Database: The Journal of Biological Databases and Curation最新文献

{"title":"GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database.","authors":"Sarthak Joshi, Shailendu Mohapatra, Dhwani Kumar, Adwait Joshi, Meenakshi Iyer, Ramanathan Sowdhamini","doi":"10.1093/database/baaf035","DOIUrl":"https://doi.org/10.1093/database/baaf035","url":null,"abstract":"<p><p>Despite the vast amount of sequence data available, a significant disparity exists between the number of protein sequences identified and the relatively few structures that have been resolved. This disparity highlights the challenge in structural biology to bridge the gap between sequence information and 3D structural data, and the necessity for robust databases capable of linking distant homologs to known structures. Studies have indicated that there are a limited number of structural folds, despite the vast diversity of proteins. Hence, computational tools can enhance our ability to classify protein sequences, much before their structures are determined or their functions are characterized, thereby bridging the gap between sequence and structural data. GenDiS (Genomic Distribution of Superfamilies) is a repository with information on the genomic distribution of protein domain superfamilies, involving a one-time computational exercise to search for trusted homologs of protein domains of known structures against the vast sequence database. We have updated this database employing advanced bioinformatics tools, including DELTA-BLAST (domain enhanced lookup time accelerated BLAST) for initial detection of hits and HMMSCAN for validation, significantly improving the accuracy of domain identification. Using these tools, over 151 million sequence homologs for 2060 superfamilies [SCOPe (Structural Classification of Proteins extended)] were identified and 116 million out of them were validated as true positives. Through a case study on glycolysis-related enzymes, variations in domain architectures of these enzymes are explored, revealing evolutionary changes and functional diversity among these essential proteins. We present another case, LOG gene, where one can tune in and find significant mutations across the evolutionary lineage. The GenDiS database, GenDiS3, and the associated tools made available at https://caps.ncbs.res.in/gendis3/ offer a powerful resource for researchers in functional annotation and evolutionary studies. Database URL: https://caps.ncbs.res.in/gendis3/.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126776","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CancerPPD2: an updated repository of anticancer peptides and proteins.","authors":"Milind Chauhan, Amisha Gupta, Ritu Tomer, Gajendra P S Raghava","doi":"10.1093/database/baaf030","DOIUrl":"https://doi.org/10.1093/database/baaf030","url":null,"abstract":"<p><p>CancerPPD2 (http://webs.iiitd.edu.in/raghava/cancerppd2/) is an updated version of CancerPPD, developed to maintain comprehensive information about anticancer peptides and proteins. It contains 6521 entries, each entry provides detailed information about an anticancer peptide/protein that include origin of the peptide, cancer cell line, type of cancer, peptide sequence, and structure. These anticancer peptides have been tested against 392 types of cancer cell lines and 28 types of cancer-associated tissues. In addition to natural anticancer peptides, CancerPPD2 contains 781 entries for chemically modified and 3018 entries for N-/C- terminus modified anticancer peptides. Few entries are also linked with 47 clinical studies and have provided the cross reference to Uniprot, DrugBank, and ThPDB2. The possible entries also linked with clinical trials. On average, CancerPPD2 contains around 85% more information than its previous version, CancerPPD. The structures of these anticancer peptides and proteins were either obtained from the Protein Data Bank (PDB) or predicted using PEPstrMOD, I-TASSER, and AlphaFold. A wide range of tools have been integrated into CancerPPD2 for data retrieval and similarity searches. Additionally, we integrated a REST API into this repository to facilitate automatic data retrieval via program. Database URL: https://webs.iiitd.edu.in/raghava/cancerppd2/api/rest.html.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A longitudinal analysis of function annotations of the human proteome reveals consistently high biases.","authors":"An Phan, Parnal Joshi, Claus Kadelka, Iddo Friedberg","doi":"10.1093/database/baaf036","DOIUrl":"https://doi.org/10.1093/database/baaf036","url":null,"abstract":"<p><p>The resources required to study gene function are limited, especially when considering the number of genes in the human genome and the complexity of their function. Therefore, genes are prioritized for experimental studies based on many different considerations, including, but not limited to, perceived biomedical importance, such as disease-associated genes, or the understanding of biological processes, such as cell signalling pathways. At the same time, most genes are not studied or are under-characterized, which hampers our understanding