEGG (Kyoto Encyclopedia of Genes and Genomes) Automatic Annotation Server. GAEV generates an easy-to-read table that summarizes the query gene name, the KO (KEGG Orthology) number, name of gene orthologs, functional definition of the ortholog, and the functional pathways that query gene has been mapped to. Via links to KEGG pathway maps, users can directly examine the interaction between gene products involved in the same molecular pathway. We provide a usage example by annotating the newly published freshwater microcrustacean\n                    <ns4:italic>Daphnia pulex<\/ns4:italic>\n                    genome. This gene-centered view of gene function and pathways will greatly facilitate the genome annotation of non-model species and metagenomics data. GAEV runs on a Windows or Linux system equipped with Python 3 and provides easy accessibility to users with no prior Unix command line experience.\n                  <\/ns4:p>","DOI":"10.12688\/f1000research.14012.1","type":"journal-article","created":{"date-parts":[[2018,3,29]],"date-time":"2018-03-29T11:30:08Z","timestamp":1522323008000},"page":"416","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["Gene Annotation Easy Viewer (GAEV): Integrating KEGG\u2019s Gene Function Annotations and Associated Molecular Pathways"],"prefix":"10.12688","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3878-2151","authenticated-orcid":false,"given":"Trung","family":"Huynh","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1304-9968","authenticated-orcid":false,"given":"Sen","family":"Xu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"2560","published-online":{"date-parts":[[2018,3,29]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"D158-D169","DOI":"10.1093\/nar\/gkw1099","article-title":"UniProt: the universal protein knowledgebase.","volume":"45","author":"A Bateman","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref-2","doi-asserted-by":"publisher","first-page":"W29-W33","DOI":"10.1093\/nar\/gkt282","article-title":"BLAST: a more efficient report with usability improvements.","volume":"41","author":"G Boratyn","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref-3","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications.","volume":"10","author":"C Camacho","year":"2009","journal-title":"BMC Bioinformatics."},{"key":"ref-4","doi-asserted-by":"publisher","first-page":"D190-D199","DOI":"10.1093\/nar\/gkw1107","article-title":"InterPro in 2017-beyond protein family and domain annotations.","volume":"45","author":"R Finn","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref-5","doi-asserted-by":"publisher","first-page":"1236-1240","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: genome-scale protein function classification.","volume":"30","author":"P Jones","year":"2014","journal-title":"Bioinformatics."},{"key":"ref-6","doi-asserted-by":"publisher","first-page":"D353-D361","DOI":"10.1093\/nar\/gkw1092","article-title":"KEGG: new perspectives on genomes, pathways, diseases and drugs.","volume":"45","author":"M Kanehisa","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref-7","doi-asserted-by":"publisher","first-page":"27-30","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: kyoto encyclopedia of genes and genomes.","volume":"28","author":"M Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref-8","doi-asserted-by":"publisher","first-page":"D457-D462","DOI":"10.1093\/nar\/gkv1070","article-title":"KEGG as a reference resource for gene and protein annotation.","volume":"44","author":"M Kanehisa","year":"2016a","journal-title":"Nucleic Acids Res."},{"key":"ref-9","doi-asserted-by":"publisher","first-page":"726-731","DOI":"10.1016\/j.jmb.2015.11.006","article-title":"BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences.","volume":"428","author":"M Kanehisa","year":"2016b","journal-title":"J Mol Biol."},{"key":"ref-10","doi-asserted-by":"publisher","first-page":"e121","DOI":"10.1093\/nar\/gkt263","article-title":"Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions.","volume":"41","author":"J Mistry","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref-11","doi-asserted-by":"publisher","first-page":"324","DOI":"10.1186\/1471-2105-10-324","article-title":"KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database.","volume":"10","author":"K Moutselos","year":"2009","journal-title":"BMC Bioinformatics."},{"key":"ref-12","doi-asserted-by":"publisher","first-page":"2314-2315","DOI":"10.1093\/bioinformatics\/btr377","article-title":"KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats.","volume":"27","author":"C Wrzodek","year":"2011","journal-title":"Bioinformatics."},{"key":"ref-13","doi-asserted-by":"publisher","first-page":"1405-1416","DOI":"10.1534\/g3.116.038638","article-title":"A New Reference Genome Assembly for the Microcrustacean Daphnia pulex.","volume":"7","author":"Z Ye","year":"2017","journal-title":"G3 (Bethesda)."}],"updated-by":[{"DOI":"10.12688\/f1000research.14012.2","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,6,28]],"date-time":"2018-06-28T00:00:00Z","timestamp":1530144000000}},{"DOI":"10.12688\/f1000research.14012.3","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,5,9]],"date-time":"2019-05-09T00:00:00Z","timestamp":1557360000000}}],"container-title":["F1000Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/f1000research.com\/articles\/7-416\/v1\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/7-416\/v1\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/7-416\/v1\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,12,6]],"date-time":"2018-12-06T06:04:54Z","timestamp":1544076294000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/articles\/7-416\/v1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,3,29]]},"references-count":13,"URL":"https:\/\/doi.org\/10.12688\/f1000research.14012.1","relation":{"has-review":[{"id-type":"doi","id":"10.5256\/f1000research.15230.r32636","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.15230.r32642","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.15230.r32642","asserted-by":"object"},{"id-type":"doi","id":"10.5256\/f1000research.15230.r32636","asserted-by":"object"}]},"ISSN":["2046-1402"],"issn-type":[{"value":"2046-1402","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,3,29]]},"assertion":[{"value":"Approved