{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T04:28:09Z","timestamp":1768969689982,"version":"3.49.0"},"reference-count":15,"publisher":"Springer Science and Business Media LLC","issue":"S3","license":[{"start":{"date-parts":[[2023,12,15]],"date-time":"2023-12-15T00:00:00Z","timestamp":1702598400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,12,15]],"date-time":"2023-12-15T00:00:00Z","timestamp":1702598400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000002","name":"national institutes of health","doi-asserted-by":"publisher","award":["75N91020C00017"],"award-info":[{"award-number":["75N91020C00017"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"national institutes of health","doi-asserted-by":"publisher","award":["U01HG009454"],"award-info":[{"award-number":["U01HG009454"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01AI130460"],"award-info":[{"award-number":["R01AI130460"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>With more clinical trials are offering optional participation in the collection of bio-specimens for biobanking comes the increasing complexity of requirements of informed consent forms. The aim of this study is to develop an automatic natural language processing (NLP) tool to annotate informed consent documents to promote biorepository data regulation, sharing, and decision support. We collected informed consent documents from several publicly available sources, then manually annotated them, covering sentences containing permission information about the sharing of either bio-specimens or donor data, or conducting genetic research or future research using bio-specimens or donor data.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>We evaluated a variety of machine learning algorithms including random forest (RF) and support vector machine (SVM) for the automatic identification of these sentences. 120 informed consent documents containing 29,204 sentences were annotated, of which 1250 sentences (4.28%) provide answers to a permission question. A support vector machine (SVM) model achieved a F-1 score of 0.95 on classifying the sentences when using a gold standard, which is a prefiltered corpus containing all relevant sentences.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>This study provides the feasibility of using machine learning tools to classify permission-related sentences in informed consent documents.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-023-05568-7","type":"journal-article","created":{"date-parts":[[2023,12,15]],"date-time":"2023-12-15T13:02:17Z","timestamp":1702645337000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Machine learning-based donor permission extraction from informed consent documents"],"prefix":"10.1186","volume":"24","author":[{"given":"Meng","family":"Zhang","sequence":"first","affiliation":[]},{"given":"Madhuri","family":"Sankaranarayanapillai","sequence":"additional","affiliation":[]},{"given":"Jingcheng","family":"Du","sequence":"additional","affiliation":[]},{"given":"Yang","family":"Xiang","sequence":"additional","affiliation":[]},{"given":"Frank J.","family":"Manion","sequence":"additional","affiliation":[]},{"given":"Marcelline R.","family":"Harris","sequence":"additional","affiliation":[]},{"given":"Cooper","family":"Stansbury","sequence":"additional","affiliation":[]},{"given":"Huy Anh","family":"Pham","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4267-1924","authenticated-orcid":false,"given":"Cui","family":"Tao","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,12,15]]},"reference":[{"key":"5568_CR1","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1002\/cpt.461","volume":"101","author":"A Warner","year":"2017","unstructured":"Warner A, Moore H, Reinhard D, et al. Harmonizing global biospecimen consent practices to advance translational research: a call to action. Clin Pharmacol Ther. 2017;101:317\u20139.","journal-title":"Clin Pharmacol Ther"},{"key":"5568_CR2","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1177\/1054773817722690","volume":"28","author":"ER Eisenhauer","year":"2019","unstructured":"Eisenhauer ER, Tait AR, Rieh SY, et al. Participants\u2019 understanding of informed consent for biobanking: a systematic review. Clin Nurs Res. 2019;28:30\u201351.","journal-title":"Clin Nurs Res"},{"key":"5568_CR3","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1111\/bioe.12550","volume":"33","author":"NC Manson","year":"2019","unstructured":"Manson NC. The ethics of biobanking: Assessing the right to control problem for broad consent. Bioethics. 2019;33:540\u20139.","journal-title":"Bioethics"},{"key":"5568_CR4","doi-asserted-by":"publisher","first-page":"885","DOI":"10.1038\/nmeth.2142","volume":"9","author":"Z Master","year":"2012","unstructured":"Master Z, Nelson E, Murdoch B, et al. Biobanks, consent and claims of consensus. Nat Methods. 2012;9:885\u20138.","journal-title":"Nat Methods"},{"key":"5568_CR5","doi-asserted-by":"publisher","first-page":"1607","DOI":"10.1038\/ejhg.2015.27","volume":"23","author":"A Husedzinovic","year":"2015","unstructured":"Husedzinovic A, Ose D, Schickhardt C, et al. Stakeholders\u2019 perspectives on biobank-based genomic research: systematic review of the literature. Eur J Hum Genet. 2015;23:1607\u201314.","journal-title":"Eur J Hum Genet"},{"key":"5568_CR6","unstructured":"Federal Policy for the Protection of Human Subjects [Internet]. Fed. Regist. 2015 [cited 2020 Apr 23]. Available from: https:\/\/www.federalregister.gov\/documents\/2015\/09\/08\/2015-21756\/federal-policy-for-the-protection-of-human-subjects."},{"key":"5568_CR7","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1080\/15265161.2019.1587031","volume":"19","author":"LM Beskow","year":"2019","unstructured":"Beskow LM, Weinfurt KP. Exploring understanding of \u201cunderstanding\u201d: the paradigm case of biobank consent comprehension. Am J Bioeth. 2019;19:6\u201318.","journal-title":"Am J Bioeth"},{"key":"5568_CR8","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1038\/s41746-020-0302-y","volume":"3","author":"OT Inan","year":"2020","unstructured":"Inan OT, Tenaerts P, Prindiville SA, et al. Digitizing clinical trials. NPJ Digit Med. 2020;3:101.","journal-title":"NPJ Digit Med"},{"key":"5568_CR9","unstructured":"Yamada H, Takemura T, Asai T, et al. A Development of Automatic Audit System for Written Informed Consent using Machine Learning. MEDINFO 2015 EHealth-Enabled Health. 2015;926\u2013926."},{"key":"5568_CR10","unstructured":"Team CD. CLAMP | Natural Language Processing (NLP) Software [Internet]. [cited 2020 Aug 22]. Available from: https:\/\/clamp.uth.edu\/."},{"key":"5568_CR11","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1177\/001316446002000104","volume":"20","author":"J Cohen","year":"1960","unstructured":"Cohen J. A coefficient of agreement for nominal scales. Educ Psychol Meas. 1960;20:37\u201346.","journal-title":"Educ Psychol Meas"},{"key":"5568_CR12","unstructured":"spaCy \u00b7 Industrial-strength Natural Language Processing in Python [Internet]. [cited 2020 Aug 23]. Available from: https:\/\/spacy.io\/."},{"key":"5568_CR13","unstructured":"scikit-learn: machine learning in Python \u2014 scikit-learn 0.23.2 documentation [Internet]. [cited 2020 Aug 23]. 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CEUR Workshop Proc. 2014;1309:61\u20133.","journal-title":"CEUR Workshop Proc"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-023-05568-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-023-05568-7\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-023-05568-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,15]],"date-time":"2023-12-15T13:02:27Z","timestamp":1702645347000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-023-05568-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,12,15]]},"references-count":15,"journal-issue":{"issue":"S3","published-online":{"date-parts":[[2023,12]]}},"alternative-id":["5568"],"URL":"https:\/\/doi.org\/10.1186\/s12859-023-05568-7","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,12,15]]},"assertion":[{"value":"17 September 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 November 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 December 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"477"}}