Text mining and portal development for gene-specific publications on Alzheimer’s disease and other neurodegenerative diseases
Abstract Background Tremendous research efforts have been made in the Alzheimer’s disease (AD) field to understand the disease etiology, progression and discover treatments for AD. Many mechanistic hypotheses, therapeutic targets and treatment strategies have been proposed in the last few decades. R...
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| Format: | Article |
| Language: | English |
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BMC
2024-04-01
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| Series: | BMC Medical Informatics and Decision Making |
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| Online Access: | https://doi.org/10.1186/s12911-024-02501-7 |
| _version_ | 1797199436744491008 |
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| author | Jiannan Liu Huanmei Wu Daniel H. Robertson Jie Zhang |
| author_facet | Jiannan Liu Huanmei Wu Daniel H. Robertson Jie Zhang |
| author_sort | Jiannan Liu |
| collection | DOAJ |
| description | Abstract Background Tremendous research efforts have been made in the Alzheimer’s disease (AD) field to understand the disease etiology, progression and discover treatments for AD. Many mechanistic hypotheses, therapeutic targets and treatment strategies have been proposed in the last few decades. Reviewing previous work and staying current on this ever-growing body of AD publications is an essential yet difficult task for AD researchers. Methods In this study, we designed and implemented a natural language processing (NLP) pipeline to extract gene-specific neurodegenerative disease (ND) -focused information from the PubMed database. The collected publication information was filtered and cleaned to construct AD-related gene-specific publication profiles. Six categories of AD-related information are extracted from the processed publication data: publication trend by year, dementia type occurrence, brain region occurrence, mouse model information, keywords occurrence, and co-occurring genes. A user-friendly web portal is then developed using Django framework to provide gene query functions and data visualizations for the generalized and summarized publication information. Results By implementing the NLP pipeline, we extracted gene-specific ND-related publication information from the abstracts of the publications in the PubMed database. The results are summarized and visualized through an interactive web query portal. Multiple visualization windows display the ND publication trends, mouse models used, dementia types, involved brain regions, keywords to major AD-related biological processes, and co-occurring genes. Direct links to PubMed sites are provided for all recorded publications on the query result page of the web portal. Conclusion The resulting portal is a valuable tool and data source for quick querying and displaying AD publications tailored to users’ interested research areas and gene targets, which is especially convenient for users without informatic mining skills. Our study will not only keep AD field researchers updated with the progress of AD research, assist them in conducting preliminary examinations efficiently, but also offers additional support for hypothesis generation and validation which will contribute significantly to the communication, dissemination, and progress of AD research. |
| first_indexed | 2024-04-24T07:15:44Z |
| format | Article |
| id | doaj.art-e9b137248802406383495a23a70b3fe3 |
| institution | Directory Open Access Journal |
| issn | 1472-6947 |
| language | English |
| last_indexed | 2024-04-24T07:15:44Z |
| publishDate | 2024-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Medical Informatics and Decision Making |
| spelling | doaj.art-e9b137248802406383495a23a70b3fe32024-04-21T11:21:07ZengBMCBMC Medical Informatics and Decision Making1472-69472024-04-0124S31910.1186/s12911-024-02501-7Text mining and portal development for gene-specific publications on Alzheimer’s disease and other neurodegenerative diseasesJiannan Liu0Huanmei Wu1Daniel H. Robertson2Jie Zhang3Department of BioHealth Informatics, Indiana University School of Informatics & ComputingDepartment of BioHealth Informatics, Indiana University School of Informatics & ComputingIntegrated Data Sciences, Indiana Biosciences Research InstituteDept of Medical and Molecular Genetics, Indiana University School of MedicineAbstract Background Tremendous research efforts have been made in the Alzheimer’s disease (AD) field to understand the disease etiology, progression and discover treatments for AD. Many mechanistic hypotheses, therapeutic targets and treatment strategies have been proposed in the last few decades. Reviewing previous work and staying current on this ever-growing body of AD publications is an essential yet difficult task for AD researchers. Methods In this study, we designed and implemented a natural language processing (NLP) pipeline to extract gene-specific neurodegenerative disease (ND) -focused information from the PubMed database. The collected publication information was filtered and cleaned to construct AD-related gene-specific publication profiles. Six categories of AD-related information are extracted from the processed publication data: publication trend by year, dementia type occurrence, brain region occurrence, mouse model information, keywords occurrence, and co-occurring genes. A user-friendly web portal is then developed using Django framework to provide gene query functions and data visualizations for the generalized and summarized publication information. Results By implementing the NLP pipeline, we extracted gene-specific ND-related publication information from the abstracts of the publications in the PubMed database. The results are summarized and visualized through an interactive web query portal. Multiple visualization windows display the ND publication trends, mouse models used, dementia types, involved brain regions, keywords to major AD-related biological processes, and co-occurring genes. Direct links to PubMed sites are provided for all recorded publications on the query result page of the web portal. Conclusion The resulting portal is a valuable tool and data source for quick querying and displaying AD publications tailored to users’ interested research areas and gene targets, which is especially convenient for users without informatic mining skills. Our study will not only keep AD field researchers updated with the progress of AD research, assist them in conducting preliminary examinations efficiently, but also offers additional support for hypothesis generation and validation which will contribute significantly to the communication, dissemination, and progress of AD research.https://doi.org/10.1186/s12911-024-02501-7Alzheimer’s diseaseText miningNatural language processingWeb portal |
| spellingShingle | Jiannan Liu Huanmei Wu Daniel H. Robertson Jie Zhang Text mining and portal development for gene-specific publications on Alzheimer’s disease and other neurodegenerative diseases BMC Medical Informatics and Decision Making Alzheimer’s disease Text mining Natural language processing Web portal |
| title | Text mining and portal development for gene-specific publications on Alzheimer’s disease and other neurodegenerative diseases |
| title_full | Text mining and portal development for gene-specific publications on Alzheimer’s disease and other neurodegenerative diseases |
| title_fullStr | Text mining and portal development for gene-specific publications on Alzheimer’s disease and other neurodegenerative diseases |
| title_full_unstemmed | Text mining and portal development for gene-specific publications on Alzheimer’s disease and other neurodegenerative diseases |
| title_short | Text mining and portal development for gene-specific publications on Alzheimer’s disease and other neurodegenerative diseases |
| title_sort | text mining and portal development for gene specific publications on alzheimer s disease and other neurodegenerative diseases |
| topic | Alzheimer’s disease Text mining Natural language processing Web portal |
| url | https://doi.org/10.1186/s12911-024-02501-7 |
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