{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:36:00Z","timestamp":1760146560803,"version":"build-2065373602"},"reference-count":33,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2024,11,20]],"date-time":"2024-11-20T00:00:00Z","timestamp":1732060800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"State Secretary for Digitalisation and Artificial Intelligence, Ministry of Economic affairs and Digital Transformation","award":["TSI-100903-2019-11","IMIDTA\/2022\/38"],"award-info":[{"award-number":["TSI-100903-2019-11","IMIDTA\/2022\/38"]}]},{"name":"Valencian Institute for Business Competitiveness (IVACE)","award":["TSI-100903-2019-11","IMIDTA\/2022\/38"],"award-info":[{"award-number":["TSI-100903-2019-11","IMIDTA\/2022\/38"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BDCC"],"abstract":"<jats:p>In this work, we describe the implementation of an infrastructure of conversational chatbots by using natural language processing and training within the Rasa framework. We use this infrastructure to create a chatbot assistant for the users of a bioinformatics suite. This suite provides a customized interface solution for omic pipelines and workflows, and it is named GPRO. The infrastructure has also been used to build another chatbot for a Laboratory Information Management System (LIMS). The two chatbots (namely, Genie and Abu) have been built on an open framework that uses natural language understanding (NLU) and machine learning techniques to understand user queries and respond to them. Users can seamlessly interact with the chatbot to receive support on navigating the GPRO pipelines and workflows. The chatbot provides a bridge between users and the wealth of bioinformatics knowledge available online.<\/jats:p>","DOI":"10.3390\/bdcc8110163","type":"journal-article","created":{"date-parts":[[2024,11,20]],"date-time":"2024-11-20T03:57:04Z","timestamp":1732075024000},"page":"163","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Practical Design and Implementation of Virtual Chatbot Assistants for Bioinformatics Based on a NLU Open Framework"],"prefix":"10.3390","volume":"8","author":[{"given":"Aya Allah","family":"Elsayed","sequence":"first","affiliation":[{"name":"Biotechvana, Parc Cient\u00edfic Universitat de Val\u00e8ncia, 46980 Paterna, Spain"},{"name":"VRAIN, Universitat Polit\u00e8cnica de Val\u00e8ncia, Camino de Vera s\/n, 46022 Valencia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2343-5029","authenticated-orcid":false,"given":"Ahmed Ibrahem","family":"Hafez","sequence":"additional","affiliation":[{"name":"Biotechvana, Parc Cient\u00edfic Universitat de Val\u00e8ncia, 46980 Paterna, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raquel","family":"Cepri\u00e1n","sequence":"additional","affiliation":[{"name":"Biotechvana, Parc Cient\u00edfic Universitat de Val\u00e8ncia, 46980 Paterna, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gen\u00eds","family":"Mart\u00ednez","sequence":"additional","affiliation":[{"name":"Biotechvana, Parc Cient\u00edfic Universitat de Val\u00e8ncia, 46980 Paterna, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alejandro","family":"Granados","sequence":"additional","affiliation":[{"name":"VRAIN, Universitat Polit\u00e8cnica de Val\u00e8ncia, Camino de Vera s\/n, 46022 Valencia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8355-5911","authenticated-orcid":false,"given":"Beatriz","family":"Soriano","sequence":"additional","affiliation":[{"name":"Biotechvana, Parc Cient\u00edfic Universitat de Val\u00e8ncia, 46980 Paterna, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1402-4743","authenticated-orcid":false,"given":"Carlos","family":"Llorens","sequence":"additional","affiliation":[{"name":"Biotechvana, Parc Cient\u00edfic Universitat de Val\u00e8ncia, 46980 Paterna, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2393-9224","authenticated-orcid":false,"given":"Jos\u00e9 M.","family":"Sempere","sequence":"additional","affiliation":[{"name":"VRAIN, Universitat Polit\u00e8cnica de Val\u00e8ncia, Camino de Vera s\/n, 46022 Valencia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,11,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Caldarini, G., Jaf, S., and McGarry, K. (2022). A literature survey of recent advances in chatbots. Information, 13.","DOI":"10.3390\/info13010041"},{"key":"ref_2","first-page":"225","article-title":"A literature review on chatbots in healthcare domain","volume":"8","author":"Bhirud","year":"2019","journal-title":"Int. J. Sci. Technol. Res."