of their function and potential effects on human health and wellness. Understanding function annotation disparity is a necessary first step toward understanding how much functional knowledge is gained from the human genome, and toward guidelines for better targeting future studies of the genes in the human genome effectively. Here, we present a comprehensive longitudinal analysis of the human proteome utilizing data analysis tools from economics and information theory. Specifically, we view the human proteome as a population of proteins within a knowledge economy: we treat the quantified knowledge of the protein's function as the analogue of wealth and examine the distribution of information in a population of proteins in the proteome in the same manner distribution of wealth is studied in societies. Our results show a highly skewed distribution of information about human proteins over the last decade, in which the inequality in the annotations given to the proteins remains high. Additionally, we examine the correlation between the knowledge about protein function as captured in databases and the interest in proteins as reflected by mentions in the scientific literature. We show a large gap between knowledge and interest and dissect the factors leading to this gap. In conclusion, our study shows that research efforts should be redirected to less studied proteins to mitigate the disparity among human proteins both in databases and literature.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A longitudinal analysis of function annotations of the human proteome reveals consistently high biases.","authors":"An Phan, Parnal Joshi, Claus Kadelka, Iddo Friedberg","doi":"10.1093/database/baaf036","DOIUrl":"10.1093/database/baaf036","url":null,"abstract":"<p><p>The resources required to study gene function are limited, especially when considering the number of genes in the human genome and the complexity of their function. Therefore, genes are prioritized for experimental studies based on many different considerations, including, but not limited to, perceived biomedical importance, such as disease-associated genes, or the understanding of biological processes, such as cell signalling pathways. At the same time, most genes are not studied or are under-characterized, which hampers our understanding of their function and potential effects on human health and wellness. Understanding function annotation disparity is a necessary first step toward understanding how much functional knowledge is gained from the human genome, and toward guidelines for better targeting future studies of the genes in the human genome effectively. Here, we present a comprehensive longitudinal analysis of the human proteome utilizing data analysis tools from economics and information theory. Specifically, we view the human proteome as a population of proteins within a knowledge economy: we treat the quantified knowledge of the protein's function as the analogue of wealth and examine the distribution of information in a population of proteins in the proteome in the same manner distribution of wealth is studied in societies. Our results show a highly skewed distribution of information about human proteins over the last decade, in which the inequality in the annotations given to the proteins remains high. Additionally, we examine the correlation between the knowledge about protein function as captured in databases and the interest in proteins as reflected by mentions in the scientific literature. We show a large gap between knowledge and interest and dissect the factors leading to this gap. In conclusion, our study shows that research efforts should be redirected to less studied proteins to mitigate the disparity among human proteins both in databases and literature.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12060720/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143984205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CancerPPD2: an updated repository of anticancer peptides and proteins.","authors":"Milind Chauhan, Amisha Gupta, Ritu Tomer, Gajendra P S Raghava","doi":"10.1093/database/baaf030","DOIUrl":"10.1093/database/baaf030","url":null,"abstract":"<p><p>CancerPPD2 (http://webs.iiitd.edu.in/raghava/cancerppd2/) is an updated version of CancerPPD, developed to maintain comprehensive information about anticancer peptides and proteins. It contains 6521 entries, each entry provides detailed information about an anticancer peptide/protein that include origin of the peptide, cancer cell line, type of cancer, peptide sequence, and structure. These anticancer peptides have been tested against 392 types of cancer cell lines and 28 types of cancer-associated tissues. In addition to natural anticancer peptides, CancerPPD2 contains 781 entries for chemically modified and 3018 entries for N-/C- terminus modified anticancer peptides. Few entries are also linked with 47 clinical studies and have provided the cross reference to Uniprot, DrugBank, and ThPDB2. The possible entries also linked with clinical trials. On average, CancerPPD2 contains around 85% more information than its previous version, CancerPPD. The structures of these anticancer peptides and proteins were either obtained from the Protein Data Bank (PDB) or predicted using PEPstrMOD, I-TASSER, and AlphaFold. A wide range of tools have been integrated into CancerPPD2 for data retrieval and similarity searches. Additionally, we integrated a REST API into this repository to facilitate automatic data retrieval via program. Database URL: https://webs.iiitd.edu.in/raghava/cancerppd2/api/rest.html.