A framework for community curation of interspecies interactions literature.

The quantity and complexity of data being generated and published in biology has increased substantially, but few methods exist for capturing knowledge about phenotypes derived from molecular interactions between diverse groups of species, in such a way that is amenable to data-driven biology and research. To improve access to this knowledge, we have constructed a framework for the curation of the scientific literature studying interspecies interactions, using data curated for the Pathogen-Host Interactions database (PHI-base) as a case study. The framework provides a curation tool, phenotype ontology, and controlled vocabularies to curate pathogen-host interaction data, at the level of the host, pathogen, strain, gene, and genotype. The concept of a multispecies genotype, the 'metagenotype,' is introduced to facilitate capturing changes in the disease-causing abilities of pathogens, and host resistance or susceptibility, observed by gene alterations. We report on this framework and describe PHI-Canto, a community curation tool for use by publication authors.

The increasingly vast amount of data being produced in research communities can be difficult to manage, making it challenging for both humans and computers to organise and connect information from different sources. Currently, software tools that allow authors to curate peer-reviewed life science publications are designed solely for single species, or closely related species that do not interact. Although most research communities are striving to make their data FAIR (Findable, Accessible, Interoperable and Reusable), it is particularly difficult to curate detailed information based on interactions between two or more species (interspecies), such as pathogen-host interactions. As a result, there was a lack of tools to support multi-species interaction databases, leading to a reliance on labour-intensive curation methods. To address this problem, Cuzick et al. used the Pathogen-Host Interactions database (PHI-base), which curates knowledge from the text, tables and figures published in over 200 journals, as a case study. A framework was developed that could capture the many observable traits (phenotype annotations) for interactions and link them directly to the combination of genotypes involved in those interactions across multiple scales ­ ranging from microscopic to macroscopic. This demonstrated that it was possible to build a framework of software tools to enable curation of interactions between species in more detail than had been done before. Cuzick et al. developed an online tool called PHI-Canto that allows any researcher to curate published pathogen-host interactions between almost any known species. An ontology ­ a collection of concepts and their relations ­ was created to describe the outcomes of pathogen-host interactions in a standardised way. Additionally, a new concept called the 'metagenotype' was developed which represents the combination of a pathogen and a host genotype and can be easily annotated with the phenotypes arising from each interaction. The newly curated multi-species FAIR data on pathogen-host interactions will enable researchers in different disciplines to compare and contrast interactions across species and scales. Ultimately, this will assist the development of new approaches to reduce the impact of pathogens on humans, livestock, crops and ecosystems with the aim of decreasing disease while increasing food security and biodiversity. The framework is potentially adoptable by any research community investigating interactions between species and could be adapted to explore other harmful and beneficial interspecies interactions.

[Status quo of and challenges for research on rust disease in medicinal plants].

Medicinal plants are beneficial to human health. However,most of the major producing regions of medicinal plants suffer from rust disease,which threatens the yield and quality of Chinese medicinal materials,thus causes huge economic loss,and hinders the sustainable development of the Chinese medicine industry. By the end of 2020,rust disease had been reported in medicinal plants of 76 species and 33 families. In the 76 species,79 rust pathogens were detected. The majority of these pathogens belonged to Puccinia( 33,39. 24%),Coleosporium( 14,15. 19%),and Aecidium( 11,13. 92%). Of these 79 rust pathogens,10 were autoecious and 13 were heteroecious. Through literature research,this study reviewed the symptoms,pathogen species,severity and distribution,prevalence and occurrence conditions,and control measures of rust disease in medicinal plants,and thereby summarized the research status of rust disease in medicinal plants and the gap with other plants,which is expected to serve as a reference for further research on rust disease in medicinal plants.

Status quo of and challenges for research on rust disease in medicinal plants / 中国中药杂志

Medicinal plants are beneficial to human health. However,most of the major producing regions of medicinal plants suffer from rust disease,which threatens the yield and quality of Chinese medicinal materials,thus causes huge economic loss,and hinders the sustainable development of the Chinese medicine industry. By the end of 2020,rust disease had been reported in medicinal plants of 76 species and 33 families. In the 76 species,79 rust pathogens were detected. The majority of these pathogens belonged to Puccinia( 33,39. 24%),Coleosporium( 14,15. 19%),and Aecidium( 11,13. 92%). Of these 79 rust pathogens,10 were autoecious and 13 were heteroecious. Through literature research,this study reviewed the symptoms,pathogen species,severity and distribution,prevalence and occurrence conditions,and control measures of rust disease in medicinal plants,and thereby summarized the research status of rust disease in medicinal plants and the gap with other plants,which is expected to serve as a reference for further research on rust disease in medicinal plants.