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Almansor, E.H., and Hussain, F.K. (2020). Survey on intelligent chatbots: State-of-the-art and future research directions. Complex, Intelligent, and Software Intensive Systems: Proceedings of the 13th International Conference on Complex, Intelligent, and Software Intensive Systems (CISIS-2019), Sydney, Australia, 3\u20135 July 2019, Springer.","DOI":"10.1007\/978-3-030-22354-0_47"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Wollny, S., Schneider, J., Mitri, D.D., Weidlich, J., Rittberger, M., and Drachsler, H. (2021). Are we there yet?\u2014A systematic literature review on chatbots in education. Front. Artif. Intell., 4.","DOI":"10.3389\/frai.2021.654924"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Goel, R., Goswami, R.P., Totlani, S., Arora, P., Bansal, R., and Vij, D. (2022, January 28\u201329). Machine learning based healthcare chatbot. Proceedings of the 2022 2nd International Conference on Advance Computing and Innovative Technologies in Engineering (ICACITE), Greater Noida, India.","DOI":"10.1109\/ICACITE53722.2022.9823901"},{"key":"ref_6","unstructured":"Ayanouz, S., Abdelhakim, B., and Benhmed, M. (April, January 31). A smart chatbot architecture based NLP and machine learning for health care assistance. Proceedings of the 3rd International Conference on Networking, Information Systems & Security, Marrakech, Morocco."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1016\/j.jbusres.2018.10.004","article-title":"Chatbot e-service and customer satisfaction regarding luxury brands","volume":"117","author":"Chung","year":"2020","journal-title":"J. Bus. Res."},{"key":"ref_8","first-page":"13","article-title":"How chatbot e-services motivate communication credibility and lead to customer satisfaction: The perspective of Thai consumers in the apparel retailing context","volume":"18","author":"Jansom","year":"2022","journal-title":"Innov. Mark."},{"key":"ref_9","unstructured":"Bocklisch, T., Faulkner, J., Pawlowski, N., and Nichol, A. (2017). Rasa: Open source language understanding and dialogue management. arXiv."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Boonstra, L. (2021). Definitive Guide to Conversational AI with Dialogflow and Google Cloud, Springer.","DOI":"10.1007\/978-1-4842-7014-1"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1055\/s-0038-1634431","article-title":"What is bioinformatics? A proposed definition and overview of the field","volume":"40","author":"Luscombe","year":"2001","journal-title":"Methods Inf. Med."},{"key":"ref_12","unstructured":"Barh, D., and Azevedo, V. (2018). Overview and Principles of Bioengineering: The Drivers of Omics Technologies. Omics Technologies and Bio-Engineering, Academic Press."},{"key":"ref_13","unstructured":"Barh, D., and Azevedo, V. (2018). Next-Generation Sequencing and Data Analysis: Strategies, Tools, Pipelines and Protocols. Omics Technologies and Bio-Engineering, Academic Press."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Ouzounis, C.A. (2012). Rise and Demise of Bioinformatics? Promise and Progress. PLoS Comput. Biol., 8.","DOI":"10.1371\/journal.pcbi.1002487"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"2520","DOI":"10.1093\/bioinformatics\/bts480","article-title":"Snakemake - a scalable bioinformatics workflow engine","volume":"28","author":"Rahmann","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_16","unstructured":"Barh, D., and Azevedo, V. (2018). Computational Techniques in Data Integration and Big Data Handling in Omics. Omics Technologies and Bio-Engineering, Academic Press."