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12060709/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143981885","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"STCDB4ND: a signal transduction classification database for neurological diseases.","authors":"Boyan Gong, Sida Li, Yifan Chen, Liya Liu, Ralf Hofestädt, Ming Chen","doi":"10.1093/database/baaf032","DOIUrl":"10.1093/database/baaf032","url":null,"abstract":"<p><p>Neurological disorders pose significant global health challenges due to their complex etiology and insufficient understanding of underlying mechanisms. Signal transduction pathways are critical in the pathophysiology of these diseases and have been extensively studied to develop therapeutic interventions. However, existing databases for biological signal pathways often overlook the dynamic interactions between entities within these pathways and lack standardized representations of the signaling processes. To address these limitations, we present STCDB4ND, a specialized database focused on signal transduction pathways associated with neurological diseases. Utilizing the ST classification system, STCDB4ND provides a unified framework for pathway representation, emphasizing interactions and pathway characteristics. The database features advanced visualization tools, network analysis capabilities, and a key factor identification module, enabling researchers to comprehensively study these complex networks. Our analysis of neurological disease-related pathways using STCDB4ND revealed key signaling factors and supported existing findings on pathogenic mechanisms STCDB4ND serves as a valuable resource for advancing the understanding of neurological disease pathways and promoting novel therapeutic approaches. And we believe that STCDB will provide greater convenience for researchers in various fields as we expand the STCDB system's database in the future. Database URL: https://bis.zju.edu.cn/STCDB.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12047452/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143968084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"STCDB4ND: a signal transduction classification database for neurological diseases.","authors":"Boyan Gong, Sida Li, Yifan Chen, Liya Liu, Ralf Hofestädt, Ming Chen","doi":"10.1093/database/baaf032","DOIUrl":"https://doi.org/10.1093/database/baaf032","url":null,"abstract":"<p><p>Neurological disorders pose significant global health challenges due to their complex etiology and insufficient understanding of underlying mechanisms. Signal transduction pathways are critical in the pathophysiology of these diseases and have been extensively studied to develop therapeutic interventions. However, existing databases for biological signal pathways often overlook the dynamic interactions between entities within these pathways and lack standardized representations of the signaling processes. To address these limitations, we present STCDB4ND, a specialized database focused on signal transduction pathways associated with neurological diseases. Utilizing the ST classification system, STCDB4ND provides a unified framework for pathway representation, emphasizing interactions and pathway characteristics. The database features advanced visualization tools, network analysis capabilities, and a key factor identification module, enabling researchers to comprehensively study these complex networks. Our analysis of neurological disease-related pathways using STCDB4ND revealed key signaling factors and supported existing findings on pathogenic mechanisms STCDB4ND serves as a valuable resource for advancing the understanding of neurological disease pathways and promoting novel therapeutic approaches. And we believe that STCDB will provide greater convenience for researchers in various fields as we expand the STCDB system's database in the future. Database URL: https://bis.zju.edu.cn/STCDB.