College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, China.
Brief Bioinform. 2021 Sep 2;22(5). doi: 10.1093/bib/bbaa432.
Fertility refers to the ability of animals to maintain reproductive function and give birth to offspring, which is an important indicator to measure the productivity of animals. Fertility is affected by many factors, among which environmental factors may also play key roles. During the past years, substantial research studies have been conducted to detect the factors related to fecundity, including genetic factors and environmental factors. However, the identified genes associated with fertility from countless previous studies are randomly dispersed in the literature, whereas some other novel fertility-related genes are needed to detect from omics-based datasets. Here, we constructed a fertility index factor database FifBase based on manually curated published literature and RNA-Seq datasets. During the construction of the literature group, we obtained 3301 articles related to fecundity for 13 species from PubMed, involving 2823 genes, which are related to 75 fecundity indicators or 47 environmental factors. Eventually, 1558 genes associated with fertility were filtered in 10 species, of which 1088 and 470 were from RNA-Seq datasets and text mining data, respectively, involving 2910 fertility-gene pairs and 58 fertility-environmental factors. All these data were cataloged into FifBase (http://www.nwsuaflmz.com/FifBase/), where the fertility-related factor information, including gene annotation and environmental factors, can be browsed, retrieved and downloaded with the user-friendly interface.
生育力是指动物维持生殖功能并产生后代的能力，是衡量动物生产力的重要指标。生育力受多种因素影响，其中环境因素也可能发挥关键作用。在过去的几年中，已经进行了大量的研究来检测与生育力相关的因素，包括遗传因素和环境因素。然而，从无数先前的研究中确定的与生育力相关的基因在文献中是随机分散的，而需要从基于组学的数据集检测其他一些新的与生育力相关的基因。在这里，我们基于人工编辑的已发表文献和 RNA-Seq 数据集构建了一个生育力指数因子数据库 FifBase。在构建文献组时，我们从 PubMed 获得了 13 个物种与生育力相关的 3301 篇文章，涉及 2823 个基因，这些基因与 75 个生育力指标或 47 个环境因素有关。最终，在 10 个物种中筛选出与生育力相关的 1558 个基因，其中 1088 个和 470 个分别来自 RNA-Seq 数据集和文本挖掘数据，涉及 2910 个生育力基因对和 58 个生育力环境因素。所有这些数据都被编入 FifBase（http://www.nwsuaflmz.com/FifBase/），用户可以通过友好的界面浏览、检索和下载与生育力相关的因子信息，包括基因注释和环境因素。