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Dudley, J.T., and Butte, A.J. (2009). A Quick Guide for Developing Effective Bioinformatics Programming Skills. PLoS Comput. Biol., 5.","DOI":"10.1371\/journal.pcbi.1000589"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1016\/j.csbj.2017.10.001","article-title":"Challenges in the Setup of Large-scale Next-Generation Sequencing Analysis Workflows","volume":"15","author":"Kulkarni","year":"2017","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1272","DOI":"10.1093\/bioinformatics\/bts128","article-title":"SEQanswers: An open access community for collaboratively decoding genomes","volume":"28","author":"Li","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Parnell, L.D., Lindenbaum, P., Shameer, K., Dall\u2019Olio, G.M., Swan, D.C., Jensen, L.J., Cockell, S.J., Pedersen, B.S., Mangan, M.E., and Miller, C.A. (2011). BioStar: An online question & answer resource for the bioinformatics community. PLoS Comput. Biol., 7.","DOI":"10.1371\/journal.pcbi.1002216"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"Tommaso","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Hafez, A.I., Soriano, B., Elsayed, A.A., Futami, R., Ceprian, R., Ramos-Ruiz, R., Martinez, G., Roig, F.J., Torres-Font, M.A., and Naya-Catala, F. (2023). Client Applications and Server-Side Docker for Management of RNASeq and\/or VariantSeq Workflows and Pipelines of the GPRO Suite. Genes, 14.","DOI":"10.3390\/genes14020267"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/j.eswa.2005.09.042","article-title":"Applications of artificial intelligence in bioinformatics: A review","volume":"30","author":"Ezziane","year":"2006","journal-title":"Expert Syst. Appl."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Tang, B., Pan, Z., Yin, K., and Khateeb, A. (2019). Recent Advances of Deep Learning in Bioinformatics and Computational Biology. Front. Genet., 10.","DOI":"10.3389\/fgene.2019.00214"},{"key":"ref_26","unstructured":"Futami, R., Mu\u00f1oz-Pomer, A., Viu, J.M., Dominguez-Escriba, L., Covelli, L., Bernet, G.P., Sempere, J.M., Moya, A., and Llorens, C. (2011). GPRO: The professional tool for annotation, management and functional analysis of omic sequences and databases. Biotechvana Bioinform., SOFT3."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"D492","DOI":"10.1093\/nar\/gkp858","article-title":"The NCBI BioSystems database","volume":"38","author":"Geer","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1109\/MS.2009.144","article-title":"Web Application Tests with Selenium","volume":"26","author":"Bruns","year":"2009","journal-title":"IEEE Softw."},{"key":"ref_29","first-page":"5883","article-title":"Using JSON for Data Exchanging in Web Service Applications","volume":"7","author":"Peng","year":"2011","journal-title":"J. Comput. Inf. Syst."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Cer, D., Yang, Y., Kong, S., Hua, N., Limtiaco, N., John, R.S., Constant, N., Guajardo-Cespedes, M., Yuan, S., and Tar, C. (2018). Universal Sentence Encoder. arXiv.","DOI":"10.18653\/v1\/D18-2029"},{"key":"ref_31","unstructured":"(2024, July 29). YAML. Available online: https:\/\/ymlthis.r-lib.org\/."},{"key":"ref_32","unstructured":"(2024, July 29). NLTK UDHR Corpus Reader. Available online: https:\/\/www.nltk.org\/api\/nltk.corpus.reader.udhr.html."},{"key":"ref_33","unstructured":"Powers, D.M.W. (2020). Evaluation: From precision, recall and F-measure to ROC, informedness, markedness and correlation. arXiv."}],"container-title":["Big Data and Cognitive Computing"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2504-2289\/8\/11\/163\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T16:35:41Z","timestamp":1760114141000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2504-2289\/8\/11\/163"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,20]]},"references-count":33,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2024,11]]}},"alternative-id":["bdcc8110163"],"URL":"https:\/\/doi.org\/10.3390\/bdcc8110163","relation":{},"ISSN":["2504-2289"],"issn-type":[{"type":"electronic","value":"2504-2289"}],"subject":[],"published":{"date-parts":[[2024,11,20]]}}}