Deciphering the comprehensive knowledgebase landscape featuring infertility with IDDB Xtra

• Published in: Computers in biology and medicine Vol. 170; p. 108105
• Main Authors: Li, Qian, Hu, Zhijie, He, Jiayin, Liu, Xinyi, Liu, Yini, Wei, Jiale, Wu, Binjian, Lu, Xun, He, Hongxi, Zhang, Yuqi, He, Jixiao, Li, Mingyu, Wu, Chengwei, Lv, Lijun, Wang, Yang, Zhou, Linxuan, Zhang, Quan, Zhang, Jian, Cheng, Xiaoyue, Shao, Hongfang, Lu, Xuefeng
• Format: Journal Article
• Language: English
• Published: United States Elsevier Ltd 01.03.2024; Elsevier Limited
• Subjects: Abnormalities; Animals; Chromosome aberrations; Chromosome abnormalities; Data collection; Databases, Factual; Datasets; Developmental stages; Diagnosis; Disease; DNA methylation; Epigenetics; Fertility; Genes; Genetic counseling; Genetic disorders; Genetic screening; Genomes; Genomics; Genotype & phenotype; Health services; Humans; Infertility; Infertility - genetics; Infertility-caused genes; Knowledge Bases; Knowledge bases (artificial intelligence); Knowledge graph; Knowledge representation; Medical diagnosis; Mice; Modulators; Mutation; Mutations; Next-generation sequencing; Ontology; Patients; Phenotype; Phenotypes; Proteins; R&D; Research & development; Research applications; Mutations; Phenotypes; Chromosome abnormalities; Infertility; Genomics; Infertility-caused genes; Epigenetics; Research applications; Modulators; Knowledge graph
• ISSN: 0010-4825; 1879-0534
• DOI: 10.1016/j.compbiomed.2024.108105

Infertility affects ∼15% of couples globally and half of cases are related to genetic disorders. Despite growing data and unprecedented improvements in high-throughput sequencing technologies, accumulated fertility-related issues concerning genetic diagnosis and potential treatment are urgent to be solved. However, there is a lack of comprehensive platforms that characterise various infertility-related records to provide research applications for exploring infertility in-depth and genetic counselling of infertility couple. To solve this problem, we provide IDDB Xtra by further integrating phenotypic manifestations, genomic datasets, epigenetics, modulators in collaboration with numerous interactive tools into our previous infertility database, IDDB. IDDB Xtra houses manually-curated 2369 genes of human and nine model organisms, 273 chromosomal abnormalities, 884 phenotypes, 60 genomic datasets, 464 epigenetic records, 1144 modulators relevant to infertility diagnosis and treatment. Additionally, IDDB Xtra incorporated customized graphical applications for researchers and clinicians to decipher in-depth disease mechanisms from the perspectives of developmental atlas, mutation effects, and clinical manifestations. Users can browse genes across developmental stages of human and mouse, filter candidate genes, mine potential variants and retrieve infertility biomedical network in an intuitive web interface. In summary, IDDB Xtra not only captures valuable research and data, but also provides useful applications to facilitate the genetic counselling and drug discovery of infertility. IDDB Xtra is freely available at https://mdl.shsmu.edu.cn/IDDB/and http://www.allostery.net/IDDB. •Built the most comprehensive resource integrating infertility associated genetic, clinical factors and modulators.•Design a series of customized research applications for researchers and clinicians to decipher in-depth disease mechanisms.•Facilitate precise diagnosis and drug discovery for infertility as well as serve as a benchmark for developing computational methods for infertility studies.