with reservations, Approved with reservations","URL":"https:\/\/f1000research.com\/articles\/7-416\/v1#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.15230.r32636, Fragiskos N Kolisis, Efthymios Ladoukakis, Laboratory\u00a0of\u00a0Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece, 16 Apr 2018, version 1, 2 approved with reservations","URL":"https:\/\/f1000research.com\/articles\/7-416\/v1#referee-response-32636","order":0,"name":"referee-response-32636","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Trung Huynh<\/b>; \n<i>Posted: 23 May 2018<\/i>;  Dear Dr. Kolisis, &nbsp; Thanks very much for your comments on our manuscript. Please see below for how we revised our manuscript to address your concerns. &nbsp; 1. \n<i>Nevertheless this reviewer considers this endeavour to have already been covered by other bioinformatic tools with which a comparison would be necessary to underline the importance of the new tool. For example tools like MEGAN can provide a thorough investigation of the existing KEGG pathways in a genome\/metagenome (although by using an older and not commercial version of the KEGG database). Furthermore MinPath can be also used in combination with KEGG generated datasets in order to provide a similar pathway reconstruction analysis.<\/i>  \n<b>Response<\/b>: Our goal with our new tool is to provide a gene-centric view of molecular pathways, where each gene is accompanied by all the pathways where this gene is predicted to play a role. This is different from the purposes of MEGAN and Minpath. We emphasized this idea in the last paragraph of Introduction and drew comparison with MEGAN and Minpath.  2\n<i>. Moreover during the Conclusions section the authors do not seem to explain the methodology in order to examine the differences between Daphnia and Drosophila and how that (and similar analyses) can be achieved solely (or more intuitively) by exploiting this particular tool.<\/i>  \n<b>Response<\/b>: This example of \n<i>Daphnia<\/i> circadian pathway is to demonstrate using this tool for initial exploration of non-model organisms\u2019 genomes to understand the conservation of specific pathways compared to established model systems (i.e., Drosophila). The Drosophila circadian pathway is provided through KEGG database. Users can directly examine their interested pathways from the results of GAEV (click on the link in the generated html file) and view the pathways and mapped genes on KEGG website. We provide a brief explanation of how to technically view the pathway on KEGG server in Discussion.","URL":"https:\/\/f1000research.com\/articles\/7-416\/v1#referee-comment-3674","order":1,"name":"referee-comment-3674","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.15230.r32642, Tonia S. Schwartz, Department of Biological Sciences, Auburn University, Auburn, AL, USA, 02 May 2018, version 1, 2 approved with reservations","URL":"https:\/\/f1000research.com\/articles\/7-416\/v1#referee-response-32642","order":2,"name":"referee-response-32642","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Trung Huynh<\/b>; \n<i>Posted: 23 May 2018<\/i>;  Dear Dr. Schwartz, Thanks very much for your comments on our manuscript. Please see below for how we revised our manuscript to address your concerns. \n<i>1. Although I can start the python script running using python3, the example_input.txt file cannot be found when I enter the relative path or the absolute path. This is despite the input file being in the same folder as the script. My bioinformatics technician also encountered the same problem. Thus it seems there is an error in the script that would need to be corrected prior to acceptance of the manuscript.<\/i> \n<b>Response<\/b>: We have found the bug in our code that prevented the script from finding files on Linux and Mac OS properly. This bug has been fixed as of version 1.1.1.  \n<i>2. This tool is presented as accessible and user-friendly, and the authors use the example from Ye et al. 2017 of&nbsp; \u201cthe query protein sequences in a fasta file\u201d. But a protein sequence file is not provided with that paper (that I could find). Thus there an assumed knowledge gap that your reader needs to be able to use this tool as you describe. I suggest you provide additional information on how users can go from a genome with predicted genes (i.e. a .gtf or .gff3 file) to obtain those query sequences for input into the KEGG.&nbsp;<\/i> \n<b>Response<\/b>: We provide a fasta file of Daphnia protein sequence through the github page for GAEV. Moreover, in the manuscript we recommend users to use tools such as gff2sequence to create query sequences using information from gtf\/gff files. See 2\n<sup>nd<\/sup> paragraph of Use Cases.  \n<i>3. You may also want to mention that researchers working with non-model organisms could start with a de novo transcriptome or as an input file.<\/i> \n<b>Response<\/b>: Addressed accordingly. See 2\n<sup>nd<\/sup> paragraph of Use Cases.","URL":"https:\/\/f1000research.com\/articles\/7-416\/v1#referee-comment-3675","order":3,"name":"referee-comment-3675","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"University of Texas at Arlington. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":4,"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"}]}}