Clinical records anonymisation and text extraction (CRATE): an open-source software system
Abstract Background Electronic medical records contain information of value for research, but contain identifiable and often highly sensitive confidential information. Patient-identifiable information cannot in general be shared outside clinical care teams without explicit consent, but anonymisation...
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| Format: | Article |
| Language: | English |
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BMC
2017-04-01
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| Series: | BMC Medical Informatics and Decision Making |
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| Online Access: | http://link.springer.com/article/10.1186/s12911-017-0437-1 |
| _version_ | 1819177838824128512 |
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| author | Rudolf N. Cardinal |
| author_facet | Rudolf N. Cardinal |
| author_sort | Rudolf N. Cardinal |
| collection | DOAJ |
| description | Abstract Background Electronic medical records contain information of value for research, but contain identifiable and often highly sensitive confidential information. Patient-identifiable information cannot in general be shared outside clinical care teams without explicit consent, but anonymisation/de-identification allows research uses of clinical data without explicit consent. Results This article presents CRATE (Clinical Records Anonymisation and Text Extraction), an open-source software system with separable functions: (1) it anonymises or de-identifies arbitrary relational databases, with sensitivity and precision similar to previous comparable systems; (2) it uses public secure cryptographic methods to map patient identifiers to research identifiers (pseudonyms); (3) it connects relational databases to external tools for natural language processing; (4) it provides a web front end for research and administrative functions; and (5) it supports a specific model through which patients may consent to be contacted about research. Conclusions Creation and management of a research database from sensitive clinical records with secure pseudonym generation, full-text indexing, and a consent-to-contact process is possible and practical using entirely free and open-source software. |
| first_indexed | 2024-12-22T21:33:01Z |
| format | Article |
| id | doaj.art-3263fb23b6504cedb56d9ea757d38660 |
| institution | Directory Open Access Journal |
| issn | 1472-6947 |
| language | English |
| last_indexed | 2024-12-22T21:33:01Z |
| publishDate | 2017-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Medical Informatics and Decision Making |
| spelling | doaj.art-3263fb23b6504cedb56d9ea757d386602022-12-21T18:11:51ZengBMCBMC Medical Informatics and Decision Making1472-69472017-04-0117111210.1186/s12911-017-0437-1Clinical records anonymisation and text extraction (CRATE): an open-source software systemRudolf N. Cardinal0Behavioural and Clinical Neuroscience Institute, Department of Psychiatry, University of CambridgeAbstract Background Electronic medical records contain information of value for research, but contain identifiable and often highly sensitive confidential information. Patient-identifiable information cannot in general be shared outside clinical care teams without explicit consent, but anonymisation/de-identification allows research uses of clinical data without explicit consent. Results This article presents CRATE (Clinical Records Anonymisation and Text Extraction), an open-source software system with separable functions: (1) it anonymises or de-identifies arbitrary relational databases, with sensitivity and precision similar to previous comparable systems; (2) it uses public secure cryptographic methods to map patient identifiers to research identifiers (pseudonyms); (3) it connects relational databases to external tools for natural language processing; (4) it provides a web front end for research and administrative functions; and (5) it supports a specific model through which patients may consent to be contacted about research. Conclusions Creation and management of a research database from sensitive clinical records with secure pseudonym generation, full-text indexing, and a consent-to-contact process is possible and practical using entirely free and open-source software.http://link.springer.com/article/10.1186/s12911-017-0437-1AnonymisationDe-identificationClinical informaticsElectronic medical recordsOpen-source softwarePseudonymisation |
| spellingShingle | Rudolf N. Cardinal Clinical records anonymisation and text extraction (CRATE): an open-source software system BMC Medical Informatics and Decision Making Anonymisation De-identification Clinical informatics Electronic medical records Open-source software Pseudonymisation |
| title | Clinical records anonymisation and text extraction (CRATE): an open-source software system |
| title_full | Clinical records anonymisation and text extraction (CRATE): an open-source software system |
| title_fullStr | Clinical records anonymisation and text extraction (CRATE): an open-source software system |
| title_full_unstemmed | Clinical records anonymisation and text extraction (CRATE): an open-source software system |
| title_short | Clinical records anonymisation and text extraction (CRATE): an open-source software system |
| title_sort | clinical records anonymisation and text extraction crate an open source software system |
| topic | Anonymisation De-identification Clinical informatics Electronic medical records Open-source software Pseudonymisation |
| url | http://link.springer.com/article/10.1186/s12911-017-0437-1 |
| work_keys_str_mv | AT rudolfncardinal clinicalrecordsanonymisationandtextextractioncrateanopensourcesoftwaresystem |