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mapping assays to the key characteristics of carcinogens to support decision-making.","authors":"Gabrielle Rigutto, Cliona M McHale, Ettayapuram Ramaprasad Azhagiya Singam, Iemaan Rana, Luoping Zhang, Martyn T Smith","doi":"10.1093/database/baaf026","DOIUrl":"10.1093/database/baaf026","url":null,"abstract":"<p><p>The key characteristics (KCs) of carcinogens are the properties common to known human carcinogens that can be used to search for, organize, and evaluate mechanistic data in support of hazard identification. A limiting factor in this approach is that relevant in vitro and in vivo assays, as well as corresponding biomarkers and endpoints, have been only partially documented for each of the 10 KCs (Smith MT, Guyton KZ, Kleinstreuer N et al. The key characteristics of carcinogens: relationship to the hallmarks of cancer, relevant biomarkers, and assays to measure them. Cancer Epidemiol Biomarkers Prev 2020;29:1887-903. https://doi.org/10.1158/1055-9965.EPI-19-1346). To address this limitation, a comprehensive database is described that catalogues these previously described methods and endpoints/biomarkers pertinent to the 10 KCs of carcinogens as well as those referenced as supporting evidence for each KC in the International Agency of Research on Cancer Monograph Volumes 112-131. Our comprehensive mapping of KCs to assays and endpoints can be used to facilitate mechanistic data searches, presents a useful tool for searching for assays and endpoints relevant to the 10 KCs, and can be used to create a roadmap for utilizing data to evaluate the strength of the evidence for each KC. The KC-Assay database is available to the public on the web at https://kcad.cchem.berkeley.edu and acts as a 'living document', with the ability to be updated and refined. Database URL: https://kcad.cchem.berkeley.edu.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12013474/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143968082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mapping assays to the key characteristics of carcinogens to support decision-making.","authors":"Gabrielle Rigutto, Cliona M McHale, Ettayapuram Ramaprasad Azhagiya Singam, Iemaan Rana, Luoping Zhang, Martyn T Smith","doi":"10.1093/database/baaf026","DOIUrl":"https://doi.org/10.1093/database/baaf026","url":null,"abstract":"<p><p>The key characteristics (KCs) of carcinogens are the properties common to known human carcinogens that can be used to search for, organize, and evaluate mechanistic data in support of hazard identification. A limiting factor in this approach is that relevant in vitro and in vivo assays, as well as corresponding biomarkers and endpoints, have been only partially documented for each of the 10 KCs (Smith MT, Guyton KZ, Kleinstreuer N et al. The key characteristics of carcinogens: relationship to the hallmarks of cancer, relevant biomarkers, and assays to measure them. Cancer Epidemiol Biomarkers Prev 2020;29:1887-903. https://doi.org/10.1158/1055-9965.EPI-19-1346). To address this limitation, a comprehensive database is described that catalogues these previously described methods and endpoints/biomarkers pertinent to the 10 KCs of carcinogens as well as those referenced as supporting evidence for each KC in the International Agency of Research on Cancer Monograph Volumes 112-131. Our comprehensive mapping of KCs to assays and endpoints can be used to facilitate mechanistic data searches, presents a useful tool for searching for assays and endpoints relevant to the 10 KCs, and can be used to create a roadmap for utilizing data to evaluate the strength of the evidence for each KC. The KC-Assay database is available to the public on the web at https://kcad.cchem.berkeley.edu and acts as a 'living document', with the ability to be updated and refined. Database URL: https://kcad.cchem.berkeley.edu.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CPDMS: a database system for crop physiological disorder management.","authors":"Jae-Hyeon Oh, Hwang-Weon Jeong, Il Pyung Ahn, Seon-Hwa Bae, Sung Mi Kim, Eunhee Kim, Su Jung Ra, Jinjeong Lee, Hye Yeon Choi, Young-Joo Seol","doi":"10.1093/database/baaf031","DOIUrl":"10.1093/database/baaf031","url":null,"abstract":"<p><p>As the importance of precision agriculture grows, scalable and efficient methods for real-time data collection and analysis have become essential. In this study, we developed a system to collect real-time crop images, focusing on physiological disorders in tomatoes. This system systematically collects crop images and related data, with the potential to evolve into a valuable tool for researchers and agricultural practitioners. A total of 58 479 images were produced under stress conditions, including bacterial wilt (BW), Tomato Yellow Leaf Curl Virus (TYLCV), Tomato Spotted Wilt Virus (TSWV), drought, and salinity, across seven tomato varieties. The images include front views at 0 degrees, 120 degrees, 240 degrees, and top views and petiole images. Of these, 43 894 images were suitable for labeling. Based on this, 24 000 images were used for AI model training, and 13 037 images for model testing. By training a deep learning model, we achieved a mean Average Precision (mAP) of 0.46 and a recall rate of 0.60. Additionally, we discussed data augmentation and hyperparameter tuning strategies to improve AI model performance and explored the potential for generalizing the system across various agricultural environments. The database constructed in this study will serve as a crucial resource for the future development of agricultural AI. Database URL: https://crops.phyzen.com/.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12013473/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143968636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}