Biomarker_nlp: A Python Package for Mining Biomarker Information for Targeted Cancer Therapies
This article describes biomarker_nlp, a Python package that aims to provide natural language processing (NLP) functionalities for mining and processing biomarker information from the drug labels in DailyMed for targeted cancer therapies approved by the U.S. Food and Drug Administration (FDA), as wel...
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| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Ubiquity Press
2024-12-01
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| Series: | Journal of Open Research Software |
| Subjects: | |
| Online Access: | https://account.openresearchsoftware.metajnl.com/index.php/up-j-jors/article/view/502 |
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| _version_ | 1841554896036298752 |
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| author | Junxia Lin Yuezheng He Subha Madhavan Chul Kim Simina M. Boca |
| author_facet | Junxia Lin Yuezheng He Subha Madhavan Chul Kim Simina M. Boca |
| author_sort | Junxia Lin |
| collection | DOAJ |
| description | This article describes biomarker_nlp, a Python package that aims to provide natural language processing (NLP) functionalities for mining and processing biomarker information from the drug labels in DailyMed for targeted cancer therapies approved by the U.S. Food and Drug Administration (FDA), as well as other biomedical free text. It contains modules and functions supporting the recognition and extraction of a variety of biomarkers, such as gene/protein, therapy, disease, and drug label. This package may be helpful for users who want to extract and analyze biomarker information related to FDA-approved products, focusing on FDA-approved targeted cancer therapies. |
| format | Article |
| id | doaj-art-ceca3a7d963b431a8090fbf3ba35a623 |
| institution | Kabale University |
| issn | 2049-9647 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Ubiquity Press |
| record_format | Article |
| series | Journal of Open Research Software |
| spelling | doaj-art-ceca3a7d963b431a8090fbf3ba35a6232025-01-08T08:37:33ZengUbiquity PressJournal of Open Research Software2049-96472024-12-01121151510.5334/jors.502491Biomarker_nlp: A Python Package for Mining Biomarker Information for Targeted Cancer TherapiesJunxia Lin0https://orcid.org/0000-0001-6348-5015Yuezheng He1Subha Madhavan2https://orcid.org/0000-0001-7617-3547Chul Kim3https://orcid.org/0000-0003-0191-8684Simina M. Boca4https://orcid.org/0000-0002-1400-3398Georgetown University Medical Center (work performed while at Georgetown University, currently employee at Chemonics International), Washington D.C.Georgetown University Medical Center, Washington D.C.Georgetown University Medical Center (work performed while at Georgetown University, currently employee at Pfizer), Washington D.C.Georgetown University Medical Center, Washington D.C.Georgetown University Medical Center (work performed while at Georgetown, currently employee and minor shareholder at AstraZeneca), Washington D.C.This article describes biomarker_nlp, a Python package that aims to provide natural language processing (NLP) functionalities for mining and processing biomarker information from the drug labels in DailyMed for targeted cancer therapies approved by the U.S. Food and Drug Administration (FDA), as well as other biomedical free text. It contains modules and functions supporting the recognition and extraction of a variety of biomarkers, such as gene/protein, therapy, disease, and drug label. This package may be helpful for users who want to extract and analyze biomarker information related to FDA-approved products, focusing on FDA-approved targeted cancer therapies.https://account.openresearchsoftware.metajnl.com/index.php/up-j-jors/article/view/502biomarker_nlpbiomarkerinformation retrievaltargeted cancer therapydailymednegation detectionnatural language processingtext mining |
| spellingShingle | Junxia Lin Yuezheng He Subha Madhavan Chul Kim Simina M. Boca Biomarker_nlp: A Python Package for Mining Biomarker Information for Targeted Cancer Therapies Journal of Open Research Software biomarker_nlp biomarker information retrieval targeted cancer therapy dailymed negation detection natural language processing text mining |
| title | Biomarker_nlp: A Python Package for Mining Biomarker Information for Targeted Cancer Therapies |
| title_full | Biomarker_nlp: A Python Package for Mining Biomarker Information for Targeted Cancer Therapies |
| title_fullStr | Biomarker_nlp: A Python Package for Mining Biomarker Information for Targeted Cancer Therapies |
| title_full_unstemmed | Biomarker_nlp: A Python Package for Mining Biomarker Information for Targeted Cancer Therapies |
| title_short | Biomarker_nlp: A Python Package for Mining Biomarker Information for Targeted Cancer Therapies |
| title_sort | biomarker nlp a python package for mining biomarker information for targeted cancer therapies |
| topic | biomarker_nlp biomarker information retrieval targeted cancer therapy dailymed negation detection natural language processing text mining |
| url | https://account.openresearchsoftware.metajnl.com/index.php/up-j-jors/article/view/502 |
| work_keys_str_mv | AT junxialin biomarkernlpapythonpackageforminingbiomarkerinformationfortargetedcancertherapies AT yuezhenghe biomarkernlpapythonpackageforminingbiomarkerinformationfortargetedcancertherapies AT subhamadhavan biomarkernlpapythonpackageforminingbiomarkerinformationfortargetedcancertherapies AT chulkim biomarkernlpapythonpackageforminingbiomarkerinformationfortargetedcancertherapies AT siminamboca biomarkernlpapythonpackageforminingbiomarkerinformationfortargetedcancertherapies |