{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T13:16:11Z","timestamp":1761743771012,"version":"build-2065373602"},"reference-count":4,"publisher":"Walter de Gruyter GmbH","issue":"2","license":[{"start":{"date-parts":[[2025,3,31]],"date-time":"2025-03-31T00:00:00Z","timestamp":1743379200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100010801","name":"Xunta de Galicia","doi-asserted-by":"publisher","award":["ED431C 2022\/03-GRC"],"award-info":[{"award-number":["ED431C 2022\/03-GRC"]}],"id":[{"id":"10.13039\/501100010801","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ministry of Science and Innovation, Spain","award":["PID2022-138936OB-C31"],"award-info":[{"award-number":["PID2022-138936OB-C31"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Family structures play a crucial role in personal development, social dynamics, and mental health. Traditional systems for encoding genealogical data, such as Ahnentafel and the Register System, offer methods to document lineage but face limitations, particularly in accommodating horizontal relationships or handling changes in family datasets. Modern computational systems like LINKAGE and PED, while powerful for genetic analysis, lack human readability and are challenging to apply in fields where unstructured, narrative data is common, such as sociology or psychiatry. This paper aims to bridge this gap by enhancing Fcodes, a flexible and intuitive algorithm for encoding kinship relationships that is suited for both manual and computational use. Building on our previous work, we present improvements to the Fcodes core algorithm and command-line interface (CLI), as well as the development of F-Tree, a new graphical user interface (GUI) to streamline the encoding process. Additionally, we introduce a method for estimating the coefficient of inbreeding using Fcodes and explore the application of artificial intelligence, namely large language models (LLMs), to automatically infer family relationships from narrative text. These advancements highlight the potential of Fcodes in a wide range of research contexts, from social studies to genetics and mental health research.<\/jats:p>","DOI":"10.1515\/jib-2024-0046","type":"journal-article","created":{"date-parts":[[2025,3,28]],"date-time":"2025-03-28T21:56:19Z","timestamp":1743198979000},"source":"Crossref","is-referenced-by-count":0,"title":["Fcodes update: a kinship encoding framework with F-Tree GUI &amp; LLM inference"],"prefix":"10.1515","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8110-3567","authenticated-orcid":false,"given":"Daniel","family":"P\u00e9rez-Rodr\u00edguez","sequence":"first","affiliation":[{"name":"Dept. of Telematics Engineering, ESEI-Escuela Superior de Ingenier\u00eda Inform\u00e1tica, Universidade de Vigo , 32004 Ourense , Spain"},{"name":"Science and Business S.L. , Edificio CITEXVI , R\u00faa Fonte das Abelleiras s\/n., Local 41.2, Vigo University Campus, 36310 , Vigo , Spain"}]},{"given":"Roberto C.","family":"Ag\u00eds-Balboa","sequence":"additional","affiliation":[{"name":"Neuro Epigenetics Lab, Health Research Institute of Santiago de Compostela (IDIS) , Santiago University Hospital Complex , 15706 Santiago de Compostela , Spain"},{"name":"Translational Research in Neurological Diseases Group, Health Research Institute of Santiago de Compostela (IDIS) , Santiago University Hospital Complex , 15706 Santiago de Compostela , Spain"},{"name":"Servicio de Neurolog\u00eda , Hospital Cl\u00ednico Universitario de Santiago , 15706 Santiago de Compostela , Spain"}]},{"given":"Hugo","family":"L\u00f3pez-Fern\u00e1ndez","sequence":"additional","affiliation":[{"name":"SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS UVIGO , 36213 Vigo , Spain"}]}],"member":"374","published-online":{"date-parts":[[2025,3,31]]},"reference":[{"key":"2025102907580413248_j_jib-2024-0046_ref_001","unstructured":"Curran, JF, Crane, MC, Wray, JH. Numbering your genealogy: basic systems, complex families, and international kin. Falls Church, Virginia: National Genealogical Society; 2008."},{"key":"2025102907580413248_j_jib-2024-0046_ref_002","doi-asserted-by":"crossref","unstructured":"Purcell, S, Neale, B, Todd-Brown, K, Thomas, L, Ferreira, MAR, Bender, D, et al.. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007;81:559\u201375. https:\/\/doi.org\/10.1086\/519795.","DOI":"10.1086\/519795"},{"key":"2025102907580413248_j_jib-2024-0046_ref_003","doi-asserted-by":"crossref","unstructured":"P\u00e9rez Rodr\u00edguez, D, Ag\u00eds Balboa, RC, L\u00f3pez Fern\u00e1ndez, H. Fcodes: a straightforward algorithm for kinships encoding. In: 18th international conference on practical applications of computational biology & bioinformatics: PACBB 2024. Salamanca, Spain; in press. Available from: http:\/\/hdl.handle.net\/11093\/7494.","DOI":"10.1007\/978-3-031-87873-2_10"},{"key":"2025102907580413248_j_jib-2024-0046_ref_004","doi-asserted-by":"crossref","unstructured":"Barker, M, Chue Hong, NP, Katz, DS, Lamprecht, AL, Martinez-Ortiz, C, Psomopoulos, F, et al.. Introducing the FAIR principles for research software. Sci Data 2022;9:622. https:\/\/doi.org\/10.1038\/s41597-022-01710-x.","DOI":"10.1038\/s41597-022-01710-x"}],"container-title":["Journal of Integrative Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.degruyterbrill.com\/document\/doi\/10.1515\/jib-2024-0046\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyterbrill.com\/document\/doi\/10.1515\/jib-2024-0046\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T07:59:54Z","timestamp":1761724794000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.degruyterbrill.com\/document\/doi\/10.1515\/jib-2024-0046\/html"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,31]]},"references-count":4,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2025,7,14]]},"published-print":{"date-parts":[[2025,10,30]]}},"alternative-id":["10.1515\/jib-2024-0046"],"URL":"https:\/\/doi.org\/10.1515\/jib-2024-0046","relation":{},"ISSN":["1613-4516"],"issn-type":[{"type":"electronic","value":"1613-4516"}],"subject":[],"published":{"date-parts":[[2025,3,31]]},"article-number":"20240046"}}